Gerstner Scholars

 
Courtesy of Zoe Kulik

Zoe Kulik

Research Focus: My research as an NSF Postdoctoral Fellow (EAR-2304875) and Gerstner Scholar focuses on illuminating the developmental patterns and life history traits in the synapsid forerunners of mammals. The synapsid lineage spans over 300 million years and includes a vast array of extinct lineages with different ecologies, physiologies, and life histories. While living mammals are also very ecologically diverse, they all share a homeothermic endothermic physiology. However, there is a longstanding hypothesis that synapsids arose from an ectothermic common ancestor and achieved endothermy in the immediate ancestors of living mammals. I am interested in testing this hypothesis by analyzing the bone tissue of deeply nested synapsid groups. Bone histology is one of the best and most informative lines of evidence to understand growth rates in the fossil record and is in turn used as a proxy for physiological capacity. By comparing the bone tissue of different synapsid groups, I aim to understand when, how, or how many times mammal-like growth rates and developmental patterns evolved. This requires a comparative approach that synthesizes bone tissue from multiple lineages to robustly assess the life histories and growth rates at different evolutionary stages along the mammalian stem.

Biography: Zoe Kulik received her B.A. in Geology from Macalester College in 2016, where she and Kristi Curry Rogers worked to reconstruct titanosaur life histories. She then worked as Macalester’s paleohistology lab manager as a post-bacc. In 2023, Zoe earned her PhD from the University of Washington in Christian Sidor’s lab. Her dissertation research focused on growth trajectories, life history, and community age structure in the mammalian stem lineage. Zoe uses a combination of traditional histological techniques, advanced imaging methods such as micro-CT, and cutting-edge synchrotron tomography to unveil the developmental patterns of the fossil relatives and ancestors of mammals.

 
Courtesy of Pedro H. N. Bragança

Pedro H. N. Bragança

Research Focus: The main goal of my postdoctoral research at the AMNH is to understand the evolution of the Congo River within the past 15 million years through the analysis of miniature Congolese Cyprinodontiform fishes (families Nothobranchiidae and Procatopodidae), popularly known as killifishes. Based on the different species and populations distribution patterns, the project aims to understand if the hypothesized low land forest refugia played a major role in the process of speciation in the system.

The Congo River basin harbors the highest freshwater fish diversity in the African continent, but little is known about the processes that shaped this mega diversity. To address this knowledge gap, combined morphological and molecular data of different species and populations of miniature killifishes belonging to the genera Congopanchax, Hylopanchax, Fenerbahce, and Aphyoplatys, all of them inhabiting similar low land forest swamps, will be assessed. Through a comparative analysis of the populational structuring seen in the different genera, it will be possible, for the first time, to identify common historical patterns in the Congo. The selection of miniature species is a critical aspect of this research given that extremely small species generally have a lower vagility and are considered to be habitat specific. Thus, the resulting genetic diversity and distribution patterns are more likely to correspond with historical events that affected the Congo River drainage and the extent of its forest cover than patterns retrieved from larger species. In the past 10 million years, the Congo experienced increased aridification and many abrupt shifts between arid and moist periods, resulting in subsequent expansions and contractions of the rainforest. Have these climatic fluctuations affected the diversity and distribution of miniature fishes in the Congo?

During my Ph.D. research a fossil calibrated multigene phylogeny for the family Procatopodidae was published, allowing a first insight into the family biogeography in which it was possible to estimate the origin of the genera Congopanchax and Hylopanchax. A similar comprehensive phylogeny is not available for the Nothobranchiidae, thus the present research project also aims to build a time calibrated phylogeny for the family, allowing the estimate of the origin dates for Fenerbahce and Aphyoplatys.

The research will be based on specimens from the AMNH fish collection and other natural history collections, as well as on specimens that will be sampled in an expedition to the Congo River basin. For the first time UCEs will be used to understand the genetic diversity within taxa belonging to these two families, and to establish the relationships within the Nothobranchiidae.  

Biography: Pedro H. N. Bragança received his B.Sc. from the Federal University of Rio de Janeiro, Brazil, in 2011 and his M.Sc. from the same institution in 2014. During his master’s thesis, he studied the Amazon miniature lampeye killifish Fluviphylax resulting in the first molecular phylogeny for the genus and the description of two new species. He earned his Ph.D. in 2018 from the Museu Nacional/Federal University of Rio de Janeiro, Brazil, including a 10-month program of doctoral research at the Royal Museum for Central Africa in Tervuren, Belgium. His dissertation research focused on the systematics and biogeography of the Cyprinodontoidei fishes, with a focus on the African lampeyes (Procatopodidae). Between the end of 2019 and 2023, Pedro was a postdoctoral researcher at the South African Institute for Aquatic Biodiversity in Makhanda (former Grahamstown), South Africa.

Courtesy of Sofia Paz Sedano

Sofía Paz-Sedano

Research Focus: My postdoctoral research as a Gerstner Scholar at theAmerican Museum of Natural History focuses on investigating the molecular mechanisms and genes involved in autotomy and regeneration of tissues in Nudibranchia (Mollusca, Gastropoda), as well as the evolution of this defense method in different lineages. Nudibranchs are soft-bodied mollusks that lost the shell. However, these sea slugs have developed defensive strategies to compensate the loss of this typical gastropod defensive structure. Some species of nudibranchs can synthesize de novo or sequester through their prey bioactive compounds. Other species can sequester stinging cells from the cnidarians which they feed. Another defensive strategy is autotomy/regeneration.

It has been observed that different species of nudibranchs can autotomize different parts of the body, including the mantle, or the cerata. In the most extreme cases in Heterobranchia, the species may even free the entire body. The defense mechanisms of nudibranchs have been of interest over the years, highlighting the study of bioactive compounds and the sequestration of nematocysts. However, the ability of autotomy and regeneration has received less attention. With the aim to better understand the autotomy process in nudibranchs, one of the aims of the postdoctoral research is to study the differential gene expression and gene regulatory network of autotomy/regeneration mechanisms in the Cladobranch Berghia stephanieae (Á. Valdés, 2005) through the analyses of transcriptomes.

The second aim of the research is to study the origin and evolution of autotomy/regeneration in nudibranchs through ancestral state reconstruction analyses, which combines the phylogenetic relationships between species with data on their ability to autotomize different body parts.

Biography: Sofía Paz-Sedano received her B.Sc. in Biology from the Autonomous University of Madrid (Spain) in 2016 and her M.Sc. in Marine Biology, Biodiversity and Conservation from the University of La Laguna (Spain) in 2018. Her work has focused on studying the biodiversity and evolution of Nudibranchia sea slugs. For her bachelor thesis, she studied and described one species of nudibranch belonging to the genus Okenia from the Azores Archipelago, using morphological and molecular analyses. For her master thesis, she increased the number of species and molecular data, and carried out a review of Okenia species inhabiting the Mediterranean Sea through integrative taxonomic approach, including morphological, phylogenetic and species delimitation analyses. She earned her position as assistant professor in Zoology and she carried out her Ph.D from the Autonomous University of Madrid. Her dissertation research focused on the phylogenetics, diversification and biodiversity of the nudibranch family Goniodorididae, performing a world-wide review of species. Her work included morphological studies using computed microtomography, scanning electron microscopy and dissections, as well as molecular analyses by sanger sequencing of mitochondrial and nuclear markers, and ultraconserved elements.

 
Courtesy of Rene Martin

Rene Martin

Research Focus: My postdoctoral research as a Gerstner Scholar at the American Museum of Natural History focuses on investigating a key innovation of deep-sea fishes, bioluminescence. Fishes create bioluminescent displays either intrinsically, through the innervation of light-producing photophores, or by housing symbiotic bioluminescent bacteria in light organs in their bodies. Fishes have independently evolved the ability to produce bioluminescence at least 27 times and it occurs in over 1,500 species. Bioluminescence is used in behaviors such as camouflaging, predation, and communication, and fish lineages with bioluminescent courtship displays have significantly higher rates of species accumulation compared to their non-luminous sister clades. Within these over 1,500 bioluminescent fish, there exists numerous adaptations and alterations to the light organs possessed by these species. Fishes have evolved different light-organ morphologies, and many have evolved various filters and shutters that change the color of emitted light or obscure it completely.

My work focuses on using various methods (e.g., histology, micro-CT, SEM) combined with phylogenetic comparative methods to describe and understand the evolution of light-organ morphology in a diverse group of deep-sea fishes, the lanternfishes (Myctophidae). Lanternfishes possess intrinsic bioluminescence and emit light from primary scale-associated photophores located in ventral and lateral positions on their bodies. Many species also possess additional light organs, often sexually dimorphic, on their heads and tails. My research will also focus on analyzing the light organ morphology and control of the shuttering system in a more shallow-water group of fishes, the ponyfishes (Leiognathidae). Unlike lanternfishes, ponyfishes instead have bacterially mediated bioluminescence through a symbiosis with bioluminescent bacteria housed in an esophageal light organ. The light organ morphology in many species is sexually dimorphic, being larger in males, and often-times the males of these species also possess uniquely patterned ‘windows’ that they emit light through. Their symbiotic bacteria emit light continuously, so it is important to understand how ponyfishes control how this light is emitted and shuttered.

Biography: Rene Martin received her BS and MS in Biology from St. Cloud State University in 2014 and 2017 respectively and her PhD in Ecology and Evolutionary Biology from the University of Kansas in 2022. Most of her graduate work focused on investigating the macroevolution and adaptation in deep-sea lanternfishes and blackchins (Myctophiformes). Lanternfishes are extremely abundant and are prey for a variety of organisms, playing a major role in oceanic ecosystems. Lanternfishes are also bioluminescent and are considered diverse for a mesopelagic fish lineage. This work included creating phylogenetic hypotheses of genus-level relationships within the Myctophiformes using ultraconserved elements, gene sequences, and morphological characters. Resulting trees furthered the understanding of lanternfish relationships and were integral in investigating macroevolutionary questions associated with feeding and dentition, body-shape evolution, and olfactory organs.

Courtesy of Audrey Lin

Audrey Lin

Research Focus — My research utilizes recovering ancient biomolecules from archaeological and museum specimens and objects to answer diverse questions on human-mediated evolutionary processes, including domestication, extinction, and mechanisms of zoonoses. My multidisciplinary approach integrates tools and theories from the life sciences (palaeogenomics, biology, zoology), the humanities (history), and social sciences (archaeology and cultural anthropology).

My primary research focus for the Gerstner Scholarship involves utilizing novel museomics methods to explore the genetic roots of virulence in historical viral diseases. Studying ancient viral genomes offers valuable insights into the dynamics of present-day emerging and re-emerging infectious diseases. It is rare to observe adaptive mutations over the course of an infectious disease outbreak, but the study of ancient viral genomes can allow us to observe ‘evolution in action’, by reconstructing the evolutionary history of how and why a pathogen's virulence may change over time.

Bats are the natural reservoir hosts for many coronaviruses (CoVs), and Rhinolophus bats in particular have been identified as the most likely origin of SARS-CoV-2, based on genetic sequences of bat CoVs collected through wildlife surveillance. However, there are an unknown number of extinct viral lineages that may have been the progenitors of SARS-CoV-2 and other CoVs – including those yet to emerge. I will use preexisting viral sequences and information on co-roosting of different bat species to examine the network of co-evolutionary relationships among viruses and their bat hosts. I am developing methods to recover viral RNA from “wet” ethanol-preserved bats housed in the American Museum of Natural History. I will use bioinformatic methods to develop and optimize a pipeline to study low-coverage virus genomes from museum specimens and perform phylogenomic and phylodynamic analyses. These viral ‘time capsules’ can reveal lost viral diversity and evolution of these current and future health threats.

Biography —Audrey T. Lin received her B.S. in Biological Sciences (2012) from University of Nevada Las Vegas and M.Sc. in Infection and Immunity (2014) from University College London. She received her D.Phil from the Department of Zoology (2020) where she used bioinformatic methods to investigate the consequences of genome evolution and its impact on molecular rate, demographic spread, and its physiological and functional changes over time. While at Oxford, Audrey joined the Palaeogenomics & Bio-Archaeology Research Network (PalaeoBARN) under the supervision of Professor Greger Larson where she made her research home in the field of palaeogenomics. Prior to joining AMNH, Audrey was at the Smithsonian National Museum of Natural History’s Anthropology Department where she held the Peter Buck Postdoctoral Fellowship and the George Burch Postdoctoral Fellowship in Theoretical Medicine and Affiliated Theoretical Science. While at NMNH, she led several collections-based projects, including two fully-funded projects with the aim of recovering viral RNA from museum specimens to better understand the molecular evolution of zoonotic viruses of biomedical interest — particularly the 1918 pandemic influenza virus and bat coronaviruses. The last project she led was in collaboration with Coast Salish weavers, Knowledge Keepers, Elders, and artists, utilizing “Two-Eyed Seeing” to view the world through the combined strengths of Indigenous knowledge and western science. This holistic approach revealed the deep history and recent decline of the Coast Salish woolly dog due to colonialism.

