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Manakins (Pipridae) are well know for elaborate male sexual displays and ornate plumage coloration, both of which are thought to have evolved as a consequence of lekking breeding, the prevalent mating system in the family. Less attention has been paid to a handful of 'drab' manakin species, in which sexual dimorphism appears to be reduced or absent. Using character reconstruction, we show that these 'exceptions to the rule' represent phylogenetically independent cases of losses in sexual dimorphism, and as such could provide a focal group to investigate the link between changes in morphology and in life history (e.g. mating system). We take a first step in this direction by focusing on two subspecies of the putatively monomorphic green manakin Xenopipo holochlora to formally confirm that the species is sexually monomorphic in size and plumage color and test the prediction that sexual monomorphism is associated with the loss of lekking behavior in this species. Our results show that size dimorphism is present but limited in the green manakin, with substantial overlap in male and female morphometric measures, and that sexes are largely monochromatic (including from an avian perspective), despite marked coloration differences between subspecies. Behavioral observations indicate that males do not form leks and do not engage in elaborate sexual displays, that there is no stable pair bond formation, and that females provide parental care alone. These findings are consistent with the idea that changes in mating behavior may have driven changes in morphology in Pipridae, and we encourage similar studies on other drab manakins to better understand this relationship.

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species., (© The American Genetic Association. 2024.)

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome., (© The American Genetic Association. 2023.)

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest., (© The American Genetic Association. 2023.)

The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata . This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays ( C. argentigula , C. pumilo , C. mirabilis , and C. nanus ). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species ( C. mitrata and C. cucullata ). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white-throated magpie-jay ( Calocitta formosa ) and black-throated magpie-jay ( Calocitta colliei ) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre-1973) and modern (post-2005) time periods-a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white-throated individuals in the northern range of the black-throated magpie-jay hints at the possibility of prehistorical long-distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species., Competing Interests: The authors declare no competing interests., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages., (© The Author(s) 2022. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE).)

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-Jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.]., (© The Author(s) 2022. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Sceloporus subniger Poglaygen Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing thousands of genomic regions from 12 specimens to specifically evaluate the genetic distinctiveness of populations from western Michoacán and adjacent Jalisco along with the newly discovered population in the Sierra de Mascota in western Jalisco. We also recorded morphological data from 47 museum specimens to compare to our genetic data. Results from our analyses of the genetic data, augmented by specimen measurements and scale counts, support the notion that S. subniger is indeed a composite of distinct species. Montane bunchgrass lizards from western Michoacán and adjacent Jalisco, and from the Sierra de Mascota in western Jalisco, each represent distinct new species, which we describe and name here.

Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols., (© 2019 John Wiley & Sons Ltd.)

Natural history collections are yielding more information as digitization brings specimen data to researchers, connects specimens across museums, and as new technologies allow for more large-scale data collection. Therefore, a key goal in specimen digitization is developing methods that both increase access and allow for the highest yield of phenomic data. 3D digitization is increasingly popular because it has the potential to meet both aspects of that key goal. However, current methods overlook or do not prioritize some of the most sought-after phenotypic traits, those involving the external appearance of specimens, especially color. Here, we introduce an efficient and cost-effective pipeline for 3D photogrammetry to capture the external appearance of natural history specimens and other museum objects. 3D photogrammetry aligns and compares sets of dozens, hundreds, or even thousands of photos to create 3D models. The hardware set-up requires little physical space and around $3,000 in initial investment, while the software pipeline requires $1,400/year for proprietary software subscriptions (with open-source alternatives). The creation of each 3D model takes 1-2 hours/specimen and much of the software pipeline is automated with minimal supervision required, including the onerous step of mesh processing. We showcase the method by creating 3D models for most of the type specimens in the Moore Laboratory of Zoology bird collection and show that digital bill measurements are comparable to hand-taken measurements. Color data, while not included as part of this pipeline, is easily extractable from the models and one of the most promising areas of data collection. Future advances can adapt the method for ultraviolet reflectance capture and increased efficiency and model quality. Combined with genomic data, phenomic data from 3D models including photogrammetry will open new doors to understanding organismal evolution., Competing Interests: The authors have declared that no competing interests exist.

