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At least 235 records · Page 13Linked to original sources

USGS2012

Genetic analysis of a novel nidovirus from fathead minnows

A bacilliform virus was isolated from diseased fathead minnows ( Pimephales promelas ). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream ( Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales . In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus . A PCR assay was developed for the identification of future FHMNV-like isolates.

Journal of General Virology↗

USGS2009

Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

Molecular Ecology Resources↗

USGS2013

Characterization of the OmyY1 region on the rainbow trout Y chromosome

We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescence in situ hybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed.

International Journal of Genomics↗

USGS2022

Microbial source tracking and evaluation of best management practices for restoring degraded beaches of Lake Michigan

Attempts to mitigate shoreline microbial contamination require a thorough understanding of pollutant sources, which often requires multiple years of data collection (e.g., point/nonpoint) and the interacting factors that influence water quality. Because restoration efforts can alter shoreline or beach morphology, revisiting source inputs is often necessary. Microbial source tracking (MST) using source-specific molecular markers, genomic community analyses, and physical modeling was used to identify contamination sources along three Lake Michigan beaches of the Laurentian Great Lakes with historically high fecal indicator bacteria (FIB, E. coli ) concentrations. Genetic markers for human (Bacteroides HF183) and mixed gull species ( Catellicoccus marimammalium ) fecal sources were tested from water and sediment. Gene sequencing (16S rRNA) was used to identify similarities in bacterial communities in nearshore water, river inputs, sand, sediment, and groundwater. Synoptic surveys of water exchange were conducted to determine nearshore-offshore interactions of FIB. In addition to these MST studies, best management practices to mitigate FIB, including gull deterrence, slope grading, wetland establishment, and shoreline plantings, were reviewed for their effectiveness at reducing FIB concentrations over time. Using multiple tools for MST helped identify primary and secondary sources of FIB (gulls, stormwater inputs) and the physical processes that exacerbate FIB concentrations (onshore currents, limited circulation). Management actions were successful in the short-term at reducing FIB, but scope of success was temporally limited, with FIB concentrations often rebounding. Results highlight the usefulness of MST to inform best management practices and the need for a sustained adaptive approach that adjusts for changes in the coastal system.

Illinois, Wisconsin↗

USGS2014

Avian influenza virus ecology in Iceland shorebirds: intercontinental reassortment and movement

Shorebirds are a primary reservoir of avian influenza viruses (AIV). We conducted surveillance studies in Iceland shorebird populations for 3 years, documenting high serological evidence of AIV exposure in shorebirds, primarily in Ruddy Turnstones ( Arenaria interpres ; seroprevalence = 75%). However, little evidence of virus infection was found in these shorebird populations and only two turnstone AIVs (H2N7; H5N1) were able to be phylogenetically examined. These analyses showed that viruses from Iceland shorebirds were primarily derived from Eurasian lineage viruses, yet the H2 hemagglutinin gene segment was from a North American lineage previously detected in a gull from Iceland the previous year. The H5N1 virus was determined to be low pathogenic, however the PB2 gene was closely related to the PB2 from highly pathogenic H5N1 isolates from China. Multiple lines of evidence suggest that the turnstones were infected with at least one of these AIV while in Iceland and confirm Iceland as an important location where AIV from different continents interact and reassort, creating new virus genomes. Mounting data warrant continued surveillance for AIV in wild birds in the North Atlantic, including Canada, Greenland, and the northeast USA to determine the risks of new AI viruses and their intercontinental movement in this region.