Courtesy of Jose Barba-Montoya

Jose Barba-Montoya

Research Focus — I study patterns of molecular evolution and species diversification across the tree of life by integrating phylogenetics/phylogenomics with systematics and ecology. My primary focus lies in inferring evolutionary relationships and divergence times of species and subspecies. The inference of accurate timetrees is crucial for understanding major transitions in the evolution of genomes and species. Despite the abundance of data and powerful analysis methods, challenges persist in constructing reliable timetrees. Understanding the different sources of errors and uncertainties, as well as the strategies to address them, is fundamental for constructing an accurate tree of life. Given these considerations, another aspect of my research is dedicated to developing methods for phylogenomic analysis and molecular clock dating that effectively control sources of error and uncertainty.

Arachnid phylogeny has emerged as one of the most challenging problems in phylogenomics due to an ancient rapid radiation. Recent phylogenomic studies have both confirmed and refuted the monophyly of Arachnida with implications for understanding the evolution of terrestrialization: Did arachnids colonize land once or on multiple occasions? As a Gerstner Scholar in Bioinformatics and Computational Biology at the American Museum of Natural History I am investigating arachnid monophyly and the evolution of terrestrialization, using phylogenomic data for all living orders of Chelicerata; (2) developing a bioinformatics pipeline for identifying specific genomic regions or loci that affect phylogenetic signal, causing incongruence among gene trees and species trees; (3) undertaking further phylogenomic and divergence dating analyses of specific arachnid orders to build a more complete dated tree of life for Arachnida; and (4) developing an algorithm for automatically updating dated phylogenies with new sequences. I expect that the methods implemented will achieve robust estimates of relationships and divergence times for Arachnida.

Biography — Jose Barba-Montoya received his BSc in Biology (2009) and MSc in Systematics (2012) from the Universidad Nacional Autónoma de México under the supervision of Professor Susana Magallón. His dissertations research focused on the evolution of columnar cacti and pollination syndromes. Then, he received his PhD in Molecular Evolution (2017) from University College London under the supervision of Professor Ziheng Yang. His dissertation explored the use of phylogenomic data, combined with statistical summaries of the fossil record, to estimate divergence times of angiosperms and primates. Specifically, the impact of different interpretations of the fossil record and relaxed molecular clock models, among other factors, on Bayesian divergence time estimation was explored. This work highlighted that the main factors impacting time estimates are data partitioning, fossil calibration uncertainty, discrepancy between the specified time prior and the effective time prior, and relaxed clock model. Prior to joining AMNH, Dr. Barba-Montoya was a postdoctoral fellow with Professor Sudhir Kumar at Temple University. His research mainly focused on investigating and developing models and methods for phylogenetic inference and divergence time estimation. Overall, his work had applied implications for molecular clock dating and provided valuable insights into the evolution of angiosperms and primates.

Courtesy of Daniel Hooper

Daniel M. Hooper

Research Focus -Gene flow, following hybridization, can play a large and often counterintuitive role in a variety of evolutionary processes related to trait evolution and the development of reproductive isolation. My research at the AMNH utilizes a comparative genomic approach to investigate topics such as: (a) How chromosome inversions evolve and their effectiveness as barriers to gene flow. (b) The evolutionary forces that shape sex chromosome evolution and their large contribution to speciation. (c) How mitonuclear coevolution within species can lead to mitonuclear incompatibilities between species. Towards these aims, I am currently evaluating the potential of a new approach to recover population-level haplotype information for non-model organisms called ‘haplotagging’. This new, rapid-run, low-cost, high-throughput approach maintains haplotype information by generating linked-read sequence data from large DNA molecules that are uniquely barcoded with custom beadTags. I am currently evaluating the utility of this new linked-read data towards better understanding inversions, sex chromosomes, and mitonuclear coevolution in the long-tailed finch hybrid system.

Biography – Daniel M. Hooper received his B.S. from the University of California Davis in 2009 and his Ph.D. from the University of Chicago in 2017 with Dr. Trevor Price. His dissertation examined chromosome inversion evolution in birds, explicitly testing support for the hypothesis that inversions – as potent recombination modifiers – are contextually selectively favored in certain conditions: i.e., maladaptive hybridization between divergent species or eco-types. Evaluating decades of cytological work on passerines in a phylogenetic context and using comparative genomic techniques to examine an Australian hybrid zone, this work suggested that inversions may often contribute to speciation in birds. His postdoctoral work has pursued these findings.

Courtesy of Edson Abreu

Dr. Edson Abreu Junior

Research Focus: My postdoctoral research at the AMNH focuses on the systematics, taxonomy, and phenotypic evolution of a charismatic and diverse group of mammals, the tree squirrels (Sciuridae, Sciurini). My objectives include undertaking a comprehensive taxonomic review of Sciurini using an integrative approach to reconcile genomic and morphological data, and investigating phenotypic evolution and morphological disparification in the adaptive radiation of tree squirrels.

Sciurini represents a diverse radiation that originated around 14 Mya, most likely in North America, and successfully colonized the Holarctic and Neotropical regions. Tree squirrels exhibit strikingly high rates of diversification, especially in the Neotropics, where they experienced an explosive diversification after invading South America around 6 Mya. They are conspicuous inhabitants of forested ecosystems throughout their distribution, and they play important ecological roles as predators and dispersers of tree seeds. Tree squirrels are also often used as model organisms to address a wide range of ecological and evolutionary questions, both in their native ecosystems and as invasive species. However, unresolved taxonomic problems obscure many potentially important aspects of tree-squirrel research.

Until quite recently, the genetic diversity and molecular systematics of tree squirrels were poorly known, particularly regarding the Neotropical taxa. During my Ph.D. research, I proposed heretofore the most comprehensive phylogenetic hypotheses for tree squirrels based on mitogenomes and thousands of UCE loci recovered from almost all valid species of the tribe Sciurini. The phylogenomic results allowed the advancement of a preliminary and tentative nomenclatural designation for the taxa at the genus-group level. However, a detailed taxonomic investigation is still in very much needed to carefully evaluate the application of generic names, to provide taxon diagnoses and descriptions, as well as to evaluate the species-level taxonomy within genera.

Biography: Edson F. Abreu received his B.Sc. from the University of Santa Cruz do Sul, Brazil, in 2009 and his M.Sc. from the University of São Paulo, Brazil, in 2014. For his masters thesis, he studied the non-volant small mammal fauna of the southeastern Brazilian Atlantic Forest, and described a new rodent species. He earned his Ph.D. from the University of São Paulo, including a one-year program of doctoral research at the Smithsonian Institution’s Center for Conservation Genomics in 2020. His dissertation research focused on the phylogenomics, diversification, and biogeography of Neotropical squirrels (Sciurillinae and Sciurinae: Sciurini).

Courtesy of Jesse Delia

Dr. Jesse Delia

Research focus: My postdoctoral research focuses on why and how certain frogs attain transparency—a rare occurrence in terrestrial vertebrates. Glassfrogs are well known for their highly transparent skin and muscle tissue, through which their organs are visible. Under the supervision of my advisor Christopher Raxworthy, this comparative project aims to identify (i) the underlying specializations that balance the physical requirements for tissue transparency with the physiological demands of living cells, and (ii) the broader eco-evolutionary processes that explain these adaptations.

Biography: Jesse Delia received an MSc from East Carolina University (2011), where he was advised by Kyle Summers. He studied the social lives of Mexican glassfrogs in the understory cafetales of San Gabriel Mixtepec (Oaxaca). This work formed the foundation for his PhD thesis on the co-evolutionary dynamics of family life in glassfrogs, which spanned across the Americas. He received his PhD (2018) from Boston University under the supervision of Karen Warkentin. Prior to this fellowship, Jesse was a postdoctoral researcher in Lauren O’Connell’s lab at Stanford University, where he developed a protocol for in vivo cell labeling using non-model amphibians. He also began investigating the physiology of glassfrogs in collaboration with Carlos Taboada, Sönke Johnsen, and Junjie Yao at Duke University.

Courtesy of Maxwell Bernt

Dr. Maxwell Bernt

Research Focus -My research has been primarily focused on biodiversity in large tropical river systems. I am broadly interested in the evolution of fishes and particularly the origins of phenotypic diversity. Freshwater fishes exhibit a dramatic range of morphological disparity and while our knowledge of their evolutionary relationships continues to grow, we still have little understanding of the relationship between morphological evolution and lineage diversification for most taxa.

The African clariid catfishes comprise an ideal group to study this relationship as they show a remarkable array of phenotypic extremes. These include a range of body plans from fusiform to highly elongate (anguilliform), the loss or reduction of fins and eyes, and a flattening of the head with hypertrophied jaw muscles. This body elongation is of particular interest as anguilliform species are associated with both stagnant swamp habitats as well as swift, rocky river channels. Several phylogenetic studies have suggested that these phenotypes have independently evolved several times in Clariidae, however these analyses show substantial discordance and relatively low resolution. This group poses a number of questions including, how many times did anguilliform phenotypes evolve? Is anguilliformity discrete, or is it merely an extension of the phenotypic trajectories observed in other species? Are extreme phenotypes associated with higher rates of evolution?

My postdoctoral research will combine phylogenomic and morphometric data in an integrative framework in order to reconstruct the evolutionary history of Clariidae. The first stage of this study will be generating a robust phylogeny for the family using ultraconserved elements (UCEs). The UCEs will be tested against a molecular clock model and then filtered by clocklikeness with the goal of improving phylogenetic accuracy and computational efficiency. The filtered dataset will be incorporated with all available fossil data to generate a time-calibrated phylogeny. The second stage of the project will involve gathering morphological data from clariids to analyze in a phylogenetic and temporal context. Body shape will be quantified using a series of size-corrected linear measurements, while the shape of the skull will be analyzed independently using 3D geometric morphometric data taken from micro-CT scans. In order to assess the origins of extreme morphologies, I will perform a series of tests for correlation between phenotype and rates of lineage diversification as well as habitat type. Additional tests for correlation will be performed between each of three morphological datasets to determine the degree of convergence across anguilliform phenotypes.

Biography - Maxwell Bernt received his BA in biology from Carroll College (Helena, MT) in 2013. He earned his PhD in ecology and evolutionary biology from the University of Louisiana at Lafayette in 2013 under the supervision of James Albert. His dissertation research focused on the evolutionary history of the ghost knifefishes (Apteronotidae) a poorly-known group of weakly-electric fishes from South America. The project involved extensive collection of specimens and tissues, building a multilocus phylogeny, the description of new taxa, and analysis of the clade’s biogeographic history.

Courtesy of Johanna Harvey

Dr. Johanna Harvey

Research Focus - My postdoctoral work at the AMNH focuses on the effects of climate change on the distribution and virulence of avian malaria parasites and the effects on avian host immune response along the northern extent of the North American Atlantic flyway.

Biography - Johanna A. Harvey received her BS from Texas A&M University in 2010 and her PhD from Texas A&M University in 2018 under the supervision of Gary Voelker. Her dissertation focused on the using the phylogenetic relationships of avian malaria and related haemosporidians along with their host associations and environment to determine how these factors synergistically shape the resulting diversity and distributions across Africa. Results inform the association of phylogenetic haemosporidian subgenera groups with bioclimatic variables and host associations. Results found that internal clades are restricted to various bioclimate variables and host group associations, whereas broader patterns were not found at the level of genera. Results suggest that host specificity and generalism of malaria parasites are also constrained at lower taxonomic levels. These results inform possible climate change scenarios and highlight malaria clades which may be more prone to invasion and host shifting. Prior to the Gerstner Fellowship she was a postdoctoral researcher at the University of Connecticut under the supervision of Sarah Knutie working on the effects of urbanization and an invasive parasite (Philornis downsi) on Darwin’s finches in the Galapagos.

Dr. Chris Law

Research Focus - My current research as an NSF Postdoctoral Fellow (DBI–1906248) and Gerstner Scholar at the American Museum of Natural History focuses on the evolutionary integration of the cranial, axial, and appendicular skeleton and their contributions to mammalian body shape diversity and adaptive significance. Understanding the major patterns and adaptive significance of phenotypic variation is a central goal of evolutionary biology. In vertebrates, body shape diversity is one of the most prominent features of phenotypic variation that can lead to increased diversification, niche specialization, and innovations within a clade. However, biologists still lack a full understanding of the underlying morphological components that contribute to body shape diversity, particularly in endothermic vertebrates such as mammals. Consequently, little is known about the morphology, ecology, and evolution of mammalian body shapes as well as the underlying traits that contribute to different body plans. Therefore, I am generating the first quantitative database of mammalian body shapes using skeletal specimens. This database will enable me to document the underlying skeletal components that contribute to body shape diversity and test novel hypotheses in mammals, including the relationship between body shape and limb lengths and the influences of locomotor and dietary ecologies on the evolution of body shapes.

Biography - Chris J. Law received his B.S. from the University of California Santa Diego in 2012 and his Ph.D. from the University of California Santa Cruz in 2019 with Dr. Rita Mehta. His dissertation examined the species diversity and phenotypic disparity across Musteloidea (badgers, minks, otters, raccoons, red panda, skunks, and weasels) as well as the influences of tool use variation on individual dietary specialization on sea otters in the Monterey Bay.