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution., (© The Author(s) 2019. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Advanced age and comorbidities are recognized risk factors for adverse outcomes in elderly trauma patients. However, the contribution of the number and type of complications to in-hospital mortality in elderly blunt trauma admissions has not been extensively studied., Methods: A retrospective review of the trauma registry at a level 1 trauma center for blunt trauma patients age ≥65 y hospitalized for at least 2 d between 2010 and 2015., Results: There were 2467 admissions, with a median age of 81 y and median injury severity score of 9. The most common mechanism of injury was a low-level fall. Approximately 19.6% of admissions had a complication: 11.1% major complications, 8.6% other complications. The in-hospital mortality rate was significantly different (P < 0.001) among the three groups at 16.1% of major complications group, 7.1% of other, and 2.1% of no complications (P < 0.001). On multivariate logistic regression, each major complication increased the odds for in-hospital mortality by 1.59-fold., Conclusions: Complications are not infrequent in elderly blunt trauma admissions, despite a generally lower energy mechanism of injury. Each major complication is associated with increased odds of mortality. Multifaceted interventions for prevention and mitigation of complications are indicated., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Measurement of the angular and overlap dependence of the conduction between two identical carbon nanotubes (CNTs), with the same diameter and chirality, has only been possible through theoretical calculations; however, our observation of increased resistance adjacent to the junction between two CNTs facilitates such measurements. Since electrical resistance was found to increase with increased diameter ratio, applying 10 V to one of dissimilar diameter CNTs results in cleavage at the junction. Manipulation of the resulting identical CNTs (created by cutting a single CNT) allows for the direct measurement of the angular and parallel overlap conduction. Angular (13° < θ < 63°) dependence shows two minima (22° and 44°) and a maximum at 30°, and conduction between parallel CNTs increases with overall tip separation but shows a sinusoidal relationship with contact length, consistent with the concept of atomic scale registry.

Objective: Hybrid zones are geographic regions where genetically distinct taxa interbreed, resulting in offspring of mixed ancestry. California Scrub-Jays (Aphelocoma californica) and Woodhouse's Scrub-Jays (A. woodhouseii) come into secondary contact and hybridize in western Nevada. Although previous work investigated divergence and gene flow between these species using a handful of microsatellite markers, the hybrid zone has not been studied using genome-scale markers, providing an opportunity to assess genome-wide introgression, test for a genetic basis for ecomorphological traits, and compare these estimates to those derived from microsatellites., Results: Using variant sites flanking ultraconserved elements (UCEs), we performed population assignment and quantified hybrid ancestry for 16 individuals across the zone of secondary contact. Our study included 2468 SNPs distributed throughout the genome, allowing discrimination of genetic affinities of hybrid individuals that were similar to estimates from microsatellites. We show a relationship between bill and wing length and the genetic composition of individuals that was not found in prior work using microsatellites, suggesting a genetic basis for these traits. Our analyses demonstrate the utility of UCEs for the analysis of hybrid zones and provide a basis for future studies to identify the genomic architecture of speciation and phenotypic differences between these incipient species.

Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genus Dendrortyx. The three Dendrortyx species are found in the highlands of central Mexico and Central America south to Costa Rica. One of these species is endangered, and in general, Dendrortyx are secretive and poorly represented in tissue collections. We extracted DNA from historical museum specimens and sequenced ultraconserved elements (UCEs) and mitochondrial DNA (mtDNA) to assess their phylogeny and divergence times. Phylogenies built from hundreds to thousands of nuclear markers were well resolved and largely congruent with an mtDNA phylogeny. The divergence times revealed an unusually old avian divergence across the Isthmus of Tehuantepec in the Pliocene around 3.6 million years ago. Combined with other recent studies, our results challenge the general pattern that highland bird divergences in Mesoamerica are relatively young and influenced by the Pleistocene glacial cycles compared to the older divergences of reptiles and plants, which are thought to overlap more with periods of mountain formation. We also found evidence for monophyletic genetic lineages in mountain ranges within the widespread D. macroura, which should be investigated further with integrative taxonomic methods. Our study demonstrates the power of museum genomics to provide insight into the evolutionary histories of groups where modern samples are lacking., (Copyright © 2019 Elsevier Inc. All rights reserved.)

