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Yale Institute for Biospheric Studies Offices Environmental Science Center, Room 132
21 Sachem Street
P.O. Box 208105
New Haven, CT 06520-8105
Phone: (203) 432-9856
Fax: (203) 432-9927

Jeffrey Park, Director
Rose Rita Riccitelli, Assistant Director
Daniele Dugre-Martin, Senior Administrative Assistant

A selection of past projects in ancient DNA

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The Quagga Project

quagga

Twenty years ago the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984). This was the first extinct species from which genetic information was retrieved. We have isolated DNA from eight quaggas and an extinct population of the plains zebra (Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna. This work is in collaboration with Scott Glaberman (Graduate Student EEB) and many US and international scientists.

 

Scott Glaberman (EEB graduate student) sampling a bone for DNA analysis from a Quagga (extinct zebra species) bone from the Peabody museum at Yale.

quagga

Publication: Leonard, J.A., N. Rohland, S. Glaberman , R. C. Fleischer, S. Pääbo, A. CACCONE and M. Hofreiter. 2005. How a Zebra Lost its Stripes: 20 Years of Ancient DNA and the Origin of the Quagga. Biology Letters 1(3): 291-295.

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Extinct dwarf elephants from the Mediterranean islands

During the Pleistocene pygmy elephantids, some only a quarter of their ancestor’s size, were present on some Mediterranean islands until about 10,000 years ago (y.a.) Using a whole genomic amplification method new to the “ancient DNA world” we were able to retrieve DNA fragments from 4,200 to 800,000 y.a. samples from island and mainland pygmy and normal-sized forms. Our results challenge the prevailing view that pygmy elephantids of the Mediterranean originated exclusively from Elephas, suggesting independent histories of dwarfism and the presence of both pygmy mammoth and elephant-like taxa on the eastern Mediterranean islands. When a new ancient DNA sequence is retrieved, it is often claimed that it will rewrite the textbooks of the organism it came from. This holds true for this study as well. This work is in collaboration with Scott Glaberman (Graduate Student EEB), Nikos Poulakakis (Natural History Museum of Crete), D. Reese (Yale Peabody Museum), scientists from the University of Crete and the Crete Natural History Museum.

Poulakakis, N., A. Parmakelis, P. Lymberakis, M. Mylonas, E. Zouros, D. S. Reese, S. Glaberman, A. CACCONE. Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids. Biology Letters, 2 451-454.

 

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deer

Extinct giant and dwarf deer of Crete

One of the most interesting problems in paleontology is the occurrence in the Quaternary of a rich fauna of endemic dwarf and giant species of vertebrates on several Mediterranean islands, including Sicily, Sardinia, Malta, Tilos, Cyprus, and Crete. In Crete, elephants, hippos, cervids and murids changed; generally, smaller animals increased in size whereas larger animals decreased in size. This project focuses on one of these groups, the deer. Their evolution on Crete is more complex, with greater variation in size and morphology than in any other vertebrates that made it to the island. Different named taxa (5-8 different species) ranged in size from animals as large as a caribou or a small elk to specimens similar in size to a dik-dik or a muntjac. We are proposing to take advantage of the ability to of extract DNA from dated dental and bone remains to produce a molecular phylogeny of the extinct cervids of Crete. For comparative purposes, we also will include DNA sequences of several mainland extinct and extant species. This phylogenetic approach will help us address a series of questions regarding their phyletic relations with the mainland fauna, and the patterns and timing of colonization of Crete (i.e., Are the different named taxa distinct phyletic lineages? Which colonization model do the genetic data support? Did the lineage(s) of Cretan deer originate from one or several mainland species? This work is in collaboration with Nikos Poulakakis, D. Reese (Yale Peabody Museum) and the group of R. Fleischer from the Smithsonian Museum of Natural History.