Dr. Carrie Mongle

Research Focus - The primary focus of my postdoctoral research at the American Museum of Natural History is to address the question: What are the major phylogenetic patterns that characterize hominin diversity and evolution?

The ability to address fundamental questions about evolutionary transitions among hominins hinges on the knowledge of phylogenetic relationships among fossil species. Critically, however, no phylogenetic analysis of hominins has ever incorporated postcranial data. This represents a fundamental gap in our understanding of human evolution which could have significant implications for how we reconstruct hominin phylogenetic relationships. I am addressing this gap by undertaking an extensive character analysis of hominin postcranial fossils from both eastern and South Africa. This ongoing research builds on my previous phylogenetic work and will allow us to more directly address critical controversies in human evolution, such as the placement of Australopithecus sediba in relation to the genus Homo, and the importance of suspensory behavior as a derived or basal character in great apes. This represents a large-scale, multi-collaborator project that will form the foundation of my research program for the next 3-5 years.

In addition to the principle aims of my research outlined above, I am actively involved in the description and analysis of new hominin fossils in collaboration with Drs. Ashley Hammond, Meave Leakey, Frederick Grine, and others. In parallel with this research, I have also co-developed new software for the analysis and visualization of phylogenetic comparative data and continue to lead a collaborative project aimed at using primate teeth as a model system for linking micro and macroevolution.

Biography - Carrie S. Mongle received her BA from the University of Virginia in 2008 and her MA from Stony Brook University in 2015.  She earned her PhD from Stony Brook in 2019 under the supervision of Dr. Frederick E. Grine. For her doctoral work, Carrie developed a series of Bayesian models to understand the structure of dental variation in the fossil record in order to delimit hominin species. This work was awarded the “Anatomy in Anthropology Award for Innovative Anthropological Research” by the AAPA and the AAA professional societies, as well as the “Stony Brook President’s Award for Distinguished Doctoral Students”.  Findings from her research have been featured by international news outlets, including the BBC.

Dr. Nathan Lujan

Research Focus - My research focuses on the macroevolutionary ramifications of anatomical decoupling in the vertebrate cranium. Throughout the tree of life, the decoupling or loss of anatomical linkages is thought to be one way in which evolutionary constraints on organismal morphology are reduced, thereby accelerating the rate at which organisms diversify into different forms. Technological analogies to anatomical decoupling are common, from classical watch complications that increase time-keeping functionality to the expansion cards and subroutines of computers and computer programs that handle specialized tasks. To test the hypothesis that anatomical decoupling can increase the speed at which species diversify, my project will focus on a hyperdiverse clade of Neotropical catfishes – the Loricarioidei, which comprises six families, >140 genera, and >1,600 currently recognized species (~4.5% of all fish species).

Loricarioid catfishes occupy a wide range of aquatic habitats throughout tropical Central and South America, from coastal estuaries and deep river channels to high Andean streams and lakes over 4,500 m above sea level. Across these habitats, loricarioids have diversified to fill a wide range of mostly benthic niches. For example, many members of the family Trichomycteridae (~300 spp.) are specialized to feed on slime-coats, scales or gills of larger fishes. To facilitate host attachment while feeding, parasitic trichomycterid catfishes have a modified opercular mechanism with external teeth that can be erected to lock themselves into tight crevices, such as gill chambers. In contrast, members of the Astroblepidae (~80 spp.) and Loricariidae (~980 spp.) have a suctorial oral disk that allows them to attach to substrates while feeding, and jaws and teeth that are variously specialized for eating invertebrates, detritus, algae, and even wood. Loricariids also have an independently derived mechanism for everting opercular teeth during competitive interactions.

Throughout Loricarioidei, the cranium exhibits considerable morphological diversity, particularly related to oral and opercular mechanisms. My investigation of this diversity will interweave state-of-the-art methods in phylogenomics, anatomical visualization, comparative analyses, bioinformatics and computational biology. Across the Loricarioidei, three major intracranial ligaments have been lost, which respectively link: 1) the premaxillae to the mesethmoid, 2) bilateral mandibular rami to each other, and 3) the mandible to the operculum. I will use CT technology to capture a dense taxonomic sampling of 3D cranial shape data and will build a robust phylogeny for the entire clade using a sequence capture approach targeting hundreds of exonic (protein-coding) regions of the genome. Analysis of cranial shape data using modern phylogenetic comparative methods will allow me to determine whether cranial diversification rates change in response to individual decoupling events. Examining loricarioid catfishes in this context will provide a robust test of decoupling hypotheses, establish the tempo and mode of diversification in one of Earth’s largest vertebrate radiations, and deepen our understanding of an evolutionary process that is likely widespread throughout the tree of life.

Biography - Nathan K. Lujan received his BSc in Biology from Calvin College in 2000 and his PhD from Auburn University in 2009 under the supervision of Jonathan Armbruster. His dissertation focused on the jaw morphofunctional diversity, trophic ecology, and historical biogeography of the suckermouth armored catfish family Loricariidae. Prior to this Gerstner Fellowship, he was an NSF International Research Fellow at the Royal Ontario Museum, an NSF Postdoctoral Researcher at the Academy of Natural Sciences of Drexel University, and a Canada Department of Fisheries and Oceans Postdoctoral Researcher at the University of Toronto.

Courtesy of Ariadna Morales

Dr. Ariadna Morales

Research Focus - My postdoctoral research at the AMNH focuses on the genomic mechanisms of convergent evolution. I aim to establish a model system to study the processes linked to repeated ecological and morphological adaptation in nature, using as an example the traits and foraging strategies that have evolved in parallel in the bat genus Myotis.

Parallel evolution, the independent development of the same trait in different taxa, is a common process in nature that raises questions regarding the involved genomic mechanisms and the role of natural selection as the driver of repeated adaptations. My research implements novel genomic techniques and statistical tools to explore the genetic mechanism linked to parallel evolution of phenotypic traits, using as a model the most specious genus of bats, Myotis. This genus is found worldwide and has been classified into three ecomorphs following foraging strategies that seem to be evolved repeatedly. My approach for studying parallel evolution goes from a broad genomic perspective to explore whether homologous genes are linked to the reoccurrence of phenotypes in species that have been isolated millions of years, to detailed genotype-phenotype association approaches to explore if the presence of traits linked to foraging adaptations can be predicted by certain genomic features. This study is leading to a comprehensive understanding of the genomic mechanism of parallel trait evolution in natural conditions.

Biography - Ariadna E. Morales earned a BSc in Biology in 2009 and an MSc in Evolutionary and Environmental Biology in 2012 from the Universidad Nacional Autonoma de Mexico (UNAM) under the supervision of Dr. Daniel Piñero. She earned a Ph.D. in Evolution, Ecology, and Organismal Biology and a Graduate Minor in Statistics in 2018 from The Ohio State University under the supervision of Dr. Bryan Carstens. As part of her dissertation work, Ariadna contributed to developing computational tools for phylogeographic model selection and species delimitation that handle efficiently big datasets and helped to develop the R package “PHRAPL”. She also documented striking examples of speciation with gene flow in North American bats of the genus Myotis by integrating genomic, environmental and morphometric analyses. Finally, she investigated if the convergent evolution of foraging strategies in the genus Myotis (~70-80% of 106 extant taxa) is linked to diversification shifts using phylogenetic, biogeographic and comparative methods.

Dr. David Wright

Research Focus - I am an evolutionary paleontologist interested in the origin of major lineages, their adaptations, and the interplay between ecological and geological processes in large-scale evolutionary radiations throughout the history of life. I use a combination of specimen-based research (including specimens housed in the AMNH collections), phylogenetic methods, and mathematical modeling to study how physical and intrinsic biological processes shape macroevolutionary dynamics in the marine biosphere. My taxonomic specialty is the exclusively marine phylum Echinodermata.

Echinoderms are represented by more than 7,000 species in today’s oceans and include familiar animals such as starfish, sea urchins, and sand dollars. The apparent diversity of echinoderms alive today masks their more prodigious geologic history. For example, the Crinoidea (feather stars and sea lilies) comprises an evolutionary lineage of reef-dwelling to deep water echinoderms represented by ~600 species today, yet more than 8,000 fossil species have been described spanning ~480 million years of evolutionary history. My current research revolves around several facets of crinoid origins: both the early evolution of total-group Crinoidea during the Ordovician Radiation and the phylogenetic origin and radiation of the crown group during the Paleozoic—Mesozoic transition. The origin and radiation of crown-group crinoids is of particular interest because the early stages of their diversification spans the most severe extinction event in the history of life: the Permian-Triassic mass extinction. The results from my research will provide a means to test alternative theories predicting how biodiversity accumulates in “crowded” vs. “empty” (e.g., pre-vs. post-mass extinction) ecosystems more generally, such as whether diversification within lineages is driven more by ecological opportunities, the evolution of key innovation traits, or by “background” origination of novel adaptations.

I am also presently involved in a number of taxonomic projects describing new species from exceptionally well-preserved echinoderm faunas from around the world, including the Ordovician “Brechin Lagerstätte” of Ontario and the Permian of west Texas.

Biography - David F. Wright received his BSc in Geology (minor in Astrobology) from the University of Kansas in 2010, his MSc in Geological Sciences from Ohio University in 2012, and his PhD in Geological Sciences from The Ohio State University in December 2016. For his doctoral studies, Davey focused on the application of statistical phylogenetics and comparative methods to paleobiological data, with empirical work emphasizing fossil echinoderms. His doctoral research also featured a major systematics component in which he described several new crinoid species and comprehensively revised the higher taxonomic classification of Class Crinoidea (Echinodermata). 

Dr. Phillip Skipwith

Research Focus - My postdoctoral research focuses on the macroevolutionary dynamics of an ecologically and morphologically diverse group of snakes, the pseudoxyrhophiine lamprophiids of Madagascar. This is a diverse group of ~85 species in 20 genera representing a radiation endemic to Madagascar. Very little is known about the ecology and morphological diversity of this exceptional clade. What is known is that, since the late Paleogene, this clade has colonized a number of niches resulting in fossorial, terrestrial, and arboreal forms with accompanying variation in size and shape. Previous studies attempting account for morphological diversity have been largely descriptive in nature. Moreover, this clade represents the only insular snake radiation where there has been extensive in situ diversification. Until recently, phylogenies of the Malagasy pseudoxyrhophiines have been poorly supported and incongruous, compounding the attempts to address macroevolutionary dynamics. Using a new and fully resolved species-level phylogeny generated from hundreds of anchored tag loci, I will use morphology to investigate phenotypic diversification within this group. My project involves using 3D x-ray computed tomography (CT scanning) to generate 3D models of the skeleton and soft tissues for species within this clade. These data will be used to address: 1) morphological diversity across the entire radiation, both interspecifically and intraspecifically, 2) the dynamics of phenotypic diversification through time, 3) the relationship between net diversification and phenotypic diversification, 4) and the presence of determinism and convergent evolution. Lastly, I will examine if environmental heterogeneity, particularly climate, has influenced ecological and ecomorphogical diversification within pseudoxyrhophiines. Determining the relationships between speciation, phenotypic diversification, and extrinsic factors is critical to our understanding of how biodiversity is generated and maintained across long timescales. The Malagasy pseudoxyrhophiines represent an excellent system through which we can understand these complex patterns and processes and inform conservation initiatives.

Biography - Phillip L. Skipwith received his B.S. from the Richard Stockton College of NJ in 2008, his M.S. from Villanova University in 2011 under the supervision of Aaron Bauer, and his PhD from the University of California, Berkeley in 2017 under the supervision of Jim McGuire. His dissertation focused on the phylogenomics and macroevolutionary dynamics of the diverse diplodactyloid geckos of Australasia.

Dr. Benjamin Titus

Research Focus - My research is focused on understanding how biodiversity evolves in tropical marine symbioses at the species, population, and behavioral levels. I use sea anemone symbioses that live on coral reefs as models to understand the evolutionary processes and outcomes that generate and maintain diversity in these tightly linked interactions. I have primarily focused my research program on sea anemone symbioses from the Tropical Western Atlantic and Caribbean, but for my postdoctoral work I will be focusing exclusively on the evolution of sea anemones that host clownfishes in the Indo-Pacific.

Symbiosis often confers novel abilities or characteristics in at least one partner, can lead to adaptive radiation, and contributes meaningfully to the biodiversity within ecosystems. The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes, and is one of the most recognizable symbioses on the planet. There are 30 described species of clownfishes, which have adaptively radiated to live with sea anemones, but only 10 nominal species of host anemones. Why have the host anemones not undergone a radiation similar to the clownfishes? Given the co-dependent nature of the mutualism, their broad geographic and ecological distribution, extensive phenotypic variation, and that all 10 host species are only described morphologically, I hypothesize that there is undescribed cryptic species-level diversity within the host anemones.