Infection, Genetics and Evolution↗

USGS2010

Intercontinental reassortment and genomic variation of low pathogenic avian influenza viruses isolated from northern pintails ( Anas acuta ) in Alaska: examining the evidence through space and time

Migration and population genetic data for northern pintails ( Anas acuta ) and phylogenetic analysis of low pathogenic avian influenza (LPAI) viruses from this host in Alaska suggest that northern pintails are involved in ongoing intercontinental transmission of avian influenza. Here, we further refine this conclusion through phylogenetic analyses which demonstrate that detection of foreign lineage gene segments is spatially dependent and consistent through time. Our results show detection of foreign lineage gene segments to be most likely at sample locations on the Alaska Peninsula and least likely along the Southern Alaska Coast. Asian lineages detected at four gene segments persisted across years, suggesting maintenance in avian hosts that migrate to Alaska each year from Asia or in hosts that remain in Alaska throughout the year. Alternatively, live viruses may persist in the environment and re-infect birds in subsequent seasons.

Alaska↗

USGS2007

Gene expression in the liver of rainbow trout, Oncorhynchus mykiss , during the stress response

To better appreciate the mechanisms underlying the physiology of the stress response, an oligonucleotide microarray and real-time RT-PCR (QRT-PCR) were used to study gene expression in the livers of rainbow trout ( Oncorhynchus mykiss ). For increased confidence in the discovery of candidate genes responding to stress, we conducted two separate experiments using fish from different year classes. In both experiments, fish exposed to a 3 h stressor were compared to control (unstressed) fish. In the second experiment some additional fish were exposed to only 0.5 h of stress and others were sampled 21 h after experiencing a 3 h stressor. This 21 h post-stress treatment was a means to study gene expression during recovery from stress. The genes we report as differentially expressed are those that responded similarly in both experiments, suggesting that they are robust indicators of stress. Those genes are a major histocompatibility complex class 1 molecule ( MHC1 ), JunB , glucose 6-phosphatase ( G6Pase ), and nuclear protein 1 ( Nupr1 ). Interestingly, Nupr1 gene expression was still elevated 21 h after stress, which indicates that recovery was incomplete at that time.

Comparative Biochemistry and Physiology, Part D: G↗

USGS2023

Conservation genomics of an endangered montane amphibian reveals low population structure, low genomic diversity and selection pressure from disease

Wildlife diseases are a major global threat to biodiversity. Boreal toads ( Anaxyrus [Bufo] boreas ) are a state-endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis ( Bd ). We performed conservation and landscape genomic analyses using single nucleotide polymorphisms from double-digest, restriction site-associated DNA sequencing in combination with the development of the first boreal toad (and first North American toad) reference genome to investigate population structure, genomic diversity, landscape connectivity and adaptive divergence. Genomic diversity ( π = 0.00034–0.00040) and effective population sizes ( N e = 8.9–38.4) were low, likely due to post-Pleistocene founder effects and Bd -related population crashes over the last three decades. Population structure was also low, likely due to formerly high connectivity among a higher density of geographically proximate populations. Boreal toad gene flow was facilitated by low precipitation, cold minimum temperatures, less tree canopy, low heat load and less urbanization. We found >8X more putatively adaptive loci related to Bd intensity than to all other environmental factors combined, and evidence for genes under selection related to immune response, heart development and regulation and skin function. These data suggest boreal toads in habitats with Bd have experienced stronger selection pressure from disease than from other, broad-scale environmental variations. These findings can be used by managers to conserve and recover the species through actions including reintroduction and supplementation of populations that have declined due to Bd .

Colorado↗

USGS2020

High site fidelity does not equate to population genetic structure for common goldeneye and Barrow's goldeneye in North America