With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data., (© 2018 John Wiley & Sons Ltd.)

Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs ( Sarcohyla bistincta , Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as S. bistincta . Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in Sarcohyla and may have acted as a dispersal corridor for S. bistincta to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species., Competing Interests: The authors declare there are no competing interests.

The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci., (© 2018 John Wiley & Sons Ltd.)

Introduction: Isolated hip fracture (IHF) is a common injury in the elderly after a fall. However, there is limited study on elderly IHF patients' subsequent hospitalization for a new injury, that is, trauma-related recidivism., Methods: A retrospective review of the trauma registry at an ACS level I trauma center was performed for all elderly (age ≥ 65 y) blunt trauma patients admitted between 2007 and 2017, with a focus on IHF patients. IHF was defined as a fracture of the femoral head, neck, and/or trochanteric region without any other injuries except minor soft tissue trauma after a fall., Results: Of the 4986 elderly blunt trauma admissions, 974 (19.5%) had an IHF. The rate of trauma-related recidivism was 8.9% (n = 87) for a second injury requiring hospitalization. The majority of recidivist (74.7%) and nonrecidivist (66.5%) patients were females. Hospital length of stay was similar at index admission (7 d for recidivists versus 8 d for nonrecidivists). The median interval between index hospitalization and admission for a second injury was 373 d (IQR 156-1002). The most common mechanism of injury at index admission (95.4%) and at second injury-related hospitalization (95.4%) was a low-level fall. Among recidivist patients at second admission, a second hip fracture was present in 34.5% and intracranial hemorrhage in 17.2%., Conclusions: After initial admission for an IHF, 8.9% of patients were readmitted for a second injury, at a median time of approximately 1 y, overwhelmingly from a low-level fall. Emphasis on fall prevention programs and at index admission is recommended., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Background: In the general population with blunt chest trauma, pulmonary contusions (PCs) are commonly identified. However, there is limited research in the elderly. We sought to evaluate the incidence and outcomes of PCs in elderly blunt trauma admissions., Methods: We retrospectively reviewed the trauma registry at a level I trauma center for all blunt thoracic trauma patients aged ≥65 y, who were admitted between 2007 and 2015. The medical records of PC patients were reviewed., Results: There were 956 admissions with blunt thoracic trauma; of which 778 had no pulmonary contusion (NO) and 178 had PC. The major mechanisms of injury were falls (58.7% NO, 39.3% PC, P <0.001) and motor vehicle crash/motor cycle crash (35.6% NO, 51.7% PC, P <0.001). Rib fractures were present in 79.8% of PC and 73.8% of NO patients, P = 0.1. PC patients more often had serious (AIS ≥3) head/neck (30.3% versus 20.6%, P <0.001), abdomen (12.4% versus 6.6%, P <0.001), and extremity injuries (20.8% versus 11.4%, P <0.001). Complication (46.1% PC versus 26.6% NO, P <0.001) and mortality (14.0% PC versus 6.2% NO, P = 0.0003) rates were higher in PC patients. On multivariate logistic regression analyses, PC presence was significantly associated with mechanical ventilation (odds ratio 2.5), intensive care unit admission (odds ratio 2.3), and mortality (odds ratio 1.9)., Conclusions: Over 18.6% of elderly blunt thoracic trauma patients sustained PC, despite an often low energy mechanism of injury. The presence of a PC should prompt investigation for other serious intrathoracic and extrathoracic injuries. PC presence is associated with substantial morbidity and mortality., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Background: Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored., Results: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ 15 N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons., Conclusions: This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.

Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Morphologically conserved taxa such as scorpions represent a challenge to delimit. We recently discovered populations of scorpions in the genus Kovarikia Soleglad, Fet & Graham, 2014 on two isolated mountain ranges in southern California. We generated genome-wide single nucleotide polymorphism data and used Bayes factors species delimitation to compare alternative species delimitation scenarios which variously placed scorpions from the two localities with geographically adjacent species or into separate lineages. We also estimated a time-calibrated phylogeny of Kovarikia and examined and compared the morphology of preserved specimens from across its distribution. Genetic results strongly support the distinction of two new lineages, which we describe and name here. Morphology among the species of Kovarikia was relatively conserved, despite deep genetic divergences, consistent with recent studies of stenotopic scorpions with limited vagility. Phylogeographic structure discovered in several previously described species also suggests additional cryptic species are probably present in the genus.

Introduction: Blunt thoracic trauma in the elderly has been associated with adverse outcomes. As an internal quality improvement initiative, direct intensive care unit (ICU) admission of nonmechanically ventilated elderly patients with clinically important thoracic trauma (primarily multiple rib fractures) was recommended., Methods: A retrospective review of the trauma registry at a level 1 trauma center was performed for patients aged ≥65 y with blunt thoracic trauma, admitted between the 2 y before (2010-2012) and after (2013-2015) the recommendation., Results: There were 258 elderly thoracic trauma admissions post-recommendation (POST) and 131 admissions pre-recommendation (PRE). Their median Injury Severity Score (13 versus 12, P = ns) was similar. The POST group had increased ICU utilization (54.3% versus 25.2%, P < 0.001). The POST group had decreased unplanned ICU admissions (8.5% versus 13.0%, P < 0.001), complications (14.3% versus 28.2%, P = 0.001), and ICU length of stay (4 versus 6 d, P = 0.05). More POST group patients were discharged to home (41.1% versus 27.5%, P = 0.008). Of these, the 140 POST and 33 PRE patients admitted to the ICU had comparable median Injury Severity Score (14 versus 17, P = ns) and chest Abbreviated Injury Score ≥3 (66.4% versus 60.6%, P = ns). The POST-ICU group redemonstrated the above benefits, as well as decreased hospital length of stay (10 versus 14 d, P = 0.03) and in-hospital mortality (2.9% versus 15.2%, P = 0.004)., Conclusions: Admission of geriatric trauma patients with clinically important blunt thoracic trauma directly to the ICU was associated with improved outcomes., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Melanophryniscus is a bufonid frog genus with a broad geographic distribution over southeastern South America. In recent years, several new species of Melanophryniscus have been discovered in southern Brazil showing a distinctive life-history strategy for the genus - breeding in phytotelmata - as well as a strong association with high-altitude regions. In this study, we use mitogenomic data to infer the phylogenetic relationships among diurnal, phytotelm-breeding Melanophryniscus and to determine the timing of their divergence. We obtained the mitochondrial genomes (not including the control region) for eight individuals of Melanophryniscus representing all three described species (M. alipioi, M. milanoi, and M. xanthostomus), as well as some recently-discovered and potentially new species. Gene order was conserved in all species and corresponded to the general order found in bufonids. Although the phylogenetic relationships among the studied species was poorly supported, dating confirmed that they diverged during the Pleistocene, suggesting that phytotelm breeding could have arisen during drier periods in the glacial/interglacial cycles due to a decrease in the availability of permanent streams or ephemeral/temporary streams or ponds in which Melanophryniscus species commonly breed., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: A number or risk assessment tools are used in trauma victims. Because of its simplicity, we examined the ability of the recently described quick Sequential Organ Failure Assessment Score (qSOFA) to predict outcomes in blunt trauma patients presenting to the Emergency Department., Methods: We queried the trauma registry at a Level 1 Trauma Center for all adult blunt trauma admissions between 1/1/10 and 9/30/15. qSOFA scores were the sum of binary scores for 3 variables (RR ≥ 22, SBP≤100 mmHg, and GCS≤13)., Results: There were 7064 admissions (5664 admissions had qSOFA = 0, 1164 had qSOFA = 1, 223 had qSOFA = 2, and 13 had qSOFA = 3). Higher qSOFA scores were associated with greater injury severity, increased ICU admission, and higher complication rates. qSOFA scores were associated with in-hospital mortality (1.7% with qSOFA = 0; 8.7% with qSOFA = 1; 22.4% with qSOFA = 2; 23.1% with qSOFA = 3; p < 0.001). On multivariate analysis, qSOFA score was an independent predictor of mortality., Conclusions: qSOFA scores are directly associated with adverse outcomes in blunt trauma victims., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Extremity compartment syndrome is a recognized complication of trauma. We evaluated its prevalence and outcomes at a suburban level 1 trauma center., Methods: The trauma registry was reviewed for all blunt trauma patients aged ≥18 years, admitted between 2010 and 2014. Chart review of patients with extremity compartment syndrome was performed., Results: Of 6180 adult blunt trauma admissions, 83 patients developed 86 extremity compartment syndromes; two patients had compartment syndromes on multiple locations. Their (n = 83) median age was 44 years (interquartile range: 31.5-55.5). The most common mechanism of injury was motor vehicle/motor cycle accident (45.8%) followed by a fall (21.7%). The median injury severity score was 9 (interquartile range: 5-17); 65.1% had extremity abbreviate injury score ≥3. Notably, 15 compartment syndromes did not have an underlying fracture. Among patients with fractures, the most commonly injured bone was the tibia, with tibial plateau followed by tibial diaphyseal fractures being the most frequent locations. Fasciotomies were performed, in order of frequency, in the leg (n = 53), forearm (n = 15), thigh (n = 9), foot (n = 5), followed by multiple or other locations., Conclusions: Extremity compartment syndrome was a relatively uncommon finding. It occurred in all extremity locations, with or without an associated underlying fracture, and from a variety of mechanisms. Vigilance is warranted in evaluating the compartments of patients with extremity injuries following blunt trauma., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods., (© 2016 John Wiley & Sons Ltd.)

