Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

The Condor ◽  
2019 ◽  
Vol 121 (3) ◽  
Author(s):  
Iva Popovic ◽  
David P L Toews ◽  
Carson C Keever ◽  
C Toby St. Clair ◽  
Blake A Barbaree ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
River Estuary ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Migratory Connectivity ◽  
Calidris Alpina ◽  
The Pacific

Abstract Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R2 =0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.

scholarly journals Birds are islands for parasites

2014 ◽  
Vol 10 (8) ◽  
pp. 20140255 ◽  
Author(s):  
Jennifer A. H. Koop ◽  
Karen E. DeMatteo ◽  
Patricia G. Parker ◽  
Noah K. Whiteman
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Island Populations ◽  
Louse Species ◽  
Parasite Populations

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk ( Buteo galapagoensis ) and a parasitic feather louse species ( Degeeriella regalis ) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se , suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.

scholarly journals A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

2021 ◽  
Author(s):  
Souta Nakajima ◽  
Masanao Sueyoshi ◽  
Shun K. Hirota ◽  
Nobuo Ishiyama ◽  
Ayumi Matsuo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Low Temperature ◽  
Genetic Differentiation ◽  
Water Temperature ◽  
Sampling Design ◽  
Cold Water ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Sampling Strategy ◽  
Genotyping By Sequencing

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.

Population Genetic Structure of the Blood Clam,Tegillarca granosa, Along the Pacific Coast of Asia: Isolation by Distance in the Sea

Malacologia ◽  
2016 ◽  
Vol 59 (2) ◽  
pp. 303-312 ◽  
Author(s):  
Yanqing Shao ◽  
Xueliang Chai ◽  
Guoqiang Xiao ◽  
Jiongming Zhang ◽  
Zhihua Lin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Pacific Coast ◽  
Isolation By Distance ◽  
Tegillarca Granosa ◽  
The Pacific ◽  
Blood Clam

scholarly journals Mind the gap: genetic distance increases with habitat gap size in Florida scrub jays

2012 ◽  
Vol 8 (4) ◽  
pp. 582-585 ◽  
Author(s):  
Aurélie Coulon ◽  
John W. Fitzpatrick ◽  
Reed Bowman ◽  
Irby J. Lovette
Keyword(s):  
Genetic Structure ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Bird Species ◽  
Habitat Specialization ◽  
Gap Size ◽  
Movement Behaviour ◽  
Florida Scrub ◽  
Fragmented Populations

Habitat gap size has been negatively linked to movement probability in several species occupying fragmented landscapes. How these effects on movement behaviour in turn affect the genetic structure of fragmented populations at local scales is less well known. We tested, and confirmed, the hypothesis that genetic differentiation among adjacent populations of Florida scrub jays—an endangered bird species with poor dispersal abilities and a high degree of habitat specialization—increases with the width of habitat gaps separating them. This relationship was not an artefact of simple isolation-by-distance, as genetic distance was not correlated with the Euclidean distance between geographical centroids of the adjacent populations. Our results suggest that gap size affects movement behaviour even at remarkably local spatial scales, producing direct consequences on the genetic structure of fragmented populations. This finding shows that conserving genetic continuity for specialist species within fragmented habitat requires maintenance or restoration of preserve networks in which habitat gaps do not exceed a species-specific threshold distance.

scholarly journals High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas

2020 ◽  
Vol 10 (12) ◽  
pp. 4691-4705
Author(s):  
Xiaoshen Yin ◽  
Alberto Arias-Pérez ◽  
Tevfik Hamdi Kitapci ◽  
Dennis Hedgecock
Keyword(s):  
Genome Assembly ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Genotyping By Sequencing ◽  
Biological Knowledge ◽  
Linkage Maps ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
The Pacific ◽  
Chromosome Level

Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed linkage maps, to create a compendium of nearly 69 thousand SNPs mapped with high confidence. We use this compendium to assess a recently available, chromosome-level assembly of the C. gigas genome, mapping SNPs in 275 of 301 contigs and comparing the ordering of these contigs, by linkage, to their assembly by Hi-C sequencing methods. We find that, while 26% of contigs contain chimeric blocks of SNPs, i.e., adjacent SNPs mapping to different linkage groups than the majority of SNPs in their contig, these apparent misassemblies amount to only 0.08% of the genome sequence. Furthermore, nearly 90% of 275 contigs mapped by linkage and sequencing are assembled identically; inconsistencies between the two assemblies for the remaining 10% of contigs appear to result from insufficient linkage information. Thus, our compilation of linkage maps strongly supports this chromosome-level assembly of the oyster genome. Finally, we use this assembly to estimate, for the first time in a Lophotrochozoan, genome-wide recombination rates and causes of variation in this fundamental process.

scholarly journals Panmixia in a sea ice-associated marine mammal: evaluating genetic structure of the Pacific walrus (Odobenus rosmarus divergens) at multiple spatial scales

2020 ◽  
Vol 101 (3) ◽  
pp. 755-765 ◽  
Author(s):  
William S Beatty ◽  
Patrick R Lemons ◽  
Suresh A Sethi ◽  
Jason P Everett ◽  
Cara J Lewis ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Sea Ice ◽  
Spatial Scales ◽  
Pacific Walrus ◽  
Ice Dynamics ◽  
Odobenus Rosmarus Divergens ◽  
Odobenus Rosmarus ◽  
The Pacific ◽  
Kin Structure ◽  
Broad Scale

