Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management.

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.

A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor.

The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.

Bilateral Median Nerve and Brachial Artery Variations in the Arm: A Case Report.

During clinical practice, it is essential for physicians to have a sound knowledge of vascular and nerve variations. Patients who present with various clinical signs and symptoms need to be thoroughly investigated with anatomic variations in mind to prevent misdiagnosis. Most nerve variations are related to their formation or their course and are frequently associated with variability of structures that surround them. These structures most commonly include blood vessels, ligaments, and muscles. Such variations should be foremost in a physician's mind when analyzing clinical symptoms. This will aid in accurate diagnosis, and if surgical intervention is warranted, such awareness would minimize intraoperative errors. In this case study, the striking absence of median nerve and brachial artery within the cubital fossa bilaterally led to the discovery of pronator teres originating from the distal third of the humerus, associated with the bifurcation of the brachial artery at the middle third of the humerus into the ulnar and radial arteries. The median nerve ran beneath the pronator teres along with the ulnar artery and was thereby absent at the cubital fossa. Such variations observed bilaterally have not yet been reported in the literature. Knowledge of such variations can be very profound as this region involves surgical significance for several conditions, such as creation of arteriovenous fistulas (AVFs) for hemodialysis, treatment of supracondylar and radial head fractures, and cubital tunnel syndrome.

Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird (Agelaius tricolor).

Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.

Distinguishing recent dispersal from historical genetic connectivity in the coastal California gnatcatcher.

Habitat loss and fragmentation are primary threats to biodiversity worldwide. We studied the impacts of habitat loss and fragmentation on genetic connectivity and diversity among local aggregations of the California gnatcatcher (Polioptila californica californica) across its U.S. range. With a dataset of 268 individuals genotyped at 19 microsatellite loci, we analyzed genetic structure across the range using clustering analyses, exact tests for population differentiation, and a pedigree analysis to examine the spatial distribution of first-order relatives throughout the study area. In addition, we developed a habitat suitability model and related percent suitable habitat to genetic diversity indices within aggregations at two spatial scales. We detected a single genetic cluster across the range, with weak genetic structure among recently geographically isolated aggregations in the northern part of the range. The pedigree analysis detected closely related individuals across disparate aggregations and across large geographic distances in the majority of the sampled range, demonstrating that recent long-distance dispersal has occurred within this species. Genetic diversity was independent of suitable habitat at a local 5-km scale, but increased in a non-linear fashion with habitat availability at a broader, 30-km scale. Diversity declined steeply when suitable habitat within 30-km fell below 10%. Together, our results suggest that California gnatcatchers retain genetic connectivity across the majority of the current distribution of coastal sage scrub fragments, with the exception of some outlying aggregations. Connectivity may help support long-term persistence under current conservation and management strategies. However, emerging structure among more remote aggregations and associations between available habitat and genetic diversity also suggest that continued loss of habitat could threaten diversity and connectivity in the future.

Determining forward speed from accelerometer jiggle in aquatic environments.

How fast animals move is critical to understanding their energetic requirements, locomotor capacity and foraging performance, yet current methods for measuring speed via animal-attached devices are not universally applicable. Here, we present and evaluate a new method that relates forward speed to the stochastic motion of biologging devices as tag jiggle, the amplitude of the tag vibrations as measured by high sample rate accelerometers, increases exponentially with increasing speed. We successfully tested this method in a flow tank using two types of biologging devices and in situ on wild cetaceans spanning ∼3 to >20 m in length using two types of suction cup-attached tag and two types of dart-attached tag. This technique provides some advantages over other approaches for determining speed as it is device-orientation independent and relies only on a pressure sensor and a high sample rate accelerometer, sensors that are nearly universal across biologging device types.

Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus).

Achieving long-term persistence of species in urbanized landscapes requires characterizing population genetic structure to understand and manage the effects of anthropogenic disturbance on connectivity. Urbanization over the past century in coastal southern California has caused both precipitous loss of coastal sage scrub habitat and declines in populations of the cactus wren (Campylorhynchus brunneicapillus). Using 22 microsatellite loci, we found that remnant cactus wren aggregations in coastal southern California comprised 20 populations based on strict exact tests for population differentiation, and 12 genetic clusters with hierarchical Bayesian clustering analyses. Genetic structure patterns largely mirrored underlying habitat availability, with cluster and population boundaries coinciding with fragmentation caused primarily by urbanization. Using a habitat model we developed, we detected stronger associations between habitat-based distances and genetic distances than Euclidean geographic distance. Within populations, we detected a positive association between available local habitat and allelic richness and a negative association with relatedness. Isolation-by-distance patterns varied over the study area, which we attribute to temporal differences in anthropogenic landscape development. We also found that genetic bottleneck signals were associated with wildfire frequency. These results indicate that habitat fragmentation and alterations have reduced genetic connectivity and diversity of cactus wren populations in coastal southern California. Management efforts focused on improving connectivity among remaining populations may help to ensure population persistence.

Improving Quality and Safety through Positive Patient Identification.

The World Health Organization recognizes that patient misidentification can contribute to medication, surgical and charting errors. Accreditation Canada has set national standards and the Joint Commission on Accreditation of Healthcare Organizations has listed patient identification as a national patient safety goal. A qualitative and observational evaluation of patient identification practices in the Pre-Admission Clinic, Admitting Department and the Perioperative Care Center uncovered confusion, with 90% (n = 55) of patient verification occurrences not matching current policies. These discrepancies identify an opportunity to reassess and standardize workflow, clarify what identification methods are acceptable and determine additional appropriate identification verification practices with ID bracelets and patient charts.

Fluctuating fire regimes and their historical effects on genetic variation in an endangered shrubland specialist.

The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire-dependent communities. We studied an endangered juniper-oak shrubland specialist, the black-capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, predation, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long-term history of the fire regime and ecological niche models representing the mid-Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present.

Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii).

Populations forming the edge of a species range are often imperiled by isolation and low genetic diversity, with proximity to human population centers being a major determinant of edge stability in modern landscapes. Since the 1960s, the California red-legged frog (Rana draytonii) has undergone extensive declines in heavily urbanized southern California, where the range edge has rapidly contracted northward while shifting its cardinal orientation to an east-west trending axis. We studied the genetic structure and diversity of these frontline populations, tested for signatures of contemporary disturbance, specifically fire, and attempted to disentangle these signals from demographic events extending deeper into the past. Consistent with the genetic expectations of the 'abundant-center' model, we found that diversity, admixture, and opportunity for random mating increases in populations sampled successively further away from the range boundary. Demographic simulations indicate that bottlenecks in peripheral isolates are associated with processes extending tens to a few hundred generations in the past, despite the demographic collapse of some due to recent fire-flood events. While the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.

Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla).

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.

Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery.

Black-capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (F(ST) = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.

Habitat fragmentation and genetic diversity of an endangered, migratory songbird, the golden-cheeked warbler (Dendroica chrysoparia).

Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler (Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration.