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At least 613 records · Page 34Linked to original sources
USGS2017

Protection of bats (Eptesicus fuscus) against rabies following topical or oronasal exposure to a recombinant raccoon poxvirus vaccine

Rabies is an ancient neglected tropical disease that causes tens of thousands of human deaths and millions of cattle deaths annually. In order to develop a new vaccine for potential use in bats, a reservoir of rabies infection for humans and animals alike, an in silico antigen designer tool was used to create a mosaic glycoprotein (MoG) gene using available sequences from the rabies Phylogroup I glycoprotein. This sequence, which represents strains more likely to occur in bats, was cloned into raccoonpox virus (RCN) and the efficacy of this novel RCN-MoG vaccine was compared to RCN-G that expresses the glycoprotein gene from CVS-11 rabies or luciferase (RCN- luc , negative control) in mice and big brown bats ( Eptesicus fuscus ). Mice vaccinated and boosted intradermally with 1 x 10 7 plaque forming units (PFU) of each RCN-rabies vaccine construct developed neutralizing antibodies and survived at significantly higher rates than controls. No significant difference in antibody titers or survival was noted between rabies-vaccinated groups. Bats were vaccinated either oronasally (RCN-G, RCN-MoG) with 5x10 7 PFU or by topical application in glycerin jelly (RCN-MoG, dose 2x10 8 PFU), boosted (same dose and route) at 46 days post vaccination (dpv), and then challenged with wild-type big brown variant RABV at 65 dpv. Prior to challenge, 90% of RCN-G and 75% of RCN-MoG oronasally vaccinated bats had detectable levels of serum rabies neutralizing antibodies. Bats from the RCN- luc and topically vaccinated RCN-MoG groups did not have measurable antibody responses. The RCN-rabies constructs were highly protective and not significantly different from each other. RCN-MoG provided 100% protection (n = 9) when delivered oronasally and 83% protection (n = 6) when delivered topically; protection provided by the RCN-G construct was 70% (n = 10). All rabies-vaccinated bats survived at a significantly (P ≤ 0.02) higher rate than control bats (12%; n = 8). We have demonstrated the efficacy of a novel, in silico designed rabies MoG antigen that conferred protection from rabies challenge in mice and big brown bats in laboratory studies. With further development, topical or oronasal administration of the RCN-MoG vaccine could potentially mitigate rabies in wild bat populations, reducing spillover of this deadly disease into humans, domestic mammals, and other wildlife.

PLoS Neglected Tropical Diseases↗
USGS2024

Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

The diagnosis of anthrax, a zoonotic disease caused by Bacillus anthracis can be complicated by detection of closely related species. Conventional diagnosis of anthrax involves microscopy, culture identification of bacterial colonies and molecular detection. Genetic markers used are often virulence gene targets such as B. anthracis protective antigen ( pagA , also called BAPA, occurring on plasmid pXO1), lethal factor ( lef , on pXO1), capsule-encoding capB/C (located on pXO2) as well as chromosomal Ba-1. Combinations of genetic markers using real-time/quantitative polymerase chain reaction (qPCR) are used to confirm B . anthracis from culture but can also be used directly on diagnostic samples to avoid propagation and its associated biorisks and for faster identification. We investigated how the presence of closely related species could complicate anthrax diagnoses with and without culture to standardise the use of genetic markers using qPCR for accurate anthrax diagnosis. Using blood smears from 2012–2020 from wildlife mortalities (n = 1708) in Kruger National Park in South Africa where anthrax is endemic, we contrasted anthrax diagnostic results based on qPCR, microscopy, and culture. From smears, 113/1708 grew bacteria in culture, from which 506 isolates were obtained. Of these isolates, only 24.7% (125 isolates) were positive for B . anthracis based on genetic markers or microscopy. However, among these, merely 4/125 (3.2%) were confirmed B . anthracis isolates (based on morphology, microscopy, and sensitivity testing to penicillin and gamma-phage) from the blood smear, likely due to poor survival of spores on stored smears. This study identified B . cereus sensu lato , which included B . cereus and B . anthracis , Peribacillus spp., and Priestia spp. clusters using gyrB gene in selected bacterial isolates positive for pagA region using BAPA probe. Using qPCR on blood smears, 52.1% (890 samples) tested positive for B . anthracis based on one or a combination of genetic markers which included the 25 positive controls. Notably, the standard lef primer set displayed the lowest specificity and accuracy. The Ba-1+BAPA+ lef combination showed 100% specificity, sensitivity, and accuracy. Various marker combinations, such as Ba-1+ capB , BAPA+ capB , Ba-1+BAPA+ capB + lef , and BAPA+ lef + capB , all demonstrated 100.0% specificity and 98.7% accuracy, while maintaining a sensitivity of 96.6%. Using Ba-1+BAPA+ lef + capB , as well as Ba-1+BAPA+ lef with molecular diagnosis accurately detects B . anthracis in the absence of bacterial culture. Systematically combining microscopy and molecular markers holds promise for notably reducing false positives. This significantly enhances the detection and surveillance of diseases like anthrax in southern Africa and beyond and reduces the need for propagation of the bacteria in culture.

