The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar.

Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world's mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.

Debugging diversity - a pan-continental exploration of the potential of terrestrial blood-feeding leeches as a vertebrate monitoring tool.

The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.

Phylogenetic relationships of South American lizards of the genus Stenocercus (Squamata: Iguania): A new approach using a general mixture model for gene sequence data.

The South American iguanian lizard genus Stenocercus includes 54 species occurring mostly in the Andes and adjacent lowland areas from northern Venezuela and Colombia to central Argentina at elevations of 0-4000m. Small taxon or character sampling has characterized all phylogenetic analyses of Stenocercus, which has long been recognized as sister taxon to the Tropidurus Group. In this study, we use mtDNA sequence data to perform phylogenetic analyses that include 32 species of Stenocercus and 12 outgroup taxa. Monophyly of this genus is strongly supported by maximum parsimony and Bayesian analyses. Evolutionary relationships within Stenocercus are further analyzed with a Bayesian implementation of a general mixture model, which accommodates variability in the pattern of evolution across sites. These analyses indicate a basal split of Stenocercus into two clades, one of which receives very strong statistical support. In addition, we test previous hypotheses using non-parametric and parametric statistical methods, and provide a phylogenetic classification for Stenocercus.

Phylogenetic relationships and molecular evolution in uropeltid snakes (Serpentes: Uropeltidae): allozymes and albumin immunology.

Multilocus electrophoretic methods and microcomplement fixation comparisons of serum albumin are used to assess phylogenetic relationships among species of uropeltid snakes, to infer aspects of their population biology and biogeography, and to evaluate their relationships to other primitive snakes (Henophidia). There is very good agreement between phylogenetic inferences derived from the electrophoretic data and those derived from the albumin immunological data. Protein variation detected by electrophoresis is relatively high among 17 operational taxonomic units (OTUs) examined. The mean number of alleles per locus (5.1 across all OTUs), levels of polymorphism (25% of loci), and heterozygosity (4-6%), are typical of, or greater than, values reported for other snakes. Species of uropeltids are genetically highly differentiated, as measured by genetic distances (lowest interspecific Nei's unbiased genetic distances, 0.22-0.27 among several Sri Lankan species; 2.3 between Teretrurus of India and other uropeltines). The phylogenetic tree most consistent with both the immunological and electrophoretic data shows uropeltines from Sri Lanka to be monophyletic, but the Indian species are paraphyletic with respect to those from Sri Lanka. Rhinophis travancoricus of India is inferred to be the sister taxon to the Sri Lankan radiation. As the genera are presently understood, neither Rhinophis nor Uropeltis appears to be monophyletic. A biogeographic scenario derived from the phylogenetic hypothesis suggests an early diversification of uropeltids in India, followed by a single invasion into the lowlands of Sri Lanka. Subsequent evolution on Sri Lanka resulted in occupation of montane biotopes. Cylindrophis is the sister group to uropeltines and is considered a member of the Uropeltidae. The immunological data indicate no phylogenetic association between uropeltids and other 'anilioid' taxa, specifically Anilius, Loxocemus or Xenopeltis, although we cannot rule out a very remote relationship. We specifically reject the hypothesis that uropeltines and scolecophidians form a clade relative to henophidians. High levels of genetic variation and a trend toward negative FIS values for polymorphic loci in three populations suggest generally large effective population sizes and outbreeding in these species. The niche-width variation hypothesis for allozyme loci is not supported by the uropeltid data. In comparison to other vertebrates, the relationship between Nei's genetic distance and albumin immunological distance in uropeltids suggests either conservative albumin evolution or strong differentiation at electrophoretic loci.