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)

Escalante, Marco A.; Perrier, Charles; León, Francisco J. Garcı́a de; Ruiz‐Luna, Arturo; Ortega-Abboud, Enrique; Manel, Stéphanie

doi:10.1007/s10592-020-01297-z

Cited by 10 publications

(5 citation statements)

References 115 publications

(126 reference statements)

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“…Effective population size (Ne), usually less than the census population size, influences genetic diversity in a population. Our results showed lower levels of Ne ranging from 0.8 to 1.2, and similar observations were reported by Escalante et al (2020) and Diaz et al (2021) . Inbreeding and genetic drift are expected to reduce genetic diversity as Ne decreases ( Frankham, 2005 ).…”

Section: Discussionsupporting

confidence: 93%

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Sahoo,

Das,

Nandanpawar

et al. 2023

Front. Genet.

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Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

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Section: Discussionsupporting

confidence: 93%

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Sahoo,

Das,

Nandanpawar

et al. 2023

Front. Genet.

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“…These inconsistencies may be associated with the lower number of loci analyzed in microsatellites studies when compared to SNP datasets, hence SNPs reflect genome-wide genetic diversity of populations more accurately than microsatellites 6 . The overall low genetic diversity values found for M. margaritifera are commonly found in other endangered freshwater organisms, such as Australian freshwater crocodiles and Mexican golden trout 44 , 45 and have also been estimated for North American M. margaritifera 24 and M. hembeli 26 , suggesting a strong relation between the loss of genetic diversity and the poor conservation status of these species. The low genetic diversity values found in the Iberian populations have been explained by strong genetic drift effects due to population bottlenecks 20 , 21 .…”

Section: Discussionmentioning

confidence: 93%

Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model

Perea‍

Mendes

Sousa-Santos³

et al. 2022

Sci Rep

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Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide.

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“…One reason for this may be that the complex geographical environment and evolutionary history of the QTP have a longlasting impact on species survival and promote species adaptation to local conditions (Mao et al, 2021;Shen et al, 2021). Studies have indicated that local adaptations may affect the genetic diversity of populations (Escalante et al, 2020;Zhao et al, 2020). For commercially exploited salt lakes (ABL, YC, and QXC) that have low genetic diversity, exploiters must consider rational exploitation.…”

Section: Discussionmentioning

confidence: 99%

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

Li,

Zhang,

Sui

et al. 2024

Front. Mar. Sci.

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This study investigated the population genetics and distribution patterns of Artemia populations from ten inland salt lakes in China. A total of 1,274,698 Artemia single nucleotide polymorphisms (SNPs) were identified. The results showed that these populations could be geographically and genetically divided into four distinct groups, and that the Tibetan populations were further divided into two subpopulations with a trend of decreasing genetic diversity from west to east. The Tibetan population had the highest genetic diversity, whereas the Shanxi population had the lowest. There was moderate genetic differentiation between the Tibetan populations and greater genetic differentiation between the Xinjiang and Shanxi populations. IBD (isolation by distance) suggested that geographical isolation contributes to genetic differentiation. In addition, there was some degree of gene flow among the ten populations, with A. sinica showing unidirectional gene flow in all populations in the eastern Nagri region. Species distribution modeling showed that mean annual temperature, temperature seasonality, and annual precipitation were the main environmental factors affecting the distribution of Artemia populations and suitable habitats for Tibetan populations will be further reduced in the future. It is necessary to strengthen the protection of germplasm resources and formulate scientific protocols for the sustainable development and utilization of Artemia resources.

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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)

Abstract: 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).

Cited by 10 publications

References 115 publications

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

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