Delineation of population structure provides valuable information for conservation and management of species, as levels of demographic and genetic connectivity not only affect population dynamics but also have important implications for adaptability and resiliency of populations and species. Here, we measure population genetic structure and connectivity across the ranges of two sister species of sea ducks: Barrow's goldeneye Bucephala islandica and common goldeneye B. clangula . We use two different marker types: 7–8 nuclear microsatellite loci assayed across 229 samples and 3678 double digest restriction‐site associated DNA sequencing (ddRAD‐seq) loci assayed across 61 samples. First, both datasets found no evidence of genetic structure within common or Barrow's goldeneye, including between North American and European samples of common goldeneye. These results are in contrast with previous mitochondrial DNA, band recovery and telemetry data which suggest that goldeneyes are structured across their range. We posit that the discordance between autosomal genetic markers and other data types suggests that males, possibly subadult males, may be maintaining genetic connectivity across each species' respective ranges. Next, although mate choice consequences resulting from inter‐specific brood parasitism was hypothesized to cause some level of gene flow between goldeneye species, we only identified a single F1 hybrid with no further evidence of contemporary or historical gene flow. Despite ddRAD‐seq demographic analyses which recovered an optimum evolutionary model of split‐with‐migration (i.e. secondary contact), estimates of gene flow were <<1 migrant per generation in both directions. Together, we conclude that either strong ecological barriers or assortative mating are likely playing a role in preventing further backcrossing. Finally, demographic analyses estimated a relatively deep divergence time between Barrow's goldeneye and common goldeneye of ~1.6 million years before present and suggests that the genomes of both species have been under similar evolutionary constraints.

Journal of Avian Biology↗

USGS2015

Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater ( Centrocercus urophasianus ) and Gunnison sage-grouse ( C. minimus ), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index ( F ST ) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly ( F ST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other Greater Sage-Grouse. The level of differentiation is much less than the divergence between Greater and Gunnison sage-grouse, supporting the idea that the Bi-State represents a unique population within the Greater Sage-Grouse. New genomic methods like the restriction-site-associated DNA (RAD-tag) method used here illustrate how increasing the number of markers and coverage of the genome can better characterize patterns of genetic variation, particularly among recently diverged taxa, providing vital information for conservation and management.

The Condor↗

USGS2017

Divergence and gene flow in the globally distributed blue-winged ducks

The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler (A. clypeata) and the more sedentary, African Cape shoveler (A. smithii) into the Australasian shoveler (A. rhynchotis), although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.

Journal of Avian Biology↗

USGS2024

The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population

Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse ( Centrocercus urophasianus ) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity ( H O = 0.65) was higher in the recipient population than predicted had no augmentation occurred ( H O = 0.58) but less than what was predicted by our model ( H O = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index ( F ST ) (143 genes) or local environmental variables (97 and 157 genes for each genotype–environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.

Conservation Biology↗

USGS2022

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.)

Groups of sympatric taxa with low interspecific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes ( Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the last was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as Coregonus hoyi and C. zenithicus , which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent data sets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

Michigan, Minnesota, Ontario, Wisconsin↗

USGS2017

Low-pathogenic influenza A viruses in North American diving ducks contribute to the emergence of a novel highly pathogenic influenza A(H7N8) virus

Introductions of low-pathogenic avian influenza (LPAI) viruses of subtypes H5 and H7 into poultry from wild birds have the potential to mutate to highly pathogenic avian influenza (HPAI) viruses, but such viruses' origins are often unclear. In January 2016, a novel H7N8 HPAI virus caused an outbreak in turkeys in Indiana, USA. To determine the virus's origin, we sequenced the genomes of 441 wild-bird origin influenza A viruses (IAVs) from North America and subjected them to evolutionary analyses. The results showed that the H7N8 LPAI virus most likely circulated among diving ducks in the Mississippi flyway during autumn 2015 and was subsequently introduced to Indiana turkeys, in which it evolved high pathogenicity. Preceding the outbreak, an isolate with six gene segments (PB2, PB1, PA, HA, NA, and NS) sharing >99% sequence identity with those of H7N8 turkey isolates was recovered from a diving duck sampled in Kentucky, USA. H4N8 IAVs from other diving ducks possessed five H7N8-like gene segments (PB2, PB1, NA, MP, and NS; >98% sequence identity). Our findings suggest that viral gene constellations circulating among diving ducks can contribute to the emergence of IAVs that affect poultry. Therefore, diving ducks may serve an important and understudied role in the maintenance, diversification, and transmission of IAVs in the wild-bird reservoir.

