Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

Comparison of tandem ureteral stents, cryoplasty, and cutting balloon ureteroplasty in treatment of refractory transplant ureteral strictures.

The objective of study was to compare clinical outcome of cryoplasty, tandem stents, and cutting balloon ureteroplasty as "bailout procedures" to prevent surgical intervention or stent dependency in renal transplant patients with refractory ureteral stricture. All patients who underwent a bailout procedure from June 11, 2003, to August 8, 2015, at a single institution were reviewed retrospectively. Refractory ureteral stricture was defined as ureteral stenosis not responding to at least two prior percutaneous plain balloon ureteroplasties. Primary patency was defined as stable allograft function following the procedure with unobstructed urine outflow, not requiring indwelling ureteral stent, repeat ureteroplasty, or surgical revision. Sixty-one procedures were performed on 51 patients. Patients were followed up for a median of 286 days. Overall primary patency rate was 26.1%. Primary patency rate by method was 38.1%, 23.1%, and 14.3% after cryoplasty, tandem stent placement, and cutting balloon dilatation, respectively (P = .260). Primary patency rate was higher in early (<3 months post-transplant) ureteral strictures (35.7% vs 13.3%; P = .047). More complications identified in patients who had tandem ureteral stents (P = .00754). As some renal transplant patients may not be good operative candidates for ureteral revision, it would be reasonable to attempt one of these "bailout" interventions as long as the clinical team and patient are aware of overall low potential for achieving primary patency.

A Case Report of Thoracic Endovascular Aneurysm Repair under Local Anesthesia with Resolution of Acute Onset Lower Extremity Paraplegia from an Acute Complicated Type B Aortic Dissection.

Spinal cord ischemia (SCI) is a rare presenting symptom of acute complicated type B aortic dissection, occurring in approximately 3% of patients . We present a case report of a patient with this presentation who had observed resolution of his paraplegia symptoms immediately after placement of a thoracic stent graft under local anesthesia. The temporal association between true lumen flow restoration and paraplegia resolution intraoperatively is a novel finding. We feel that this case report may provide support for recognized cord perfusion theory , as well as contribute to the understanding of the time frame associated with SCI and reversibility of paraplegia.

Decreased mortality with local versus general anesthesia in endovascular aneurysm repair for ruptured abdominal aortic aneurysm in the Vascular Quality Initiative database.

BACKGROUND: Endovascular aneurysm repair (EVAR) is an accepted approach for patients presenting with ruptured abdominal aortic aneurysm (rAAA) and suitable anatomy. The effect of anesthesia modality on mortality outcomes in rAAA has not been well described. Using the Vascular Quality Initiative database, this study compares local anesthesia (LA) vs general anesthesia (GA) in EVAR for rAAA. METHODS: The Vascular Quality Initiative database was queried for patients presenting with rAAA managed with open surgical repair, EVAR under LA (rEVAR-LA), and EVAR under GA (rEVAR-GA) between 2003 and 2017. Patients were observed until the earlier end point of either death or 1-year follow-up. Kaplan-Meier event rates are presented at 30 days and 1 year. Cox proportional hazards regression was used to model risk of death, with adjustment for demographic and clinical factors. Additional multivariate Cox hazards analyses were used to assess effect modifiers for 1-year mortality for the different repair methods. RESULTS: A total of 3330 patients (77.4% male) met the inclusion criteria (1594 [47.9%] open surgical repair, 226 [6.8%] rEVAR-LA, and 1510 [45.3%] rEVAR-GA). Patients treated with rEVAR-LA compared with rEVAR-GA had decreased intraoperative time, number of intraoperative blood transfusions, intraoperative crystalloid administration, intensive care unit length of stay, and postoperative pulmonary complications. Mortality rates with rEVAR-LA were lower compared with rEVAR-GA at 30 days (15.5% vs 23.3%; adjusted hazard ratio [AHR], 0.70; 95% confidence interval [CI], 0.49-0.99; P = .04) and at 1 year (22.5% vs 32.3%; AHR, 0.71; 95% CI, 0.53-0.96; P = .02). Patients undergoing EVAR who were <75 years old and those without preoperative hypotension had the greatest survival benefit from LA compared with GA (both factors: AHR, 0.14 [95% CI, 0.03-0.57]; single factor: AHR, 0.57 [95% CI, 0.36-0.91]). CONCLUSIONS: This study demonstrates that rEVAR-LA for rAAA may be a safe alternative to rEVAR-GA for certain patients, with lower morbidity and improved mortality. Further prospective study is warranted to confirm mortality benefit in rEVAR-LA for rAAA.

MetaWin 3: open-source software for meta-analysis.

