Location-level processes drive the establishment of alien bird populations worldwide.

Human-mediated translocation of species to areas beyond their natural distribution (which results in 'alien' populations1) is a key signature of the Anthropocene2, and is a primary global driver of biodiversity loss and environmental change3. Stemming the tide of invasions requires understanding why some species fail to establish alien populations, and others succeed. To achieve this, we need to integrate the effects of features of the introduction site, the species introduced and the specific introduction event. Determining which, if any, location-level factors affect the success of establishment has proven difficult, owing to the multiple spatial, temporal and phylogenetic axes along which environmental variation may influence population survival. Here we apply Bayesian hierarchical regression analysis to a global spatially and temporally explicit database of introduction events of alien birds4 to show that environmental conditions at the introduction location, notably climatic suitability and the presence of other groups of alien species, are the primary determinants of successful establishment. Species-level traits and the size of the founding population (propagule pressure) exert secondary, but important, effects on success. Thus, current trajectories of anthropogenic environmental change will most probably facilitate future incursions by alien species, but predicting future invasions will require the integration of multiple location-, species- and event-level characteristics.

RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data.

SUMMARY: Here, we introduce RatesTools, an automated pipeline to infer de novo mutation rates from parent-offspring trio data of diploid organisms. By providing a reference genome and high-coverage, whole-genome resequencing data of a minimum of three individuals (sire, dam and offspring), RatesTools provides a list of candidate de novo mutations and calculates a putative mutation rate. RatesTools uses several quality filtering steps, such as discarding sites with low mappability and highly repetitive regions, as well as sites with low genotype and mapping qualities to find potential de novo mutations. In addition, RatesTools implements several optional filters based on post hoc assumptions of the heterozygosity and mutation rate of the organism. Filters are highly customizable to user specifications in order to maximize utility across a wide range of applications. AVAILABILITY AND IMPLEMENTATION: RatesTools is freely available at https://github.com/campanam/RatesTools under a Creative Commons Zero (CC0) license. The pipeline is implemented in Nextflow (Di Tommaso et al., 2017), Ruby (http://www.ruby-lang.org), Bash (https://www.gnu.org/software/bash/) and R (R Core Team, 2020) with reliance upon several other freely available tools. RatesTools is compatible with macOS and Linux operating systems. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Regional invasion history and land use shape the prevalence of non-native species in local assemblages.

The ecological impact of non-native species arises from their establishment in local assemblages. However, the rates of non-native spread in new regions and their determinants have not been comprehensively studied. Here, we combined global databases documenting the occurrence of non-native species and residence of non-native birds, mammals, and vascular plants at regional and local scales to describe how the likelihood of non-native occurrence and their proportion in local assemblages relate with their residence time and levels of human usage in different ecosystems. Our findings reveal that local non-native occurrence generally increases with residence time. Colonization is most rapid in croplands and urban areas, while it is slower and variable in natural or semi-natural ecosystems. Notably, non-native occurrence continues to rise even 200 years after introduction, especially for birds and vascular plants, and in other land-use types rather than croplands and urban areas. The impact of residence time on non-native proportions is significant only for mammals. We conclude that the continental exchange of biotas requires considerable time for effects to manifest at the local scale across taxa and land-use types. The unpredictability of future impacts, implied by the slow spread of non-native species, strengthens the call for stronger regulations on the exchange of non-native species to reduce the long-lasting invasion debt looming on ecosystems' future.

The crucial role of genome-wide genetic variation in conservation.

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

Medical demography at stroke centers: Current situation in France.

INTRODUCTION: Following the 2010-2014 French national stroke action plan, the number of stroke center (SC) has gradually increased in France, allowing a homogeneous coverage and access to neurovascular care in organized and territorially defined structures. However, operational difficulties within SCs have been progressively reported over the last few years. The objective of this study was to identify the medical staff shortages in SC that may contribute to these difficulties. METHODS: A survey on the medical staffing level as of January 1, 2021 was sent to all French SC managers. Specific questions related on vacancies, need of interim medical staff, and participation in out-of-hour healthcare services. RESULTS: Among the 139 SC managers contacted, 122 (88%) filled in the questionnaire. Analysis of the data showed that over 879 physician positions opened, 163 (18.5%) remained vacant for a mean of two years, and that in 51 SCs (41.9%), more than two positions were unfilled. In 13 of these 51 SCs, the out-of-hour healthcare services relied on less than four practitioners, defining a critical situation, and three other SCs had to close temporarily (2) or permanently (1). Moreover, 39.2% of SCs with at least one vacancy used interim physicians, for a median period of 12.5 weeks/year (IQR 5-18). CONCLUSION: This study highlights the significant medical staff shortage in French SCs. In the absence of urgent measures, more SCs will close, jeopardizing the regional network and access to care for stroke patients.

Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research.

We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection.

Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers. With 70% of the world's wild tigers living in India, such knowledge is critical. We re-sequenced 65 individual tiger genomes representing most extant subspecies with a specific focus on tigers from India. As suggested by earlier studies, we found strong genetic differentiation between the putative tiger subspecies. Despite high total genomic diversity in India, individual tigers host longer runs of homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small and fragmented protected areas. We suggest the impacts of ongoing connectivity loss on inbreeding and persistence of Indian tigers be closely monitored. Surprisingly, demographic models suggest recent divergence (within the last 20,000 years) between subspecies and strong population bottlenecks. Amur tiger genomes revealed the strongest signals of selection related to metabolic adaptation to cold, whereas Sumatran tigers show evidence of weak selection for genes involved in body size regulation. We recommend detailed investigation of local adaptation in Amur and Sumatran tigers prior to initiating genetic rescue.

A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates.

The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawai'i, and outgroup taxa on older islands, we tested whether each component of the "holobiont" (spider hosts, intracellular endosymbionts and gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. To investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. The results showed that the host A. waikula is indeed structured by geographical isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawai'i. Conversely, the gut microbiota, which we suspect is generally environmentally derived, was largely conserved across all populations and species. Our results show that different components of the holobiont respond in distinct ways to the dynamic environment of the volcanic archipelago. This highlights the necessity of understanding the interplay between different components of the holobiont, to properly characterize its evolution.

Global rise in emerging alien species results from increased accessibility of new source pools.

Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history. Emerging alien species-those never encountered as aliens before-therefore pose a significant challenge to biosecurity interventions worldwide. Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools. Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide. Even after many centuries of invasions the rate of emergence of new alien species is still high: One-quarter of first records during 2000-2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa. Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions. Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change. This process compensates for the depletion of the historically important source species pool through successive invasions. We estimate that 1-16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species. These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict.

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data.

BACKGROUND: The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS: Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS: We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

Horizontal Transfer of Bacterial Cytolethal Distending Toxin B Genes to Insects.

Horizontal gene transfer events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here, we report horizontal gene transfer of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that confers resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies.

The Global Distribution and Drivers of Alien Bird Species Richness.

Alien species are a major component of human-induced environmental change. Variation in the numbers of alien species found in different areas is likely to depend on a combination of anthropogenic and environmental factors, with anthropogenic factors affecting the number of species introduced to new locations, and when, and environmental factors influencing how many species are able to persist there. However, global spatial and temporal variation in the drivers of alien introduction and species richness remain poorly understood. Here, we analyse an extensive new database of alien birds to explore what determines the global distribution of alien species richness for an entire taxonomic class. We demonstrate that the locations of origin and introduction of alien birds, and their identities, were initially driven largely by European (mainly British) colonialism. However, recent introductions are a wider phenomenon, involving more species and countries, and driven in part by increasing economic activity. We find that, globally, alien bird species richness is currently highest at midlatitudes and is strongly determined by anthropogenic effects, most notably the number of species introduced (i.e., "colonisation pressure"). Nevertheless, environmental drivers are also important, with native and alien species richness being strongly and consistently positively associated. Our results demonstrate that colonisation pressure is key to understanding alien species richness, show that areas of high native species richness are not resistant to colonisation by alien species at the global scale, and emphasise the likely ongoing threats to global environments from introductions of species.

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range FST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence.

Metal-Polycyclic Aromatic Hydrocarbon Mixture Toxicity in Hyalella azteca. 2. Metal Accumulation and Oxidative Stress as Interactive Co-toxic Mechanisms.

Mixtures of metals and polycyclic aromatic hydrocarbons (PAHs) are commonly found in aquatic environments. Emerging reports have identified that more-than-additive mortality is common in metal-PAH mixtures. Individual aspects of PAH toxicity suggest they may alter the accumulation of metals and enhance metal-derived reactive oxygen species (ROS). Redox-active metals (e.g., Cu and Ni) are also capable of enhancing the redox cycling of PAHs. Accordingly, we explored the mutual effects redox-active metals and PAHs have on oxidative stress, and the potential for PAHs to alter the accumulation and/or homeostasis of metals in juvenile Hyalella azteca. Amphipods were exposed to binary mixtures of Cu, Cd, Ni, or V, with either phenanthrene (PHE) or phenanthrenequinone (PHQ). Mixture of Cu with either PAH produced striking more-than-additive mortality, whereas all other mixtures amounted to strictly additive mortality following 18-h exposures. We found no evidence to suggest that interactive effects on ROS production were involved in the more-than-additive mortality of Cu-PHE and Cu-PHQ mixtures. However, PHQ increased the tissue concentration of Cu in juvenile H. azteca, providing a potential mechanism for the observed more-than-additive mortality.

Metal-Polycyclic Aromatic Hydrocarbon Mixture Toxicity in Hyalella azteca. 1. Response Surfaces and Isoboles To Measure Non-additive Mixture Toxicity and Ecological Risk.