Using high-throughput sequencing (i.e. RADseq, Ultra-conserved elements), molecular species delimitation, and a comparative phylogeographic framework, I will test allopatric and ecological speciation hypotheses to search for cryptic species and reconstruct the evolutionary histories of the two most common sea anemone host species from the tropical Indo-West Pacific (IWP) oceans: Entacmaea quadricolor and Heteractis crispa. A genomic perspective is likely to be critical for understanding sea anemone diversity given the inherent challenges with classic morphological studies in this group. Ultimately, the existence of undescribed cryptic anemone host species has the potential to re-write much of our understanding of this symbiosis and impact the evolutionary, ecological, and behavioral theory that has been generated from the study of these charismatic relationships. This work will also have important conservation implications as these species are among the most heavily collected species in the ornamental aquarium trade.

Biography - Benjamin Titus received his BSc in Ecology from Otterbein University in 2008, his MSc in Marine Biology from Auburn University in 2011, and his PhD from the Dept. of Evolution and Ecology from The Ohio State University. For his doctoral work he studied the comparative phylogeography of sea anemone symbioses on coral reefs in the Tropical Western Atlantic and was advised by Meg Daly.

Website - https://reefsymbiosis.com/

Dr. Federico Lopez-Osorio

Research Focus – I study the evolutionary relationships and molecular basis of social behavior in wasps. Specifically, I focus on the subfamily Vespinae (yellowjackets and hornets). These wasps live in colonies usually including a single reproductive queen, and hundreds to thousands of sterile workers that raise the queen's offspring. Worker and queen castes in advanced societies of yellowjackets and hornets can be morphologically different and, unlike groups of primitively social wasps, individuals cannot switch between castes as adults. The field of sociogenomics aims to understand the origin of social behavior in molecular terms. The Vespinae are particularly interesting for comparative studies in sociogenomics because its close relatives in the family Vespidae exhibit a full range of social phenotypes, from solitary to primitively social. Moreover, the Vespinae include socially parasitic species, which have secondarily lost the worker caste and rely on parental care from workers of host species. Therefore, social parasites may allow the identification of changes in genetic architecture associated with the loss of free-living traits, such as maternal care and nest founding, or the gain of parasitic behavior.

For my research as a Gerstner Scholar, I will address three objectives. First, I will augment existing transcriptomic data, identify single-copy genes, and conduct a phylogenomic analysis of vespine wasps. Second, I will use the inferred phylogeny to search for evidence of positive selection, and I will test the ‘novel’ genes hypothesis, which states that sociality is the product of the evolution of genes lacking detectable sequence similarity to known genes. Lastly, I will characterize the transcriptomes of socially parasitic species and test for the predicted loss (or lack of expression) of genes associated with maternal care.

Biography - Federico Lopez-Osorio received his B.Sc. from the Universidad Industrial de Santander in Colombia in 2009, and completed his Ph.D. in 2016 at the University of Vermont, where Dr. Kurt M. Pickett and Dr. Ingi Agnarsson were his advisors. In his doctoral studies, he focused on molecular phylogenetics and comparative transcriptomics of yellowjackets and hornets. 

Website - https://www.qmul.ac.uk/sbcs/staff/federicolopez-osorio.html

Dr. Edward A. Myers

Research Focus – My postdoctoral research is focused on understanding variation in rattlesnake venom. Viperids, the family of snakes that includes rattlesnakes (Crotalus and Sistrurus), have venoms that are largely characterized as hemotoxic or hemorrhagic. However, a number of rattlesnake species and populations posses a potent neurotoxin. Despite these species being widespread within North America and being of medical importance, how these venoms have evolved is still unresolved. Recent studies have suggested that neurotoxic venoms are shared between rattlesnake species or populations because of past hybridization events (e.g. Zancolli et al. 2016 and Rokyta et al. 2015). However, other studies have concluded that the ancestor to all rattlesnakes possessed the genes responsible for these neurotoxins, and therefore species that lack this component in their venom have lost these genes at some point during their evolutionary history. My work will focus on addressing these competing hypotheses. In order to do so I will be generating RNA-seq data from venom glands and designing a set of DNA-probes to sequence venom genes across Crotalus. Ultimately this work will address how many times neurotoxin genes have evolved and whether hybridization plays a large role in the distribution of this trait across the rattlesnake phylogeny, which may contribute to our understanding of venom evolution in other snake groups as well as trait evolution in general.

In addition to the rattlesnake work, I will continue to work on population genomics and species delimitation in a number of North American snake taxa. This work seeks to address the mechanisms of speciation, while quantifying biodiversity within the US and Mexico. For example, collaborators and I are generating a genomic data set for the genus Pantherophis (rat snakes and corn snakes) to test species boundaries and to understand color pattern evolution in snakes.

Biography - Edward A. Myers received his B.Sc. in Zoology from Washington State University in 2009 and Ph.D. from the City University of New York in Biology in 2016, under the supervision of Dr. Frank Burbrink. His dissertation focused on comparative population genomics and ecological speciation of codistributed snakes across the desert southwest of North America.

Website - https://edwardamyers.wordpress.com/

Dr. Lu Yao

Research Focus – My research interests thus far have utilized phylogeographic analysis and phylogenetic comparative methods to answer a number of questions concerning the evolution of mammals on islands. For my postdoctoral work, I will be expanding on this research by studying gibbon evolution through a combination of genetics and morphology to better understand the intraspecific variation and level of hybridization within this highly endangered family of primates in Southeast Asia. 

Gibbons (Hylobatidae) are relatively more speciose compared to other apes. Although some species are relatively well known, so far no attempts have been made to sample widely within each gibbon species to understand intraspecific variation and hybridization. My research is designed to use a combination of next generation sequencing techniques with morphometric analyses of wild gibbon specimens housed in museum collections around the world, including the extensive collections at AMNH, to expand knowledge about gibbon phylogeography, molecular evolution, and morphology at the population level. I will generate mitogenome, exome and single nucleotide polymorphism (SNP) data for a large selection of gibbon individuals across as many species as possible. With these data, I will be able to reconstruct a well-resolved intraspecific phylogeny, recognize hybridization events that may have occurred, and identify specific genes that experienced positive selection in different lineages. In addition to the genetic data, I am also collecting 3D morphological data from extant museum specimens along with alleged Hylobatidae fossils in order to analyze size and morphological variation between and within extant and fossil species. With this combination of genetic and morphological data, I intend to explore and illuminate the importance of intraspecific-level analyses, particularly in this group of understudied primates.

Biography - Lu Yao received her B.A. degree in 2011 from Northwestern University in the Integrated Science Program, Anthropology, and Biology. For her doctoral work, she was advised by Robert D. Martin and Corrie S. Moreau and studied the evolution of mammals on islands with a focus on long-tailed macaques. She received her Ph.D in 2016 from the Committee on Evolutionary Biology at University of Chicago.

Website - https://luyaobiology.com/

Dr. James Herrera

Research Focus – For my postdoctoral fellowship, I am expanding my prior studies of diversification to investigate the mode and tempo of primate evolution. I am investigating how diversification has varied with biogeography, time, paleoenvironments and community composition for all primates across the globe and in deep time.

The first step is to infer a combined phylogeny for all primates, including both extinct and living taxa. I am gathering published and new morphological data for living and fossil primates from museum collections, including the extraordinary collections at the AMNH. I will combine these with molecular data available for almost all living species and several subfossil species. I then will apply a total evidence dating approach that determines the inferred speciation and extinction rates of the tree based on the fossils included in the analyses.

The second step is to compare speciation and extinction dynamics inferred from the phylogeny of only living species to those inferred from fossils. Estimates of speciation and extinction have been made from phylogenies of only living species, but the validity of these methods is contentious. I will compare the diversification dynamics estimated from different methods and test the most likely processes explaining diversification dynamics in deep time over the 65 million year history of Primates. I will quantify how species diversity varies across the evolutionary tree and test if age, diversification rate, biogeography and intrinsic traits explain the variation in observed species diversity.

My research also investigates the biogeography and community ecology in Madagascar by expanding from my previous studies of lemurs to include more taxonomic groups, including bats, carnivores, tenrecs, birds, amphibians, reptiles, fishes, and plants. I am seeking collaborations with specialists in these other groups to test if the patterns observed for lemurs hold for other groups as well. Finally, I am collaborating with other researchers to quantify the habitat loss around the measured communities to assess their threat status.

Biography - James Herrera received his Bachelors in Arts degree in 2009 from the University of Miami (FL) in Anthropology. He then earned his Master of Arts degree in 2011 from Stony Brook University (NY) in Anthropology and received his Ph.D. in 2015 from the Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University (NY).

Website - https://herrerajamesp.weebly.com/

Dr. Brendan Reid

Research Focus – My research interests lie in understanding and conserving turtle diversity.  Turtles represent both an enormously charismatic and highly threatened group of reptiles, with approximately two-thirds of all turtle species considered to be at risk of extinction.  They are morphologically and biogeographically extremely distinctive.  While many other taxonomic groups are at their most diverse in the tropics, turtles instead exhibit their highest levels of species diversity in subtropical areas.  In fact, the United States is home to more turtle species than any other nation, and the southeastern US is considered to be a global hotspot of turtle diversity.  A better understanding of the processes responsible for creating and maintaining turtle diversity will help us understand how this diversity has survived in the face of shifting climates and habitats over the past several million years and how turtles may fare in the future.

Several roadblocks, however, still exist to understanding turtle diversity.  Reproductive barriers among turtle taxa develop slowly, and ancient introgression as well as contemporary gene flow can obscure our understanding of past and ongoing speciation processes.  Turtle DNA in general evolves relatively slowly compared to other vertebrate groups, and some recently-diverged turtle groups that exhibit a great deal of morphological diversity (such as the American map turtles) are still highly similar or identical for many traditional molecular markers used in evolutionary studies.

For my research at the AMNH, I will generate genomic single nucleotide polymorphism (SNP) data for an array of turtle species, focusing on pond turtles (family Emydidae) and mud turtles (family Kinosternidae) in North America.  These data will be used to refine our understanding of recent evolution in these groups as well as to test hypotheses generated from paleophylogeographic species distribution models (which use present-day ranges, past climate reconstructions, and phylogenetic relationships to project species’ distributions into the past and to infer changes in distribution over time).  By explicitly incorporating genetic data into range modeling, I intend to improve our understanding of how species’ ranges change over time, discriminate the effects of different potential drivers of species distributions (including climatic tolerances, local adaptation, and competitive interactions), and develop more accurate methods for predicting future changes in species ranges and the distribution of biodiversity.

Biography - Brendan Reid received his Masters degree in Conservation Biology from Columbia University in 2009.  His Masters thesis project on genetic barcoding of turtles developed from a research internship at the AMNH, where he worked extensively with Museum research associates Dr. Eugenia Naro-Maciel and Dr. Minh Le.  He has continued to work on various research topics (ranging from the genetic structure of spiny lobsters and New Guinea snapping turtles to the historical demography of green sea turtles) with AMNH scientists and other collaborators in the years since.  For his Ph.D., Brendan studied under Dr. Zach Peery at the University of Wisconsin-Madison, where he investigated the ecology and conservation status of three wetland turtle species (including the endangered Blanding’s turtle) in the Midwest using demographic and landscape genetic approaches, obtaining his doctorate in 2015. 

Dr. Nelson Salinas

Research Focus – I am trained as a botanist and have worked on Neotropical plant diversity over the last 15 years. Most of my previous research has been devoted to either floristics of the NW Amazon flora, or systematics of Neotropical plant groups, including blueberries (family Ericaceae), bromeliads (Bromeliaceae), and spiral gingers (Costaceae). More recently, I have become interested in biogeography, particularly in the estimation of ancestral ranges of tropical taxa, such as Ericaceae, and improving the delimitation of their geographical areas of endemism.

As a Gerstner Scholar, I am continuing my research on biogeography from a bioinformatics perspective. My current project aims to assess the adequacy of statistical models to describe patterns of geographic distributions of a variety of organisms. Attaining such a widely-applicable class of models will allow biogeographers to advance new tools for analysis, helping to incorporate uncertainty of geographical distribution data into historical range reconstructions and to implement more elaborate hypothesis testing procedures. As a first approximation to these models, I am beginning by developing an algorithm to infer areas of endemism, that is, geographic regions to which two or more taxa are likely to be restricted. This new algorithm will be tested against both simulated and empirical data, and implemented as a Python program that will be available to other researchers.

The empirical part of my Gerstner Scholar project includes biogeographic analyses of Neotropical blueberries (Ericaceae: Vaccinieae). These plants are ecologically important elements of the montane flora across Latin America, where they are usually found in well-preserved rain forests. Most species are epiphytic shrubs, which have bright, colorful flowers that are often pollinated by hummingbirds. Their diversity (around 600 species) and multiplicity of distribution patterns (from narrow endemics to widespread taxa) make them an excellent group to examine the efficacy of different methods to uncover areas of endemism.

Biography - Nelson Salinas received his B.Sc. in 2004 from the Universidad Nacional de Colombia, and his Ph.D. in 2015 in Biology from the City University of New York, in collaboration with the New York Botanical Garden. His doctoral research was focused on the taxonomy, phylogenetics, and biogeography of Neotropical blueberries.