Objectives: To evaluate the incidence of spinal fractures and their outcomes in the elderly who fall from low-levels in a suburban county., Design: Retrospective county-wide trauma registry review from 2004 to 2013., Setting: Suburban county with regionalized trauma care consisting of 11 hospitals., Participants: Adult trauma patients aged ≥65 years who were admitted after falling from <3 feet., Measurements: Demographic characteristics, comorbidities, and outcomes., Results: Spinal fractures occurred in 18% of 4,202 older adult patients admitted following trauma over this 10-year time period, in the following distribution: 43% cervical spine, 5.7% thoracic, 4.9% lumbar spine, 36% sacrococcygeal, and 9.6% multiple spinal regions. As compared to non-spinal fracture patients, more spinal fracture patients went to acute/subacute rehabilitation (47% vs 34%, P < .001) and fewer were discharged home (21% vs 35%, P < .001). In-hospital mortality rate in spinal and non-spinal fracture patients was similar (8.5% vs 9.3%, P = .5)., Conclusion: Low-level falls often resulted in a spinal fracture at a variety of levels. Vigilance in evaluation of the entire spine in this population is suggested., (© 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.)

Background: The prevalence and outcomes of older trauma patients with implantable cardioverter defibrillators (ICDs) or permanent pacemakers (PPMs) is unknown., Methods: The trauma registry at a regional trauma center was reviewed for blunt trauma patients, aged ≥ 60 years, admitted between 2007 and 2014. Medical records of cardiac devices patients were reviewed., Results: Of 4,193 admissions, there were 146 ICD, 233 PPM, and 3,814 no device patients; median Injury Severity Score was 9. Most cardiac device patients had substantial underlying heart disease. Patients with ICDs (13.0%) and PPMs (8.6%) had higher mortality rates than no device patients (5.6%, P = .0002). Among cardiac device patients who died, the device was functioning properly in all that were interrogated; the most common cause of death was intracranial hemorrhage. On propensity score analysis, cardiac devices were not independent predictors of mortality but rather surrogate variables associated with other predictors of mortality., Conclusions: Approximately 9.0% of admitted older patients had cardiac devices. Their presence identified patients who had higher mortality rates, likely because of their underlying comorbidities, including cardiac dysfunction., (Published by Elsevier Inc.)