PLoS Neglected Tropical Diseases↗
USGS2025

Population genomics of Aedes albopictus across remote Pacific islands for genetic biocontrol considerations

Remote Pacific islands (RPI) are characterized by ecological isolation, diverse endemic species, and vulnerability to invasive organisms due to globalization-driven connectivity. Among these species, Aedes albopictus , a highly invasive vector of flaviviruses, has spread extensively across the RPI via human-mediated dispersal, posing significant health and economic burdens. While the population structure and the degree of gene flow between mosquito populations can inform the dispersal pathways critical for disease vector management, the population genetics of Ae. albopictus in Northern RPI remains understudied. The present work investigated the population structure and connectivity of Ae. albopictus populations from Guam, Hawaiian Islands, and the Republic of the Marshall Islands (RMI) to inform disease and vector-based biosecurity risks and develop targeted management strategies. This is the first assessment to develop and analyze whole genome sequences of Ae. albopictus for RPI, enabling more accurate estimates of differentiation, admixture, and ancestry. We found distinct genetic clustering between regions, distinct ancestry of populations across RPI, and potential invasions that originated from Hawaii and spread into the RMI, and invasions from North America that spread to Guam. These findings can inform biosecurity protocols to limit the invasion of Ae. albopictus and their associated diseases within Hawaii and around the Pacific. Given the significant degree of genetic differentiation, we found between islets, islands, and regions, the genome data from this study can be used to enable the development of locally confined geographically isolated gene drives. These drives may be used to prevent and control outbreaks of dengue, chikungunya, and Zika, diseases that have had devastating consequences in these remote island communities.

PLoS Neglected Tropical Diseases↗
USGS2010

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

Background: Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding. Methodology/Principal Findings: We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation. Conclusions/Significance: Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

California↗
USGS2013

Molecular detection and genotyping of Japanese Encephalitis Virus in mosquitoes during a 2010 outbreak in the Republic of Korea

Japanese encephalitis virus (JEV), a mosquito-borne zoonotic pathogen, is one of the major causes of viral encephalitis. To reduce the impact of Japanese encephalitis among children in the Republic of Korea (ROK), the government established a mandatory vaccination program in 1967. Through the efforts of this program only 0-7 (mean 2.1) cases of Japanese encephalitis were reported annually in the ROK during the period of 1984-2009. However, in 2010 there was an outbreak of 26 confirmed cases of Japanese encephalitis, including 7 deaths. This represented a >12-fold increase in the number of confirmed cases of Japanese encephalitis in the ROK as compared to the mean number reported over the last 26 years and a 3.7-fold increase over the highest annual number of cases during this same period (7 cases). Surveillance of adult mosquitoes was conducted during the 2010 outbreak of Japanese encephalitis in the ROK. A total of 6,328 culicine mosquitoes belonging to 12 species from 5 genera were collected at 6 survey sites from June through October 2010 and assayed by reverse-transcription polymerase chain reaction (RT-PCR) for the presence of JEV. A total of 34/371 pooled samples tested positive for JEV (29/121 Culex tritaeniorhynchus, 4/64 Cx. pipiens, and 1/26 Cx. bitaeniorhynchus) as confirmed by sequencing of the pre-membrane and envelope protein coding genes. The maximum likelihood estimates of JEV positive individuals per 1,000 culicine vectors for Cx. tritaeniorhynchus, Cx. pipiens, and Cx. bitaeniorhynchus were 11.8, 5.6, and 2.8, respectively. Sequences of the JEV pre-membrane and envelope protein coding genes amplified from the culicine mosquitoes by RT-PCR were compared with those of JEV genotypes I-V. Phylogenetic analyses support the detection of a single genotype (I) among samples collected from the ROK in 2010.

