Dr. MacPhee studies the historical biogeography of the West Indies, using a combined tectonic/paleontological approach. This program of research has been in operation for more than 20 years and has involved work on all major and many of the smaller islands in the West Indies. His research has focused on systematic and functional anatomical investigations of the groups concerned. Dr. MacPhee also studies recent mammalian extinctions (last 40,000 years). Loss of species during geologically recent times is a worldwide phenomenon that has been blamed either on direct impacts involving people, or less direct impacts caused by environmental change. His research aims to clarify the causal patterns behind these losses, most recently by studying population dynamics of fossil species using ancient DNA methods.
- Pere Bover (2006-2008)
- Alex Greenwood (1999-2001)
- Manuel Iturralde-Vinent (1997-1998)
- Siobhan Cooke, Doctoral Program in Anthropology, Graduate Center, City University of New York. [email protected]
- Rob Asher (PhD '00, Stony Brook University, Department of Anatomical Sciences)
- Ines Horovitz (PhD '97, Stony Brook University, Department of Anatomical Sciences)
- Jennifer White (PhD '93, Stony Brook University, Department of Anatomical Sciences)
- Hendrik Poinar, Associate Professor, Departments of Anthropology and Pathology and Molecular Medicine, McMaster University, Canada. [email protected]
- Eske Willerslev, Centre for GeoGenetics, University of Copenhagen, Denmark. [email protected]
- Lee Arnold, Luminescence Dating Laboratory, Geochronology Research Group, National Research Centre on Human Evolution (CENIEH), Spain. [email protected]
Dr. Simmons' research group focuses on systematics and evolutionary biology of bats (Chiroptera). Projects range from large-scale phylogenetic studies of bats and their place in the Mammalian Tree of Life to descriptions of new species, biogeographic analyses, investigations of details of bat morphology (e.g., cranial and dental structures), analyses of DNA sequence data, host-parasite coevolution, and descriptions and analyses of rare Eocene fossil bats. Simmons and her collaborators and students employ both morphological and molecular data in their work, and field research is a frequent component of projects.
Simmons Group Research Projects
Dr. Simmons is part of a large team of researchers working with NSF support to build a "Tree of Life" (large-scale phylogeny) for mammals using molecular and morphological data collected from representatives of both extant and extinct lineages. This collaborative effort involves over 30 researchers at over a dozen institutions. Three institutions comprise the core of the morphology team -- the AMHH, SUNY Stony Brook, and the Carnegie Museum of Natural History. Simmons is one of the principal organizers of the AToL Mammal Morphology Team and leads the group responsible for scoring bats for the project. The bat group also includes Postdoctoral Fellows Norberto Giannini (AMNH and Universidad Nacional de Tucumann, Argentina) and Paul Velazco (AMNH).
Thus far the AToL Mammal Morphology Team has assembled a dataset of over 4,500 morphological characters archived in an online database using MorphoBank. This data set includes cranial, dental, postcranial, and soft tissue characters. Each character has verbal descriptions, bibliographic citations, and illustrations for each character state. Scoring of the first set of taxa (representing all extant mammalian orders and several extinct lineages) is nearing completion and plans for the first publication of the data set are underway.
The Order Chiroptera is the second most diverse order of mammals with over 1100 extant species placed in 19 families. Together with Dr. Giannini, Dr. Simmonshas been working for several years to complete a data matrix of several hundred morphological characters scored in nearly 100 species representing all major clades of bats.These data will ultimately be combined with mitochondrial and nuclear DNA data from at least 17 genes.With funding of the ATOL-Mammals grant, they have now turned much of their attention to integrating their characters into the larger matrices under development for that project, but the ultimate goals remain the same:to produce well-resolved, well-supported phylogenies that resolve both the place of bats in the mammal tree and relationships among all the major lineages of bats.Along the way they are trying to sort out a number of long-standing problems with particular character compexes.Publications have already been completed resolving issues with dental homologies in megabats (Pteropodidae) and documenting the extensive variation seen in the chiropteran premaxilla (Giannini and Simmons, 2007a, 2007b). In the future Simmons and Giannini plan to return to work on the bat data set and integrate many new characters discovered in the course of the AToL project as well as data from many fossil bats.