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation., (© 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.)

New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources., (© 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.)

The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate-induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low-dispersing species to shed light on small-scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots., (© 2016 John Wiley & Sons Ltd.)

Background: The prevalence and outcomes of trauma patients requiring an unplanned return to the intensive care unit (ICU) and those initially admitted to a step-down unit or floor and subsequently upgraded to the ICU, collectively termed unplanned ICU (UP-ICU) admission, are largely unknown., Methods: A retrospective review of the trauma registry of a suburban regional trauma center was conducted for adult patients who were admitted between 2007 and 2013, focusing on patients requiring ICU admission. Prehospital or emergency department intubations and patients undergoing surgery immediately after emergency room evaluation were excluded., Results: Of 5411 admissions, there were 212 UP-ICU admissions, 541 planned ICU (PL-ICU) admissions, and 4658 that were never admitted to the ICU (NO-ICU). Of the 212 UP-ICU admits, 19.8% were unplanned readmissions to the ICU. Injury Severity Score was significantly different between PL-ICU (16), UP-ICU (13), and NO-ICU (9) admits. UP-ICU patients had significantly more often major (Abbreviated Injury Score ≥ 3) head/neck injury (46.7%) and abdominal injury (9.0%) than the NO-ICU group (22.5%, 3.4%), but significantly less often head/neck (59.5%) and abdominal injuries (17.9%) than PL-ICU patients. Major chest injury in the UP-ICU group (27.8%) occurred at a statistically comparable rate to PL-ICU group (31.6%) but more often than the NO-ICU group (14.7%). UP-ICU patients also significantly more often underwent major neurosurgical (10.4% vs 0.7%), thoracic (0.9% vs 0.1%), and abdominal surgery (8.5% vs 0.4%) than NO-ICU patients. Meanwhile, the PL-ICU group had statistically comparable rates of neurosurgical (6.8%) and thoracic surgical (0.9%) procedures but lower major abdominal surgery rate (2.0%) than the UP-ICU group. UP-ICU admission occurred at a median of 2 days following admission. UP-ICU median hospital LOS (15 days), need for mechanical ventilation (50.9%), and in-hospital mortality (18.4%) were significantly higher than those in the PL-ICU (9 days, 13.9%, 5.4%) and NO-ICU (5 days, 0%, 0.5%) groups., Conclusions: UP-ICU admission, although infrequent, was associated with significantly greater hospital length of stay, rate of major abdominal surgery, need for mechanical ventilation, and mortality rates than PL-ICU and NO-ICU admission groups., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Tranexamic acid (TXA) is an antifibrinolytic agent that is listed as an essential medication by the World Health Organization for traumatic hemorrhage. We determined United States-based surgeons' familiarity with TXA and their use of TXA. An online survey was sent to the 1291 attending surgeon members of a national trauma organization. The survey was organized into three general parts: respondent demographics, perceptions of TXA, and experience with TXA. The survey was completed by 35 per cent of members. TXA was available at 89.1 per cent of centers. Experience with TXA was variable: 38.0 per cent use regularly, 24.9 per cent use it 1 to 2 times per year, 12.3 per cent use it rarely, and 24.7 per cent had never used it. Among surgeons who had used TXA, 77.1 per cent noted that TXA had reduced bleeding, but 22.9 per cent indicated that it had not. Reasons for not routinely using TXA included uncertain clinical benefit (47.7%) and unfamiliarity (31.5%). Finally, 90.5 per cent of respondents indicated that are looking toward national organizations to develop practice guidelines. TXA is widely available in civilian United States trauma centers. Although a majority of surveyed surgeons had used TXA, only 38 per cent use TXA regularly for significant traumatic hemorrhage; principal reasons for this are uncertainty regarding clinical benefit and unfamiliarity with the drug. National guidelines are sought.

