The Experts below are selected from a list of 1245 Experts worldwide ranked by ideXlab platform
Matthew C Brandley - One of the best experts on this subject based on the ideXlab platform.
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the phylogenetic systematics of blue tailed skinks plestiodon and the family Scincidae
Zoological Journal of the Linnean Society, 2012Co-Authors: Matthew C Brandley, Xianguang Guo, Hidetoshi Ota, Tsutomu Hikida, Adrian Nietomontes De Oca, Manuel Feriaortiz, Yuezhao WangAbstract:Blue-tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well-supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine-locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent-based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re-evaluate deep relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of scincines and the inter-relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large scincine clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large-bodied species inhabiting northern Indochina, south-eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent-based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter-relationships of the primarily small-bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results.
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partitioned bayesian analyses partition choice and the phylogenetic relationships of scincid lizards
Systematic Biology, 2005Co-Authors: Matthew C Brandley, Andreas Schmitz, Tod W ReederAbstract:Partitioned Bayesian analyses of approximately 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean -lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2 ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
Tod W Reeder - One of the best experts on this subject based on the ideXlab platform.
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partitioned bayesian analyses partition choice and the phylogenetic relationships of scincid lizards
Systematic Biology, 2005Co-Authors: Matthew C Brandley, Andreas Schmitz, Tod W ReederAbstract:Partitioned Bayesian analyses of approximately 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean -lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2 ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
David G Chapple - One of the best experts on this subject based on the ideXlab platform.
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conservation status of the world s skinks Scincidae taxonomic and geographic patterns in extinction risk
Biological Conservation, 2021Co-Authors: David G Chapple, Uri Roll, Monika Bohm, Rocio Aguilar, Andrew Amey, Christopher C Austin, Marleen Baling, Anthony J Barley, Michael BatesAbstract:Abstract Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation status of skinks (Scincidae), a speciose reptile family with a worldwide distribution. Using International Union for Conservation of Nature (IUCN) criteria, we report that ~20% of species are threatened with extinction, and nine species are Extinct or Extinct in the Wild. The highest levels of threat are evident in Madagascar and the Neotropics, and in the subfamilies Mabuyinae, Eugongylinae and Scincinae. The vast majority of threatened skink species were listed based primarily on their small geographic ranges (Criterion B, 83%; Criterion D2, 13%). Although the population trend of 42% of species was stable, 14% have declining populations. The key threats to skinks are habitat loss due to agriculture, invasive species, and biological resource use (e.g., hunting, timber harvesting). The distributions of 61% of species do not overlap with protected areas. Despite our improved knowledge of the conservation status of the world's skinks, 8% of species remain to be assessed, and 14% are listed as Data Deficient. The conservation status of almost a quarter of the world's skink species thus remains unknown. We use our updated knowledge of the conservation status of the group to develop and outline the priorities for the conservation assessment and management of the world's skink species.
