Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers.

Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced.

Use of object-oriented classification and fragmentation analysis (1985-2008) to identify important areas for conservation in Cockpit Country, Jamaica.

Forest fragmentation is one of the most important threats to global biodiversity, particularly in tropical developing countries. Identifying priority areas for conservation within these forests is essential to their effective management. However, this requires current, accurate environmental information that is often lacking in developing countries. The Cockpit Country, Jamaica, contains forests of international importance in terms of levels of endemism and overall diversity. These forests are under severe threat from the prospect of bauxite mining and other anthropogenic disturbances. In the absence of adequate, up-to-date ecological information, we used satellite remote sensing data and fragmentation analysis to identify interior forested areas that have experienced little or no change as priority conservation sites. We classified Landsat images from 1985, 1989, 1995, 2002, and 2008, using an object-oriented method, which allowed for the inclusion of roads. We conducted our fragmentation analysis using metrics to quantify changes in forest patch number, area, shape, and aggregation. Deforestation and fragmentation fluctuated within the 23-year period but were mostly confined to the periphery of the forest, close to roads and access trails. An area of core forest that remained intact over the period of study was identified within the largest forest patch, most of which was located within the boundaries of a forest reserve and included the last remaining patches of closed-broadleaf forest. These areas should be given highest priority for conservation, as they constitute important refuges for endemic or threatened biodiversity. Minimizing and controlling access will be important in maintaining this core.

Tail injuries increase the risk of mortality in free-living lizards (Uta stansburiana).

Caudal autotomy is an effective anti-predator mechanism used by many lizard species. Fitness benefits of surviving a predatory attack are obvious, although lizards that autotomize their tails may be at greater risk during subsequent encounters with predators than lizards with complete tails. In previous laboratory studies, tail-less lizards were more vulnerable to capture by predators, but little is known about the relative survival of tailed versus tail-less lizards in nature. This study reports on significant associations between naturally incurred tail injuries and the subsequent risk of mortality in 7 populations of the lizard Uta stansburiana. I used standard mark-recapture techniques to document survival and quantified tail injuries by estimating tail completeness. I then used sampled randomization tests to compare intitial tail completeness values of surviving versus non-surviving lizards. I evaluated overall patterns by comparising the means of tail completeness values of survivors versus non-survivors among mark-recapture sequences. Lizards with incomplete tails suffered higher mortality in the field, although this was not true for every comparison considered (i.e., for every mark-recapture sequence analyzed), and the overall trend was much stronger for adult males than for either adult females or juveniles. Higher mortality among lizards with incomplete tails is presumably a consequence of increased vulnerability to capture by predators. Vulnerability to predation of tail-injured lizards may be confounded by reduced social status in this species, because social subordination can result in the occupation of an inferior home range.

DNA barcoding of an invasive mammal species, the small Indian mongoose (Herpestes javanicus; E. Geoffroy Saint-Hillaire 1818) in the Caribbean and Hawaiian Islands.

BACKGROUND AND AIM: The use of DNA barcodes has been proposed as a promising tool for identifying species. The efficacy of this tool for invasive species requires further exploration. The species status of the small Indian mongoose, an exotic invasive in several parts of the world, has been contentious due to morphological similarity with its congeners in its natural habitat. Although the small Indian mongoose is recognized as Herpestes javanicus, this nomenclature has been used interchangeably with Herpestes auropunctatus. MATERIALS AND METHODS: Here, we demonstrate the utility of using DNA barcoding approaches with mtDNA cytochrome b to discriminate between the two species and other sympatric members of the genus Herpestes (Herpestes naso, Herpestes urva, and Herpestes edwardsii). Using the diagnostic DNA positions we obtain, we can identity specimens of nonnative populations of the small Indian mongoose from the Caribbean and Hawaiian Islands to their species of origin. RESULTS: A singe diagnostic site accomplishes the identification of H. javanicus versus H. auropunctatus. CONCLUSION: Our results indicate that the nonnative mongoose populations from the Caribbean and Hawaiian Islands are H. auropunctatus, and not H. javanicus.