Mixtures of metals and polycyclic aromatic hydrocarbons (PAHs) occur ubiquitously in aquatic environments, yet relatively little is known regarding their potential to produce non-additive toxicity (i.e., antagonism or potentiation). A review of the lethality of metal-PAH mixtures in aquatic biota revealed that more-than-additive lethality is as common as strictly additive effects. Approaches to ecological risk assessment do not consider non-additive toxicity of metal-PAH mixtures. Forty-eight-hour water-only binary mixture toxicity experiments were conducted to determine the additive toxic nature of mixtures of Cu, Cd, V, or Ni with phenanthrene (PHE) or phenanthrenequinone (PHQ) using the aquatic amphipod Hyalella azteca. In cases where more-than-additive toxicity was observed, we calculated the possible mortality rates at Canada's environmental water quality guideline concentrations. We used a three-dimensional response surface isobole model-based approach to compare the observed co-toxicity in juvenile amphipods to predicted outcomes based on concentration addition or effects addition mixtures models. More-than-additive lethality was observed for all Cu-PHE, Cu-PHQ, and several Cd-PHE, Cd-PHQ, and Ni-PHE mixtures. Our analysis predicts Cu-PHE, Cu-PHQ, Cd-PHE, and Cd-PHQ mixtures at the Canadian Water Quality Guideline concentrations would produce 7.5%, 3.7%, 4.4% and 1.4% mortality, respectively.

Global patterns of freshwater species diversity, threat and endemism.

AIM: Global-scale studies are required to identify broad-scale patterns in the distributions of species, to evaluate the processes that determine diversity and to determine how similar or different these patterns and processes are among different groups of freshwater species. Broad-scale patterns of spatial variation in species distribution are central to many fundamental questions in macroecology and conservation biology. We aimed to evaluate how congruent three commonly used metrics of diversity were among taxa for six groups of freshwater species. LOCATION: Global. METHODS: We compiled geographical range data on 7083 freshwater species of mammals, amphibians, reptiles, fishes, crabs and crayfish to evaluate how species richness, richness of threatened species and endemism are distributed across freshwater ecosystems. We evaluated how congruent these measures of diversity were among taxa at a global level for a grid cell size of just under 1°. RESULTS: We showed that although the risk of extinction faced by freshwater decapods is quite similar to that of freshwater vertebrates, there is a distinct lack of spatial congruence in geographical range between different taxonomic groups at this spatial scale, and a lack of congruence among three commonly used metrics of biodiversity. The risk of extinction for freshwater species was consistently higher than for their terrestrial counterparts. MAIN CONCLUSIONS: We demonstrate that broad-scale patterns of species richness, threatened-species richness and endemism lack congruence among the six freshwater taxonomic groups examined. Invertebrate species are seldom taken into account in conservation planning. Our study suggests that both the metric of biodiversity and the identity of the taxa on which conservation decisions are based require careful consideration. As geographical range information becomes available for further sets of species, further testing will be warranted into the extent to which geographical variation in the richness of these six freshwater groups reflects broader patterns of biodiversity in fresh water.

Genomics and conservation: Guidance from training to analyses and applications.

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

The University of Texas Houston Stroke Registry (UTHSR): implementation of enhanced data quality assurance procedures improves data quality.

BACKGROUND: Limited information has been published regarding standard quality assurance (QA) procedures for stroke registries. We share our experience regarding the establishment of enhanced QA procedures for the University of Texas Houston Stroke Registry (UTHSR) and evaluate whether these QA procedures have improved data quality in UTHSR. METHODS: All 5093 patient records that were abstracted and entered in UTHSR, between January 1, 2008 and December 31, 2011, were considered in this study. We conducted reliability and validity studies. For reliability and validity of data captured by abstractors, a random subset of 30 records was used for re-abstraction of select key variables by two abstractors. These 30 records were re-abstracted by a team of experts that included a vascular neurologist clinician as the "gold standard". We assessed inter-rater reliability (IRR) between the two abstractors as well as validity of each abstractor with the "gold standard". Depending on the scale of variables, IRR was assessed with Kappa or intra-class correlations (ICC) using a 2-way, random effects ANOVA. For assessment of validity of data in UTHSR we re-abstracted another set of 85 patient records for which all discrepant entries were adjudicated by a vascular neurology fellow clinician and added to the set of our "gold standard". We assessed level of agreement between the registry data and the "gold standard" as well as sensitivity and specificity. We used logistic regression to compare error rates for different years to assess whether a significant improvement in data quality has been achieved during 2008-2011. RESULTS: The error rate dropped significantly, from 4.8% in 2008 to 2.2% in 2011 (P < 0.001). The two abstractors had an excellent IRR (Kappa or ICC ≥ 0.75) on almost all key variables checked. Agreement between data in UTHSR and the "gold standard" was excellent for almost all categorical and continuous variables. CONCLUSIONS: Establishment of a rigorous data quality assurance for our UTHSR has helped to improve the validity of data. We observed an excellent IRR between the two abstractors. We recommend training of chart abstractors and systematic assessment of IRR between abstractors and validity of the abstracted data in stroke registries.