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origin diversification and systematics of the new zealand skink fauna reptilia Scincidae
Molecular Phylogenetics and Evolution, 2009Co-Authors: David G Chapple, Peter A Ritchie, Charles H DaughertyAbstract:Abstract The diverse scincid lizard fauna of the largely submerged subcontinent of Zealandia (which incorporates New Zealand, New Caledonia, Lord Howe Island, Norfolk Island, and the Chatham Islands) forms a monophyletic lineage within the Eugongylus group of skinks. We use 4062 bp of mitochondrial (ND2, ND4, Cytochrome b, 12SrRNA, 16SrRNA) and nuclear (Rag-1) DNA sequence data to recover a molecular phylogeny for the New Zealand skink fauna, and investigate the origin and diversification of skinks in New Zealand. Our phylogeny includes 32 of the 33 extant described New Zealand skink species (Cyclodina and Oligosoma), the Lord Howe Island skink (C. lichenigera), and representatives from several New Caledonian genera. Neighbour-joining, Maximum Parsimony, Maximum Likelihood, and Bayesian phylogenetic analyses are used to demonstrate that the New Zealand skink species form a single monophyletic lineage, with C. lichenigera representing a closely related sister lineage to the New Zealand radiation. Our relaxed molecular clock analyses indicate that skinks colonised New Zealand in the early Miocene (16–22.6 mya), shortly after the ‘Oligocene drowning’ event (∼25 mya). We propose that skinks reached New Zealand from New Caledonia via long-distance overwater dispersal, with C. lichenigera persisting on volcanic islands along the Lord Howe Rise and Norfolk Ridge. Eight major genetic clades are evident within the New Zealand skink fauna, with the divergences among these clades during the early to mid-Miocene resulting in distinct open habitat, forest, and coastal radiations. Subsequent diversification in the late Miocene–Pliocene appears to coincide with tectonic activity along the Alpine Fault and the uplift of the Southern Alps. We were unable to resolve the phylogenetic affinities of O. suteri, New Zealand’s only native oviparous skink. We use the phylogeny and topology tests to resolve several taxonomic issues and assess the taxonomic status of several suspected undescribed taxa. We complete a generic revision for the New Zealand skink fauna, placing C. lichenigera and all native New Zealand species into a single genus.
Richard Shine - One of the best experts on this subject based on the ideXlab platform.
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cues for communal egg laying in lizards bassiana duperreyi Scincidae
Biological Journal of The Linnean Society, 2013Co-Authors: Melanie J Elphick, David A Pike, Chalene N Bezzina, Richard ShineAbstract:Animals may aggregate either because the presence of conspecifics provides information about habitat suitability, or because the presence of conspecifics directly enhances individual viability. For a female lizard, the advantage of laying her eggs in a communal nest may entail either information transfer (hatched eggshells show that the site has been successful in previous seasons) or direct physiological benefits (recently-laid eggs can enhance water availability to other eggs). We tested the relative importance of these two mechanisms in the three-lined alpine skink (Bassiana duperreyi Gray, 1838) by offering gravid females a choice between sites with hatched eggshells versus freshly-laid eggs. Females selectively oviposited beside fresh eggs. In this species, early-nesting females use information transfer (i.e. the presence of old eggshells) as a nest-site criterion, whereas later nesters switch to a reliance on direct benefits of conspecific presence (i.e. the presence of freshly-laid eggs).
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evolutionary diversification of the lizard genus bassiana Scincidae across southern australia
PLOS ONE, 2010Co-Authors: Sylvain Dubey, Richard ShineAbstract:Background: Relatively recent (Plio-Pleistocene) climatic variations had strong impacts on the fauna and flora of temperatezone North America and Europe; genetic analyses suggest that many lineages were restricted to unglaciated refuges during this time, and have expanded their ranges since then. Temperate-zone Australia experienced less severe glaciation, suggesting that patterns of genetic structure among species may reflect older (aridity-driven) divergence events rather than Plio-Pleistocene (thermally-mediated) divergences. The lizard genus Bassiana (Squamata, Scincidae) contains three species that occur across a wide area of southern Australia (including Tasmania), rendering them ideally-suited to studies on the impact of past climatic fluctuations. Methodology/Principal Findings: We performed molecular phylogenetic and dating analyses using two partial mitochondrial genes (ND2 and ND4) of 97 samples of Bassiana spp. Our results reveal a pattern of diversification beginning in the Middle Miocene, with intraspecific diversification arising from 5.7 to 1.7 million years ago in the Upper Miocene-Lower Pleistocene. Conclusions/Significance: In contrast to the temperate-zone Northern Hemisphere biota, patterns of evolutionary diversification within southern Australian taxa appear to reflect geologically ancient events, mostly relating to east-west discontinuities imposed by aridity rather than (as is the case in Europe and North America) relatively recent recolonisation of northern regions from unglaciated refugia to the south.