Another long-term research project focuses on Old World Fruit Bats (Family Pteropodidae = Megachiroptera). Lead byDr. Giannini and in collaboration with Simmons, Postdoctoral Fellow Francisca Almeida (now at theUniversitat de Barcelona), and Kris Helgen (US National Museum), the group hascompiled a large data set of molecular and morphological data for resolving relationships among pteropodids.They now have over 300 morphological characters for over 70 species, and DNA sequence data from 4 mitochondrial and 4 nuclear genes.Publications thus far have focused on the "big picture" of pteropodid relationships (Giannini and Simmons, 2003, 2005), relationships of harypionycterine pteropodids (Gianinni et al., 2006, in press), phylogeny and taxonomy in the genus Pteropus (Giannini et al., 2008), andrelationships among members of the large subfamily Cynopterinae (Almeida et al., in press). Data are in hand for several additional papers as well.
Phyllostomid bats are arguably the most ecologically diverse family of mammals, including taxa that variously feed on insects, other vertebrates, fruit, pollen, nectar, and even blood. Working with Dr. Andrea Wetterer (SUNY Stony Brook and AMNH), Liliana Davalos (SUNY Stony Brook), Jonathan Geisler (NYCOM), and AMNH Postdocs Velazco and Giannini, Dr. Simmons group recently began an ambitious program to revisit phyllostomid phylogenetics and develop a complete, dated species-level phylogeny for this ecologically diverse group. A manuscript senior-authored by Dr. Wetterer will finally describe combined analyses of molecular sequences and morphological data for over 80 exemplar species, a project started years ago after publication of Wetterer et al's (2000) landmark monograrph on the family. New studies of evolutionary rates lead by Davalos should shed new light on diversification in the group, while Velazco and Simmons continue to work on new sources of morphological data (e.g., detailed dental characters) and formally integrating fossils into phylogenetic analyses. Much of the focus will be on resolving the relationships of "phyllosomines," insectivorous members of the family which seem to occupy many branches along the backbone of the family tree. Dr. Giannini's efforts will focus on analyzing and understanding the evolution of body sizes in Phyllostomidae, which contains members spanning nearly the entire size range known for echolocating bats.
Trypanosomes infect several bat species and are found in at least 4 continents. Graduate Student Miguel Pinto is spearheading a project to infer temporal and spatial patterns of speciation and host switching of bat trypanosomes by using molecular approaches. This project, based in AMNH Curator Susan Perkins' lab, will use phylogenies of bats and other mammals to identify host-switching events and patterns of coevolution in bats and their trypanosome parasites. An important component of this project is refining of molecular methodologies to extract phylogenetic information from the trypanosomes directly from bat tissues with no necessity of culturing parasites. This new methodology, if it proves successful, will be deployed in a DNA barcoding initiative of trypanosomes using tissues deposited in natural history museums. The project will also involve work on trypanosome systematics and the complex problem of delimiting species limits in these parasites.
In 2008 Simmons began a new collaborative project to develop a virtual museum of images of fossil and extant bat teeth in an online database in MorphoBank, and to analyze the morphology of these taxa in a phylogenetic context.Goals include determining rates of evolution in dental features by mapping characters onto phylogenies developed with other data (e.g., DNA sequence data), identifying patterns of correlation among characters and states, developing a method for mitigating problems of non-independance of characters to make dental characters more useful and informative in phylyogenetic analyses, and using phyogenetic analyses of dental characters to help place numerous fossil taxa in the bat family tree.
Collaboratiors in the project include Gregg Gunnell (University of Michigan),Liliana Davalos (SUNY Stony Brook), Angelique Corthals (CUNY),Joerg Habersetzer (Senkenberg Museum, Germany), Sue Hand (University of New South Wales, Australia), Postdoctoral Fellow Velazcoi, as well as two undergraduate students, Peter Smits (University of Washington and the AMNH REU program) and Dani Saks (Columbia University). The data set now includes over 275 characters scored in over 40 taxa, and the team will present results of the first analyses at the North American Society for Bat Research meetings in November 2009.
