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At least 199 records · Page 11Linked to original sources
USGS2012

Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Pacific walruses ( Odobenus rosmarus divergens ) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (Φ ST =0.051), and between the eastern Chukchi and other nonbreeding aggregations (Φ ST =0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite F ST =0.019; mtDNA Φ ST =0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite F ST =0.019–0.035; mtDNA Φ ST =0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

Journal of Mammalogy↗
USGS2015

Genetic structure, diversity, and interisland dispersal in the endangered Mariana Common Moorhen (Gallinula chloropus guami)

The Mariana Common Moorhen ( Gallinula chloropus guami ) is a highly endangered taxon, with fewer than 300 individuals estimated to occur in the wild. The subspecies is believed to have undergone population declines attributable to loss of wetland habitats on its native islands in the Mariana Islands. We analyzed mitochondrial DNA (mtDNA) sequences (control region and ND2 genes) and nuclear microsatellite loci in Mariana Common Moorhens from Guam and Saipan, the two most distal islands inhabited by the subspecies. Our analyses revealed similar nuclear genetic diversity and effective population size estimates on Saipan and Guam. Birds from Guam and Saipan were genetically differentiated (microsatellites: F ST = 0.152; control region: F ST = 0.736; ND2: F ST = 0.390); however, assignment tests revealed the presence of first-generation dispersers from Guam onto Saipan (1 of 27 sampled birds) and from Saipan onto Guam (2 of 28 sampled birds), suggesting the capability for long-distance interpopulation movements within the subspecies. The observed dispersal rate was consistent with long-term estimates of effective numbers of migrants per generation between islands, indicating that movement between islands has been an ongoing process in this system. Despite known population declines, bottleneck tests revealed no signature of historical bottleneck events, suggesting that the magnitude of past population declines may have been comparatively small relative to the severity of declines that can be detected using genetic data.

The Condor↗
USGS2019

Genetic Characterization of Non-Native African Jewelfish, Hemichromis letourneuxi Sauvage 1880, in Florida

The African Jewelfish, Hemichromis letourneuxi , is an invasive, predatory cichlid fish introduced at least once to Florida. Its native range is in northern Africa. First encountered in Miami in the 1960s, it has since been found west and north within the State of Florida. It thrives in a wide range of aquatic habitats, including shallow, vegetated or rocky areas of canals, tidal creeks, rivers, and marshes. We generated mitochondrial DNA sequences from 6 Florida localities, and 1 Mexico population. The resulting tree describes recent historical relationships among populations. Nearly all Florida populations of African Jewelfish are intermixed, supporting a single invasion, with one possible exception: samples from the Tampa Bay locality are distinct and may represent a separate introduction. Samples obtained from the Mexico locality, previously identified as Hemichromis guttatus (Spotted Jewelfish), appear to be genetically identical to, and indistinguishable from the H. letourneuxi sampled in Florida localities.

Florida↗
USGS2020

Phylogeographic analysis of Mudpuppies (Necturus maculosus)

The geology of the Pleistocene, and particularly the Last Glacial Maximum approximately 26.5 ka, is a critical driver of species’ present-day distributions and levels of genetic diversity in northern regions. Using mitochondrial DNA sequence data, we tested several predictions relating to the postglacial recolonization of the northern United States and southern Canada by Mudpuppies (Necturus maculosus). Our analyses revealed a significant split between western and eastern lineages, with the divide corresponding to the location of the Mississippi River. Our data support the presence of one or more Mississippian glacial refugia, with subsequent expansion and diversification of a western cluster into the upper Midwest, and an eastern cluster into the eastern Great Lakes and New England. As predicted in cases of postglacial colonization, each of these clusters contains a single widespread and common haplotype, along with numerous low-frequency, closely related haplotypes. Given recent conservation concerns about amphibians in general, and Mudpuppies specifically, we discuss our results in light of species conservation. Knowledge of a species’ genetic diversity allows for informed management and facilitates decisions that preserve local adaptation and evolutionary potential.

