Population Genomics Provides Insights into the Population Structure and Climate-driven Adaptation of 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.

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

BMC Genomics ◽

10.1186/s12864-021-08045-8 ◽

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.

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

Journal of Economic Entomology ◽

10.1093/jee/toz145 ◽

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.

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Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

The ISME Journal ◽

10.1038/s41396-021-01023-8 ◽

2021 ◽

Author(s):

Zhilin Yuan ◽

Irina S. Druzhinina ◽

John G. Gibbons ◽

Zhenhui Zhong ◽

Yves Van de Peer ◽

...

Keyword(s):

Membrane Trafficking ◽

Molecular Mechanisms ◽

Genomic Island ◽

Population Genomics ◽

Growth Yield ◽

Fixation Index ◽

Nucleotide Polymorphisms ◽

Evolutionary Mechanisms ◽

Melanin Biosynthesis ◽

Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

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

F1000Research ◽

10.12688/f1000research.3567.1 ◽

2014 ◽

Vol 3 ◽

pp. 66 ◽

Cited By ~ 3

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.

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

10.21203/rs.3.rs-640424/v1 ◽

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.

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

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2016-0012 ◽

2017 ◽

Vol 74 (3) ◽

pp. 377-387 ◽

Cited By ~ 13

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.

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Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges

10.1101/730911 ◽

2019 ◽

Cited By ~ 1

Author(s):

Armel S.L. Donkpegan ◽

Rosalía Piñeiro ◽

Myriam Heuertz ◽

Jérôme Duminil ◽

Kasso Daïnou ◽

...

Keyword(s):

Genetic Structure ◽

Population Genomics ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Resolving Power ◽

Timber Species ◽

Nucleotide Polymorphisms ◽

Snp Data ◽

Distribution Ranges ◽

Genetic Diversity And Structure

ABSTRACTFew studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region). Afzelia (Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana and 12 A. quanzensis individuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005 and −0.007 and bLd (SNP)= −0.008 and −0.006 for A. africana and A. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

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

10.22541/au.162597680.07818696/v1 ◽

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.

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Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽

10.3390/genes12020258 ◽

2021 ◽

Vol 12 (2) ◽

pp. 258

Author(s):

Karim Karimi ◽

Duy Ngoc Do ◽

Mehdi Sargolzaei ◽

Younes Miar

Keyword(s):

Population Genomics ◽

Association Studies ◽

American Mink ◽

Population History ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Effective Population ◽

Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

Scientific Reports ◽

10.1038/s41598-021-93000-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wei Wang ◽

Chunyan Ma ◽

Longling Ouyang ◽

Wei Chen ◽

Ming Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Structure Analysis ◽

Principal Component ◽

Genetic Constitution ◽

Southern Group ◽

Population Structure Analysis ◽

Lateolabrax Maculatus ◽

Geographic Populations ◽

Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

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