scholarly journals Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

2021 ◽  
Author(s):  
Jesse Conklin ◽  
Yvonne Verkuil ◽  
Philip Battley ◽  
Chris Hassell ◽  
James Johnson ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Annual Cycle ◽  
Secondary Contact ◽  
Migration Behavior ◽  
Nucleotide Polymorphisms ◽  
Long Distance ◽  
Calidris Canutus ◽  
Breeding Populations ◽  
Approximate Bayesian

Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide polymorphisms (SNPs) to assess the neutral genetic structure and phylogeographic history of 172 red knots representing all known global breeding populations. Using population genetics approaches, including model-based scenario-testing in an approximate Bayesian computation (ABC) framework, we infer that red knots derive from two main lineages that diverged ca. 34,000 years ago, and thus persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. In two flyways, we detected clear genetic structure between population pairs with similar migrations and substantial geographic overlap in the non-breeding season. Conversely, other populations were only weakly differentiated despite clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. In general, the magnitude of genetic differentiation did not match that of phenotypic differences among populations, suggesting that flyway-specific phenotypes developed quite rapidly and do not necessarily impose barriers to gene flow. Our results suggest that population structure and migratory phenotypes in red knots arose from a complex interplay among phylogeography, plasticity, and selective processes.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 66 ◽  
Author(s):  
Javier Monzón
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Canis Latrans ◽  
Regional Analysis ◽  
Model Organism ◽  
Nucleotide Polymorphisms ◽  
Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

scholarly journals The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

2021 ◽  
Author(s):  
Yuan Li ◽  
Fangrui Lou ◽  
Hai Li ◽  
Rui Wang ◽  
Zizi Cai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Expansion ◽  
Nucleotide Polymorphisms ◽  
Stress Reactions ◽  
Long Distance ◽  
Evolutionary Mechanisms ◽  
Inflammatory Reactions ◽  
Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

scholarly journals Population Genomics Provides Insights into the Population Structure and Climate-driven Adaptation of Collichthys Lucidus

2021 ◽  
Author(s):  
Linlin Zhao ◽  
Fangyuan Qu ◽  
Na Song ◽  
Zhiqiang Han ◽  
Tianxiang Gao ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genomics ◽  
Anthropogenic Activities ◽  
Thermal Adaptation ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Southern Group ◽  
Northern Group ◽  
Collichthys Lucidus

Abstract Background: Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the conservation and management of biological resources. Collichthys lucidus is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results: To elucidate the fine-scale genetic structure and local thermal adaptation of C. lucidus, we performed restriction site-associated DNA tag sequencing (RAD-seq) of 177 individuals from 8 populations, and a total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified. All the results revealed significant population structure with high support for two distinct genetic clusters, namely, the northern group (populations DL, TJ, LYG, NT, ZS, and WZ) and southern group (populations XM and ZH). The genetic diversity of the southern group was evidently lower than that of the northern group, which indicated that the southern group was possibly under climate-driven natural selection. In addition, a total of 314 SNPs were found to be significantly associated with temperature variation. Annotations of temperature-related SNPs suggested that genes involved in material (protein, lipid, and carbohydrate) metabolism and immune responses were critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. Conclusion: In the context of anthropogenic activities and environmental change, the results of the present population genomic work could make important contributions to the understanding of genetic differentiation and adaptation to changing environments.

scholarly journals Genetic structure and long-distance dispersal in populations of the wingless pest springtail, Sminthurus viridis (Collembola: Sminthuridae)

2011 ◽  
Vol 93 (1) ◽  
pp. 1-12 ◽  
Author(s):  
JOHN M. K. ROBERTS ◽  
ANDREW R. WEEKS
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cytochrome Oxidase ◽  
Isolation By Distance ◽  
Control Strategies ◽  
Single Species ◽  
Coi Gene ◽  
Effective Control ◽  
Long Distance Dispersal ◽  
Long Distance

SummaryThe lucerne flea, Sminthurus viridis (Collembola: Sminthuridae) (L.) is a major pest of broadacre agriculture across southern Australia. Few molecular studies have been conducted on S. viridis and none have examined its population genetics, despite the importance for developing effective control strategies. Here, we characterize the genetic structure of Australian populations using three allozyme and eight microsatellite loci, as well as sequencing a fragment of the mitochondrial DNA cytochrome oxidase I gene. We found that S. viridis in Australia are diploid, sexually reproducing and exhibit significant population structure as a result of limited gene flow. Despite significant differentiation between populations, there was very low cytochrome oxidase subunit I (COI) gene sequence variation, indicating the presence of a single species in Australia. The observed structure only marginally complied with an ‘isolation by distance’ model with human-mediated long-distance dispersal likely occurring. Allozymes and microsatellites gave very similar FST estimates, although differences found for novel alternative estimates of differentiation suggest that the allozymes did not capture the full extent of the population structure. These results highlight that control strategies may need to vary for locally adapted S. viridis populations and strategies aimed at limiting the spread of any future pesticide resistance will need to manage the effects of human-mediated dispersal.

scholarly journals Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Linlin Zhao ◽  
Fangyuan Qu ◽  
Na Song ◽  
Zhiqiang Han ◽  
Tianxiang Gao ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Immune Responses ◽  
Carbohydrate Metabolism ◽  
Population Genomics ◽  
Marine Ecosystem ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Population Structure Analysis ◽  
Collichthys Lucidus

Abstract Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses. Conclusion The high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising.

scholarly journals The annual cycle for whimbrel populations using the Western Atlantic Flyway

