Workshops and Symposia
YIBS-MSCG Overview 1998-2008
Current Projects
Past Projects


Yale Institute for Biospheric Studies Offices

ESC, Room 132
21 Sachem Street
P.O. Box 208105
New Haven, CT 06520-8105
Phone: (203) 432-9856
Fax: (203) 432-9927

Oswald Schmitz, Director
Rose Rita Riccitelli, Assistant Director
LaToya Sealy, Sr Administrative Assistant

A selection of past projects in Phylogeography and Landscape Genetics


Developing AFLP markers for a genomic scan of plants in the genus Persicaria
Anne Greenburg, Yale EEB graduate student


Anne developed AFLP markers for a genomic scan of plants in the genus Persicaria. These were used to assess within- and between-species genetic variation in various Persicaria species to study hybridization and polyploidy in relation to weediness in the plant clade Persicaria. A NSF Graduate Research Fellowship Program fellowship was applied for based on this project.


Patterns of association between Symbiodinium and members of the Montastraea annularis species complex


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.

Publication: Garren, M., S.M. Walsh, A. Caccone, and N. Knowlton. 2006. Patterns of association between Symbiodinium and members of the Montastraea annularis species complex on spatial scales ranging from within colonies to between geographic regions. Coral Reefs, 25: 503-512


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)

Publication: Ketmaier, V., F. Giusti and A. Caccone. 2006. Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area. Mol. Phylog. And Evol., 39: 439-451


Reconsidering evolutionary patterns in 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 challenges 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 was in collaboration with Saverio Vicario and Sebastian Steinfartz, former members of the lab.

Publication: Steinfartz, S., S. Vicario, J. W. Arntzen and A. Caccone. 2006. A Bayesian approach on molecules, morphology and behavior: reconsidering evolutionary patterns in Triturus newts (Amphibia: Salamandridae)” J. of Exp. Zoology (Mol.Dev.Evol), 306B: 1-24.


Survey of Melanoplus femurrubrum grasshopper populations in Connecticut


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.

Publication: Jounhyoung Lee, Jonathan Marshall, Oswald J. Schmitz, and A. Caccone. 2006. Genetic divergence of Connecticut Melanoplus femurrubrum populations. Journal of Heredity, 97:290-293


Patterns of speciation in the rotifer species complex, Brachionus plicatilis
Lisa Suatoni, Yale EEB graduate student


We explored different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept).  Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species - the highest estimate for the group thus far.  A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries.  The convergence of species concepts in this group suggests that many of the species within the group may be old.  Although the diversity of the group is higher than previously understood, geographic distributions remain broad.  Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales.  These patterns concur with expectations that micro-meiofauna (0.1-1 mm) have biogeographies intermediate to microbial organisms and large vertebrates.  Sympatry of genetically distant strains is common.  

Publication: Suatoni, E., S. Vicario, S. Rice, T. Snell, and A. Caccone. 2006. An analysis of species boundaries and biogeographic patters in a cryptic species complex: The rotifer – Brachionus plicatilis. Molecular Phylogenetics and Evolution, 41: 86-98.


Molecular phylogenetic relationships among Bufo americanus and Bufo fowleri in Connecticut


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.


Xantusiid “Night” Lizards: A puzzling Phylogenetic Problem revisited
Saverio Vicario, Yale EEB graduate Student

night lizard

Contentious issues in Night Lizard (Xantusiidae) evolution were revisited using fragments from three mitochondrial genes, the ribosomal genes 12S and 16S, and the cytochrome b gene. All genes were sampled across an ingroup composed of seven xantusiid species and an outgroup of twelve-species chosen to bracket ancestral states for six additional clades of scleroglossan lizards. 

With these results we found support for the following conclusions: Xantusiidae is part of Scincomorpha, rather than being allied with Gekkota; Lepidophyma is sister to Xantusia, rather than to Cricosaura; Xantusia riversiana is imbedded within, rather than being sister to other Xantusia species; and rock-morph Xantusia are not related to one another.  Convergence, related to retarded rates of growth and development or to physical constraints imposed by living in rock crevices, may be responsible for much of the character discordance underlying conflicts in xantusiid phylogeny.

Fossil-calibrated Maximum Likelihood-based divergence time estimates suggest that although the xantusiid stem may have originated in the Mesozoic, the crown clade is exclusively Tertiary in age. Thus, the clade including extant Cricosaura does not appear to have been extant during the K-T boundary bolide impact as has been suggested. Moreover, our divergence-time estimates indicate that the xantusiid island endemics, Cricosaura typica on Cuba and Xantusia riversiana on the California Channel Islands, arrived via dispersal rather than vicariance as previously proposed.  

Publication:  Vicario, S., A. Caccone and J. Gauthier. 2003. Xantusiid "Night" lizards: a puzzling phylogenetic problem revisited using likelihood-based Bayesian methods on mtDNA sequences. Molecular Phylogenetics and Evolution, 26: 243-261.


Genetic structure of Mesoamerican populations of Big-leaf mahogany, Swietenia macrophylla
Rachel Roth Novick, Yale Forestry and Environemntal Studies masters student

mahagony tree

We assessed the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries.  Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation.

Publication: Roth R., C. Dick, M.R. Lemes, C. Navarro, A. Caccone, and E. Bermingham. 2003. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis. Molecular Ecology, 12: 2885-2894.