Journal of Herpetology↗
USGS2010

Population structure and relatedness among female Northern Pintails in three California wintering regions

Female Northern Pintails ( Anas acuta ) were sampled in California's three main Central Valley wintering regions (Sacramento Valley, Suisun Marsh, San Joaquin Valley) during September–October before most regional movements occur and microsatellite and mitochondrial DNA were analyzed to examine population structure and relatedness. Despite reportedly high rates of early-fall pairing and regional fidelity, both sets of markers indicated that there was little overall genetic structuring by region. Pintails from Suisun Marsh did exhibit higher relatedness among individuals and capture groups than in the Sacramento or San Joaquin Valleys, likely reflecting a sample comprised of a greater proportion of local breeders. The lack of genetic structuring among regions indicates that a high degree of movement and interchange occurs among pintails wintering in the Central Valley. Thus, although maintaining the existing distribution of pintails among Central Valley regions is important for other reasons, it does not appear to be critical to retain current patterns of population genetic variation. Because of potential lack of independence among highly related study individuals, researchers should consider regional differences in relatedness when designing sampling schemes and interpreting research findings.

California↗
USGS2010

Genetic characterization of Neotropical Jabiru Storks: Insights for conservation

Jabiru Stork (Jabiru mycteria is listed under Appendix I of CITES and considered threatened in Central America. The first population genetic analysis of Jabiru Storks was carried out using mitochondrial DNA (mtDNA) control region sequences (520 bp) and five heterologous microsatellite loci. Samples were collected from the field (N = 49) and museum skins (N = 22) in Central (mainly Belize, Nicaragua and Costa Rica) and South America (Colombia, Venezuela, Peru and Brazil). A decline of mtDNA diversity was observed in comparisons between past (N = 20) and present (N = 40) samples collected in Central America and northern South America. Similar levels of microsatellite loci diversity were observed among contemporary samples. Lower levels of mtDNA variability were observed in samples from Central America and northern South America when compared to the Brazilian Pantanal region. Significant levels of genetic differentiation were found between contemporary locations sampled, whereas non-significant results were observed for historic samples. The non-geographic association of haplotypes observed at the cladograms and the recent divergence times estimated between locations are indicative of an evolutionary history of a large population size with limited population structure. Reconnection of populations via increased gene flow, particularly in Central America, is recommended if genetic structure and status are to be restored.

Waterbirds↗
USGS2013

Genetic structure, diversity and subspecies status of Gull-billed Terns (Gelochelidon nilotica) from the United States

Gull-billed Terns (Gelochelidon nilotica) are among the most widespread, yet scarce, Charadriiformes in the world. Two subspecies are recognized in the United States: G. n. aranea breeds along the U.S. Atlantic and Gulf coasts and G. n. vanrossemi breeds in the Salton Sea and San Diego Bay of California. Conservation concerns exist for the species due to its low abundance in the United States and apparent declines in some parts of its North American range. We used nuclear microsatellite markers and mitochondrial DNA sequences to assess genetic diversity and differentiation patterns among Gull-billed Tern populations from Virginia, Texas, and California. We also tested for evidence of population bottlenecks, and evaluated the support our data provide for the North American subspecies. Genetic diversity was highest in Texas and underscored the importance of habitat in that large population. Significant population differentiation existed, but could not be consistently identified using various analytical approaches and suggested that the magnitude of differentiation was low. No evidence for bottlenecks was identified. Our data could not distinguish individuals from different subspecies and therefore do not support the current intraspecific taxonomy. Tenable explanations for many findings are related to the low site tenacity demonstrated by the species.