Another research effort lead by Giannini is aimed at complete description and documentation of morphology of the bat skull. In collaboration with Simmons and Dr. John Wible (Carnegie Museum of Natural History), Giannini produced a monograph on the skull of Pteropus (Giannini et al., 2006) which is the most complete description of the skull of a bat that has ever been published. A paper on internal anatomy of the narial capsule of Pteropus, written in collaboration with Postdoctoral Fellow Ted Macrini (now at St. Mary's University Texas)is nearing completion. The team is using both traditional morphological preparations (dried skulls, histological sections) and new technologies (high-resolution CT imaging) in this effort. Plans are underway for the next monograph in this series, a detailed analysis of the skull of an echolocating bat.
Dr. Simmons and several collaborators are working to describe what will be only the second endemic mammal from the Hawaiian islands, a new genus and species of extinct bat.Simmons inhereted this project after the death of one of the original discoverers of the bat, Alan Ziegler. Simmons is working on completing a manuscript begun by Ziegler with co-discoverer Frank Howarth (Bishop Museum), and entomologist and expert on Hawaiian cave faunas.The paper describing the new bat will include a small phylogenetic analysis placing the new taxon relative to extant vesperilionine bats.In 2008 Postdoctoral Fellow Kevin Olival (now at the Wildlife Trust) joined the team, and he is working on extracting DNA from the bones of this animal. If this "ancient DNA" work is successful, it will give us invaluable information about relationships of the new bat.
Dr. Simmons is collaborating on description of a new Oligocene member of the family Mormoopidae and placement of this taxon in phylogenetic prespectivewith Gary Morgan (University of New Mexico) and Nick Czaplewski (Univeristy of Oklahoma).The description is complete, and the phylogenetic analysis is nearing completion.This project will be published as a monograph submitted to the Bulletin of the American Museum of Natural History.
Dr. Voss's primary research interests are the evolution of marsupials and the systematics and biogeography of other Neotropical mammals that inhabit moist-forest habitats in Amazonia and the Andes. He is actively involved in long-term revisionary studies on several groups that have radiated extensively in lowland and montane rainforests, including didelphid marsupials, caviomorph rodents (erethizontids and dasyproctids), and murid rodents. For several of these groups, he is also collaborating with molecular researchers on phylogenetic studies designed to provide a stable basis for higher-level classifications, historical biogeography, and comparative analyses of ecobehavioral adaptations. The collection and analysis of faunal inventory data, especially from long-term projects in tropical rainforest habitats, is another research focus
Robin Beck (2009;2011). Project title: "Craniodental Morphology and Phylogenetic Relationships of Living and Extinct Marsupials."
Thomas E. Macrini (2006;2008). Project title: "Anatomical Study of the Nasal Skeleton and Endocranial Cavity of Marsupials Using High-Resolution X-ray Computed Tomography."
David A. Flores (2004 2006). Project title: "A phylogenetic Study of Didelphid Marsupials Based on Postcranial Characters."
Robert P. Anderson (2001-2003). Project title: "Ecogeographic modeling and systematic revision of spiny pocket mice (Heteromys)."
Sharon A. Jansa (1998-2000). Project titles: "Phylogeny and Biogeography of the Native Rodents of Madagascar" (1998-1999); "Intraspecific Phylogeography of Madagascar's Native Rodents" (1999-2000).
Mario de Vivo (1991-1992). Project title: "Review of the South American Sciuridae (Mammalia, Rodentia)."
Marcelo Weksler (1998-2004). Thesis title: "Phylogeny of oryzomyine rodents (Muridae) based on morphological and molecular datasets." Ph.D., CUNY.
Victor Pacheco (1994-2003). Thesis title: "Phylogenetic analysis of thomasomyine rodents (Rodentia, Sigmodontinae)." Ph.D., CUNY.
Thomas C. Giarla (2008-present). No thesis title yet. Ph.D. student, University of Minnesota.
Eliecer Gutierrez (2007-present). No thesis title yet. Ph.D. student, CUNY.
Adrian Tejedor (2002-2007). Thesis title: "Systematics and phylogeny of the New World bat family Natalidae." Ph.D., CUNY.
Valeria Taveres (2002-present). Thesis title: "Revisionary systematics and phylogenetic relationships of Vampyressa (Chiroptera: Phyllostomidae)." Ph.D. candidate, CUNY.
Patricia Escalante (1987-1991). Thesis title: "Phylogenetic relationships of Geothlypis (Aves: Parulidae)." Ph.D., CUNY.