Journal of Virology↗

USGS2001

Green fluorescent protein is lighting up fungal biology

Prasher ( 42 ) cloned a cDNA for the green fluorescent protein (GFP) gene from the jellyfish Aequorea victoria in 1992. Shortly thereafter, to the amazement of many investigators, this gene or derivatives thereof were successfully expressed and conferred fluorescence to bacteria and Caenorhabditis elegans cells in culture ( 10 , 31 ), followed by yeast ( 24 , 39 ), mammals ( 40 ), Drosophila ( 66 ), Dictyostelium ( 23 , 30 ), plants ( 28 , 49 ), and filamentous fungi ( 54 ). The tremendous success of GFP as a reporter can be attributed to unique qualities of this 238-amino-acid, 27-kDa protein which absorbs light at maxima of 395 and 475 nm and emits light at a maximum of 508 nm. The fluorescence of GFP requires only UV or blue light and oxygen, and therefore, unlike the case with other reporters (β-glucuronidase, β-galacturonidase, chloramphenicol acetyltransferase, and firefly luciferase) that rely on cofactors or substrates for activity, in vivo observation of gfp expression is possible with individual cells, with cell populations, or in whole organisms interacting with symbionts or environments in real time. Complications caused by destructive sampling, cell permeablization for substrates, or leakage of products do not occur. Furthermore, the GFP protein is extremely stable in vivo and has been fused to the C or N terminus of many cellular and extracellular proteins without a loss of activity, thereby permitting the tagging of proteins for gene regulation analysis, protein localization, or specific organelle labeling. The mature protein resists many proteases and is stable up to 65°C and at pH 5 to 11, in 1% sodium dodecyl sulfate or 6 M guanidinium chloride (reviewed in references 17 and 67 ), and in tissue fixed with formaldehyde, methanol, or glutaraldehyde. However, GFP loses fluorescence in methanol-acetic acid (3:1) and can be masked by autofluorescent aldehyde groups in tissue fixed with glutaraldehyde. Fluorescence is optimal at pH 7.2 to 8.0 ( 67 ). Limitations on GFP as a reporter for some applications are its low turnover rate, 2-h lag time for autoactivation of its chromophore, improper folding at high temperatures (37°C), which results in nonfluorescent and insoluble forms of the protein, and requirement for oxygen, which is not present in equal concentrations in all subcellular locations or cell types (reviewed in references 17 and 67 ). These characteristics of GFP, however, have not posed a problem for many applications, and mutant forms of GFP that have an ability to fold properly at high temperatures, increased solubility and fluorescence, reduced photobleaching ( 16 , 17 , 51 ), and reduced half-lives ( 1 ) have been developed. Coupled with fluorescence-activated cell sorting, confocal microscopy or quantitative image analysis techniques, GFP technology can be used to isolate transformed cells or specific cell types from populations of cells ( 14 ), to quantify gene expression of individual cells within whole organisms ( 8 ), or to assess the dispersal and biomass of organisms in complex environments, such as in animal or plant hosts ( 38 , 59 ), in biofilms ( 55 ), in fermentors ( 41 ), on leaf surfaces ( 53 , 61 ), or in soils ( 2 ). The vast majority of studies utilizing GFP expression in fungi have been with yeast (reviewed in reference 13 ). Ustilago maydis was the first filamentous fungus for which successful expression of gfp was reported ( 54 ), followed closely by Aspergillus nidulans ( 22 , 57 ) and Aureobasidium pullulans ( 61 ). Presently, gfp expression has been reported for 16 species comprising 12 genera of filamentous fungi, including Colletotrichum ( 21 , 44 ), Mycosphaerella ( 52 ), Magnaporthe ( 32 , 35 ), Cochliobolus ( 38 ), Trichoderma ( 2 , 70 ), Podospora ( 5 ), Sclerotinia ( 63 ), Schizophyllum ( 37 ), Aspergillus ( 20 , 47 , 50 ) and Phytophthora ( 7 , 62 ). In this review we draw on published reports, with the goal of providing an overview of GFP technology as it applies to the biology of filamentous fungi. These reports are not exhaustive of potential applications of GFP technology, as examples of genomic approaches to utilizing GFP in bacterial and yeast systems attest ( 4 , 46 , 60 , 65 ). Expression of gfp in filamentous fungi requires a gfp variant that is efficiently translated in fungi, a transformation system, and a fungal promoter that satisfies the requirements of a given experimental objective. Transformation of fungi has recently been reviewed by Gold et al. ( 26 ). Robinson and Sharon ( 44 ) suggest that GFP can actually be used to optimize transformation protocols. In addition to reporting the construction of a new fungal transformation vector that expresses SGFP under the control of the ToxA gene promoter from Pyrenophora tritici-repentis ( 12 ) and demonstrating its use in plant pathogens belonging to eight different genera of filamentous fungi ( Fusarium, Botrytis, Pyrenophora, Alternaria, Cochliobolus, Sclerotinia, Colletotrichum , and Verticillium ), in this review we also enumerate and describe a comprehensive list of vectors for expressing GFP in fungi.

