Investigating the prevalence of three medically important pathogens in from southern Oregon.

Introduction: In the far western United States of America, is the primary vector of several pathogens of public health and veterinary importance including the Lyme disease spirochete sensu lato (s.l.), as well as and is common in southern Oregon yet there are few published studies on the distribution of tick-borne pathogens in this region.

A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins.

Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times.

Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys).

The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies.

Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines).

Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.

Phylogeny and temporal diversification of the New World pond turtles (Emydidae).

We present a comprehensive multigene phylogeny and time tree for the turtle family Emydidae. Our phylogenetic analysis, based on 30 nuclear and four mitochondrial genes (23,330 total base pairs) sequenced for two individuals for each of the currently recognized species of the subfamily Emydinae and two species from each of the more species-rich Deirochelyinae genera, yielded a well-supported tree that provides an evolutionary framework for this well-studied clade and a basis for a stable taxonomy. We calibrated an emydid time tree using three well-vetted fossils, modeled uncertainty in fossil ages to reflect their accuracy in node dating, and extracted stem/crown ages of a number of key diversification events.

Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group.

A goal of modern taxonomy is to develop classifications that reflect current phylogenetic relationships and are as stable as possible given the inherent uncertainties in much of the tree of life. Here, we provide an in-depth phylogenetic analysis, based on 14 nuclear loci comprising 10,305 base pairs of aligned sequence data from all but two species of the turtle family Kinosternidae, to determine whether recent proposed changes to the group's classification are justified and necessary. We conclude that those proposed changes were based on (1) mtDNA gene tree anomalies, (2) preliminary analyses that do not fully capture the breadth of geographic variation necessary to motivate taxonomic changes, and (3) changes in rank that are not motivated by non-monophyletic groups.

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle.

As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle (Emys marmorata).

Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys.

Reconstructing species trees for clades containing weakly delimited or incorrectly identified taxa is one of the most serious challenges facing systematists because building phylogenetic trees is generally predicated on correctly identifying species membership for the terminals in an analysis. A common practice, particularly in large-scale phylogenetic analyses, is to use single-exemplar sampling under the implicit assumption that the resulting phylogenetic trees will be poorly supported if the sampled taxa are not good species. We examine this fundamental assumption in the North American turtle genus Pseudemys, a group of common, widely distributed freshwater turtles whose species boundaries and phylogenetic relationships have challenged systematists for over half a century.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.

Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle.

Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora.

Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships.

Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California.

The historical biogeography of California's taxa has been the focus of extensive research effort. The western pond turtle (Emys marmorata) is an example of a wide-ranging taxon that spans several well-known California diversity hotspots. Using a dataset comprised of one mitochondrial and five nuclear loci, we elucidate the major biogeographic patterns of the western pond turtle across the California landscape.

Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life.

Advances in molecular biology have expanded our understanding of patterns of evolution and our ability to infer phylogenetic relationships. Despite many applications of molecular methods in attempts at resolving the evolutionary relationships among the major clades of turtles, some nodes in the tree have proved to be extremely problematic and have remained unresolved. In this study, we use 14 nuclear loci to provide an in depth look at several of these troublesome nodes and infer the systematic relationships among 11 of the 14 turtle families.

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles.

Background: Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data.

Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization.

Understanding the mechanisms by which widely disjunct members of a clade came to occupy their current distribution is one of the fundamental challenges of biogeography. Here, we used data from 7 nuclear and 1 mitochondrial gene to examine the phylogenetic and biogeographic history of Emys, a clade of turtles that is broadly disjunct in western and eastern North America and Europe. We found strong disagreement between mitochondrial and nuclear gene trees, with mitochondrial DNA supporting the monophyly of the North American taxa (marmorata + blandingii) to the exclusion of the European orbicularis, and nuclear genes supporting the monophyly of (blandingii + orbicularis) to the exclusion of marmorata.

Moraxella bovoculi sp. nov., isolated from calves with infectious bovine keratoconjunctivitis.

Eighteen isolates of a Gram-negative coccus (strain 237(T)) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; 'pinkeye') in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity.

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications.

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico.

Phylogenetic hypotheses for the turtle family Geoemydidae.

The turtle family Geoemydidae represents the largest, most diverse, and most poorly understood family of turtles. Little is known about this group, including intrafamilial systematics. The only complete phylogenetic hypothesis for this family positions geoemydids as paraphyletic with respect to tortoises, but this arrangement has not been accepted by many workers.