Waterbirds↗
USGS2009

Genetic differentiation between sympatric and allopatric wintering populations of Snow Geese

Blackwater National Wildlife Refuge on the Delmarva Peninsula, Maryland, USA has been the wintering area of a small population of Lesser Snow Geese (Chen caerulescens caerulescens; LSGO) since the 1930s. Snow Geese primarily pair in wintering areas and gene flow could be restricted between this and other LSGO wintering populations. Winter pair formation also could facilitate interbreeding with sympatric but morphologically differentiated Greater Snow Geese (C. c. atlantica; GSGO).We sequenced 658 bp of the mitochondrial DNA control region for 68 Snow Geese from East Coast and Louisiana wintering populations to examine the level of genetic differentiation among populations and subspecies. We found no evidence for genetic differentiation between LSGO populations but, consistent with morphological differences, LSGO and GSGO were significantly differentiated. We also found a lack of genetic differentiation between different LSGO morphotypes from Louisiana. We examined available banding data and found the breeding range of Delmarva LSGO overlaps extensively with LSGO that winter in Louisiana, and documented movements between wintering populations. Our results suggest the Delmarva population of LSGO is not a unique population unit apart from Mid-Continent Snow Geese. ?? 2009 by the Wilson Ornithological Society.

Wilson Journal of Ornithology↗
USGS2005

Population genetics of Gunnison sage-grouse: Implications for management

The newly described Gunnison sage-grouse ( Centrocercus minimus ) is a species of concern for management because of marked declines in distribution and abundance due to the loss and fragmentation of sagebrush habitat. This has caused remaining populations to be unusually small and isolated. We utilized mitochondrial DNA sequence data and data from 8 nuclear microsatellites to assess the extent of population subdivision among Gunnison sage-grouse populations in southwestern Colorado and southeastern Utah, USA. We found a high degree of population structure and low amounts of gene flow among all pairs of populations except the geographically adjacent Gunnison and Curecanti populations. Population structure for Gunnison sage-grouse was significantly higher than has been reported for greater sage-grouse ( C. urophasianus ). Further, we documented low levels of genetic diversity in some populations (particularly Dove Creek/Monticello and Piñon Mesa with an average of only 3.00 and 2.13 alleles per locus respectively) indicating that translocations from larger, more genetically diverse populations may be warranted. Bayesian analysis identified 3 potential migrants (involving San Miguel, Dove Creek/Monticello, Crawford, and Curecanti). Further, this analysis showed that 4 individuals from Cerro/Cimarron were more closely related to birds from San Miguel than to its geographically closer neighbors Gunnison and Curecanti. This suggests the Cerro/Cimarron area may act as a stepping stone for gene flow between San Miguel and Gunnison and that habitat restoration and protection in areas between these 2 basins should be a priority in an attempt to facilitate natural movement among these populations. Conservation plans should include monitoring and maintaining genetic diversity, preventing future habitat loss and fragmentation, enhancing existing habitat, and restoring converted sagebrush communities.

Journal of Wildlife Management↗
USGS2009

Molecular Population Genetic Structure in the Piping Plover

The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect differences in spatiotemporal stability of Piping Plover nesting habitat between regions.

Open-File Report↗
USGS2021

Genetic connectivity of the West Indian manatee in the southern range and limited evidence of hybridization with Amazonian manatees