Dr. Abigail Curtis

Research Focus – I am studying the role of paranasal sinuses in the evolution of morphological disparity and species diversity in bats using microCT scans. Paranasal sinuses are air-filled cavities in the bones surrounding the nasal chamber in mammals that appear to opportunistically develop in space where bone is mechanically unnecessary. Sinuses functionally decouple the inner and outer tables of the bones they pneumatize, which may allow external skull shape to be more easily modified without affecting the morphology of more functionally constrained regions, such as the nasal chamber and braincase. Thus, paranasal sinuses may facilitate evolution of skull size and shape disparity. Bats are an excellent framework in which to test this hypothesis because they represent over one fifth of living mammals species, and show remarkable disparity in skull size and shape. Clades of bats that show the greatest species diversity also show some of the greatest morphological disparity, and the literature suggests that some species with highly derived morphologies also have unusual sinus morphologies that have yet to be described. My work will provide the first quantitative data on bat paranasal sinuses, and will generate a large collection of CT scans from AMNH specimens. This research will aid our understanding of how mammal skulls evolve to meet the demands of differing diets, and may reveal factors that facilitate evolution of cranial shape disparity and allow species to adopt novel ecologies.

Biography - Abigail Curtis received her Ph.D. in Biology at UCLA in 2014, and was advised by Dr. Blaire Van Valkenburgh. She earned her B.S. in Biological Sciences from SUNY at Albany in 2008. Her interest in anatomy and functional morphology was sparked during her time as a mammalogy research and collections intern at the New York State Museum during her junior and senior years of college. This experience also gave her an appreciation for museums as an invaluable resource to the scientific community as well as the public. 

Website - https://abigailacurtis.wixsite.com/abigailcurtis

Dr. Steven Davis

Research Focus - My research centers in weevil (Curculionoidea) systematics, exploring the morphology, patterning, and evolutionary development of these remarkably diverse and curious beetles. My research centers in weevil (Curculionoidea) systematics, exploring the morphology, patterning, and evolutionary development of these remarkably diverse and curious beetles. While my interests are strongly nested within comparative morphology and weevil systematics, I desire to employ a broad range of tools in evolutionary biology to better understand the taxonomy, classification, and evolution of one of the largest radiations in the tree of life.

Emanating from these interests, I have been integrating techniques of evo-devo and developmental biology to better understand the genetic basis of morphological structure and evolution. I began by exploring the development and patterning of the weevil rostrum, a feature of this group which is believed to represent a key evolutionary innovation permitting them to undergo a spectacular radiation.

Current and future work includes understanding the specific functions of these genes, their expression patterns, and determine the utility of such developmental data in a comparative phylogenetic context, using RNA interference (RNAi) and in situ hybridization. While it is a primary goal to understand how the rostrum forms (i.e., how the head elongates), throughout the weevil superfamily, this structure (defined as an extension of various head segments and bearing the mouthparts at the apex) has also magnificently diversified into countless forms and demonstrates amazing modifications traversing the different weevil lineages. The rice weevil, Sitophilus oryzae, has been the main experimental candidate for this research, though other weevil taxa which transcend the range of rostral diversity, are significant to agriculture and forestry, and can be reared in the laboratory, are being utilized for comparison, including Dendroctonus ponderosae (Mountain Pine Beetle), Diaprepes abbreviatus (Citrus Root Weevil), Hypothenemus hampei (Coffee Berry Borer), and Curculio spp. (Acorn Weevils).

Weevils, however, are not the only beetles (nor insects) to possess a rostrum. Other insect groups, such as Diptera (flies), Lepidoptera (moths and butterflies), Hemiptera (true bugs), and Siphonaptera (fleas), possess structures that resemble a rostrum, though these structures are formed through elongation of different mouthparts. Of the insect groups that bear a true rostrum, including various lineages within Coleoptera (beetles), Hymenoptera (bees and wasps), and Mecoptera (scorpionflies), weevils have maximized the diversity in rostral forms. As a comparison to weevil rostrum formation and patterning, rostrum development in lineages within Lycidae (Net-winged beetles) and Mecoptera also is being investigated.

New insect systems in developmental biology are being developed through such developmental research, in which the relationships between morphological change and structural genes responsible for phenotypic change are examined. These results will also have remarkable influence in understanding homology statements in phylogenetics, can be used in phylogenetic reconstruction, and can allow for rigorous interpretation of character and developmental evolution across groups. Examination of rostrum formation in other beetle families and insect orders will address a key question in evolutionary developmental biology concerning the degree of novelty of evolutionary innovations and convergence of morphological features.

Biography - Steve Davis received his B.S. in entomology from the University of Maryland, College Park, in 2005, completing his undergraduate thesis with Dr. Charles Mitter (UMCP) and Dr. Patricia Gentili-Poole (Smithsonian, USNM) on carpenter moth (Cossidae) systematics; thesis entitled " A revision of the Cossulinae of Costa Rica and cladistic analysis of the world species (Lepidoptera: Cossidae)." He went on to complete his M.A. in entomology from the University of Kansas in 2008, studying weevil systematics with Dr. Michael Engel, the thesis entitled " Morphology and phylogeny of the weevil subfamily Baridinae (Coleoptera: Curculionidae)." He then continued on at Univ. of Kansas with Dr. Engel to receive his Ph.D. in 2014 studying weevil systematics, morphology, and evolutionary developmental biology. 

Dr. Christopher Martinez

Research Focus – I am broadly interested in the evolution of form and function and enjoy applying morphological analyses in different systems. During my Ph.D. I assessed the diversity of pectoral fin shape in batoids and also linked sexual dimorphism in skate fins to the development of their reproductive organs. Currently, my research as a Gerstner Scholar is focused on understanding modes of oral jaw diversification in teleost fishes. I am primarily working on two of the lesser-known cichlid subfamilies, Etroplinae and Ptychochrominae. Etroplinae includes two genera, Etroplus of India/Sri Lanka and Paretroplus, whose species are endemic to Madagascar. Ptychochrominae consists of five genera that are also endemic to Madagascar. Variation in overall body form and jaw morphology is larger in the ptychochromines, although etropline cichlids also display interesting morphological patterns that appear to be habitat specific.

I am using geometric morphometrics to quantify and compare morphological diversity of body shape and internal structure of oral jaws between the two cichlid subfamilies. In addition, I am evaluating jaw variation in terms of a four-bar linkage system, which has been used as a model for jaw mechanics in a number of fish groups. As an essential component of this research, we are currently updating the phylogenetic relationships of Malagasy and South Asian cichlids in order to estimate ancestral states of jaw form and their corresponding functional properties. This information will be used in a modeling framework that is designed to simulate hypothetical morphological pathways that represent transitions between functional states of ancestors to that of their descendants. Due to the complex nature of the form-function relationship in four-bar linkages, we expect starting ancestral morphologies to be a vital determinant of the ability and ease by which a species may respond to selection for new functional states. This research will give us valuable context with which to understand current jaw diversity and will also provide a framework to pursue a number of questions. For instance, among species whose jaws are suited to a diet of snails (durophagy), which is most likely to evolve the ability to capture mobile prey (e.g. piscivory)?

Biography – Christopher Martinez received his B.Sc. from the University of California, Santa Barbara in 2006 where he researched a mutualistic relationship between corals and amphipods. He completed his Ph.D. at Stony Brook University in 2014, with his dissertation research concerning the morphological diversity of batoid fishes (i.e. skates and rays) and also spatial modeling of marine communities. 

Dr. Aaron Heiss

Research Focus - My research focuses on the morphology and evolution of protists (those eukaryotes that are not also plants, animals, or fungi).  I am particularly interested in organisms from 'orphan' lineages (those without known close relatives) and those representing ancestral forms, which in most cases are unicellular, heterotrophic flagellates.

My studies in morphology have centred around the use of transmission electron microscopy (TEM).  I use serial sections from a single cell to make a computer-based model of the cytoskeleton, referring to series from additional cells for consistency.  I combine this with observations using contrast-enhanced light microscopy (LM) and scanning electron microscopy (SEM) to produce a comprehensive view of the cell’s structure.  One exciting development of this is that my models can be made into physical objects through the use of 3D printers and related technology.  Physically or virtually, these models can be compared with one another, as well as with models developed from previous research, to give an idea of the evolution of the morphology of the eukaryotic cell.

That comparison requires a solid evolutionary framework, which is unfortunately lacking in many critical cases.  Molecular phylogenies (evolutionary trees based on genetic data) have proven surprisingly dependent upon such factors as selection of gene, which organisms are included, the method used to translate genetic data into a tree, and the individual researcher’s often-subjective preparation of that data.  Rather than solid answers, the last few decades of phylogenetic research have given us a series of (usually) increasingly consistent hypotheses.  In some cases, such as the relationships amongst the major eukaryotic lineages, those hypotheses remain tentative.  One factor that remains definitely lacking is representation of the same groups that I am most interested in.  To that end, I sequence genetic data on both the small (individual gene) and large (transcriptomic) scales.  In addition to solidifying our understanding of the relationships of major lineages, the trees that I generate also yield both questions and (sometimes) answers about the evolution of critical features of the eukaryotic cell.

The data that we are able to obtain from any organism is contingent upon that organism being sampled in the first place.  Surprisingly, new organisms, representing very deeply divergent lineages, continue to be discovered on an almost-regular basis.  In some cases, organisms are rediscovered after decades of not having been reported; in others, completely new lineages are found that had not been anticipated.  I have been sampling the environment for such organisms, discovering and culturing both new and rediscovered strains, and assisting others with similar work.  This provides the raw material for my ongoing phylogenetic and morphological studies.

Biography - Aaron Heiss completed his B.S. in Biology at Portland State University in 2002.  He then worked in PSU’s Museum of Vertebrate Biology for two years, until starting graduate school.  He earned an M.Sc. in Botany from the University of British Columbia in 2006, working in the lab of Dr. Patrick Keeling, and a Ph.D. in Biology from Dalhousie University, working under Dr. Alastair Simpson.  After additional work in Dr. Simpson’s lab as a postdoctoral researcher, he was awarded a Japan Society for the Promotion of Science postdoctoral fellowship, for which he spent eight months in Japan at the University of Tsukuba.  His research at the American Museum of Natural History is an extension of his work in Japan.

Website - https://www.amnh.org/research/invertebrate-zoology/staff/postdoctoral-fellows/aaron-a.-heiss-ph.d

Dr. Adrien Perrard

Research Focus - I am interested in the use of the wing shape as a new marker to reconstruct relationships among social wasp species. The wing venation is a long-known marker in insect identification. Geometric morphometrics methods enable to quantify the shape of the venation using landmarks in order to detect subtle morphological differences. During my PhD I developed a method to measure the wing shape of pinned specimens from natural history collections without damaging them. I used this method to study the caste and sex dimorphism of the wing shape in hornets and the variation between populations of a single hornet species and between the different species of hornets. My results confirmed that the wing shape enables to identify species of hornets, sex, castes and isolated populations, and that this structure presents a significant phylogenetic signal, i.e. that the wing shape similarity of insect species is congruent with the phylogeny.

My Gerstner project aims at determining whether the wing shape could be a good marker for phylogenetic reconstructions. The wing shape can be measured on ancient material from Natural History collections, and the wing is one of the best structures preserved in fossil insects. Using wing shape as a phylogenetic marker could improve phylogenetic inferences of rare or extinct species for which no molecular data could be available. The use of data from geometric morphometrics in phylogenies has long been a subject of debate because of their multivariate continuous nature, but a new method was recently developed for using landmark data in phylogeny outside from the framework of regular geometric morphometrics. Using this method, I will test the efficiency of wing shape for reconstructing the phylogeny of the Vespinae.

The subfamily of social wasps Vespinae comprises hornets and yellow-jackets. However these insects are well-known due to their large colonies and feared stings, the phylogeny of this group, comprising 70 species, has been surprisingly poorly studied. During this project, I will develop a comprehensive analysis of the phylogeny of the Vespinae integrating molecular markers and traditional morphological characters. This analysis will serve as a framework for estimating the suitability of wing shapes as markers for phylogenetic reconstruction and to test the methods of integration of geometric morphometrics data in phylogenies.

Biography- Adrien Perrard graduated at the University of Toulouse, in the South of France. He studied there the biology of a new invasive hornet. He completed his master’s degree in Palaeontology, Systematics and Evolution at the University Pierre & Marie Curie (Paris). For his master thesis, he worked on the phylogeny of hornets (genus Vespa) at the University of Vermont with Kurt M. Pickett and at the American Museum of Natural History with James M. Carpenter. He did his Ph.D. between 2009 and 2012 at the Muséum National d’Histoire Naturelle in Paris under the co-direction of Claire Villemant and James M. Carpenter. Before his Gerstner appointment in October 2013, he worked on a French collection of amber fossils with André Nel at the Paris Museum as a part-time employee. 