PLoS ONE↗
USGS2016

Loss of genetic diversity and increased subdivision in an endemic Alpine Stonefly threatened by climate change

Much remains unknown about the genetic status and population connectivity of high-elevation and high-latitude freshwater invertebrates, which often persist near snow and ice masses that are disappearing due to climate change. Here we report on the conservation genetics of the meltwater stonefly Lednia tumana (Ricker) of Montana, USA, a cold-water obligate species. We sequenced 1530 bp of mtDNA from 116 L. tumana individuals representing “historic” (>10 yr old) and 2010 populations. The dominant haplotype was common in both time periods, while the second-most-common haplotype was found only in historic samples, having been lost in the interim. The 2010 populations also showed reduced gene and nucleotide diversity and increased genetic isolation. We found lower genetic diversity in L. tumana compared to two other North American stonefly species, Amphinemura linda (Ricker) and Pteronarcys californica Newport. Our results imply small effective sizes, increased fragmentation, limited gene flow, and loss of genetic variation among contemporary L. tumana populations, which can lead to reduced adaptive capacity and increased extinction risk. This study reinforces concerns that ongoing glacier loss threatens the persistence of L. tumana, and provides baseline data and analysis of how future environmental change could impact populations of similar organisms.

Montana↗
USGS2016

Nuclear and mitochondrial DNA analyses of golden eagles (Aquila chrysaetos canadensis) from three areas in western North America; initial results and conservation implications

Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles ( Aquila chrysaetos canadensis ) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles. Our results indicate high genetic diversity, low genetic structure and high connectivity. Nuclear DNA Fst values between Idaho and California were low but significantly different from zero (0.026). Bayesian clustering methods indicated a single population, and we were unable to distinguish summer breeding residents from different regions. Results of the mtDNA AMOVA showed that most of the haplotype variation (97%) was within the geographic populations while 3% variation was partitioned among them. One haplotype was common to all three areas. One region-specific haplotype was detected in California and one in Idaho, but additional sampling is required to determine if these haplotypes are unique to those geographic areas or a sampling artifact. We discuss potential sources of the high gene flow for this species including natal and breeding dispersal, floaters, and changes in migratory behavior as a result of environmental factors such as climate change and habitat alteration. Our preliminary findings can help inform the USFWS in development of golden eagle management strategies and provide a basis for additional research into the complex dynamics of the North American subspecies.

Alaska, California, Idaho, Oregon↗
USGS2017

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

Subspecies relationships within the peregrine falcon ( Falco peregrinus ) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20 th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons– F . p . tundrius , anatum , and pealei –for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20 th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei , was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius . Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping ( pealei ) and a boreal/Arctic grouping (currently anatum and tundrius )–each comprised of discrete populations that are variously intra-regionally connected.

Alaska↗
USGS2022

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: a Greater Sage-grouse case study

Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse ( Centrocercus urophasianus ), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.

