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Presents an analysis of seismic reflection profiles that cover the southern half of the Cache Valley basin in northern Utah. Combination of subsurface data with surface geologic data; Geologic setting of basin; Factors affecting nonuniformity of basin and fault geometry; Non-conclusive deduction of geologic history from single cross sections.

Investigates the immunogenicity of an inactivated Hepatitis A vaccine. Methodology; Results; Discussion of findings.

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a "super-spreading" event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands' landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.

AbstractThe scarcity of asexual reproduction in vertebrates alludes to an inherent cost. Several groups of asexual vertebrates exhibit lower endurance capacity (a trait predominantly sourced by mitochondrial respiration) compared with congeneric sexual species. Here we measure endurance capacity in five species of Aspidoscelis lizards and examine mitochondrial respiration between sexual and asexual species using mitochondrial respirometry. Our results show reduced endurance capacity, reduced mitochondrial respiration, and reduced phenotypic variability in asexual species compared with parental sexual species, along with a positive relationship between endurance capacity and mitochondrial respiration. Results of lower endurance capacity and lower mitochondrial respiration in asexual Aspidoscelis are consistent with hypotheses involving mitonuclear incompatibility.

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show that previous estimates of co-expansion among five Alaskan populations of three-spine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations., (© 2020 The Authors. Evolution © 2020 The Society for the Study of Evolution.)

A new gekkonid lizard, Cyrtodactylus maelanoi sp. nov., from Mae Hong Son Province of the Thai Highlands is described using an integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs. Phylogenetic analyses place the new species within clade 1 of the C. sinyineensis group and as the sister species to C. inthanon with an uncorrected pairwise sequence divergence of 3.9%. Collection data gathered in the field indicate that C. maelanoi sp. nov. is a habitat generalist. Reconstruction of the ancestral habitat preference for the C. sinyineensis group by way of stochasitc character mapping (SCM) indicates that karstic environments were the ancestral condition out of which the general habitat preference of the ancestor of C. maelanoi sp. nov. and C. inthanon and that of C. amphipetreaus and C. doisuthep evolved three times independently. Additionally, SCM demonstrated that the evolution of a granitic habitat preference from a karst-adapted ancestor happened in C. aequalis. The discovery of a new upland species in the Thai Highlands brings into focus the understudied nature of the mountain systems of western Thailand and the need for their continued exploration and conservation.

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina., (Copyright © 2020 Elsevier Inc. All rights reserved.)

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number of species in Cambodia to at least seven. Species of this relatively small group vary widely in habitat preference, occurring in general, terrestrial, karstic, or granitic habitats. Ancestral character state mapping recovered a general habitat preference as the ancestral condition from which all others independently evolved even though this did not covary with morphology. The description of another new species of reptile from Cambodia continues to underscore the potentially significant amount of unrealized biodiversity in Indochina and Southeast Asia and the continued need for field surveys in unexplored or poorly explored areas.

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf., (© 2020 John Wiley & Sons Ltd.)

Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be absent or idiosyncratic. We conducted a Bayesian analysis of shared evolutionary events to test models of population divergence for 20 species of anurans (frogs) and squamates (lizards and snakes) that are distributed across the Dahomey Gap, a climate change-induced savanna barrier responsible for fragmenting previously contiguous rain forests of Ghana into two regions: the Togo-Volta Hills and the Southwestern Forests. A model of asynchronous diversification is supported for anurans and squamates, suggesting that drivers of diversification are not specifically related to ecological and life history associations with habitat types. Instead, the wide variability of genetic divergence histories exhibited by these species suggests that biodiversity in this region has been shaped by diversification events that extend beyond the Holocene. Comparisons of the genealogical divergence index, a measure of the genetic divergence between populations due to the combined effects of genetic isolation and gene flow, illustrate that these populations represent a broad sampling of the speciation continuum., (© 2020 The Authors. Evolution © 2020 The Society for the Study of Evolution.)

Background: Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting., Methods: To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa., Results: Overall, we found ω to be more similar between lineages descended from speciation events ( p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions., Competing Interests: The authors declare that they have no competing interests., (© 2020 David et al.)

An integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene ND2 recovered four new species of Hemiphyllodactylus Bleeker that are endemic to the Shan Plateau or Salween Basin in eastern Myanmar. Hemiphyllodactylus ngwelwini sp. nov. from the Shan Plateau is part of the earlier described "eastern Myanmar clade" renamed herein as the north lineage and H. kyaiktiyoensis sp. nov. and H. pinlaungensis sp. nov. of the Shan Plateau and H. zwegabinensis sp. nov. of the Salween Basin compose an entirely new Burmese clade herein referred to as the south lineage. Although the north and south lineages come within 46 km of one another on the Shan Plateau, they are not sister lineages but sequentially separated by two lineages from Yunnan, China and another from northwestern Thailand. Hemiphyllodactylus zwegabinensis sp. nov. is the first species of this genus to be recorded from the Salween Basin and is known only from a wind-blown cloud forest on the top of the insular, karstic mountain Zwegabin in Kayin State. All other Burmese species except for H. typus, are endemic to the various localities throughout the Shan Plateau. These four new species bring the total number of Hemiphyllodactylus in Myanmar to at least 10 which is certainly an extreme underestimate of the diversity of this genus given that we discover new species at every upland locality we survey.

A survey of a limestone forest at Gunung Baling, Kedah, West Malaysia lead to the discovery of an undescribed species of Bent-toed Gecko from the Cyrtodactylus pulchellus complex. Cyrtodactylus evanquahi sp. nov. can be distinguished from all other species in the C. pulchellus complex by a suite of morphological and color pattern characteristics: prominent tuberculation, higher number of dark body bands, and a smaller maximum SVL. It is further differentiated from all other species as follows; no tubercles on the ventral surface of the forelimbs, gular region, or in the ventrolateral folds; 31-34 paravetebral dorsal tubercles; 18-23 longitudinal rows of tubercles; 29-33 ventral scales; 22-23 subdigital lamellae on the fourth toe; 32-36 femoroprecloacal pores; a shallow precloacal groove in males; body bands and nuchal loop edged with a thin white line bearing tubercles; no scattered white spots on the dorsum; six or seven dark body bands much thinner than interspaces; 9-11 dark caudal bands on original tail; bands on the original tail separated by immaculate white caudal bands. It is further differentiated by an uncorrected pairwise genetic divergence of 6.50-15.67% from all other congeners in the C. pulchellus complex. It is most closely related to C. pulchellus from Penang Island ∼76 km to the southwest. In addition to the new samples from Gunung Baling, we added four samples of C. bintangrendah from the new locality of Belukar Semang, Perak. The discovery of yet another new species of the C. pulchellus complex from a limestone habitat continues to underscore the high degree of endemism and the importance of these unique habitats for biodiversity, and the continued need for their conservation.

An integrative taxonomic analysis of the 10 species of the Cyrtodactylus sinyineensis group based on squamation, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNA regions, recovered the newly discovered populations from Datt Kyaik and Taung Wine Hills in Kayin State as the new species Cyrtodactylus dattkyaikensis sp. nov. and C. taungwineensis sp. nov. The Maximum Likelihood and Bayesian phylogenetic estimates supported C. dattkyaikensis sp. nov. as the sister species of C. bayinnyiensis and C. taungwineensis sp. nov. as the sister species of C. sinyineensis. Each new species is differentially diagnosable from all other C. sinyineensis group species based on their morphological placement in multivariate space and several statistically significant mean differences is meristic squamation and color pattern data. The C. sinyineensis group ranges across an archipelago of karstic habitat-islands in the Salween Basin of southern Myanmar. The discovery of these new species continues to underscore the unprecedented high degree of diversity and site-specific endemism in this relatively small region and the urgent need for the conservation of its karstic terranes.

Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. Additionally, we review the literature on teaching practices to support the development of these skills. We pay special attention to meeting the needs of diverse learners, and consider how different ways of delivering course content can be leveraged to provide a more inclusive classroom experience. Our goal is to enable biologists to teach computational skills and use computing in the classroom successfully., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Wright AM et al.)

A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but differs from it and other congeners by at least a 5.0% sequence divergence. It is further differentiated by the following combination of morphological characters: (1) maximum SVL 24 mm in males and females; (2) first finger shorter than second; (3) absence of interorbital and tarsal ridges; (4) presence of light-coloured interscapular spot; (5) presence of yellow rictal tubercle; (6) absence of wide, light-coloured patch below eye; (7) presence of large, discrete, bright-yellow submandibular spots along the underside of lower jaw; (8) iris yellow-gold; (9) presence of markings on the snout consisting of streaks below the eye to the lip, and on the canthus rostralis to the nostril; (10) dorsum grey-brown with orange-beige spots, a dark-brown X-shaped marking on the back surrounding the interscapular spot, and dark-coloured markings on rump; (11) fore- and hind limbs with orange-beige cross-bars; and (12) venter light-gray with yellow spotting, especially near flanks and underside of hind limbs. Ansonia kyaiktiyoensis sp. nov. is the westernmost known record for the genus and the only species west of the Salween Basin. Its discovery echoes the increasing number of herpetological discoveries being made in upland regions fringing the Ayeyarwady and Salween Basins.

