The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus) are globally distributed zoonotic RNA viruses with pathogenic strains carried by a diverse group of rodent hosts. The marsh rice rat (Oryzomys palustris) is the reservoir host of Orthohantavirus bayoui, a hantavirus that causes fatal cases of hantavirus cardiopulmonary syndrome in humans. We performed a genome wide association study (GWAS) using the rice rat "immunome" (i.e., all exons related to the immune response) to identify genetic variants associated with infection status in wild-caught rice rats naturally infected with their endemic strain of hantavirus. First, we created an annotated reference genome using 10× Chromium Linked Reads sequencing technology. This reference genome was used to create custom baits which were then used to target enrich prepared rice rat libraries (n = 128) and isolate their immunomes prior to sequencing. Top SNPs in the association test were present in four genes (Socs5, Eprs, Mrc1, and Il1f8) which have not been previously implicated in hantavirus infections. However, these genes correspond with other loci or pathways with established importance in hantavirus susceptibility or infection tolerance in reservoir hosts: the JAK/STAT, MHC, and NFκB. These results serve as informative markers for future exploration and highlight the importance of immune pathways that repeatedly emerge across hantavirus systems. Our work aids in creating cross-species comparisons for better understanding mechanisms of genetic susceptibility and host-pathogen coevolution in hantavirus systems.

Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high-throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: (1) double-stranded DNA (dsDNA), single tube (KAPA); (2) single-stranded DNA (ssDNA), multi-tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi-tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best-performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.

North American grassland birds colonized emerging habitat created by expanding agriculture in a pattern of eastward expansions from the mid-1800s to mid-1900s. These birds have been declining, since at least the mid-1900s, largely as result of anthropogenic landscape change. Only one bird that now breeds predominantly in southeastern pine savannas is thought to have experienced a concurrent range expansion into this region: Peucaea aestivalis (Bachman’s Sparrow). However, our understanding of the P. aestivalis expansion, and subsequent retraction to the southeastern United States, is largely based on a contemporaneous review of only a subset of historical records from beyond its modern, northern limit. We suggest an alternative explanation for these historical records is that P. aestivalis historically occurred more broadly than was recognized in contemporaneous literature. To evaluate these hypotheses, we reviewed field observations from literature, natural history collections, and eBird to show how P. aestivalis presence throughout eastern North America has shifted since the mid-1800s. To confirm that these findings were not the result of detection bias, we repeated our analysis on a common sparrow species (Spizella pusilla) with a largely overlapping breeding range, but no history of expansion and retraction. We confirm that P. aestivalis expanded its range, but add that prior to that expansion, its historical distribution was broader than commonly acknowledged today. As a result, we identify the northwestern historical limit of P. aestivalis, the Ouachita and Ozark highlands, as a potential source region for an eastward expansion that is consistent with those of other North American grassland birds of the era. We discuss the potential evolutionary and conservation implications of this range expansion on P. aestivalis given our more nuanced understanding of it. Anthropogenic landscape change initially provided additional habitat for P. aestivalis but has ultimately resulted in a reduction of the P. aestivalis distribution.

As an obligate salt marsh species, Seaside Sparrows (Ammospiza maritima) are vulnerable to numerous threats including climate change, coastal erosion, sea-level rise, and both natural and anthropogenic disasters. Of the 9 recognized subspecies, 2 are extinct and 1 is endangered. Previous genetic analyses of mitochondrial DNA (mtDNA) and microsatellite loci showed that current taxonomy does not accurately reflect underlying genetic diversity, with possible consequences for the distribution of conservation resources. To further inform Seaside Sparrow management, we comprehensively describe genetic structure among 24 range-wide sampling locations that include all extant subspecies. We inferred population structure from several thousand single-nucleotide polymorphisms collected from 272 individuals via restriction-site-associated DNA sequencing. Principal components, pairwise FST values, and clustering approaches suggest that Seaside Sparrows on the Atlantic and Gulf Coasts are distinct and consist of at least 5 genetic clusters: 1 in southern Texas, 1 ranging from Aransas County, Texas, to Mississippi; 1 in western Florida; and 2 or 3 genetic groups intermixed along a gradient on the Atlantic Coast. These genetic clusters are not consistent with current subspecies taxonomy and could be used as distinct population segments (DPSs) to inform the most efficient allocation of resources to Seaside Sparrow conservation. Our results regarding the endangered subspecies, A. m. mirabilis, from southern Florida are inconclusive due to low sample size, but indicate that it is distinct and may represent a sixth DPS. Based on our genetic results, we recommend additional song and morphometric analyses in western Florida and a closer study of the boundary between the breeding distributions of A. m. maritima and A. m. macgillivraii to ensure the proper identification of DPSs.