The Antillean subspecies of the West Indian manatee is classified as endangered by the International Union for the Conservation of Nature (IUCN) Red List. In Brazil, the manatee population is listed as endangered with an estimated population size of 500–1,000. Historic hunting, recent habitat degradation, and fisheries bycatch have decreased the population size. The Amazonian manatee is listed as vulnerable by the IUCN with unknown population sizes within Brazil. The Antillean manatee occurs in sympatry with the Amazonian manatee in Brazil and hybridization has been previously indicated. To provide information on the genetic structure, diversity, and degree of hybridization in the sympatric zone near the Amazon River mouth, the mitochondrial DNA control region and 13 nuclear microsatellite markers were assessed on the two species. Samples were analyzed from the Antillean subspecies across its distribution in Brazil ( n = 78) and from the Amazonian species ( n = 17) at the Amazon River mouth and inland mainstem river. To assess the previously defined evolutionary significant units of Antillean manatees in the area, an additional 11 samples from Venezuela and Guyana were included. The Antillean manatee was found to be a single population in Brazil and had lower than average number of alleles (3.00), expected heterozygosity (0.34), and haplotype diversity (0.15) when compared to many other manatee populations. The low values may be influenced by the small population size and extended pressures from anthropogenic threats. Gene flow was identified with Venezuela/Guyana in admixed Antillean Brazil samples, although the two populations were found to be moderately divergent. The nuclear loci in Venezuela/Guyana Antillean manatee samples indicated high differentiation from the samples collected in the Amazon River ( F ST = 0.35 and R ST = 0.18, p = 0.0001). No indication of nuclear hybridization was found except for a single sample, “Poque” that had been identified previously. The distribution of Antillean manatees in Brazil is extensive and the areas with unique habitat and threats would benefit from independent management and conservation actions. Gene flow, resulting in genetic diversity and long-term population stability, could be improved in the southern range through habitat restoration, and the establishments of travel corridors and protected areas, which are particularly important for successful parturition and neonatal calf survival.

Frontiers in Marine Science↗
USGS2023

United States Gulf of Mexico waters provide important nursery habitat for Mexico’s green turtle nesting populations

Resolving natal populations for juvenile green turtles is challenging given their potential for extensive dispersal during the oceanic stage and ontogenetic shifts among nursery habitats. Mitochondrial DNA markers have elucidated patterns of connectivity between green turtle nesting populations (rookeries) and juvenile foraging aggregations. However, missing rookery baseline data and haplotype sharing among populations have often impeded inferences, including estimating origins of Gulf of Mexico juveniles. Here, we assessed genetic structure among seven foraging aggregations spanning southern Texas (TX) to southwestern Florida (SWFL), including Port Fourchon, Louisiana (LA); a surface-pelagic aggregation (SP) offshore of Louisiana and Florida; Santa Rosa Island, Florida (SRI); St. Joseph Bay, Florida (SJB); and the Big Bend region, Florida (BB). We estimated source contributions to aggregations with novel genetic data (excluding SP and BB) using a Bayesian many-to-one mixed stock analysis (MSA) approach. Haplotype frequencies for western (TX, LA, SP, SRI) and eastern (SJB, BB, SWFL) aggregations were significantly differentiated. The largest shift in haplotype frequencies between proximal nursery sites occurred between SRI and SJB, separated by only 150 km, highlighting the lack of a geographic yardstick for predicting genetic structure. In contrast to previous MSA results, there was no signal of Florida juveniles at any foraging site. Mexican contributions dominated in all aggregations, with strong connectivity between western Bay of Campeche (Tamaulipas/Veracruz) rookeries and western foraging aggregations. MSA indicated more diverse Mexican origins for eastern aggregations, with larger inputs from the eastern Bay of Campeche (Campeche/Yucatán), Campeche Bank, and Quintana Roo rookeries. These results demonstrate the significance of the Gulf of Mexico coast and offshore waters of the United States as important nursery habitat for green turtles of Mexican origin and highlight the need for international coordination for management of these populations.

Alabama, Florida, Louisiana, Mississippi, Texas↗
USGS2021

Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: The rusty blackbird

The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird ( Euphagus carolinus ) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change.

Diversity↗
USGS2023

Movement and genomic methods reveal mechanisms promoting connectivity in a declining shorebird: The lesser yellowlegs

Integrating tracking technology and molecular approaches provides a comprehensive picture of contemporary and evolutionary mechanisms promoting connectivity. We used mitochondrial DNA and double digest restriction-site associated DNA (ddRAD) sequencing combined with satellite telemetry to investigate the connectivity of geographically disparate breeding populations of a declining boreal shorebird, the lesser yellowlegs ( Tringa flavipes ). We were able to track 33 individuals on their round-trip migrations to Central and South America and back to the boreal wetlands of North America. Nearly all (93%) adults captured on the breeding grounds returned to within 5 km of the original capture site, with a median dispersal distance of 629 m. While our telemetry data revealed limited breeding dispersal in adults, genetic data uncovered significant interconnectedness across the species’ range. Very little genetic structure was estimated at ddRAD autosomal ( Φ ST = 0.001), Z-linked ( Φ ST = 0.001), and mtDNA loci ( Φ ST = 0.020), and maximum likelihood-based clustering methods placed all individuals in a single cluster regardless of capture location, indicating the species is panmictic. Our data indicate that large-scale juvenile dispersal is the main mechanism maintaining connectivity in this species, resulting in the absence of genomic structure.