Website - https://adrienperrard.wordpress.com/about/

Dr. Sara Ruane

Research Focus - My research interests include many aspects of herpetology, but are particularly strong within the realm of evolutionary biology and systematics and focus extensively on snakes. My current research, working with Dr. Chris Raxworthy, is on the systematics and phylogenetics of the Malagasy Pseudoxyrhophiine snakes. Madagascar has frequently been considered an ideal model system for understanding basic evolutionary processes including diversification and the interaction between ecology and speciation. The Pseudoxyrhophiinae snakes are a striking example of a group in Madagascar showing both high species diversity and encompassing a wide range of morphologies, habitat use, and diets. This monophyletic subfamily is one lineage of the largely continental African snake radiation Lamprophiidae, which makes up >98% of the Madagascan colubroid snake assemblage. Pseudoxyrhophiinae is represented by 88 described species in 21 genera, with 18 of these genera forming the Malagasy radiation of 83 described species (Reptile Database). This group provides an opportunity to examine causes of speciation, and the ecological and morphological diversity found in these snakes is comparable with other continental radiations. However, the advantage here is that pseudoxyrhophiines are almost entirely endemic to Madagascar, with little outside influence from colonization of other snake groups.

To estimate broad patterns relating to the tempo of diversification in extant taxa and to understand basic taxonomy, it is imperative to have a phylogeny of Pseudoxyrhophiinae. However, <50% of the described species have so far been included in the broadest published molecular study. In addition, preliminary work suggests that species diversity has been greatly underestimated for these snakes, likely due to cryptic species and poor sampling. By using next generation sequencing techniques we are generating 100’s of homologous loci across all taxa in this group in order to properly estimate phylogeny and divergence times. Understanding relationships among pseudoxyrhophiines, and the timing of origin and diversification, requires a precisely estimated and dated species tree. The species richness of the Malagasy pseudoxyrhophiine radiation, coupled with their ecological diversity (arboreal, surface dwelling, fossorial, and aquatic) and high levels of regional endemism for most species make this an ideal group to explore patterns and process of species radiations, especially concerning the tempo of species diversification in relation to both morphological and ecological evolution. My most recent work is focused on screening our current tissue collection for potentially cryptic species using a handful of informative loci, as well as targeted collecting of species in Madagascar that we are missing from our dataset.

Biography - Sara received her doctorate (Ecology, Evolution, and Behavior) from the CUNY Graduate Center in November 2012. Her dissertation, entitled “Phylogenetics, Phylogeography, Historical Demography and Morphology of Milksnakes (genus Lampropeltis)”, disentangled the systematics of the species formerly known as Lampropeltis triangulum. Her research experience is primarily within evolution and systematics, with a strong focus on herpetology, especially snakes. She also has additional training in ecological research as well, having done a MS examining ecology and population demography of Blanding’s turtles. You can read more about Sara’s research at sararuane.wordpress.com.

Website - https://ncas.rutgers.edu/about-us/faculty-staff/sara-ruane

Dr. J. Angel Soto-Centeno

Research Focus - I am fascinated by population genetics, phylogeography, distribution models, fossils, and the application of computer software to solve population level evolutionary problems. I use climate based ecological niche models and fossils to understand the changes that occurred in insular populations of bat from the late Pleistocene (ca. 20 thousand years ago) to the present and to assess how available habitat has changed with climate fluctuations. Also, I model population genetic data under a coalescent framework (i.e. projected towards the past) to explore how different climate change scenarios affected populations of bat on Caribbean Islands. Climate based ecological niche models can be projected to infer the potential distributions of organisms at different time intervals. Radiocarbon dated fossils provide the hard data of when and where different species occurred. Finally, DNA serves as a distinctive marker for each population and can give us information about evolutionary processes that occur today and in the past. For example, DNA analysis can help us understand island bat population sizes, movement of bats among islands, etc. The combined use of DNA, coalescent methods, distribution models, and fossils is very powerful and allows me to learn about the evolutionary processes that shaped island bat populations and how bats reacted to climate change in the past. In the face of current climate change trends, my research plays an important part to better understand what happens to these bats today and to be able to predict what may happen to them in the future.

Biography - Dr. J. Angel Soto-Centeno received his B.Sc. in 2000 from Interamerican University of Puerto Rico where he studied physiological ecology of bats on Puerto Rico. He earned his M.Sc. from Eastern Michigan University studying dietary ecology of nectarivorous bats on Puerto Rico in 2004. He completed his Ph.D. from University of Florida in 2013 where he researched phylogeography of multiple species of bat in the Caribbean.

Website - http://newark-rutgers.academia.edu/JAngelSotoCenteno 

Dr. Faysal Bibi

Research Focus - I currently have two main avenues of research, the evolution of bovids (horned ungulates such as antelopes, oxen, goats and their relatives), and the discovery of fossils of around 7 million years in age from the United Arab Emirates.

I study the modern and fossil bovids to reconstruct evolutionary, ecological, and biogeographic histories. Bovidae is a large, diverse, and widespread clade of horned ungulates that is subject to a broad range of investigation, from evolutionary studies to conservation and agricultural sciences. The earliest fossil bovids are at least 18 million years old, and since that time the fossil record of Eurasia and Africa is rich in bovid remains.  My main focus is on bovid fossils ranging from the last 10 million years, from Ethiopia (Middle Awash, Omo), Turkey (Sivas), Kenya (Baringo), United Arab Emirates (Baynunah), and Pakistan and India (Siwaliks). My work consists of: description and taxonomic identification of specimens; comparative and phylogenetic analyses for determination of evolutionary relationships; analysis of functional morphology and ecological proxies (tooth wear, stable isotopes, etc.) for paleoecological reconstruction; and comparative biogeography for reconstruction of evolutionary dispersal patterns.

I am also co-director (with Andrew Hill of Yale University) of the Baynunah Paleontology Project. Each year, our team spends a month conducting fieldwork surveys of the region of Al Gharbia in Abu Dhabi Emirate, United Arab Emirates, to recover fossil remains from the Baynunah Formation.  These sediments preserve fossil remains of plants and animals that indicate an age of somewhere between 8 and 6 million years ago. In addition to bone and plant remains, among the Baynunah sites are also elephant trackways preserving the earliest evidence for herding behavior in this group of mammals.

My Gerstner Scholar project, Combined Morphological-Molecular Systematics of Bovidae (Mammalia: Ruminantia), willintegrate molecular and morphological character datasets to produce the most comprehensive phylogeny for Bovidae. Recent efforts to integrate living and fossil taxa into a single phylogeny using combined molecular and morphological datasets have produced encouraging results in many clades.  The resulting phylogeny of fossil and living Bovidae would be the first of its kind, providing a large and comprehensive phylogenetic framework that would be of direct relevance to biologists and paleobiologists alike. This analysis would also provide the best-calibrated chronological estimates for diversification events within this clade. The resulting data would span almost the entire Neogene (23 million years ago to present) and may be used to directly test hypotheses of diversification associated with global and regional climate and environmental changes.  The resulting phylogeny will also comprise a primary reference for conservation biologists, namely for the identification of unique clades (genera to sub-species) susceptible to perturbation and extinction. The proposed project complements concurrent AMNH-related projects such as the mammalian portion of the Assembling the Tree of Life project. 

Biography - Faysal Bibi received his Ph.D. in Geology & Geophysics from Yale University in 2009. Since then he has spent two years at the Institute de Paléoprimatologie, Paléontologie Humaine (IPHEP) in Poitiers, France, as an International Research Fellow of the N.S.F., and one year at the Museum für Naturkunde in Berlin, Germany, as a D.A.A.D.-Leibniz scholar. 

Website - https://www.museumfuernaturkunde.berlin/en/taxonomy/term/234/faysal.bibi

Dr. Jo Wolfe

Research Focus - I am interested in the relationship between ontogeny (development from embryo to adult) and our understanding of phylogenetic relationships. My Ph.D. involved testing the relationships of Cambrian (500+ million year old) fossil crustacean larvae to living clades. To achieve this, I studied the morphology of each discrete ontogenetic stage (in arthropods these are separated by molt events) and coding each stage as a separate row in a cladistic matrix. Resulting phylogenetic trees placed fossil larvae on the stem lineages of important extant clades, and supported molecular estimates of divergence in the Cambrian.

My Gerstner Scholar research will expand this ontogenetic approach to transcriptomics of living crustaceans. Decapods (crabs, shrimps, lobsters, and relatives) are some of the most charismatic and economically important crustaceans. Many species undergo radical metamorphosis multiple times in their ontogeny. Transcriptomes are the set of genes expressed in a particular tissue at a particular time in ontogeny. Different genes are expected to be expressed depending on ontogenetic timing (as they play roles in development). I will sequence transcriptomes from multiple life stages (embryo, larva, adult) of each of several species to examine the influence of ontogenetic gene expression on phylogeny reconstruction.

In order to accurately link gene expression with its specific larval or adult morphology, all sequenced life stages will also be documented with high-resolution scanning electron micrographs. The morphological data I gather will also be used for the NSF-funded AVAToL project: “Next-generation phenomics for the tree of life”. My images will be test cases for developing new approaches to automate morphological character discovery and scoring. See http://www.avatol.org. 

Biography - Jo Wolfe received her H.B.Sc. from the University of Toronto in 2007, and her Ph.D. from Yale University in 2012. Her doctoral research focused on the combination of different types of datasets (fossil, phylogenomic, and developmental) for reconstructing the pattern and tempo of deep (500+ million year) divergences of pancrustacean clades.

Dr. Mercer R. Brügler

Research Focus - Reconstructing relationships among cnidarians is complicated by extremely low rates of mitochondrial (mt) DNA sequence evolution within anthozoans (anemones, corals, zoanthids and corallimorphs). With the exception of some stony corals, anthozoans examined to date are characterized by synonymous substitution rates 50-100 times slower than most metazoans and variation is almost nonexistent at the intraspecific level. Currently applied nuclear markers are not sufficiently variable to differentiate some putative species.

Anthozoan systematists and taxonomists face a daunting challenge: in addition to slow mt sequence evolution and a lack of variable nuclear markers, simple body plans reduce the number of morphological characters available to define a species or provide phylogenetic information. Sea anemones (order Actiniaria) are among the most diverse members of the subclass Hexacorallia and are considered an emerging model system as they represent a basal eumetazoan lineage that serves as an outgroup to studies analyzing the origin and evolution of bilaterian animals. Mosaics of characters currently distinguish actiniarians, and proposed evolutionary relationships have been largely based on an absence of features. Thus, my primary focus is to search for variable, single-copy nuclear DNA markers for species-level identification. Variable markers will ultimately help determine which external / internal morphological characters are species-specific. My secondary focus is elucidating systematic relationships within, and the evolutionary history of, the order Actiniaria (1,200 species; 46 families) using 44 newly sequenced complete mitochondrial genomes (~16-18K nucleotides per individual).

To locate novel nuclear markers for reliable species-level identification and phylogenetic analysis, I am focusing on two largely Antarctic anemones: Hormathia (Hormathiidae) and Isosicyonis (Actiniidae). Markers also are being located forAiptasia and Metridium because of their broad applicability to the scientific community. I am implementing three strategies to locate markers: building a recombinant library from whole genomic DNA; constructing a complementary DNA (cDNA) library from messenger RNA (mRNA) and screening for expressed sequence tags (ESTs); and de-novo sequencing of the transcriptome utilizing a 454 ultra-high-throughput Next Generation DNA Sequencer (the complete nuclear genome ofNematostella vectensis serves as a control). Defining species and deeper phylogenetic relationships is imperative, representing a critical step in advancing knowledge and understanding of sea anemone taxonomy and systematics. 

Biography - Mercer R. Brügler is a Texas native who was born in Hurst on December 8, 1978 to Mercer L. and Donna J. Brügler. He attended the University of Miami (Florida, 1997-2001) where he earned a Bachelor of Science in Marine Biology. He then pursued a Master of Science in Marine Biology at the College of Charleston’s Grice Marine Laboratory (South Carolina, 2001-2004) and a Doctor of Philosophy in Environmental and Evolutionary Biology at the University of Louisiana at Lafayette (2004-2011).

Website - http://www.citytech.cuny.edu/faculty/MBrugler

Dr. Timothy Guiher

Research Focus - I am interested in the evolutionary history of the subfamily Crotalinae, the venomous snakes commonly known as pitvipers. Despite recent efforts to reconstruct the phylogenetic history of this medically important group of snakes, using mtDNA, several key nodes remain unresolved, also leaving several unanswered biogeographic questions. For instance, estimates of time of dispersal into the New World vary from the Miocene to the Late Cretaceous. In addition, inter-generic relationships remain poorly resolved, making it difficult to identify patterns of dispersal into temperate and tropical environments.

Pitvipers are responsible for the majority of mortality and morbidity due to envenomation in many parts of the world. Antivenom effectiveness is reduced by substantial variation in composition among crotaline snakes. In contrast, venom proteins have received a great deal of interest from the medical community to develop treatments. Recent studies have identified venom proteins with properties suitable to the treatment of breast cancer, colon cancer, and tumor suppression. Describing the variability in venom composition at all taxonomic levels requires a phylogenetic framework. Providing a robust hypothesis of phylogenetic (evolutionary) relationships, which can be accomplished by combining extensive sampling with a large number of unlinked genetic loci. This study will explore applications of novel genomic techniques and next generation sequencing to greatly improve the sampling of loci and individuals that can efficiently be achieved for phylogenetic study. Recent efforts to sequence entire genomes for an increasing number of vertebrate taxa, including several squamate taxa, have identified a large number of potentially informative nuclear loci suitable for examining phylogenetic relationships. Taking advantage of this is limited by the cost and effort required to sequence a large number of markers for many individuals using standard Sanger sequencing. However, recently proposed sample barcoding techniques pool samples making it possible to simultaneously sequence hundreds of loci for hundreds of individuals. This study will be among the first to apply next generation sequencing to the field of phylogenetics. By combining extensive sampling with 48 nuclear loci I will provide new insight into the biogeographic history of Crotalinae and the evolution of venom proteins within this subfamily. Specific efforts will be made to elucidate when Crotalines invaded the New World and identify patterns of dispersal into temperate and tropical niches. 