Applied and Environmental Microbiology↗

USGS2023

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus ( U. americanus ), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos , and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10 −13 ). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 ( TYRP1 ) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.

Current Biology↗

USGS2018

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate‐sensitive mammal

The American pika is a thermally sensitive, alpine lagomorph species. Recent climate-associated population extirpations and genetic signatures of reduced population sizes range-wide indicate the viability of this species is sensitive to climate change. To test for potential adaptive responses to climate stress, we sampled pikas along two elevational gradients (each ~470 to 1640 m) and employed three outlier detection methods, BAYESCAN, LFMM, and BAYPASS, to scan for genotype-environment associations in samples genotyped at 30,763 SNP loci. We resolved 173 loci with robust evidence of natural selection detected by either two independent analyses or replicated in both transects. A BLASTN search of these outlier loci revealed several genes associated with metabolic function and oxygen transport, indicating natural selection from thermal stress and hypoxia. We also found evidence of directional gene flow primarily downslope from large high-elevation populations and reduced gene flow at outlier loci, a pattern suggesting potential impediments to the upward elevational movement of adaptive alleles in response to contemporary climate change. Finally, we documented evidence of reduced genetic diversity associated the south-facing transect and an increase in corticosterone stress levels associated with inbreeding. This study suggests the American pika is already undergoing climate-associated natural selection at multiple genomic regions. Further analysis is needed to determine if the rate of climate adaptation in the American pika and other thermally sensitive species will be able to keep pace with rapidly changing climate conditions.

Washington↗

USGS2008

Genetic evidence of intercontinental movement of avian influenza in a migratory bird: The northern pintail (Anas acuta)

The role of migratory birds in the movement of the highly pathogenic (HP) avian influenza H5N1 remains a subject of debate. Testing hypotheses regarding intercontinental movement of low pathogenic avian influenza (LPAI) viruses will help evaluate the potential that wild birds could carry Asian-origin strains of HP avian influenza to North America during migration. Previous North American assessments of LPAI genetic variation have found few Asian reassortment events. Here, we present results from whole-genome analyses of LPAI isolates collected in Alaska from the northern pintail (Anas acuta), a species that migrates between North America and Asia. Phylogenetic analyses confirmed the genetic divergence between Asian and North American strains of LPAI, but also suggested inter-continental virus exchange and at a higher frequency than previously documented. In 38 isolates from Alaska, nearly half (44.7%) had at least one gene segment more closely related to Asian than to North American strains of LPAI. Additionally, sequences of several Asian LPAI isolates from GenBank clustered more closely with North American northern pintail isolates than with other Asian origin viruses. Our data support the role of wild birds in the intercontinental transfer of influenza viruses, and reveal a higher degree of transfer in Alaska than elsewhere in North America. ?? 2008 The Authors.

Alaska↗