California, Colorado, Idaho, Montana, Nevada, Nort↗
USGS2023

Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity

Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise continues to decline as disturbance increases across the Mojave Desert in the southwestern United States. While underground crossing structures, like hydrological culverts, have begun receiving attention, population density has not been considered in tortoise connectivity. Our work asks a novel question: How do culverts and population density affect connectivity and potentially drive genetic and demographic patterns? To explore the role of culverts and population density, we used agent-based spatially explicit forward-in-time simulations of gene flow. We constructed resistance surfaces with a range of barriers to movement and representative of tortoise habitat with anthropogenic disturbance. We predicted connectivity under variable population densities. Simulations were run for 200 non-overlapping generations (3400 years) with 30 replicates using 20 microsatellite loci. We evaluated population genetic structure and diversity and found that culverts would not entirely negate the effects of linear barriers, but gene flow improved. Our results also indicated that density is important for connectivity. Low densities resulted in declines regardless of the landscape barrier scenario (> 75% population census size, > 97% effective population size). Results from our simulation using current anthropogenic disturbance predicted decreased population connectivity over time. Genetic and demographic effects were detectable within five generations (85 years) following disturbance with estimated losses in effective population size of 69%. The pronounced declines in effective population size indicate this could be a useful monitoring metric. We suggest management strategies that improve connectivity, such as roadside fencing tied to culverts, conservation areas in a connected network, and development restricted to disturbed areas.

California, Nevada↗
USGS2012

Genetic and morphological divergence among Cooper's Hawk ( Accipiter cooperii ) populations breeding in north-central and western North America

Cooper's Hawk ( Accipiter cooperii ) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits ( P ST) and genetic markers ( F ST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite F ST= 0.031-0.050; mitochondrial DNA Φ ST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits ( P ST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of F ST and Φ ST interpopulation estimates. Comparison of P STand F STestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

The Auk↗
USGS1997

Genetic differentiation of sockeye salmon subpopulations from a geologically young Alaskan lake system

The Tustumena Lake drainage in southcentral Alaska is glacially turbid and geologically young (<2,000 years old). Previous field studies identified at least three subpopulations of sockeye salmon Oncorhynchus nerka at Tustumena Lake, based on the distribution and timing of spawners. The subpopulations included early‐run salmon that spawned in six clearwater tributaries of the lake (mid August), lake shoreline spawners (late August), and late‐run fish that spawned in the lakeˈs outlet, the Kasilof River (late September). Our objective was to determine the degree of genetic differentiation among these subpopulations based on restriction enzyme analyses of the cytochrome b gene of mitochondrial DNA and analyses of four polymorphic allozyme loci. Mitochondrial DNA haplotype frequencies for outlet‐spawning sockeye salmon differed significantly from those of all other subpopulations. The most common (36%) haplotype in the outlet subpopulation did not occur elsewhere, thus suggesting little or no gene flow between outlet spawners and other spatially close subpopulations at Tustumena Lake. Allele frequencies at two allozyme loci also indicated a degree of differentiation of the outlet subpopulation from the shoreline and tributary subpopulations. Allele frequencies for three tributary subpopulations were temporally stable over approximately 20 years (based on a comparison to previously published results) despite initiation of a hatchery program in two of the tributaries during the intervening period. Collectively, our results are consistent with the hypothesis that significant genetic differentiation has occurred within the Tustumena Lake drainage since deglaciation approximately 2,000 years ago.

Alaska↗
USGS2002

Optimization of nested polymerase chain reaction assays for identification of Aeromonas salmonicida, Yersinia ruckeri and Flavobacterium psychrophilum

Nested polymerase chain reaction (PCR) assays were developed using first-round primers complementary to highly conserved regions within the bacterial 16S ribosomal RNA (rRNA) gene (universal eubacterial primers) and second-round primers specific for sequences within the 16S rRNA genes of Aeromonas salmonicida , Yersinia ruckeri , and Flavobacterium psychrophilum . Following optimization of the MgCl 2 concentration and primer annealing temperature, PCR employing the universal eubacterial primers was used to amplify a 1,500-base-pair (bp) product visible in agarose gels stained with ethidium bromide. The calculated detection limit of this single-round assay was less than 1.4 &times; 10 4 colony-forming units (CFU) per reaction for all bacterial species tested. Single-round PCR using primer sets specific for A. salmonicida , Y. ruckeri , and F. psychrophilum amplified bands of 271, 575, and 1,100 bp, respectively, with detection limits of less than 1.4 &times; 10 4 , 1.4 &times; 10 5 , and 1.4 &times; 10 5 CFU per reaction. Using the universal eubacterial primers in the first round and the species-specific primer sets in the second round of nested PCR assays improved the detection ability by approximately four orders of magnitude to fewer than 14 CFU per sample for each of the three bacterial species. Such nested assays could be adapted to a wide variety of bacterial fish pathogens for which 16S sequences are available.