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as "species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to "first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Do Not Resuscitate (DNR) orders have been associated with poor outcomes in surgical patients. There is limited literature on admitted trauma patients with advanced directives indicating DNR status before admission (preadmission DNR [PADNR])., Methods: A retrospective review of the trauma registry of a suburban county was carried out for admitted trauma patients with age ≥41 years, who were admitted between 2008 and 2013., Results: Of 7,937 admitted patients, 327 had a preadmission advanced directive indicating DNR. PADNR patients were significantly older (87 vs 69 years), with more frequent comorbidities, and were more often admitted after a fall (94.2% vs 65.8%). PADNR patients had a higher Injury Severity Score (14 vs 11). They also had significantly increased rates of pneumonia, sepsis, myocardial infarction, and death (33.6% vs 5.9%). On multivariate logistic regression, the presence of a preadmission advanced directive indicating DNR status was independently associated with a 5.2-fold increased odds of mortality., Conclusion: An advanced directive indicating DNR is associated with adverse outcomes following trauma., (Published by Elsevier Inc.)

Background: There is limited literature on early unplanned hospital readmission after acute traumatic injury, especially at suburban facilities., Methods: A retrospective review of the trauma registry at a suburban, state-designated, level-I academic trauma center from July 2009 to June 2012 was performed for all admitted (≥24 hours) adult (age ≥18 years) trauma patients who were discharged alive, including unplanned readmissions within 30 days of discharge., Results: Of 3,622 admitted adult trauma patients, 6.57% were readmitted at a median of 9 days. Major surgery was required in 15.9% patients on readmission. The mortality rate at readmission was 4.6%. Multiple factors were associated with readmission on univariate analysis; however, on multivariate analysis, only major comorbidities (odds ratio [OR], 1.53), hospital length of stay (OR, 1.01), abdominal Abbreviated Injury Score greater than or equal to 3 (OR, 2.10), and discharge to a skilled nursing facility or subacute facility (OR, 1.56) were significant predictors. Meanwhile, index admission to surgical services was associated with a significantly lower readmission risk (OR, .60)., Conclusions: Trauma patients are infrequently readmitted. Index admission to a surgical service reduces the risk of readmission. Earlier medical follow-up should be considered., (Published by Elsevier Inc.)

Background: The care of mechanically ventilated patients at high-volume centers in select nontrauma populations has variable effects on outcomes. We evaluated outcomes for trauma patients requiring prolonged mechanical ventilation (PMV). We further hypothesized that the higher mechanical ventilator volume trauma center would have better outcomes., Methods: A retrospective review of a county's trauma registry was performed for trauma patients who were at least 18 years old admitted from 2006 to 2010. Eleven hospitals serve this suburban county, with a population of approximately 1.5 million people. The state has designated them as nontrauma centers (n = 6), area trauma centers (ATCs, n = 4), or regional trauma center (RTC, n = 1), where the last one provides the highest echelon of care. Patients requiring mechanical ventilation for at least 96 hours following injury were evaluated., Results: A total of 3,382 trauma patients were admitted to the RTC, and 5,870 were admitted to the other 10 hospitals in the county. Seven hundred seventy-one received mechanical ventilation at the RTC, and 687 at the other 10 hospitals combined. Of these patients, 407 at the RTC and 308 at the remaining facilities (291 at ATCs and 17 at nontrauma centers) required PMV. Median (interquartile range [IQR]) Injury Severity Score (ISS) at the RTC was higher (29 [21-41] vs. 22 [16-29] p < 0.001) than that at ATCs. Hospital length of stay (in days) was comparable between the RTC and ATCs (28 [18-45] vs. 26 [16-44.7]). With regard to complications, rates of renal failure, sepsis, and myocardial infarction were similar. The RTC had higher pneumonia rates (59% vs. 45.4%, p < 0.001) and venous thromboembolic disease rates (20.4% vs. 10.4%, p < 0.001) than did ATCs. In-hospital mortality was 17% at the RTC and 34.4% at ATCs (p < 0.001)., Conclusion: A mortality benefit but higher VTE and pneumonia rate for PMV patients at the RTC was noted. Collaborative practice initiatives are warranted to reduce morbidity and mortality across the region., Level of Evidence: Epidemiologic study, level IV.

Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.