Spatial Genetic Structure of Long-tailed Ducks (Clangula hyemalis) among Alaskan, Canadian, and Russian Breeding Populations + Supplementary Appendix Tables S1 and S2 (See Article Tools)

ARCTIC ◽  
2016 ◽  
Vol 69 (1) ◽  
pp. 65 ◽  
Author(s):  
Robert E. Wilson ◽  
Judy R. Gust ◽  
Margaret R. Petersen ◽  
Sandra L. Talbot
Keyword(s):  
Population Structure ◽  
Microsatellite Loci ◽  
Spatial Genetic Structure ◽  
Nuclear Genome ◽  
Migratory Connectivity ◽  
Arctic Ecosystems ◽  
Breeding Populations ◽  
The Pacific ◽  
Autosomal Microsatellite Loci ◽  
Clangula Hyemalis

<p class="Pa5" style="text-align: justify; text-justify: inter-ideograph;"><span style="font-size: 10.0pt; color: #221e1f;">Arctic ecosystems are changing at an unprecedented rate. How Arctic species are able to respond to such environmental change is partially dependent on the connections between local and broadly distributed populations. For species like the Long-tailed Duck (<em>Clangula hyemalis</em>), we have limited telemetry and band-recovery information from which to infer population structure and migratory connectivity; however, genetic analyses can offer additional insights. To examine population structure in the Long-tailed Duck, we characterized variation at mtDNA control region and microsatellite loci among four breeding areas in Alaska, Canada, and Russia. We observed significant differences in the variance of mtDNA haplotype frequencies between the Yukon-Kuskokwim Delta (YKD) and the three Arctic locations (Arctic Coastal Plain in Alaska, eastern Siberia, and central Canadian Arctic). However, like most sea duck genetic assessments, our study found no evidence of population structure based on autosomal microsatellite loci. Long-tailed Ducks use multiple wintering areas where pair formation occurs with some populations using both the Pacific and Atlantic Oceans. This situation provides a greater opportunity for admixture across breeding locales, which would likely homogenize the nuclear genome even in the presence of female philopatry. The observed mtDNA differentiation was largely due to the presence of two divergent clades: (A) a clade showing signs of admixture among all breeding locales and (B) a clade primarily composed of YKD samples. We hypothesize that the pattern of mtDNA differentiation reflects some degree of philopatry to the YKD and isolation of two refugial populations with subsequent expansion and admixture. We recommend additional genetic assessments throughout the circumpolar range of Long-tailed Ducks to further quantify aspects of genetic diversity and migratory connectivity in this species.</span></p>

scholarly journals Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

2012 ◽  
Vol 93 (6) ◽  
pp. 1512-1524 ◽  
Author(s):  
Sarah A. Sonsthagen ◽  
Chadwick V. Jay ◽  
Anthony S. Fischbach ◽  
George K. Sage ◽  
Sandra L. Talbot
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Genetic Structure ◽  
Genetic Relationships ◽  
Breeding Population ◽  
Pacific Walrus ◽  
Breeding Populations ◽  
The Pacific

Abstract 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 (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 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.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

Eight Novel Microsatellite Loci Developed from Vernal Pool Fairy Shrimp

2013 ◽  
Vol 4 (1) ◽  
pp. 134-138 ◽  
Author(s):  
Kristy Deiner ◽  
Joshua M. Hull ◽  
Bernie May
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Vernal Pool ◽  
Fairy Shrimp ◽  
Genomic Libraries ◽  
Primer Sets ◽  
Branchinecta Lynchi

Abstract We developed primer sets for eight di-, tri-, and tetranucleotide microsatellite loci for the threatened vernal pool fairy shrimp Branchinecta lynchi from CA, CAA, ATG, CAGA, and TAGA enriched genomic libraries. We tested primers in 74 individuals of B. lynchi from California, as well as 19 individuals from six other Branchinecta species: B. coloradensis, B. constricta, B. dissimilis, B. lindahli, B. mesovalensis, and B. oriena. The eight loci showed sufficient variability for investigations of B. lynchi evolution, population structure, and genetic diversity and may provide a new tool for assisting in delineation of management areas.

scholarly journals Winter activity unrelated to introgression in British bumblebee Bombus terrestris audax

Apidologie ◽  
2020 ◽  
Author(s):  
Alex F. Hart ◽  
Kevin Maebe ◽  
Gordon Brown ◽  
Guy Smagghe ◽  
Thomas Ings
Keyword(s):  
Population Structure ◽  
Microsatellite Loci ◽  
Bombus Terrestris ◽  
Geographic Range ◽  
Wild Populations ◽  
Local Adaptations ◽  
Winter Activity ◽  
Study Population

AbstractBombus terrestris is a bumblebee with a wide geographic range, with subspecies showing a variety of local adaptations. Global export of commercially-reared B. terrestris started in the 1980s; the bees are a mixture of subspecies bred for ease of rearing, bivoltinism and large nests. This paper investigated whether the increase in bivoltinism in UK resident B. terrestris audax populations was related to introgression with imported foreign subspecies. Workers were collected from wild populations in London and Bristol, as well as two commercial suppliers. Fourteen microsatellite loci were used to study population structure, hybridisation and introgression. No introgression with commercial B. t. dalmatinus was detected in wild populations. Hence, the increase in winter activity appears unrelated to introgression.