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offspring sex in a lizard depends on egg size
Current Biology, 2009Co-Authors: Rajkumar S. Radder, David A Pike, Alexander E. Quinn, Richard ShineAbstract:Current paradigms may substantially underestimate the complexity of reptilian sex determination. In previous work, we have shown that the sex of a hatchling lizard (Bassiana duperreyi, Scincidae) does not depend entirely on its genes (XX versus XY sex chromosomes); instead, low nest temperatures can override genotype to produce XX as well as XY males 1, 2 and 3. Our experimental studies now add a third mechanism to this list: sex determination via yolk allocation to the egg. Within each clutch, the eggs that produce daughters are larger than those that produce sons. If (and only if) eggs are incubated at low temperatures, removing yolk from a newly laid egg turns the offspring into a male. Adding yolk from a larger (but not smaller) egg turns the recipient egg's offspring into a female. Remarkably, then, offspring sex in this species is the end result of an interaction between three mechanisms: sex chromosomes, nest temperatures, and yolk allocation.
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Isolation and development of a molecular sex marker for Bassiana duperreyi, a lizard with XX/XY sex chromosomes and temperature-induced sex reversal
Molecular Genetics and Genomics, 2009Co-Authors: Alexander E. Quinn, Rajkumar S. Radder, Stephen D. Sarre, Arthur Georges, Tariq Ezaz, Richard ShineAbstract:Sex determination in the endemic Australian lizard Bassiana duperreyi (Scincidae) is influenced by sex chromosomes and incubation temperature, challenging the traditional dichotomy in reptilian sex determination. Analysis of those interactions requires sex chromosome markers to identify temperature-induced sex reversal. Here, we report the isolation of Y chromosome DNA sequence from B. duperreyi using amplified fragment length polymorphism PCR, the conversion of that sequence to a single-locus assay, and its combination with a single-copy nuclear gene ( C-mos ) to form a duplex PCR test for chromosomal sex. The accuracy of the assay was tested on an independent panel of individuals with known phenotypic sex. When used on offspring from field nests, our test identified the likely occurrence of a low rate of natural sex reversal in this species. This work represents the first report of Y chromosome sequence from a reptile and one of the few reptile sex tests.
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parental care protects against infanticide in the lizard egernia saxatilis Scincidae
Animal Behaviour, 2004Co-Authors: David Oconnor, Richard ShineAbstract:Reports of postpartum parental care in squamate reptiles (lizards and snakes) are rare and generally anecdotal. We investigated parental care in black rock skinks, Egernia saxatilis, from southeastern Australia. These lizards live in small family groups, with adults defending territories against conspecifics. Juvenile lizards live within their parents' territory and may thus be protected from infanticide. In staged encounters in the laboratory, adults frequently attacked unrelated juveniles but not their own offspring, and the parent's presence significantly reduced the incidence of this infanticidal aggression. This protection arose not through specific ‘parental’ behaviours, but because adults tended to ignore juveniles when another (potentially threatening) adult was present. When two family groups were placed in the same enclosure, one family rapidly became dominant over the other. Juveniles of the dominant family derived thermoregulatory and foraging benefits from their parents' status. Thus, some lizards do show postpartum parental care, and may thereby significantly benefit their progeny via reduced risk of infanticide and better access to thermal and nutritional resources.
Adam D Leache - One of the best experts on this subject based on the ideXlab platform.
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detecting the anomaly zone in species trees and evidence for a misleading signal in higher level skink phylogeny squamata Scincidae
Systematic Biology, 2016Co-Authors: Charles W Linkem, Vladimir N Minin, Adam D LeacheAbstract:: The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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detecting the anomaly zone in species trees and evidence for a misleading signal in higher level skink phylogeny squamata Scincidae
bioRxiv, 2014Co-Authors: Charles W Linkem, Vladimir N Minin, Adam D LeacheAbstract:The anomaly zone presents a major challenge to the accurate resolution of many parts of the Tree of Life. The anomaly zone is defined by the presence of a gene tree topology that is more probable than the true species tree. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data (loci) will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often implement coalescent based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve are located within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scindidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for overcoming this challenge.