An integrative taxonomic analysis of the Cyrtodactylus linnwayensis group of the Shan Plateau recovered two new populations from isolated karst habitats near Pinlaung Town, Shan State as a new species, C. pinlaungensis sp. nov. Cyrtodactylus pinlaungensis sp. nov. is most closely related to a clade comprising C. linnwayensis and C. ywanganensis from the western edge of the Shan Plateau approximately 90 km to the northwest. Cyrtodactylus pinlaungensis sp. nov. can be distinguished from all members of the C. linnwayensis group by a number of statistically different morphological characters, discrete color pattern differences, and its heavy tuberculation. It also bears an uncorrected pairwise sequence divergence of 5.0-7.6% from all other species combined based on the mitochondrial gene ND2 and its flanking tRNAs. The discovery of this new species on the Shan Plateau continues to underscore the fact that this region is rapidly emerging as a herpetological diversity hot-spot for Myanmar.

Global habitat fragmentation is associated with the emergence of infectious diseases of wildlife origins in human populations. Despite this well-accepted narrative, the underlying mechanisms driving this association remain unclear. We introduce a nuanced hypothesis, the 'coevolution effect'. The central concept is that the subdivision of host populations which occurs with habitat fragmentation causes localized coevolution of hosts, obligate parasites, and pathogens which act as 'coevolutionary engines' within each fragment, accelerating pathogen diversification, and increasing pathogen diversity across the landscape. When combined with a mechanism to exit a fragment (e.g., mosquitoes), pathogen variants will spill over into human communities. Through this combined ecoevolutionary approach we may be able to understand the fine-scale mechanisms that drive disease emergence in the Anthropocene., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago., (© 2019 The Author(s). Evolution © 2019 The Society for the Study of Evolution.)

A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions., (© The Author(s) 2018. Published by Oxford University Press.)

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6-8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data., Competing Interests: The authors have declared that no competing interests exist.

Unlabelled: •, Premise of the Study: A recurrent explanation for phylogeographic discontinuities in the Baja California Peninsula and the Sonoran Desert Region has been the association of vicariant events with Pliocene and Pleistocene seaway breaks. Nevertheless, despite its relevance for plant dispersal, other explanations such as ecological and paleoclimatic factors have received little attention. Here, we analyzed the role of several of these factors to describe the phylogeographic patterns of the desert mistletoe, Phoradendron californicum.•, Methods: Using noncoding chloroplast regions, we assess the marginal probability of 19 a priori hypotheses related to geological and ecological factors to predict the cpDNA variation in P. californicum using a Bayesian coalescent framework. Complementarily, we used the macrofossil record and niche model projections on Last Glacial Maximum climatic conditions for hosts, mistletoe, and a bird specialist to interpret phylogeographic patterns.•, Key Results: Genealogical reconstructions revealed five clades, which suggest a combination of cryptic divergence, long-distance seed dispersal, and isolating postdivergence events. Bayesian hypothesis test favored a series of Pliocene and Pleistocene geological events related to the formation of the Baja California Peninsula and seaways across the peninsula as the most supported explanation for this genealogical pattern. However, age estimates, niche projections, and fossil records show dynamic host-mistletoe interactions and evidence of host races, indicating that ecological and geological factors have been interacting during the formation and structuring of phylogeographic divergence.•, Conclusions: Variation in cpDNA across the species range results from the interplay of vicariant events, past climatic oscillations, and more dynamic factors related to ecological processes at finer temporal and spatial scales., (© 2015 Botanical Society of America, Inc.)

Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Recently, Oaks et al. () assessed the ability of an approximate-Bayesian model-choice method (msBayes) to estimate such a pattern of simultaneous divergence across taxa, to which Hickerson et al. () responded. Both papers agree that the primary inference enabled by the method is very sensitive to prior assumptions and often erroneously supports shared divergences across taxa when prior uncertainty about divergence times is represented by a uniform distribution. However, the papers differ about the best explanation and solution for this problem. Oaks et al. () suggested the method's behavior was caused by the strong weight of uniformly distributed priors on divergence times leading to smaller marginal likelihoods (and thus smaller posterior probabilities) of models with more divergence-time parameters (Hypothesis 1); they proposed alternative prior probability distributions to avoid such strongly weighted posteriors. Hickerson et al. () suggested numerical-approximation error causes msBayes analyses to be biased toward models of clustered divergences because the method's rejection algorithm is unable to adequately sample the parameter space of richer models within reasonable computational limits when using broad uniform priors on divergence times (Hypothesis 2). As a potential solution, they proposed a model-averaging approach that uses narrow, empirically informed uniform priors. Here, we use analyses of simulated and empirical data to demonstrate that the approach of Hickerson et al. () does not mitigate the method's tendency to erroneously support models of highly clustered divergences, and is dangerous in the sense that the empirically derived uniform priors often exclude from consideration the true values of the divergence-time parameters. Our results also show that the tendency of msBayes analyses to support models of shared divergences is primarily due to Hypothesis 1, whereas Hypothesis 2 is an untenable explanation for the bias. Overall, this series of papers demonstrates that if our prior assumptions place too much weight in unlikely regions of parameter space such that the exact posterior supports the wrong model of evolutionary history, no amount of computation can rescue our inference. Fortunately, as predicted by fundamental principles of Bayesian model choice, more flexible distributions that accommodate prior uncertainty about parameters without placing excessive weight in vast regions of parameter space with low likelihood increase the method's robustness and power to detect temporal variation in divergences., (© 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.)

Background: To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences times, a pattern that can be estimated using genetic data from co-distributed species. I introduce a new approximate-Bayesian method for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. The model is an extension of that implemented in msBayes., Results: By reparameterizing the model, introducing more flexible priors on demographic and divergence-time parameters, and implementing a non-parametric Dirichlet-process prior over divergence models, I improved the robustness, accuracy, and power of the method for estimating shared evolutionary history across taxa., Conclusions: The results demonstrate the improved performance of the new method is due to (1) more appropriate priors on divergence-time and demographic parameters that avoid prohibitively small marginal likelihoods for models with more divergence events, and (2) the Dirichlet-process providing a flexible prior on divergence histories that does not strongly disfavor models with intermediate numbers of divergence events. The new method yields more robust estimates of posterior uncertainty, and thus greatly reduces the tendency to incorrectly estimate models of shared evolutionary history with strong support.

We utilize robust geographical genetic sampling, a multilocus dataset, a new synthesis of numerous fossil calibration points, a time-calibrated phylogeny, and the Dispersal-Extinction-Cladogenesis model to test the prediction that widespread Southeast Asian water monitor species initially diversified on the Asian mainland and subsequently invaded the island archipelagos of the Philippines, Sundaland, and Wallacea. Our results strongly contradict these expectations and instead infer an initial water monitor radiation of range-restricted but highly divergent evolutionary lineages (now recognized as endemic species) in one archipelago around 3.6 mya, followed by an out-of-the-Philippines reinvasion of the mainland (2.2 mya), resulting in a few, widespread species that now inhabit most the islands of the Sunda Shelf and the Southeast Asian mainland as far north as Myanmar, as well as an out-of-the-Philippines invasion of Sulawesi (2.1 mya). Our analyses both confirm the importance of island archipelagos as drivers of diversification for mainland biodiversity and emphasize the global evolutionary significance and conservation priority of the Philippines for understanding processes of diversification in island archipelagos., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists., (© 2013 John Wiley & Sons Ltd.)

Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters., (© 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.)

True crocodiles (Crocodylus) are the most broadly distributed, ecologically diverse, and species-rich crocodylian genus, comprising about half of extant crocodylian diversity and exhibiting a circumtropical distribution. Crocodylus traditionally has been viewed as an ancient group of morphologically conserved species that originated in Africa prior to continental breakup. In this study, these long-held notions about the temporal and geographic origin of Crocodylus are tested using DNA sequence data of 10 loci from 76 individuals representing all 23 crocodylian species. I infer a time-calibrated species tree of all Crocodylia and estimate the spatial pattern of diversification within Crocodylus. For the first time, a fully resolved phylogenetic estimate of all Crocodylia is well-supported. The results overturn traditional views of the evolution of Crocodylus by demonstrating that the true crocodiles are not "living-fossils" that originated in Africa. Rather, Crocodylus originated from an ancestor in the tropics of the Late Miocene Indo-Pacific, and rapidly radiated and dispersed around the globe during a period marked by mass extinctions of fellow crocodylians. The findings also reveal more diversity within the genus than is recognized by current taxonomy., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

