Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

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Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation inNothofagus dombeyi(Mirb.) Oerst. in Chile

International Journal of Genomics ◽

10.1155/2016/3654093 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Rodrigo Hasbún ◽

Jorge González ◽

Carolina Iturra ◽

Glenda Fuentes ◽

Diego Alarcón ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Woody Species ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Evolutionary Forces ◽

Genome Wide ◽

Diversity Studies ◽

Nothofagus Dombeyi

Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation.Nothofagus dombeyi(Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories inNothofagus dombeyirequires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species.

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Differences in mate pairings of hatchery and natural origin coho salmon inferred from offspring genotypes

Integrative Organismal Biology ◽

10.1093/iob/obab020 ◽

2021 ◽

Author(s):

H L Auld ◽

D P Jacobson ◽

A C Rhodes ◽

M A Banks

Keyword(s):

Mate Choice ◽

Captive Breeding ◽

Population Genomics ◽

Coho Salmon ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Natural Origin ◽

In Captivity ◽

Genetic Level

Abstract Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery and natural origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared to natural origin fish at a genetic level. Using genotyping-by-sequencing (GBS), we identify single nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery and natural origin coho salmon (Oncorhynchus kisutch). In both natural origin and hatchery mate pairs, we observed more SNPs with negative assortment, than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.

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Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2104315118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2104315118

Author(s):

Pasquale Tripodi ◽

Mark Timothy Rabanus-Wallace ◽

Lorenzo Barchi ◽

Sandip Kale ◽

Salvatore Esposito ◽

...

Keyword(s):

Genetic Diversity ◽

Genotyping By Sequencing ◽

Focal Region ◽

Nucleotide Polymorphisms ◽

Trade Routes ◽

Genebank Management ◽

Capsicum Spp ◽

History Of ◽

Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

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Intraspecific genomic variation and local adaptation in a young hybrid species

10.1101/732313 ◽

2019 ◽

Author(s):

Angélica Cuevas ◽

Mark Ravinet ◽

Glenn-Peter Sætre ◽

Fabrice Eroukhmanoff

Keyword(s):

Genetic Variation ◽

Local Adaptation ◽

Climatic Variation ◽

Genomic Variation ◽

Population Divergence ◽

Parent Species ◽

Evolutionary Potential ◽

Variable Environment ◽

Hybrid Species ◽

Species Population

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

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Population Genomics of Bettongia lesueur: Admixing Increases Genetic Diversity with no Evidence of Outbreeding Depression

Genes ◽

10.3390/genes10110851 ◽

2019 ◽

Vol 10 (11) ◽

pp. 851 ◽

Cited By ~ 3

Author(s):

Kate Rick ◽

Kym Ottewell ◽

Cheryl Lohr ◽

Rujiporn Thavornkanlapachai ◽

Margaret Byrne ◽

...

Keyword(s):

Genetic Diversity ◽

Threatened Species ◽

Population Genomics ◽

Fold Increase ◽

Recruitment Rate ◽

Outbreeding Depression ◽

Nucleotide Polymorphisms ◽

Isolated Populations ◽

Genomic Markers ◽

Founder Populations

Small and isolated populations are subject to the loss of genetic variation as a consequence of inbreeding and genetic drift, which in turn, can affect the fitness and long-term viability of populations. Translocations can be used as an effective conservation tool to combat this loss of genetic diversity through establishing new populations of threatened species, and to increase total population size. Releasing animals from multiple genetically diverged sources is one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using high-resolution genomic markers through double-digest restriction site-associated sequencing (ddRAD-seq) and life history data collected over nine years of monitoring, this study investigates the genetic and fitness consequences of admixing two genetically-distinct subspecies of Bettongia lesueur in a conservation translocation. Using single nucleotide polymorphisms (SNPs) identified from 215 individuals from multiple generations, we found an almost 2-fold increase in genetic diversity in the admixed translocation population compared to the founder populations, and this was maintained over time. Furthermore, hybrid class did not significantly impact on survivorship or the recruitment rate and therefore we found no indication of outbreeding depression. This study demonstrates the beneficial application of mixing multiple source populations in the conservation of threatened species for minimizing inbreeding and enhancing adaptive potential and overall fitness.

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Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽

10.7717/peerj.2504 ◽

2016 ◽

Vol 4 ◽

pp. e2504 ◽

Cited By ~ 1

Author(s):

Katarzyna Bilska ◽

Monika Szczecińska

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Conservation Genetics ◽

Ssr Markers ◽

Full Range ◽

Mantel Test ◽

Evolutionary Potential ◽

Functional Variation ◽

Genetics Research ◽

Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽

10.3390/f11111185 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1185

Author(s):

Helena Eklöf ◽

Carolina Bernhardsson ◽

Pär K. Ingvarsson

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Picea Abies ◽

Norway Spruce ◽

Large Scale ◽

Genotyping By Sequencing ◽

Complexity Reduction ◽

Exome Capture ◽

Genome Wide ◽

Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

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Population genomics of Mycobacterium tuberculosis in the Inuit

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1507071112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13609-13614 ◽

Cited By ~ 49

Author(s):

Robyn S. Lee ◽

Nicolas Radomski ◽

Jean-Francois Proulx ◽

Ines Levade ◽

B. Jesse Shapiro ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Population Genomics ◽

Purifying Selection ◽

Synonymous Substitution ◽

Nonsynonymous Snps ◽

Recent Common Ancestor ◽

Nucleotide Polymorphisms ◽

Most Recent Common Ancestor ◽

Bacterial Genetic

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.

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Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

10.1101/2020.05.29.124685 ◽

2020 ◽

Author(s):

Godfrey Kinyori Wagutu ◽

Xiangrong Fan ◽

Wenlong Fu ◽

Wei Li ◽

Yuanyuan Chen

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Local Adaptation ◽

Landscape Heterogeneity ◽

Maximum Temperature ◽

Zizania Latifolia ◽

Precipitation Seasonality ◽

Isolation By Environment

AbstractGlobal aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Øpt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

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Assessment of coffee (coffea arabica L.) genetic erosion and genetic resources management in Ethiopia

International Journal of Agricultural Extension ◽

10.33687/ijae.007.03.2972 ◽

2020 ◽

Vol 7 (3) ◽

pp. 223-229

Author(s):

Afework Legesse

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Coffea Arabica ◽

Genetic Erosion ◽

Evolutionary Potential ◽

Arabica Coffee ◽

Resources Management ◽

Genetic Resources Management ◽

Coffee Yield ◽

Coffea Arabica L

Coffee is an important source of annual income and employment contributing significantly to the economies of many developing countries. Ethiopia is the center of origin and diversity of Coffea arabica L., there is immense genetic variability that offers great potential for improvement of the crop. The objective of this paper is to assess the status of Coffee genetic diversity, identify major factors that cause coffee genetic erosion and status of coffee genetics resources management in Ethiopia. The presences of high genetic diversity in wild Coffea arabica in Ethiopia were reported by different authors. However, the genetic diversity of coffea arabica L. are being lost rapidly due to several factors such as human population pressures leading to conversion of land to agriculture, deforestation and land degradation; low coffee prices leading to abandoning of coffee trees in forests and gardens and shifting cultivation to other more remunerative crops; and climate change. Additionally, narrow genetic basis of commercially used Arabica coffee cultivars and increased incidence of pests and diseases associated with climate change is leading to significant crop losses, threatening livelihoods in many coffee growing countries. Therefore, Conserving the wild Arabica coffee gene pool and its evolutionary potential present in Ethiopia is critically important for maintaining coffee yield, disease resistance, drought tolerant, quality and other important traits in future breeding program

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