Biography - Tim Guiher received his PhD from the City University of New York in 2011. His research focuses on using molecular techniques to investigate the processes that have resulted in current species diversity and distributions of snakes. In addition, Tim uses large empirical and simulated data sets to investigate the performance of statistical methods to delineate species and infer population dynamics, including changes in historical population sizes and migration rates. He has described two new venomous snakes in the US in addition to several phylogeographic lineages of non-venomous snakes. Currently, he is using next-generation sequencing techniques to compile a massive multi-locus data set to investigate the phylogenetic relationships within Crotalinae (pitvipers) and processes influencing the radiation of this group. Top

Dr. Jonah Choiniere

Research Focus - I am interested in the early evolution of the Coelurosauria, a clade of theropod dinosaurs closely related to birds. Although the first bird, Archaeopteryx, is known from Jurassic deposits (~150 million years old), the fossil record of contemporaneous coelurosaurs is poor. My dissertation research focused on the anatomy and systematics of new coelurosaurs that predate Archaeopteryx from the earliest Late Jurassic (~160 million years old) of China. My Gerstner Scholar research focuses on the evolution and anatomy of the Alvarezsauroidea, an enigmatic clade of theropod dinosaurs once thought to be a flightless lineage of basal birds, and the implications for understanding the non-avian dinosaur to bird transition. Alvarezsauroids are particularly fascinating because they have short, robust forelimbs, lightly-built skulls with hundreds of teeth, and long, gracile legs. Moreover, advanced alvarezsauroids share many morphological similarities with birds, including special structures of the skull, the pelvis, and the hindlimb. Recent research on alvarezsauroids shows that the lineage had evolved by the earliest Late Jurassic and that they are not as closely related to birds as previously thought. Questions remain about the phylogenetic position of alvarezsauroids within the Theropoda and about the evolution of their bird-like morphology. I am working on a detailed anatomy of alvarezsauroids from Mongolia, incorporating data from high-resolution 3D CT scans and from new, unpublished specimens. This research will clarify alvarezsauroid relationships and illuminate morphological characteristics that alvarezsauroids share with birds. 

Biography - Jonah Choiniere received his Ph.D. in Biological Sciences from the George Washington University. He studies evolution of coelurosaurian theropods, the group of meat-eating dinosaurs most closely related to birds. He has examined theropods from around the world, and his fieldwork in China, South Africa and Mongolia focuses on discovering new species of coelurosaurs and understanding dinosaur (including birds) evolution. His systematic research on theropod dinosaurs involves the use of large datasets and the application of software designed for molecular sequence alignment to questions in morphological evolution. His current research focuses on the relationships and evolution of the bizarre theropod group Alvarezsauroidea, which were previously hypothesized to be basal flightless birds.

Website - http://jonahchoiniere.weebly.com/

Dr. Jose M. Padial

Research Focus - I’m interested in species diversity, both in how it originates and how we classify it. My current research focuses on the taxonomy and phylogenetic relationships of Pristimantis. This group of Neotropical frogs, with more than 400 species, is the largest genus of Terrestrial vertebrates. These frogs are characterized by having direct development—they lay eggs in moist areas and embryos undergo direct development without the typical tadpole phase so characteristic of other anurans— and include species inhabiting the major biomes and areas of the Neotropical realm (the Amazon, the Guiana Shield, the Cerrado, diverse habitats of Central America, some islands in the Caribbean, and multiple Andean ecosystems (paramos, interandean dry valleys, cloud forests, etc.). Such an ample distribution made this group a perfect candidate to study the historical processes that shape species diversity. The first step to study the origin and biogeography of a group of organisms is to reconstruct the phylogenetic relationships of its species, so that we can identify the split of ancient species lineages and relate them to changes in the geology, climate or ecological conditions of an area. My goal as Gerstner scholar is to reconstruct a robust phylogeny of Pristimantisusing molecular and morphological data. This new phylogeny will shed light on the origin of Neotropical diversity, particularly on the diversity of the eastern slopes of the Andes and western Amazonia, for which little empirical work based on new phylogenetic hypotheses has so illuminated biogeography. Other problems that will be illuminated by an improved phylogeny and biogeography are: what is the relative role of intrinsic and extrinsic factors on the process of diversification? Has diversification occurred mainly through pulses of speciation and extinction within the same biogeographic area or through vicariance or dispersal events across different biotic zones? Do highlands promote higher diversity than lowlands? Are the Andes a diversity pump that supplies lineages to the Amazon? What’s the role of ancient areas such as the Guiana Shield in the diversification of Neotropical lineages? Has been the diversification process punctuated or constant along time? And, if punctuated, which was the period that produced a largest number of lineages and why? But also, why are so many Pristimantis out there? Ultimately, the new phylogeny will give place to an improved classification of the group. Other related projects I’m involved include, an integrative approach to Amazonian species diversity—in order to estimate how many amphibian species are still undescribed there, and how the diversity of the Amazonian forests originated; and a study on the diversity and biogeography of Andean lizards of the genus Liolaemus. 

Biography - José M. Padial received his PhD from Granada University in 2007. For his PhD research he worked at Museo Nacional de Ciencias Naturales (Madrid), and Museo de Historial Natural Noel Kemppf Mercado (Santa Cruz, Bolivia). During his PhD he was awarded with the Ernst Mayr Travel Grant in Ecology and Systematics from Harvard University and with the Travel grant of the European program “Synthesys”. In 2008 he received the 9th R.J.H. Hintelmann Scientific Award for Zoological Systematics. After his PhD he moved to Sweden for a two years postdoc at the Evolutionary Biology Centre of Uppsala University, awarded with a Marie Curie Inter-European fellowship. Since January 2009 he is associated editor for amphibians of the international taxonomic journal Zootaxa. Every year since 2002 he conducts field expeditions to the Amazon Basin and tropical Andes to search for frogs, several of which have been described by him and collaborators as new species to science. 

Website - https://www.amnh.org/research/staff-directory/jose-manuel-padial

Dr. Christian Kammerer

Research Focus - My current research as a Gerstner Scholar explores the origin and evolution of mammals from early cynodonts, a diverse group of synapsids in the Permian-Triassic (approximately 200-300 million years ago). Although the evolution of mammals from “reptilian”-grade vertebrates (sometimes incorrectly termed “mammal-like reptiles”) is one of the best-understood major evolutionary transitions in the fossil record, many questions about the base of the mammalian tree of life remain. In particular, there continues to be debate about the phylogenetic relationships of several groups of cynodonts hypothesized to be close relatives of mammals. This research is working towards the resolution of these issues through broader taxon sampling and the introduction of new character data from cynodont skulls and postcranial skeletons, including endocranial data derived from high resolution, 3-D CT-scans. In addition to addressing cynodont phylogeny, this research is elucidating the biological underpinnings of the origin of mammals. Cynodonts underwent a “size squeeze” during their evolution: most Triassic cynodonts were roughly dog-sized, but along the main branch of mammal ancestry, average body size was reduced to shrew proportions, and mammals remained generally small-bodied throughout the Mesozoic. Through histological sectioning of cynodont long bones (limb bones), data on cynodont growth history and “paleo-genomics” are being obtained. Relative ages and growth rates can be extrapolated from bone growth rings, and because genome size is correlated with cell size in extant organisms, the volumes of lacunae (the spaces containing bone cells) in fossil bones can provide an estimator of genome size in long-extinct organisms. Together, these data will be used to assess how cynodont miniaturization occurred and the implications of this for later mammalian success. 

Biography - Christian Kammerer received his PhD in Evolutionary Biology from the University of Chicago. He primarily studies evolution in the Synapsida, one of the two major groups of amniotes and the dominant terrestrial vertebrates of the late Paleozoic and early Mesozoic eras. He has extensively examined Permo-Triassic synapsid faunas around the world and utilizes rigorous quantitative methodologies and innovative imaging technologies to address major questions of diversification and extinction in the vertebrate fossil record. His current research focuses on the early Cynodontia, the most common synapsids of the Triassic Period, and their evolution into mammals.

Website - http://naturalsciences.org/staff/christian-kammerer

Dr. Cartsen Kamenz

Research Focus - Carsten is interested in the phylogeny and evolution of Chelicerata (arthropods with chelicerae, including all arachnids). The phylogenetic position of scorpions is crucial for resolving chelicerate phylogeny and fossil scorpions are especially important in this regard. Some scientists believe the earliest scorpions were aquatic, suggesting either that the invasion of land occurred twice in the evolutionary history of chelicerates or else that arachnids are not monophyletic (sharing a single common ancestor). Fossil scorpions are also important for illuminating the basal lineages of Recent scorpions. Unfortunately, little detailed morphological work, let alone phylogenetic analysis, has been done on fossil scorpion. Carsten is critically reassessing and documenting the morphology of 75 fossil scorpions, based on a re-examination of almost 200 specimens in twelve European and North American collections, using traditional palaeontological methods and new techniques like variable pressure scanning electron microscopy, and CT-scanning (for 3D specimens with morphology hidden in the matrix). He is focusing on characters with implications for terrestrialization, namely the abdominal plates, legs, specialized sensory structures called pectines and book lungs. Preliminary results of Carsten’s work suggest that fossil scorpions were not aquatic (i.e. there was a single origin of terrestrialization among chelicerates) and confirm hypotheses that arachnids are the monophyletic sister-group of eurypterids (sea scorpions). These findings are independently supported by genomic data.  

Biography - Carsten Kamenz graduated from the Humboldt University, Berlin (HUB) in 2003. He enrolled the same year for a Ph.D. on the comparative morphology of arachnid book lungs, co-supervised by Gerhard Scholtz (HUB) and Jason Dunlop (Museum für Naturkunde, Berlin). Carsten’s dissertation research, using the latest histological and micro-tomographical methods, was aided by an EU Synthesys grant to work at the Museum National de Histoire Naturelle, Paris (2005) and an Annette Kade Fellowship to work at the American Museum of Natural History, New York (2005/2006). Carsten was awarded his Ph.D. in 2009, moving immediately thereafter to take up his current postdoctoral fellowship, working on fossil scorpions at the AMNH.

Kevin Deitz

Dr. Kevin Deitz

Research Focus - The availability of thousands of individual genomes of multiple arthropod species presents an unparalleled opportunity to understand the impact of natural selection on genome evolution. My research addresses the following basic questions in genome biology, evolution, and speciation: What biological processes result in the evolution of genetic incompatibilities and reproductive isolation between incipient species? How is evolution facilitated, or constrained, by the available genetic variation within a population? How does selection act to maintain or remove exogenous elements that integrate into genomes? As a Gerstner Scholar in Bioinformatics and Computational Biology in the Institute of Comparative Genomics at AMNH, I am using open-source computational biology tools and developing new bioinformatic pipelines to address these questions in the context of rapid species radiations (Anopheles gambiae species complex) and global invasions (Aedes aegypti) of mosquitoes that are the primary vectors of some of the most devastating human diseases. I am investigating how heterogeneity in endogenous viral element integrations among arthropod populations and species impacts their resistance to viral infection, with an emphasis on arbovirus vectors such as the yellow fever mosquito Aedes aegypti. I also have ongoing research focused on understanding how recombination shapes nucleotide variation in arthropod genomes and impacts the rate of adaptive evolution.

Biography – Kevin C. Deitz received his BS in Conservation Biology from SUNY-ESF in 2008, and his MS (2011) and PhD (2017) in Entomology from Texas A&M University under the supervision of Michel Slotman. His thesis and dissertation research focused on the population, evolutionary, and speciation genetics of the Anopheles gambiae complex of African malaria mosquitoes. This work had applied implications for vector control but also provided basic insights into how genetic incompatibilities evolve and contribute to rapid species radiations. Prior to joining AMNH, Dr. Deitz was a postdoc with Peter Andolfatto at Princeton and Columbia Universities where his research focused on understanding the evolution of epistatic mutations in non-model Drosophila. Additionally, by leveraging the full genome sequences of hundreds of flies from across the Drosophila yakuba species clade, he analyzed thousands of orthologous genes in order to understand how variation in the effective population sizes of these species impacts the efficacy of selection in their genomes. This analysis helps us to understand how genetic variation within populations and species impacts their ability to adapt to their environment.

Dr. Victor Sojo

Research Focus – I am a trans-disciplinary evolutionary biologist with a background in (bio)chemistry and computer science. My main research interests are in the “major evolutionary transitions”—the times at which the greatest biological innovations occurred in the history of life on Earth. I focus on the roles that membranes (both the lipids and the proteins) played in some of these transitions.