In the Philippines, Pleistocene sea level oscillations repeatedly connected and isolated neighboring islands. Hence, an understanding of the island platforms adjoined during periods of low sea level has led biologists to a suite of expectations that, taken together, represent a paradigm for the process of recent diversification in southeast Asia. We employ statistical tests of phylogenetic topology and population genetic analyses of widespread species of bent-toed geckos (Cyrtodactylus) to ascertain whether patterns of inter- and intra-specific diversity can be explained by a Pleistocene aggregate island model of diversification. Contrary to many classic studies of Philippine vertebrates, we find complex patterns that are only partially explained by past island connectivity. In particular, we determine that some populations inhabiting previously united island groups show substantial genetic divergence and are inferred to be polyphyletic. Additionally, greater genetic diversity is found within islands, than between them. Among the topological patterns inconsistent with the Pleistocene model, we note some similarities with other lineages, but no obviously shared causal mechanisms are apparent. Finally, we infer well-supported discordance between the gene trees inferred from mitochondrial and nuclear DNA sequences of two species, which we suspect is the result of incomplete lineage sorting. This study contributes to a nascent body of literature suggesting that the current paradigm for Philippine biogeography is an oversimplification requiring revision., (Published by Elsevier Inc.)

It was demonstrated that gamma-irradiated L-929 cells support plaque formation by three strains of Rickettsia tsutsugamushi and representative species of the spotted fever and typhus group rickettsiae. Sensitivity of the plaque assay for detection of viable scrub typhus rickettsiae was similar to that achieved with intraperitoneal inoculation of random-bred mice. The concentration of irradiated cells and the temperature and length of incubation were all found to affect plaque size. A technique combining terminal dilution and plaque purification was used to obtain clones of three strains of scrub typhus rickettsiae.

A wide variety of animals have been utilized in an attempt to provide the information necessary to bring scrub typhus to the point where it is no longer a threat to man. The laboratory mouse is usually the animal of choice for the study of this disease. The discovery that certain strains of inbred mice are genetically resistant to Rickettsia tsutsugamushi, the agent of scrub typhus, has opened new avenues in the study of the immune response to the disease. The cynomolgus monkey, Macaca fascicularis, appears to be the best animal model for the study of scrub typhus as it occurs in humans and should be useful in the development of an efficacious vaccine.

The temperature range for optimum growth of Rickettsia conorii in suspension culture of gamma-irradiated L cells was 32-38 degrees C, resulting in rickettsial doubling times between 4.1 and 6.0 hr. An asynchronous release of R. conorii from host cells was suggested by the constant increase in percent cells infected over a 36 hr period. Rickettsial growth was optimal at neutral to slightly alkaline extracellular pH levels. A moderately acidic pH, however, resulted in an increase in doubling time from 4.1 to 7.8 hr.

The pathologic manifestations of the toxic death elicited by the iv injection of mice with Rickettsia tsutsugamushi strain Gilliam were examined by light and scanning electron microscopic techniques to ascertain the cause of death. Light microscopic examinations of hematoxylin and eosin-stained sections of organs suggested the presence of fluid in the lungs; this was confirmed by an increase in the weight of the lungs of moribund mice. Scanning electron microscopy of blood cells demonstrated a marked crenation of erythrocytes from these mice. Death appears to be the result of shock brought on by vascular collapse secondary to plasma leakage.

Monolayers of primary human endothelial cells were infected with the Karp strain of Rickettsia tsutsugamushi and examined by scanning and transmission electron microscopy. The results were compared with those obtained with similarly infected L-929 and MRC-5 cells and with uninfected cells of all three types. The rickettsiae grew to slightly higher titers in the human endothelial cells. Transmission electron microscopy revealed significant changes in the host cell organelles; a reduction in ribosome-coated endoplasmic reticulum and in Golgi activity, swelling of mitochondria, and an increase in vacuolation within the cytoplasm. Since human endothelial cells are known to retain their in vivo structural and functional qualities when cultured in vitro, it is likely that these effects are similar to those which occur during the infectious process in human scrub typhus.

Detailed study of post-Miocene stratigraphy in southeastern Virginia reveals at least 13 formations which show six Pliocene (?) and Pleistocene cycles of emergence and submergence, with maximum submergent sea levels near +45, +45, +20, +25, +15, and 0 feet, respectively. The newly established stratigraphic framework disproves earlier interpretations of "terrace-stratigraphy" and sea level chronologies.