Abstract The kin structure of a species at relatively fine spatial scales impacts broad-scale patterns in genetic structure at the population level. However, kin structure rarely has been elucidated for migratory marine mammals. The Pacific walrus (Odobenus rosmarus divergens) exhibits migratory behavior linked to seasonal patterns in sea ice dynamics. Consequently, information on the spatial genetic structure of the subspecies, including kin structure, could aid wildlife managers in designing future studies to evaluate the impacts of sea ice loss on the subspecies. We sampled 8,303 individual walruses over a 5-year period and used 114 single-nucleotide polymorphisms to examine both broad-scale patterns in genetic structure and fine-scale patterns in relatedness. We did not detect any evidence of genetic structure at broad spatial scales, with low FST values (≤ 0.001) across all pairs of putative aggregations. To evaluate kin structure at fine spatial scales, we defined a walrus group as a cluster of resting individuals that were less than one walrus body length apart. We found weak evidence of kin structure at fine spatial scales, with 3.72% of groups exhibiting mean relatedness values greater than expected by chance, and a significantly higher overall observed mean value of relatedness within groups than expected by chance. Thus, the high spatiotemporal variation in the distribution of resources in the Pacific Arctic environment likely has favored a gregarious social system in Pacific walruses, with unrelated animals forming temporary associations.

scholarly journals Genetic Structure of Zymoseptoria tritici in Northern France at Region, Field, Plant, and Leaf Layer Scales

2018 ◽  
Vol 108 (9) ◽  
pp. 1114-1123 ◽  
Author(s):  
Ali Siah ◽  
Myriam Bomble ◽  
Benoit Tisserant ◽  
Thierry Cadalen ◽  
Maxime Holvoet ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Control Strategies ◽  
Spatial Scales ◽  
Regional Scale ◽  
Effective Control ◽  
Zymoseptoria Tritici ◽  
Northern France ◽  
Field Plant

Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant, and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values of ≥0.44 and haplotype frequencies of ≥94%) were found at all the examined scales. Such rates of diversity are likely due to an active sexual recombination in the investigated areas, as revealed by equal proportions of the two mating types scored in all sampled populations. Interestingly, a rare occurrence of clones among lesions from a same leaf, as well as among leaves from different plant leaf layers (e.g., upper versus lower leaves), was highlighted, indicating that ascospores contribute much more than expected to Z. tritici epidemics, compared with pycnidiospores. Population structure and analyses of molecular variance revealed significant genetic differentiation at the regional scale (GST = 0.23) and, as expected, not at the other more local scales (GST ≤ 0.01). Further analyses using Bayesian and unweighted neighbor-joining statistical methods detected six genetic clusters within the regional population, overall distributed according to the locations from which the isolates were sampled. Neither clear directional relative migration linked to the geographical distribution of the locations, nor isolation by distance, were observed. Separate evolutionary trajectories caused by selection and adaptations to habitat heterogeneity could be the main forces shaping such structuration. This study provides new insights into the epidemiology and the genetic structure of Z. tritici at small local and, for the first time, at single plant and leaf layer scales. Such findings would be helpful in implementing effective control strategies.

scholarly journals Evidence of Elevational Speciation in Kerteszia cruzii (Diptera: Culicidae) in the Ribeira Valley, São Paulo, Brazil

2021 ◽  
Vol 9 ◽  
Author(s):  
Bruna Demari-Silva ◽  
Gabriel Zorello Laporta ◽  
Tatiane Marques Porangaba de Oliveira ◽  
Maria Anice Mureb Sallum
Keyword(s):  
Genetic Structure ◽  
Forest Cover ◽  
Isolation By Distance ◽  
Published Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
South Eastern ◽  
Eastern Brazil ◽  
Robust Evidence ◽  
Brazilian Atlantic Rainforest

Kerteszia cruzii [former Anopheles (Kerteszia) cruzii] is a bromeliad mosquito widespread in the Brazilian Atlantic rainforest. In South-eastern Brazil, it plays an important role in malaria transmission because it was infected with at least four Plasmodium species. There is robust evidence that Ke. cruzii is a species complex. We used single nucleotide polymorphisms (SNPs) from a nextRAD sequence (nextera-tagmented, reductively amplified DNA) to investigate the genetic structure of Ke. cruzii in the Ribeira Valley, South-eastern Brazil. Furthermore, we verified whether the genetic structure was associated with forest cover, elevation, slope, and vegetation physiognomy. Our results showed two distinct lineages in the studied region associated with elevation and isolation by distance. The first lineage included samples from coastal localities and the second comprised specimens from inland or mountain sites. At one sampling locality (Esteiro do Morro in Cananéia municipality), both lineages are sympatric. These results are in accordance with previously published data that showed elevated stratification in Ke. cruzii. However, Fst values did not indicate the existence of cryptic or sister species in Ke. cruzii in this region, we concluded that elevational speciation probably occurs, and we hypothesized that differences in population structure found might be associated with the distribution of bromeliad species.

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