The combined effects of rivers and refugia generate extreme cryptic fragmentation within the common ground skink (Scincella lateralis)

Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci. We then test several predictions of a river-refugia model of diversification. We recover 14 well-resolved mtDNA lineages distributed east-west along the Gulf Coast with a subset of lineages extending northward. In contrast, ncDNA exhibits limited phylogenetic structure or congruence among loci. However, multilocus population structure is broadly congruent with mtDNA patterns and suggests that deep coalescence rather than differential gene flow is responsible for mtDNA-ncDNA discordance. The observed patterns suggest that most lineages originated from population vicariance due to riverine barriers strengthened during the Plio-Pleistocene by a climate-induced coastal distribution. Diversification due to rivers is likely a special case, contingent upon other environmental or biological factors that reinforce riverine barrier effects. © 2009 The Society for the Study of Evolution

Parasites in a biodiversity hotspot: A survey of hematozoa and a molecular phylogenetic analysis of plasmodium in New Guinea skinks

A sample of 204 skinks (Squamata: Scincidae) from 10 genera representing 24 species were collected from 10 different localities in New Guinea and examined for blood parasites. Hemogregarines, trypanosomes, microfilarial worms, and 8 infections showing 2 distinct morphological types of malaria parasites (Plasmodium sp.) were observed. Molecular sequence data, in the form of mitochondrial cytochrome b sequences from the Plasmodium infections, showed 2 distinct clades of parasites, 1 in Sphenomorphus jobiense hosts and 1 in Emoia spp., which correspond to the 2 morphotypes. There was substantial genetic variation between the 2 clades, as well as within the clade of Emoia parasites. Nearly half of the skinks sampled had green blood pigmentation, resulting from the presence of biliverdin in the plasma; however, only 1 of these lizards was infected with Plasmodium sp. and only 2 had any blood parasites. These preliminary results suggest a high degree of phylogenetic diversity but a very low prevalence of Plasmodium spp. infections in the skinks of this globally important biodiversity hot spot. © American Society of Parasitologists 2006

Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages

Although recent radiations are fruitful for studying the process of speciation, they are difficult to characterize and require the use of multiple loci and analytical methods that account for processes such as gene flow and genetic drift. Using multilocus sequence data, we combine hierarchical cluster analysis, coalescent species tree inference, and isolation-with-migration analysis to investigate evolutionary relationships among cryptic lineages of North American ground skinks. We also estimate the extent that gene flow has accompanied or followed diversification, and also attempt to account for and minimize the influence of gene flow when reconstructing relationships. The data best support seven largely parapatric populations that are broadly concordant with mitochondrial (mt)DNA phylogeography throughout most of the species range, although they fail to fully represent extensive mtDNA divergence along the Gulf Coast. Relationships within and among three broad geographical groups are well supported, despite evidence of gene flow among them. Rejection of an allopatric divergence model partially depends on the inclusion of samples from near parapatric boundaries in the analyses, suggesting that allopatric divergence followed by recent migration may best explain migration rate estimates. Accounting for geographical variation in patterns of gene flow can improve estimates of migration-divergence parameters and minimize the influence of contemporary gene flow on phylogenetic inference. © 2012 The Linnean Society of London

Population genetic structure of the prairie skink (Eumeces septentrionalis): Nested clade analysis of post Pleistocene populations

We sequenced two regions of the mitochondrial genome, ND4 and d-loop, from 64 Eumeces septentrionales to assess intra- and interspecific population differentiation. We constructed haplotype genealogies for nine Eumeces septentrionalis septentrionalis populations in previously glaciated regions and used nested clade analysis to examine the role of vicariance and dispersal in shaping the population structure of E. s. septentrionalis in the northern part of its range following Pleistocene paleoclimatological events. In addition, we used DNA sequence data to compare populations of the northern subspecies (E. s. septentrionalis) with the southern subspecies (Eumeces septentrionalis obtusirostris) to determine whether specific level differentiation is evident. For populations of E. septentrionalis in previously glaciated areas, nested clade analyses revealed isolation by distance with restricted gene flow at both haplolype and upper clade levels as the inferred geographical pattern reflecting the lack of overlapping haplotypes in distant populations. These results suggest that colonization of E. septentrionalis into previously glaciated areas was from a single source with restricted gene flow. These results do not support past population fragmentation or colonization from multiple, genetically distinct source populations. Parsimony and maximum likelihood phylogenetic analyses showed reciprocal monophyly between northern (E. s. septentrionalis) and southern (E. s. obtusirostris) subspecies with unconnected sequence divergence ranging from 6.7-7.0%. These results, combined with the morphological differences found in previous studies, suggest that these allopatric populations are on separate evolutionary trajectories

Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes

SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising ∼4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel SINE family, Sauria SINEs, whose members are widely distributed among genomes of lizards, snakes, and tuataras. Sauria SINEs comprise a 5′ tRNA-related region, a tRNA-unrelated region, and a 3′ tail region (containing short tandem repeats) derived from LINEs. We distinguished eight Sauria SINE subfamilies in genomes of four major squamate lineages and investigated their evolutionary relationships. Our data illustrate the overall efficacy of Sauria SINEs as novel retrotransposable markers for elucidation of squamate evolutionary history. We show that all Sauria SINEs share an identical 3′ sequence with Bov-B LINEs and propose that they utilize the enzymatic machinery of Bov-B LINEs for their own retrotransposition. This finding, along with the ubiquity of Bov-B LINEs previously demonstrated in squamate genomes, suggests that these LINEs have been an active partner of Sauria SINEs since this SINE family was generated more than 200 million years ago. © Springer-Verlag New York, LLC 2004