Rapid diversification limits our ability to resolve evolutionary relationships and examine diversification history, as in the case of the Neotropical cotingas. Here we present an analysis with complete taxon sampling for the cotinga genera Lipaugus and Tijuca, which include some of the most range-restricted (e.g., T. condita) and also the most widespread and familiar (e.g., L. vociferans) forest birds in the Neotropics. We used two datasets: (1) Sanger sequencing data sampled from eight loci in 34 individuals across all described taxa and (2) sequence capture data linked to 1,079 ultraconserved elements and conserved exons sampled from one or two individuals per species. Phylogenies estimated from the Sanger sequencing data failed to resolve three nodes, but the sequence capture data produced a well-supported tree. Lipaugus and Tijuca formed a single, highly supported clade, but Tijuca species were not sister and were embedded within Lipaugus. A dated phylogeny confirmed Lipaugus and Tijuca diversified rapidly in the Miocene. Our study provides a detailed evolutionary hypothesis for Lipaugus and Tijuca and demonstrates that increasing genomic sampling can prove instrumental in resolving the evolutionary history of recent radiations.

Journal of Field OrnithologyVolume 88, Issue 1 p. 97-98 Book Review Birds: Myth, Lore, and Legend Rachel Warren Chadd and Marianne Taylor, 2016. Bloomsbury Publishing, New York, NY. 304 pages, numerous color photographs and images. ISBN 9781472922861. $40 (Hardcover). Amie Settlecowski, Amie Settlecowski asettl1@lsu.edu School of Renewable Natural Resources, Louisiana State University Baton, Rouge, LA, USASearch for more papers by this author Amie Settlecowski, Amie Settlecowski asettl1@lsu.edu School of Renewable Natural Resources, Louisiana State University Baton, Rouge, LA, USASearch for more papers by this author First published: 17 March 2017 https://doi.org/10.1111/jofo.12192Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume88, Issue1March 2017Pages 97-98 RelatedInformation

Characterizing population structure and genetic differentiation can inform the management of imperiled species and the relative influences of ecological and evolutionary factors on species evolution. One trait that is expected to influence the amount of population structure a species exhibits is vagility, or the ability to move across the landscape. Species with higher vagility may be more likely to disperse, potentially facilitating gene flow among populations and limiting population structure. My dissertation focuses on characterizing population structure in 2 imperiled sparrows that are both largely nonmigratory with broad distributions in eastern North America: Seaside Sparrow (Ammospiza maritima) and Bachman’s Sparrow (Peucaea aestivalis). Seaside Sparrow is restricted to tidal saltmarsh habitat that is temporally and spatially more stable than the fire-mediated pine savannas that Bachman’s Sparrow is closely associated with. As a result of these habitat differences these sparrows likely have differing vagility and exhibit different patterns of population structure. First, I describe the population structure of Seaside Sparrow and identify potential distinct population segments to inform future management of the species. Through comprehensive sampling of several thousand single nucleotide polymorphisms (SNPs) in 272 individuals from 24 sites across the species distribution, I identify 5 to 7 possible distinct population segments (Chapter 2). In the remainder of my dissertation, I focus on Bachman’s Sparrow and the population genetics and conservation implications of recent changes to its distribution. Through systematic review of several thousand occurrence records from historical field observations, natural history collections, and eBird I confirm that Bachman’s Sparrow experienced a rapid range expansion and subsequent retraction since the mid-1800s (Chapter 4). Finally, I infer population structure before, during, and immediately following the range expansion and modern time using approximately 1,000 SNPs sampled from 144 museum samples and 285 modern samples to determine if panmixia arose in Bachman’s Sparrow during the range shifts. I show that high gene flow is characteristic of Bachman’s Sparrow and not the result of recent range shift, but that recent anthropogenic landscape change results in barriers to dispersal that promote differentiation even in this highly vagile bird.