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Turtles are one of Earth's most instantly recognizable life forms, distinguished for over 200 million years in the fossil record. Even so, key nodes in the phylogeny of turtles remain uncertain. To address this issue, we sequenced >90% of the nuclear recombination activase gene 1 (RAG-1) for 24 species representing all modern turtle families. RAG-1(More)
Skates, rays and allies (Batoidea) comprise more than half of the species diversity and much of the morphological disparity among chondrichthyan fishes, the sister group to all other jawed vertebrates. While batoids are morphologically well characterized and have an excellent fossil record, there is currently no consensus on the interrelationships of(More)
Interest in phylogeny reconstruction has increased so rapidly during the past decade that now roughly 4,000 articles that include a phylogenetic tree are published each year and one of the key problems has been to discriminate between phy-logenetic signal and " noise. " Because constraints acting on DNA can strongly bias the assessment of homology (viz.(More)
Most methods for inferring phylogenies from sequence data assume that patterns of substitution have been stationary over time. Changes in evolutionary constraint can result in nonstationary substitution patterns that are phylogenetically misleading unless modeled appropriately. Here we present a multiple-alignment-based method to identify regions that are(More)
Squaliform sharks represent approximately 27 % of extant shark diversity, comprising more than 130 species with a predominantly deep-dwelling lifestyle. Many Squaliform species are highly specialized, including some that are bioluminescent, a character that is reported exclusively from Squaliform sharks within Chondrichthyes. The interfamiliar relationships(More)
Topological heterogeneity among gene trees is widely observed in phylogenomic analyses and some of this variation is likely caused by systematic error in gene tree estimation. Systematic error can be mitigated by improving models of sequence evolution to account for all evolutionary processes relevant to each gene or identifying those genes whose evolution(More)
The somniosid species Scymnodon ichiharai Yano and Tanaka 1984 is redescribed based on the type specimens and additional material from Taiwan and Japan. The range of this species is extended to include Taiwanese waters. Although recently allocated to the genus Zameus, this species is very similar to Scymnodon plunketi from the southern Indo-West Pacific;(More)
We commend O'Leary et al. (2003) on their reanalysis of their own data. We could take issue with their list of criticisms of our reanalysis point by point. For example, we disagree with their assertion that a heuristic search yielding 93,578 most-parsimonious trees (MPTs) is necessarily more " rigorous " than a heuristic search that yields 46,209 MPTs.(More)
Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study(More)