I work mostly on early evolution, including the emergence of life itself, the origin of free-living cells, and the evolution of complex cells (eukaryotes), but I am generally interested in the evolution of membranes throughout life’s entire history.

Why membranes? Because membranes are crucial to almost all of life’s key processes, including respiration, cell-to-cell communication, reproduction, photosynthesis, vision, motion, feeding, parasitism/immunity, energetics, and more. Membrane-associated proteins amount to approximately one third of all proteins in the genome, and they compose over three quarters of the membranes themselves. Membranes are also the point of contact between the cell and the environment. As such, they are the direct target of over half of all known drugs, whereas the remaining drugs typically have to get through the membranes before they can exert their functions inside the cell. Understanding membranes can therefore have significant implications far beyond theoretical evolutionary biology, into physiology and medicine.

My main project at the AMNH is on the origin and early evolution of eukaryotes from an “endosymbiotic” merger of bacteria and archaea. I am studying the bioenergetic role of mitochondrial respiratory membranes in the early events of eukaryogenesis. As part of my research, I am performing analyses of horizontal gene transfers across the three domains of the Tree of Life. Both topics—the relations between the branches of the tree of life, and the complexity of gene transfers between them—are central to my research in general.

I use mostly computational methods (bioinformatics and modelling) and theoretical analysis in my research, but I can also occasionally—albeit rarely—be found in the lab.

Biography – Victor Sojo received a research undergraduate degree in Chemistry from the Universidad Central de Venezuela (UCV) in Caracas, followed by a Master’s in Computer Science, also at UCV. He then pursued a second Master’s, in Modelling Biological Complexity, from the University of London – University College London (UCL). Victor completed his PhD in Evolutionary Biology in 2016, also at UCL, with Nick Lane and Andrew Pomiankowski. Prior to becoming a Gerstner Scholar at the AMNH, Victor was a Life Sciences Fellow at the Institute for Advanced Study in Berlin, a European Molecular Biology Organization (EMBO) Postdoctoral Fellow at the Ludwig-Maximilian University of Munich, and a Short-Term Postdoctoral Fellow at RIKEN in Tokyo.

Dr. Marcelo Gehara

Research Focus – Evolution happens in space and time and understanding the influence of these two variables in diversification processes is a major goal in evolutionary biology. Time is routinely modeled in population studies, but space is often implicitly considered. My goal as a postdoctoral researcher at the AMNH is to develop a simulation-based method to test the influence of space in the genetic differentiation of populations. I am currently working on a spatially explicit population genetic model that uses different distance measures, such as linear spatial distance or environmental resistance distances, to simulate gene flow between populations. Under this model, known spatial patterns of Isolation by distance and Isolation by resistance can be replicated in-silico. With this tool at hand we will be able to train machine-learning algorithms to recognize these spatial influences in real datasets. 

Biography –  Marcelo Gehara received his BA in biology by the Universidade Federal de Juiz de Fora - UFJF, Brazil in 2005. He obtained a Masters degree in Zoology by Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Brazil (2009) under the supervision of Sandro L. Bonatto, and a PhD in Zoology by the Technical University of Braunschweig, Germany (2013) under the supervision of Miguel Vences. Marcelo has authored several publications on phylogeography of amphibians and reptiles from different parts of the world. Recently he has been focusing his research in developing new methodologies for the study of evolution at the population level. Prior to being a postdoc at the RGGS, Marcelo was a postdoc in Frank Burbrink’s group, where he developed PipeMaster, an r-package for simulation-based inference in  population genetics.

Dr. Chase Nelson

Research Focus — Evolutionary genetics has long been plagued by a paucity of data. A great body of mathematical theory in the form of population genetics was developed well before data became available to test most of its predictions. Now, with the maturation of next-generation sequencing (NGS) technologies over the past decade, many previously intractable questions are within reach. In particular, the sequencing of large numbers of individuals or else pooled samples consisting of many individuals (pooled NGS) allow allele frequencies to be measured with remarkable resolution, and important population genetic parameters to be estimated. My own research aims to develop computational tools (e.g., SNPGenie) for automating such analyses, allowing researchers to draw evolutionary inferences from NGS variant (primarily single nucleotide polymorphism, or SNP) data. So far, my efforts have mainly involved data from within-host virus populations, including both natural isolates (e.g., arteriviruses infecting red colobus monkeys) and serial infection experiments (e.g., influenza viruses infecting ferrets).

My research at the American Museum of Natural History focuses mainly on (1) within- and between-host viral evolution, especially of human papillomaviruses (HPVs); (2) determining orthology within a parsimony framework; and (3) the patterns of variation among and geographic distribution of human immune alleles. I rely heavily on my Institute for Comparative Genomics mentor, Apurva Narechania, in addition to generous collaborators at the National Cancer Institute and elsewhere. Our multidisciplinary work involves the collection of samples from natural populations around the world, genome sequencing, variant calling, bioinformatic processing, and evolutionary analysis. With respect to viral evolution, specific questions to be addressed include the host and viral genetic determinants of carcinogenicity in HPV, the influence of host vs. pathogen co-evolutionary history, and the importance of Muller’s Ratchet-like processes for viral fitness. Work on orthology aims to update and expand the BigPlant OrthologID tool to incorporate more eukaryotic genomes and non-protein-coding DNA information.

Finally, human immune allele research aims to detect correlations between spatial and genetic distance, as well as to identify specific variants important in evolutionary history and immunology. It is hoped that this work will elucidate methods for drawing upon quantitative theory to make concrete predictions that will have relevance for questions both therapeutic (e.g., immune epitope identification for vaccine design) and theoretical (e.g., the importance of mutation accumulation and the relative contributions of selection and drift in molecular evolution).

Biography — Chase W. Nelson received his B.A. in Biology from Oberlin College in 2010, where he performed honors research on mutation accumulation and gene expression in Arabidopsis thaliana under Angela J. Roles. During this time, he also undertook research experiences in unsupervised motif discovery at Ohio University and the molecular biology and phylogenetics of maize at the University of Wyoming. While he completed his Ph.D. in Biological Sciences at the University of South Carolina, studying evolutionary bioinformatics under Austin L. Hughes from 2011 to 2016, he also participated in next-generation sequencing research under Wen-Hsiung Li at Academia Sinica (中央研究院) in Taipei, Taiwan. In his free time, Nelson pursues vocal and dance studies, writing, and learning Mandarin.

Research Focus – My research addresses three key evolutionary and ecological questions: 1) do larger effective population sizes improve the effectiveness of selection, 2) can ecological specialization promote larger effective population sizes, and 3) does improved selection efficacy increase the rate of adaptive evolution? The answers to these questions will produce a better understanding of the factors that facilitate adaptation and will also shed light on population divergence and the formation of new species. I predominately work in two systems, butterflies of the genus Papilio and the pathogenic, tick-vectored bacterium, Anaplasma phagocytophilum. Within Papilio, I am investigating the factors that differ between a host-generalist species, Papilio glaucus (the Eastern Tiger Swallowtail), and a host-specialist species, Papilio troilus (the Spicebush Swallowtail). These species are similar in most life history characteristics and geographic ranges, yet differ greatly in the number of larval host species they can feed upon. Within A. phagocytophilum, I have discovered that different strains vary greatly in the number of mammalian hosts they infect (host-range). I am now investigating what consequences this difference has for the evolutionary trajectory of this bacterium. In both systems, I utilized next-generation sequencing technologies and high performance computing to carry out comparative genomic analyses. These analyses allow me to assess sizes, gene flow and selection within populations and species. Other computational projects I am currently working on include thermal adaptation in clown fish using, population structure in South Africa elephants and population diversity in a rodent malaria species.

Biography - Matthew Aardema completed his B.S. in Zoology at Michigan State University (MSU) in 2008. He then went on to earn a M.S. degree at MSU in Ecology, Evolutionary Biology and Behavior. From there he went to Princeton University to earn his Ph.D. in the Department of Ecology and Evolutionary Biology under the guidance of Prof. Peter Andolfatto. Upon completion of his PhD, Matthew joined the American Museum of Natural History as a Gerstner Scholar in Bioinformatics and Computational Biology

Website - https://www.montclair.edu/profilepages/view_profile.php?username=aardemam

Dr. Robert Harbert

Research Focus - Understanding what drives the distribution of species is fundamental to the study of ecology, taxonomy, and systematics. The physiology of a given plant species restricts its distribution to a specific set of climate, soils, and biotic interactions. 

I am broadly interested in elucidating spatial patterns in global plant biodiversity through computational methods, particularly across temporal and climatic gradients. As a result, I work with large online databases of aggregated primary biodiversity data like the Global Biodiversity Information Facility (GBIF) to develop quantitative methods for the characterization of geographic distributions in terms of environmental factors, mainly climate. The unifying goal of my research is to be able to apply standard, quantitative methods to primary biodiversity data to reliably characterize environmental niches in a likelihood modeling framework for all extant taxa.

The main product of my Ph.D. work was a likelihood modeling framework that estimates climate parameters given a local vegetation community composition and distribution data for all of those species. The Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE) framework has been extensively tested on modern vegetation surveys. Relative to other related methods, CRACLE is distinctly Gleasonian in its view of vegetation assembly. That is, all species are treated as independent units in the model when parameterizing climate niche occupancy. Now, CRACLE is being turned towards paleoclimate modeling using Late Quaternary plant macrofossil communities.

Biography - Rob completed his B.S. in Biology at Roanoke College in 2011. From there, he went on to Cornell University to work on Ph.D. in the School of Integrated Plant Science and the Section of Plant Biology with a focus on Plant Systematics and Evolution with Dr. Kevin C. Nixon. Upon completion of his Ph.D. in July 2016 he joined the American Museum of Natural History as a Gerstner Scholar in Bioinformatics and Computational Biology. 

Website - https://www.stonehill.edu/directory/robert-s-harbert/

Dr. Martine Zilversmit

Research Focus – The goal of my research is to broaden our understanding of how genomes change over time by developing tools and models to study the genomes of non-model organism systems and overlooked genome regions. The focus of my work is genome structure evolution, particularly regions where it has been historically difficult to map variation or even to assemble the DNA sequence, including: gene families, low-complexity sequences, subtelomeric regions, and small regions of extreme sequence divergence. Although this “dark matter” of genome structure is often the most difficult to work with, particularly in non-model organisms, it can yield the most interesting results relevant to phenotypic change and understanding evolutionary rates. Towards this end, I have been using malaria parasites as my study system because of the large number of open questions about multiple aspects of structural change in their relatively large, but low-complexity, genomes.

 My recent work in comparative genomics is grounded in my earlier work in systematics and evolutionary genetics from my master’s research at the American Museum of Natural History and my PhD at Harvard University. The techniques of sequence alignment, tree building, and statistical models of evolution remain at the core of all my research. I have been able to use these methods to examine the evolution of low-complexity regions in coding sequence (DePristo and Zilversmit et al., 2006; Zilversmit et al. 2010), gene family evolution (Bethke et al. 2006; Ferreira, Zilversmit, and Wunderlich 2007; Zilversmit et al. 2013), and allelic and non-allelic homologous recombination (Zilversmit et al. 2010; Zilversmit et al. 2013). Analyzing all these phenomena both within and between species, in a phylogenetic framework for comparisons in the context of ancestry and evolutionary relationships, has allowed me to explore the neutral versus adaptive aspects of their evolution.

A large part of my research program now focuses on developing tools and technologies that allow for advances in comparative and evolutionary genomics. Recent developments in innovative and lower-cost sequencing technologies, and the wider use of parallel computer clusters, mean that scientists longer need to rely on the big sequencing centers for whole-genome level data, and from just a few model organisms. Since we can sequence, assemble, and annotate our own genomes, this can vastly increase the diversity of available genome data for comparative studies, which are at the core of evolutionary genomics. Currently, I am adapting both molecular and computational genomic methods to work with non-model organism systems to examine genome diversity and divergence using paired-end short read and long-read data. For this work, I have designed interworking genome analysis pipelines, using UNIX scripting and Python programs, for genome mapping (resequencing) with annotations, de novo genome assembly and annotation, and high-accuracy variant calling and in silico validation. Included in the mapping pipeline is a set of novel programs, one of which identifies regions of rapid evolutionary change that are not detectable by standard methods, and two others that show intersection and complement of variant data from multiple individuals. I have applied these techniques successfully to inter- and intraspecific studies, to identify loci associated with the evolution of drug resistance and increased disease virulence. In addition, I have been able to construct fine-scale genome maps of markers for population-level studies and quantitative trait locus analysis.

I am now applying these methods and pipelines to broader questions in malaria parasite evolution, including the origin of hemoglobin metabolism and thus the creation of the doorway to colonizing red blood cells as their ecological setting.  My research also focuses on understanding other rapidly evolving gene families such as those that code for venom proteins.

Biography -Martine Zilversmit received her MS in Biology from NYU working with Rob DeSalle on high-throughput genome sequencing techniques for studies in molecular evolution and her PhD in Biology from Harvard University in the Department of Organismic and Evolutionary Biology working with Daniel Hartl on the genome structure evolution and population genetics of malaria parasites.