Journal of Aquatic Animal Health↗
USGS2005

Growth, dispersal, mortality, and contribution of largemouth bass stocked into Chickamauga Lake, Tennessee

Marked fingerling largemouth bass Micropterus salmoides (both northern M. s. salmoides and Florida subspecies M. s. floridanus and their hybrid) were stocked into Chickamauga Lake, Tennessee, to enhance angling and introgress the Florida subspecies into the local gene pool. We evaluated mass marking and stocking success by sampling the stocked fish for 1 year poststocking. More than 128,000 fingerlings (35-64 mm total length) were immersed in a solution of 500 mg/L oxytetracycline (OTC) for 6 h and stocked into four embayments in the lake in spring 2002; two additional embayments served as controls and were not stocked (these embayments contained only wild, indigenous fish). In a blind test, 97% of sagittal otoliths were correctly scored as marked or unmarked. In a subsequent test, the OTC marks were clearly visible on every otolith removed from 240 OTC-treated bass held for 30 d. Age-0 largemouth bass were sampled with DC electrofishing gear at 7-19, 44-61, and 119-139 d after stocking, and sampling was conducted along 100-m transects within 1 km of the stocking sites in each embayment. Of all recaptures in the first sample, 31% occurred more than 600 m from the nearest stocking site, indicating rapid dispersal by some fish. Survival of stocked and wild age-0 largemouth bass was similar and low (4.5-6.9%) in two embayments; in the other two embayments, stocked fish survived at lower rates (0-4.3%) than wild fish (33.7-49.9%). Mean catches of all age-0 largemouth bass in the first sample were positively related to the number of fish stocked. By October 2002, the mean catch of all age-0 largemouth bass was similar among embayments. Contribution of stocked fish declined to approximately 2% (2 of 91 fish) the following spring. Cost per fingerling increased from US$0.35 at stocking to $12.00 at 140 d poststocking. Increasing the abundance of largemouth bass was not the primary objective of this stocking effort, but stocked fish will have to survive much better if managers hope to introgress Florida largemouth bass genes into the resident population genome.

North American Journal of Fisheries Management↗
USGS2011

Evolutionary relationships among sympatric life history forms of Dolly Varden inhabiting the landlocked Kronotsky Lake, Kamchatka, and a neighboring anadromous population

We investigated the evolutionary relationships among five sympatric morphs of Dolly Varden Salvelinus malma (white, Schmidti, longhead, river, and dwarf) inhabiting landlocked Kronotsky Lake on the Kamchatka Peninsula, Russia, and an anadromous population below the barrier waterfall on the outflowing Kronotsky River. Morphological analyses indicated phenotypic differentiation corresponding to preferred habitat, the longhead (a limnetic piscivorous morph) having a fusiform body, long jaw, and short fins and the Schmidti (a benthic morph) having a robust body, small jaw, and long fins. Analysis of molecular variance among the Kronotsky Lake morphs indicated that contemporary gene flow is restricted both among morphs within locations and among locations within morphs. Gene flow from Kronotsky Lake into the anadromous population also appears to be restricted. Our findings indicate that there are two divergent evolutionary lineages, one consisting of the white, Schmidti, river, and dwarf morphs and the other of the longhead morph and the anadromous population, which suggests that Kronotsky Lake was subject to separate waves of immigration. The Kronotsky Lake Dolly Varden morphs may represent an example of ecological speciation in progress, and we present a working hypothesis for the diversification of morphs within Kronotsky Lake.