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260339
Author(s):  
Bryan D. Watts ◽  
Fletcher M. Smith ◽  
Chance Hines ◽  
Laura Duval ◽  
Diana J. Hamilton ◽  
...  
Keyword(s):  
Annual Cycle ◽  
Migratory Birds ◽  
Hudson Bay ◽  
Mackenzie Delta ◽  
Migration Routes ◽  
Long Distance ◽  
Western Atlantic ◽  
Annual Cycles ◽  
Breeding Populations ◽  
Two Populations

Many long-distance migratory birds use habitats that are scattered across continents and confront hazards throughout the annual cycle that may be population-limiting. Identifying where and when populations spend their time is fundamental to effective management. We tracked 34 adult whimbrels (Numenius phaeopus) from two breeding populations (Mackenzie Delta and Hudson Bay) with satellite transmitters to document the structure of their annual cycles. The two populations differed in their use of migratory pathways and their seasonal schedules. Mackenzie Delta whimbrels made long (22,800 km) loop migrations with different autumn and spring routes. Hudson Bay whimbrels made shorter (17,500 km) and more direct migrations along the same route during autumn and spring. The two populations overlap on the winter grounds and within one spring staging area. Mackenzie Delta whimbrels left the breeding ground, arrived on winter grounds, left winter grounds and arrived on spring staging areas earlier compared to whimbrels from Hudson Bay. For both populations, migration speed was significantly higher during spring compared to autumn migration. Faster migration was achieved by having fewer and shorter stopovers en route. We identified five migratory staging areas including four that were used during autumn and two that were used during spring. Whimbrels tracked for multiple years had high (98%) fidelity to staging areas. We documented dozens of locations where birds stopped for short periods along nearly all migration routes. The consistent use of very few staging areas suggests that these areas are integral to the annual cycle of both populations and have high conservation value.

scholarly journals Love the one you’re with: genomic evidence of panmixia in the sablefish (Anoplopoma fimbria)

2017 ◽  
Vol 74 (3) ◽  
pp. 377-387 ◽  
Author(s):  
Andrew J. Jasonowicz ◽  
Frederick W. Goetz ◽  
Giles W. Goetz ◽  
Krista M. Nichols
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
A Priori ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Population Mixing ◽  
Anoplopoma Fimbria ◽  
The One

Understanding the genetic structure of a fishery may help delineate stocks and is directly applicable to resource management. To date, studies have not found clear population genetic structure across the range of the sablefish (Anoplopoma fimbria), yet significant biological differences are recognized. Here we use restriction site-associated DNA sequencing to develop thousands of single nucleotide polymorphisms (SNPs) throughout the sablefish genome and assess population genetic structure and examine the genome for SNPs under natural selection. Our study was unable to target spawning groups, having the potential to bias analyses that require a priori hypotheses of population structure. Low and insignificant levels of differentiation (FST = 0.0002) were observed among survey areas, and analyses of population structure suggested a single population. Only two SNPs were significantly associated with environmental variables. These results are likely due to considerable population mixing and suggest a single panmictic group of sablefish off the west coast of the United States and Alaska that is likely a consequence of a complex juvenile life history and long range movements as adults.

scholarly journals Travelling on a budget: predictions and ecological evidence for bottlenecks in the annual cycle of long-distance migrants

2007 ◽  
Vol 363 (1490) ◽  
pp. 247-266 ◽  
Author(s):  
Deborah M Buehler ◽  
Theunis Piersma
Keyword(s):  
Annual Cycle ◽  
Migratory Birds ◽  
Driving Forces ◽  
Long Distance ◽  
Annual Cycles ◽  
Calidris Canutus ◽  
Trade Offs ◽  
Breeding Grounds ◽  
Breeding Plumage ◽  
Red Knot

Long-distance migration, and the study of the migrants who undertake these journeys, has fascinated generations of biologists. However, many aspects of the annual cycles of these migrants remain a mystery as do many of the driving forces behind the evolution and maintenance of the migrations themselves. In this article we discuss nutritional, energetic, temporal and disease - risk bottlenecks in the annual cycle of long-distance migrants, taking a sandpiper, the red knot Calidris canutus , as a focal species. Red knots have six recognized subspecies each with different migratory routes, well-known patterns of connectivity and contrasting annual cycles. The diversity of red knot annual cycles allows us to discuss the existence and the effects of bottlenecks in a comparative framework. We examine the evidence for bottlenecks focusing on the quality of breeding plumage and the timing of moult as indicators in the six subspecies. In terms of breeding plumage coloration, quality and timing of prealternate body moult (from non-breeding into breeding plumage), the longest migrating knot subspecies, Calidris canutus rogersi and Calidris canutus rufa , show the greatest impact of bottlenecking. The same is true in terms of prebasic body moult (from breeding into non-breeding plumage) which in case of both C. c. rogersi and C. c. rufa overlaps with southward migration and may even commence in the breeding grounds. To close our discussion of bottlenecks in long-distance migrants, we make predictions about how migrants might be impacted via physiological ‘trade-offs’ throughout the annual cycle, using investment in immune function as an example. We also predict how bottlenecks may affect the distribution of mortality throughout the annual cycle. We hope that this framework will be applicable to other species and types of migrants, thus expanding the comparative database for the future evaluation of seasonal selection pressures and the evolution of annual cycles in long-distance migrants. Furthermore, we hope that this synthesis of recent advancements in the knowledge of red knot annual cycles will prove useful in the ongoing attempts to model annual cycles in migratory birds.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

Sign in / Sign up

Export Citation Format

Share Document