The rise of research synthesis and systematic reviews over the last 25 years has been aided by a series of software packages providing simple and accessible GUI interfaces which are intuitively easy to use by novice analysts and users. Development of many of these packages has been abandoned over time due to a variety of factors, leaving a gap in the software infrastructure available for meta-analysis. To fulfill the continued demand for a GUI-based meta-analytic system, we have now released MetaWin 3 as free, open-source, multi-platform software. MetaWin3 is written in Python and developed from scratch relative to earlier versions. The codebase is available on Github, with pre-compiled executables for both Windows and macOS available from the MetaWin website. MetaWin includes standardized effect size calculations, exploratory and publication bias analyses, and allows for both simple and complex explanatory models of variation within a meta-analytic framework, including meta-regression, using traditional least-squares/moments estimation.

A systematic review of diagnostic and interventional techniques in non-occlusive hepatic artery hypoperfusion syndrome.

OBJECTIVE: This systematic review aims to elucidate the diagnostic capabilities of imaging techniques in identifying Non-Occlusive Hepatic Artery Hypoperfusion Syndrome (NOHAH) and to evaluate the efficacy and outcomes of splenic artery embolization (SAE), including the choice and placement of embolic agents. MATERIALS AND METHODS: A comprehensive literature search was conducted using PubMed, CINAHL, and Scopus databases, adhering to PRISMA guidelines. Fifteen studies encompassing 240 patients treated with embolization (using coils or Amplatzer Vascular Plugs (AVP)) were analyzed. Key metrics assessed included patient demographics, embolization techniques, embolic agents, technical success, radiologic findings pre- and post-embolization, and complication rates. RESULTS: Among the 240 patients studied, 177 (73.8%) were reported by gender, with a majority being male (127/177, 71.7%). Doppler ultrasonography (DUS) emerged as the primary initial screening tool in 80% of studies. The hepatic arterial resistive index (RI) was a critical parameter, with mean values significantly decreasing from 0.84 pre-embolization to 0.70 post-embolization (p < 0.001). All cases confirmed technical success via digital subtraction angiography, revealing delayed hepatic arterial filling without stenosis or thrombosis. Coils were the predominant embolic agent, used in 80.8% of patients, followed by AVP in 16.3%. The overall mortality rate was 4.58%, with 29 major and 3 minor complications noted. Notably, proximal placement of coils in the splenic artery was associated with lower mortality rates compared to distal placement and showed comparable complication rates to AVPs. CONCLUSION: DUS is a reliable screening modality for NOHAH, with post-SAE assessments showing significant improvements. The choice and location of embolization significantly impact patient outcomes, with proximal placement of coils emerging as a preferable strategy due to lower mortality rates and comparable complication profiles to alternative methods.

Effects of urban-induced mutations on ecology, evolution and health.

Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

The nomenclatural status of the two "spiny-wristed" fiddler crabs: Uca spinicarpa Rathbun, 1900, and U. hesperiae Crane, 1975 (Crustacea: Brachyura: Ocypodidae).

A secondary homonymy is documented for Gelasimus [= Uca] tetragonon var. spinicarpa Kossmann, 1877 (a species from the Red Sea), and Uca spinicarpa Rathbun, 1900 (a species from the Gulf of Mexico). Although Kossmann's usage of the nomen spinicarpa has chronological priority, a reversal of precedence is required by Article 23.9 of the Code since Kossmann's use has not been applied as a valid name since the original publication in 1877, while Rathbun's use of the name has been applied over 50 times in the last half century. The species Kossmann was most likely referring to is today known as Uca hesperiae Crane, 1975, a name which may be retained in light of the reversal of precedence.

Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations.

Bone strength and the incidence and severity of skeletal disorders vary significantly among human populations, due in part to underlying genetic differentiation. While clinical models predict that this variation is largely deleterious, natural population variation unrelated to disease can go unnoticed, altering our perception of how natural selection has shaped bone morphologies over deep and recent time periods. Here, we conduct the first comparative population-based genetic analysis of the main bone structural protein gene, collagen type I α 1 (COL1A1), in clinical and 1000 Genomes Project datasets in humans, and in natural populations of chimpanzees. Contrary to predictions from clinical studies, we reveal abundant COL1A1 amino acid variation, predicted to have little association with disease in the natural population. We also find signatures of positive selection associated with intron haplotype structure, linkage disequilibrium, and population differentiation in regions of known gene expression regulation in humans and chimpanzees. These results recall how recent and deep evolutionary regimes can be linked, in that bone morphology differences that developed among vertebrates over 450 million years of evolution are the result of positive selection on subtle type I collagen functional variation segregating within populations over time.

Genie: an interactive real-time simulation for teaching genetic drift.

Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is especially challenging. Here we present Genie, a browser-based educational tool that demonstrates population-genetic concepts such as genetic drift, population isolation, gene flow, and genetic mutation. Because it does not need to be downloaded and installed, Genie can scale to large groups of students and is useful for both in-person and online instruction. Genie was used to teach genetic drift to Evolution students at Arizona State University during Spring 2016 and Spring 2017. The effectiveness of Genie to teach key genetic drift concepts and misconceptions was assessed with the Genetic Drift Inventory developed by Price et al. (CBE Life Sci Educ 13(1):65-75, 2014). Overall, Genie performed comparably to that of traditional static methods across all evaluated classes. We have empirically demonstrated that Genie can be successfully integrated with traditional instruction to reduce misconceptions about genetic drift.

Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations.

Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.

MixtureTree: a program for constructing phylogeny.

BACKGROUND: MixtureTree v1.0 is a Linux based program (written in C++) which implements an algorithm based on mixture models for reconstructing phylogeny from binary sequence data, such as single-nucleotide polymorphisms (SNPs). In addition to the mixture algorithm with three different optimization options, the program also implements a bootstrap procedure with majority-rule consensus. RESULTS: The MixtureTree program written in C++ is a Linux based package. The User's Guide and source codes will be available at http://math.asu.edu/~scchen/MixtureTree.html CONCLUSIONS: The efficiency of the mixture algorithm is relatively higher than some classical methods, such as Neighbor-Joining method, Maximum Parsimony method and Maximum Likelihood method. The shortcoming of the mixture tree algorithms, for example timing consuming, can be improved by implementing other revised Expectation-Maximization(EM) algorithms instead of the traditional EM algorithm.

Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of Sceloporus lizards.

As shown from several long-term and time-intensive studies, closely related, sympatric species can impose strong selection on one another, leading to dramatic examples of phenotypic evolution. Here, we use occurrence data to identify clusters of sympatric Sceloporus lizard species and to test whether Sceloporus species tend to coexist with other species that differ in body size, as we would expect when there is competition between sympatric congeners. We found that Sceloporus species can be grouped into 16 unique bioregions. Bioregions that are located at higher latitudes tend to be larger and have fewer species, following Rapoport's rule and the latitudinal diversity gradient. Species richness was positively correlated with the number of biomes and elevation heterogeneity of each bioregion. Additionally, most bioregions show signs of phylogenetic underdispersion, meaning closely related species tend to occur in close geographic proximity. Finally, we found that although Sceloporus species that are similar in body size tend to cluster geographically, small-bodied Sceloporus species are more often in sympatry with larger-bodied Sceloporus species than expected by chance alone, whereas large-bodied species cluster with each other geographically and phylogenetically. These results suggest that community composition in extant Sceloporus species is the result of allopatric evolution, as closely related species move into different biomes, and interspecies interactions, with sympatry between species of different body sizes. Our phyloinformatic approach offers unique and detailed insights into how a clade composed of ecologically and morphologically disparate species are distributed over large geographic space and evolutionary time.

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot.

As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

Considering spatial and temporal scale in landscape-genetic studies of gene flow.

Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field.

Understanding the genetic basis of species adaptation in the context of global change poses one of the greatest challenges of this century. Although we have begun to understand the molecular basis of adaptation in those species for which whole genome sequences are available, the molecular basis of adaptation is still poorly understood for most non-model species. In this paper, we outline major challenges and future research directions for correlating environmental factors with molecular markers to identify adaptive genetic variation, and point to research gaps in the application of landscape genetics to real-world problems arising from global change, such as the ability of organisms to adapt over rapid time scales. High throughput sequencing generates vast quantities of molecular data to address the challenge of studying adaptive genetic variation in non-model species. Here, we suggest that improvements in the sampling design should consider spatial dependence among sampled individuals. Then, we describe available statistical approaches for integrating spatial dependence into landscape analyses of adaptive genetic variation.

Utility of computer simulations in landscape genetics.

Population genetics theory is primarily based on mathematical models in which spatial complexity and temporal variability are largely ignored. In contrast, the field of landscape genetics expressly focuses on how population genetic processes are affected by complex spatial and temporal environmental heterogeneity. It is spatially explicit and relates patterns to processes by combining complex and realistic life histories, behaviours, landscape features and genetic data. Central to landscape genetics is the connection of spatial patterns of genetic variation to the usually highly stochastic space-time processes that create them over both historical and contemporary time periods. The field should benefit from a shift to computer simulation approaches, which enable incorporation of demographic and environmental stochasticity. A key role of simulations is to show how demographic processes such as dispersal or reproduction interact with landscape features to affect probability of site occupancy, population size, and gene flow, which in turn determine spatial genetic structure. Simulations could also be used to compare various statistical methods and determine which have correct type I error or the highest statistical power to correctly identify spatio-temporal and environmental effects. Simulations may also help in evaluating how specific spatial metrics may be used to project future genetic trends. This article summarizes some of the fundamental aspects of spatial-temporal population genetic processes. It discusses the potential use of simulations to determine how various spatial metrics can be rigorously employed to identify features of interest, including contrasting locus-specific spatial patterns due to micro-scale environmental selection.