Transactions of the American Fisheries Society↗
USGS2017

Molecular detection of avian influenza virus from sediment samples in waterfowl habitats on the Delmarva Peninsula, United States

Avian influenza viruses (AIV) affect many species of birds including waterfowl and may persist in sediment in aquatic habitats. Sediment samples were collected from two areas representative of prime migration and overwintering waterfowl habitat in Dorchester County, Maryland in the fall and winter of 2013–2014. Samples were screened for the presence of AIV via reverse transcriptase–quantitative PCR targeting the matrix gene. Although 13.6% of sediment samples were positive for the AIV matrix gene across all collection dates and locations, differences in detection were noted with location and collection season. Percentage of AIV-positive sediment samples recovered corresponded to trends in waterfowl abundance at collection sites both temporally and spatially. These findings provide further support for the assertion that the presence of AIV in the aquatic environment is likely affected by the total number, site-specific density, and array of waterfowl species.

Delmarva Peninsula↗
USGS2000

Genetic variation in the endangered Southwestern Willow Flycatcher

The Southwestern Willow Flycatcher ( Empidonax traillii extimus ) is an endangered Neotropical migrant that breeds in isolated remnants of dense riparian habitat in the southwestern United States. We estimated genetic variation at 20 breeding sites of the Southwestern Willow Flycatcher (290 individuals) using 38 amplified fragment length polymorphisms (AFLPs). Our results suggest that considerable genetic diversity exists within the subspecies and within local breeding sites. Statistical analyses of genetic variation revealed only slight, although significant, differentiation among breeding sites (Mantel's r = 0.0705, P < 0.0005; θ = 0.0816, 95% CI = 0.0608 to 0.1034; Φ ST = 0.0458, P < 0.001). UPGMA cluster analysis of the AFLP markers indicates that extensive gene flow has occurred among breeding sites. No one site stood out as being genetically unique or isolated. Therefore, the small level of genetic structure that we detected may not be biologically significant. Ongoing field studies are consistent with this conclusion. Of the banded birds that were resighted or recaptured in Arizona during the 1996 to 1998 breeding seasons, one-third moved between breeding sites and two-thirds were philopatric. Low differentiation may be the result of historically high rangewide diversity followed by recent geographic isolation of breeding sites, although observational data indicate that gene flow is a current phenomenon. Our data suggest that breeding groups of E. t. extimus act as a metapopulation.

The Auk↗
USGS2001

Geographic variation in the song of Willow Flycatchers: Differentiation between Empidonax traillii adastus and E. t. extimus

The vocal signatures of the primary song form (“ fitz-bew ”) of the endangered Southwestern Willow Flycatcher ( Empidonax traillii extimus ) and its northern counterpart, E. t. adastus, are distinctive. Songs of the extimus subspecies are longer (total song, note, internote) and frequencies at maximum amplitude are lower than those of adastus. I used vocal evidence to clarify the distributional limits of the Southwestern Willow Flycatcher and that of the geographically adjacent subspecies, E. t. adastus. Unweighted pair-group method using averaging (UPGMA) cluster analysis and canonical discriminant analysis revealed that (1) low elevation, southerly desert populations (Arizona, New Mexico, and southern Utah) have a unique vocal identity corresponding to populations in the range of E. t. extimus ; (2) northerly song groups (Oregon, Colorado, and northern Utah) share a different song type corresponding to populations in the range of E. t. adastus; and (3) a departure from vocal and morphological congruence occurs for a population of high-elevation Arizona birds that, although in the currently accepted range of E. t. extimus, sings songs acoustically similar to more northern populations ( E. t. adastus ). Multiple regression of song distance on latitude and elevation, and a comparison of a matrix of song distances with a matrix of latitude and elevation dissimilarities, demonstrated that song populations sort out by both latitude and elevation: birds with the vocal identity of extimus occur as far north as 37°N if at low elevation, and those acoustically similar to adastus occur as far south as 33.7°N if at high elevation. The vocal background of northern New Mexico birds appears to be intermediate between that of extimus and adastus, suggesting that northern New Mexico is a zone of intermixing and intergradation between the subspecies. Pure forms of E. t. extimus apparently do not occur in Colorado because even the southernmost populations are acoustically similar to more northerly populations of adastus. A low-elevation population in western Colorado, however, stands apart from other adastus populations, suggesting moderate introgression of extimus genes into the adastus gene pool.

The Auk↗