scholarly journals Migratory connectivity in the context of differential migration

2018 ◽  
Vol 14 (12) ◽  
pp. 20180679 ◽  
Author(s):  
Martins Briedis ◽  
Silke Bauer
Keyword(s):  
Population Dynamics ◽  
Differential Mortality ◽  
Breeding Period ◽  
Migratory Connectivity ◽  
Differential Migration ◽  
Relative Contribution ◽  
Breeding Populations ◽  
Conservation Actions ◽  
Carry Over ◽  
The Times

Understanding how breeding populations are spatially and temporarily associated with one another over the annual cycle has important implications for population dynamics. Migratory connectivity typically assumes that populations mix randomly; yet, in many species and populations, sex-, age- or other subgroups migrate separately, and/or spend the non-breeding period separated from each other—a phenomenon coined differential migration. These subgroups likely experience varying environmental conditions, which may carry-over to affect body condition, reproductive success and survival. We argue that environmental or habitat changes can have disproportional effects on a population's demographic rates under differential migration compared to random mixing. Depending on the relative contribution of each of these subgroups to population growth, environmental perturbations may be buffered (under-proportional) or amplified (over-proportional). Thus, differential migration may result in differential mortality and carry-over effects that can have concomitant consequences for dynamics and resilience of the populations. Recognizing the role of differential migration in migratory connectivity and its consequences on population dynamics can assist in developing conservation actions that are tailored to the most influential demographic group(s) and the times and places where they are at peril.

Hybridization between Gulls (Larus glaucescens and L. occidentalis) in the Pacific Northwest

The Auk ◽  
1978 ◽  
Vol 95 (3) ◽  
pp. 441-458 ◽  
Author(s):  
Wayne Hoffman ◽  
John A. Wiens ◽  
J. Michael Scott
Keyword(s):  
Pacific Northwest ◽  
High Frequency ◽  
Equilibrium System ◽  
Mixed Composition ◽  
Mating Patterns ◽  
Hybrid Individual ◽  
Breeding Populations ◽  
The Pacific ◽  
Wing Tip ◽  
Larus Glaucescens

Abstract Interbreeding between Glaucous-winged Gulls (Larus glaucescens) and Western Gulls (L. occidentalis) occurs extensively within a 180-km zone along the Washington coast, producing a high frequency of intermediate morphs in breeding populations. We conducted intensive studies on Destruction Island, Washington, in the midst of the zone of hybridization. There over half of the breeding birds were phenotypically intergrades between pure Glaucous-winged and Western gulls in characters of iris and eye-ring coloration, mantle shade, and wing tip pattern. Mating patterns of Destruction Island gulls were assortative, individuals pairing with mates similar to themselves. Pairs composed of pure Glaucous-winged or Western gulls hatched significantly fewer eggs than pairs containing at least one hybrid individual. The greater apparent reproductive success of the intergrades would seem to be countered by the assortative mating patterns, possibly providing conditions sufficient to maintain an equilibrium system containing both pure types as well as intergrades. These conditions are explored in a simulation model that considered immigration, density-dependent fecundity, pairing and reproduction, and mortality. A stable colony of mixed composition may be maintained by a regular but small influx of pure types into the colony.

scholarly journals Seasonal survival and migratory connectivity of the Eurasian Oystercatcher revealed by citizen science

The Auk ◽  
2019 ◽  
Vol 136 (1) ◽  
Author(s):  
Andrew M Allen ◽  
Bruno J Ens ◽  
Martijn Van de Pol ◽  
Henk Van der Jeugd ◽  
Magali Frauendorf ◽  
...  
Keyword(s):  
Citizen Science ◽  
Avian Species ◽  
Future Research ◽  
Migratory Connectivity ◽  
Space And Time ◽  
Demographic Rates ◽  
Breeding Populations ◽  
Spatio Temporal ◽  
Using Data ◽  
Model Structures

Abstract Migratory connectivity describes linkages between breeding and non-breeding areas. An ongoing challenge is tracking avian species between breeding and non-breeding areas and hence estimating migratory connectivity and seasonal survival. Collaborative color-ringing projects between researchers and citizen scientists provide opportunities for tracking the annual movements of avian species. Our study describes seasonal survival and migratory connectivity using data from more than 4,600 individuals with over 51,000 observations, predominantly collected by citizen scientists. Our study focuses on the Eurasian Oystercatcher (Haematopus ostralegus), a species that has experienced a substantial and ongoing decline in recent decades. Multiple threats have been described, and given that these threats vary in space and time, there is an urgent need to estimate demographic rates at the appropriate spatio-temporal scale. We performed a seasonal multi-state (5 geographical areas within The Netherlands) live- and dead-recoveries analysis under varying model structures to account for biological and data complexity. Coastal breeding populations were largely sedentary, while inland breeding populations were migratory and the direction of migration varied among areas, which has not been described previously. Our results indicated that survival was lower during winter than summer and that survival was lower in inland areas compared with coastal areas. A concerning result was that seasonal survival of individuals over-wintering in the Wadden Sea, an internationally important site for over-wintering shorebirds, appeared to decline during the study period. We discuss the outcomes of our study, and how citizen science was integral for conducting this study. Our findings identify how the demographic rates of the oystercatcher vary in space and time, knowledge that is vital for generating hypotheses and prioritizing future research into the causes of decline.

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