Dataset Information

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.

ABSTRACT: High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.

SUBMITTER: Brandley MC

PROVIDER: S-EPMC4434831 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.

Brandley Matthew C MC Bragg Jason G JG Singhal Sonal S Chapple David G DG Jennings Charlotte K CK Lemmon Alan R AR Lemmon Emily Moriarty EM Thompson Michael B MB Moritz Craig C

BMC evolutionary biology 20150411

<h4>Background</h4>High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic sc ...[more]

PMID: 25880916

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Project description:BACKGROUND:The Australian scincid clade Lerista provides perhaps the best available model for studying limb reduction in squamates (lizards and snakes), comprising more than 75 species displaying a remarkable variety of digit configurations, from pentadactyl to entirely limbless conditions. We investigated the pattern and rate of limb reduction and loss in Lerista, employing a comprehensive phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. RESULTS:The inferred phylogeny reveals extraordinary evolutionary mutability of limb morphology in Lerista. Ancestral state reconstructions indicate at least ten independent reductions in the number of digits from a pentadactyl condition, with a further seven reductions proceeding independently from a tetradactyl condition derived from one of these reductions. Four independent losses of all digits are inferred, three from pentadactyl or tetradactyl conditions. These conclusions are not substantially affected by uncertainty in assumed rates of character state transition or the phylogeny. An estimated age of 13.4 million years for Lerista entails that limb reduction has occurred not only repeatedly, but also very rapidly. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within 3.6 million years. CONCLUSION:The exceptionally high frequency and rate of limb reduction inferred for Lerista emphasise the potential for rapid and substantial alteration of body form in squamates. An absence of compelling evidence for reversals of digit loss contrasts with a recent proposal that digits have been regained in some species of the gymnophthalmid clade Bachia, possibly reflecting an influence of differing environmental and genetic contexts on the evolution of limb morphology in these clades. Future study of the genetic, developmental, and ecological bases of limb reduction and loss in Lerista promises the elucidation of not only this phenomenon in squamates, but also the dramatic evolutionary transformations of body form that have produced the extraordinary diversity of multicellular organisms.

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Project description:Here, I review phylogenetic studies of the lizard family Pygopodidae, a group of 47 extant species that diversified in Australia and New Guinea. The goal of this study was to examine published phylogenetic and phylogenomic hypotheses on pygopodids to identify the strengths and weaknesses in our understanding of their phylogeny. Many parts of the pygopodid family tree are well established by multiple independent tree inferences including: (1) all multispecies genera (i.e., Aprasia, Delma, Lialis, Pletholax, and Pygopus) are monophyletic groups; (2) the root of the pygopodid tree is located along the branch leading to the Delma clade, thus showing that Delma is the sister group to all other pygopodid genera; (3) the Aprasia repens group, Delma tincta group, and several other groups of closely related species are demonstrated to be monophyletic entities; and (4) the monotypic Paradelma orientalis is the sister lineage to the Pygopus clade. Based on accumulated phylogenetic evidence, two taxonomic recommendations are given: Paradelma merits generic status rather than being subsumed into Pygopus as some earlier studies had suggested, and the monotypic Aclys concinna should be recognized as a member of Delma (following current practice) until future studies clarify its placement inside or outside the Delma clade. One chronic problem with phylogenetic studies of pygopodids, which has limited the explanatory power of many tree hypotheses, concerns the undersampling of known species. Although the continual addition of newly described species, especially over the past two decades, has been a major reason for these taxon sampling gaps, deficits in species sampling for ingroups and/or outgroups in several studies of pygopodid species complexes has confounded the testing of some ingroup monophyly hypotheses. Ancient hybridization between non-sister lineages may also be confounding attempts to recover the relationships among pygopodids using molecular data. Indeed, such a phenomenon can explain at least five cases of mito-nuclear discordance and conflicts among trees based on nuclear DNA datasets. Another problem has been the lack of consensus on the relationships among most pygopodid genera, an issue that may stem from rapid diversification of these lineages early in the group's history. Despite current weaknesses in our understanding of pygopodid phylogeny, enough evidence exists to clarify many major and minor structural parts of their family tree. Accordingly, a composite tree for the Pygopodidae was able to be synthesized. This novel tree hypothesis contains all recognized pygopodid species and reveals that about half of the clades are corroborated by multiple independent tree hypotheses, while the remaining clades have less empirical support.

Dataset Information

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.

Publications

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.

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