Conservation Genetics

Salt-water crocodiles

In recent years we have concluded a molecular assay on blood and tissue samples of the saltwater crocodile, Crocodylus porosus, indigenous to the Republic of Palau. The objectives of this study was to determine: 1. If the Palauan crocodile population is composed of one or more separate species. 2. If the population reflects the genetic influence of crocodilian species other than Crocodylus porosus, which may, inadvertently, have been introduced into the population. 3. The genetic and morphological characterization of Palauan crocodilians. These samples were used in conjunction with blood, skin and bone samples from other crocodilian species that may have been introduced into the population prior to WWII. These include the Siamese crocodile, Crocodylus siamensis; the Philippine crocodile, Crocodylus mindorensis; and the New Guinea crocodile, Crocodylus novaeguineae. Scalation morphology of Palauan crocodilians was also characterized. This project was a collaboration with Michael Russello, Gregory Watkins-Colwell, J. Gratten, and P. Braziatis, and several Yale undergraduates.

Publications

Evolutionary and Behavioral Ecology

Our lab is involved in a series of projects in collaboration with PI’s from other laboratories working on evolutionary ecology projects. Our main input is to provide support for the collection and analyses of genetic data.

Wood Frogs

Molecular techniques such as microsatellite analysis make it possible to identify individual organisms and infer relatedness. We used these techniques to evaluate the importance of kin level structure and variation on the population ecology of wood frogs (Rana sylvatica) in the wild. Wood frogs are ideal organisms in which to conduct this research because of the discrete nature of the breeding ponds and larval habitat, the relatively brief generation time, and the fact that many influential studies in population and community ecology have already been conducted on these and similar pond-breeding amphibians. This project is in collaboration with D. Skelly (Yale Forestry School) and his group.

Publications

Corals

Patterns of associations between corals and the major clades of zooxanthellae can vary across scales ranging from individual colonies to widely separated regions. This was clearly illustrated in our study of members of the Montastraea annularis species complex in comparisons of six sites on the Mesoamerican Reef, Belize and nine sites in the Bocas del Toro archipelago, Panama. Because molecular types vary in their resistance to temperature resistant and some are found in environments characterized by high levels of irradiance and sedimentation, these Panamanian reefs may have considerable importance as reservoirs of corals better able to tolerate conditions associated with human impacts. This project is in collaboration with Nancy Knowlton and M. Garren (Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography). This project was M Garren's senior thesis in this laboratory.

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Phylogeography and Phylogenetics

Our lab continues to be involved in a variety of projects aimed at understanding the evolutionary patterns underlying the spatial and temporal structuring of genetic variation, especially in recently diverged taxa from insular systems, including islands and other isolated system such as caves. We are integrating genetic studies with morphological data, life history traits, and data from recently extinct taxa. The selection below shows a partial list of the projects in this area.

Evolutionary genetics of CT populations of Alewife (Alosa pseudoharengus)

Alewife, Alosa pseudoharengus, populations occur in two discrete life history variants, an anadromous form and a landlocked (freshwater resident) form.  Landlocked populations display a consistent pattern of life history divergence from anadromous populations, including earlier age at maturity, smaller adult body size, and reduced fecundity. We are using mtDNA sequence and microsatellites to ask whether coastal Connecticut landlocked alewife populations are independently evolved from anadromous populations or whether they share a common freshwater ancestor.  We are also interested in timing the divergence between anadromous and landlocked populations using microsatellite data to calculate to calculate the rate of evolution for foraging traits. This project is part of a large long-term research project coordinated by David Post, it was part of Eric Palkovacs, Ph.D. thesis. Kirstin Dion (EEB) collected data for this project.

Publications

Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area

The land snail genus Solatopupa consists of six species and has a peri-Tyrrhenian distribution; most of the species have a very narrow range and all of them except one (Solatopupa cianensis, which inhabits porphyritic rocks) are strictly bound to calcareous substrates. One species (Solatopupa guidoni) is limited to Sardinia, Corsica, and Elba Island. Because the potential for dispersal of these snails is low, the insular range of this species has been traditionally related to the Oligocenic detachment of the Sardinia–Corsica microplate from the Iberian plate and its subsequent rotation towards the Italian peninsula. In this study, we used sequences of three mitochondrial and one nuclear gene to reconstruct the evolutionary history of the genus. Our phylogenetic results are consistent with the genetic relationships found using allozymes, but contrast with the phylogenetic hypotheses based on karyology and morphology. Molecular clock estimates indicate that the main cladogenetic events in the genus occurred between the middle Miocene and the middle-late Pliocene. Patterns of phylogenetic relationships and geological considerations suggest that the cladogenesis of the genus can be explained by vicariant (tectonic) processes. Our datings do not support a causal relation between the split of S. guidoni from its continental sister taxon and the initial phases of the detachment of the Corsica–Sardinia microplate from the mainland. On the contrary, time estimates coincide with the very last phase of detachment of the microplate (from 5 to 3 Myrs ago). Overall, our molecular clock estimates are in good agreement with the latest geological views on the tectonic evolution of the peri-Tyrrhenian area. (pdf)

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Triturus salamanders

The genus Triturus is a problem for taxonomists. One member, the Southern Crested Newt, has been classified eighteen different ways. The monophyletic origin of European newts within this genus, family Salamandridae, has for decades rested on presumably homologous characters from behavior and morphology. Molecular data challenge this hypothesis, but the phylogenetic position of Triturus newts within the Salamandridae has not yet been convincingly resolved. We addressed this issue and that of the temporal divergence of Triturus within the Salamandridae with novel Bayesian approaches applied to DNA sequence data from three mitochondrial genes (12S, 16S and cytb). Using the molecular phylogeny we map the evolution of life history and courtship traits displayed by Triturus species. Given that their evolution is best explained by multiple independent evolutionary gains, we suggest that new conceptual and experimental approaches are required to explain how complex courtship traits, for a long time assumed to be homologous, might have evolved in parallel. This work is in collaboration with Saverio Vicario and Sebastian Steinfartz, former members of the lab.

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Grasshoppers

We surveyed Melanoplus femurrubrum grasshopper populations within the state of Connecticut for genetic diversity at multiple genetic markers, including three mitochondrial (CO1, ND2, and AT-rich) and one nuclear (ITS-1) gene regions. This study shows for the first time genetic variation for the ND2, AT-rich, and ITS genes within populations from a small geographic area from a Melanoplus species, and our methods and results should be useful for other researchers interested in conducting population level studies on closely related species. This project is in collaboration with Professor Oswald Schmitz from the Yale School of Forestry and Environmental Studies.

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Toads

Connecticut is home to two species of Bufo toads: Bufo americanus and Bufo fowleri. Bufo species are found throughout North America and commonly hybridize in nature. Our study aims at understanding the molecular phylogenetic relationships among Bufo americanus and Bufo fowleri in Connecticut.  How does their mtDNA compare to their morphology with respect to phylogenetic inference?  What is the phylogenetic relationship between Bufo toads in Connecticut to Bufo toads in the rest of their United States range? This project is in collaboration with Greogory Watkins-Colwell, of the Yale Peabody Museum.

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The Quagga Project

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.

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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.

Publications

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.

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