2009-2012. National Science Foundation, Antarctic Organisms and Ecosystems Program, Antarctic Sciences Division. Genomic approaches to resolving phylogenies of Antarctic notothenioid fishes. $491,000.

The teleost fish fauna in the waters surrounding Antarctica are completely dominated by a single clade of closely related species, the Notothenioidei. This clade offers an unprecedented opportunity to investigate the effects of deep time paleogeographic transformations and periods of global climate change on lineage diversification and facilitation of adaptive radiation. With over 100 species, the Antarctic notothenioid radiation has been the subject of intensive investigation of biochemical, physiological, and morphological adaptations associated with freezing avoidance in the subzero Southern Ocean marine habitats. However, broadly sampled time-calibrated phylogenetic hypotheses of notothenioids have not been used to examine patterns of adaptive radiation in this clade. The goals of this project are to develop an intensive phylogenomic scale dataset for 90 of the 124 recognized notothenioid species, and use this genomic resource to generate time-calibrated molecular phylogenetic trees. The results of pilot phylogenetic studies indicate a very exciting correlation of the initial diversification of notothenioids with the fragmentation of East Gondwana approximately 80 million years ago, and the origin of the Antarctic Clade adaptive radiation at a time of global cooling and formation of polar conditions in the Southern Ocean, approximately 35 million years ago. This project will provide research experiences for undergraduates, training for a graduate student, and support a postdoctoral researcher. In addition the project will include three high school students from New Haven Public Schools for summer research internships.

2009. National Science Foundation, Systematic Biology and Biodiversity Inventories, Division of Environmental Biology. REU Supplement to Collaborative Research: Phylogenetics and key innovations in labroid fishes. $7,500.

2009-2012. National Science Foundation, Biological Research Collections, Division of Biological Infrastructure. Curation of vertebrate spirit specimens of the Yale Peabody Museum of Natural History. $350,000 (P.I. R.O. Prum, Co-PI T.J. Near).

The Yale Peabody Museum (YPM) houses a world-renowned collection of vertebrate specimens. Approximately 30 percent of the entire holdings of the Division of Vertebrate Zoology (VZ) are fluid-preserved specimens. The goal of this project is to recurate the entire fluid-preserved vertebrate zoology collections of YPM, to facilitate accessibility of the collections, and to promote their use in research and education. YPM-VZ?s fluid-preserved collections have been amassed over more than 160 years by Yale academics, researchers from other institutions, and government agencies. We will recurate of the entire spirit specimen collections in the YPM-VZ including fishes, amphibians, reptiles, birds and mammals. These activities will include rejarring, relabeling, changing fluids, checking identifications, evaluating data quality, etc.

The rehousing and improvement of storage conditions of the VZ spirit collections will help preserve these unique materials, and foster comparative biological research on them. Recuration will foster accessibility to visitors, faculty, and students wishing to use the collections. The project will provide curation, identification, and database training for Yale undergraduates, and high school interns (most of whom are under-represented minority students) through the YPM’s after-school intern program.

2007–2010. National Science Foundation, Systematic Biology and Biodiversity Inventories, Division of Environmental Biology. Collaborative Research: Phylogenetics and key innovations in labroid fishes. $324,800 PI T.J. Near PI, Co-PI W.L. Smith.

This research will focus on the evolution and diversity of labroid fishes - including cichlids, labrids (wrasses and parrotfish), pomacentrids (damselfishes) and embiotocids (surfperch). At over 3,000 species, these are among the most successful and diverse groups of bony fishes. Hypotheses will be tested about the effect of major innovations found in the pharyngeal jaws of these fishes on speciation rate, morphological diversity, and ecological diversity. The research has two major components. DNA sequence from 9 genes and 650 species will be obtained to determine the phylogenetic relationships between labroids and other fishes. The resulting phylogenetic trees will be used as the basis for making comparisons of diversity between groups that possess the modified pharyngeal jaw, and close relatives that lack the specialization.

The major contribution of this research will be to improve our understanding of how breakthroughs in functional design impact the evolutionary success of lineages. New insights will be gained into evolutionary relationships within one of the least understood branches of the bony-fish tree of life. Training and mentoring will be provided for two post-doctoral researchers and one graduate student. Teaching modules will be developed from this research for undergraduate and graduate courses. An undergraduate internship program will be developed to recruit students from disadvantaged backgrounds into research opportunities provided by this project.