Diversity↗
USGS2025

Relatedness of white-tailed deer from culling efforts within chronic wasting disease management zones in Minnesota

In white-tailed deer ( Odocoileus virginianus ), closely related females form social groups, avoiding other social groups. Consequently, females infected with chronic wasting disease (CWD) are more likely to infect social group members. Culling has been used to reduce CWD transmission in high-risk areas; however, its effectiveness in removing related individuals has not been assessed. We analyzed 11 microsatellites and a mitochondrial DNA fragment to assess: (1) the genetic structure in white-tailed deer in Minnesota, USA and (2) the effectiveness of localized culling to remove related deer. For (1), we genotyped deer culled in 2019 and 2021 in three CWD management zones, and deer collected in between zones. For (2), we only included culled deer, defining “culled groups” as deer obtained in the same township-range-section and year. We compared mean relatedness among deer from the same culled group (intra-group relatedness) and among deer from different culled groups (inter-group relatedness). We did not find evidence of genetic structure, suggesting that an outbreak in any of the management zones could naturally spread to the others. Culling removed deer that were on average more related than expected by chance (intra-group relatedness > inter-group relatedness), and most highly-related deer were culled in the same bait site.

Minnesota↗
USGS2017

Between hot rocks and dry places: The status of the Dixie Valley toad

In Dixie Valley, Nevada, an isolated population of toads has been the subject of proactive conservation measures by the Nevada Department of Wildlife and the U.S. Fish and Wildlife Service since 2008 due to concerns about potential habitat degradation resulting from exploitation of nearby geothermal energy resources. These toads appear to belong within the Anaxyrus boreas species group but are commonly referred to as Dixie Valley toads (DVTs). The DVT is currently confined to an extremely narrow habitat range (370 ha) that is geographically isolated from any other A. boreas population. In this study, genetic variations in mitochondrial genes and 11 microsatellite loci were used to assess the affinities of DVTs in relation to members of the A. boreas species group. We compared results from DVTs with previously published data spanning much of the range of A. boreas in the United States and new data from a nearby toad population within Dixie Valley. Data from both mitochondrial DNA and microsatellites placed DVTs inside the A. boreas species group. In particular, DVTs fell into a cluster of A. boreas from Washington and California, along with other species from the A. boreas species group, namely A. nelsoni, A. canorus, and A. exsul. Genetic differentiation of DVTs was lowest between A. boreas populations in Washington and California. However, allele frequencies were significantly different between DVTs and all other populations, including a nearby locality within Dixie Valley. This genetic differentiation, along with the DVT's geographical isolation and restricted habitat, warrants recognition of the DVT as a distinct management unit.

Nevada↗
USGS2020

Brood parasitism of greater sage-grouse by California Quail in Idaho

We describe a case of brood parasitism of a Greater Sage-Grouse ( Centrocercus urophasianus ; hereafter, sage-grouse) nest by California Quail ( Callipepla californica ; hereafter, quail) in southwestern Idaho during 2019. We observed one quail egg in the parasitized nest; the egg partially hatched, but the chick was dead upon the final nest check. Of the 6 sage-grouse eggs in the nest, only 2 hatched, although the eggs contained chicks that appeared nearly completely developed. Identification of the quail chick was confirmed using mitochondrial DNA. Additional monitoring and documentation of this behavioral interaction is warranted to better understand its prevalence and any reproductive consequences for sage-grouse.

Idaho↗
USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