Simmons Research Group
Current 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 instiutions (the AToL Mammals web page can be accessed here) 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 Tucumánn, 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.
Morphology and higher-level relationships of bats.
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. Simmons has 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.
Phylogeny of Old World Fruit bats (Pteropodidae).
Another long-term research project focuses on Old World Fruit Bats (Family Pteropodidae = Megachiroptera). Lead by Dr. Giannini and in collaboration with Simmons, Postdoctoral Fellow Francisca Almeida (now at the Universitat de Barcelona), and Kris Helgen (US National Museum), the group has compiled 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), and relationships among members of the large subfamily Cynopterinae (Almeida et al., in press). Data are in hand for several additional papers as well.
Phylogeny and rates of evolution in New World Leaf-nosed Bats (Phyllostomidae).
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.
Biogeography and phylogeny of bat trypanosomes
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.
Morphology and evolution of the chiropteran dentition.
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.
Morphology of the chiropteran skull.
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.
A new fossil bat from Hawaii.
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.
Phylogeny of Mormoopid bats and a new fossil member of the family.
Dr. Simmons is collaborating on description of a new Oligocene member of the family Mormoopidae and placement of this taxon in phylogenetic prespective with 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.
Current Postdoctoral Fellows
- Norberto Giannini
- Paul Velazco
Current Graduate Students
- Miguel Pinto
Former Postdoctoral Fellows
- Bill Schutt
- Jonathan Geisler
- Albert Ditchfield
- Francisca Almeida
- Adrian Tejedor
- Valeria Tavares
- Liliana Davalos
- Andrea Wetterer
- Scott Cardiff