A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

AbstractGenomic architecture, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics are in freshwater fish, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n=345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed for alternate genotypes in each Canadian lake. These patterns exist despite several opportunities for gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptative divergence between the two lakes despite gene flow. Our study illuminates the importance of genomic architecture for facilitating local adaptation in freshwater fish and provides additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

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Gene flow influences the genomic architecture of local adaptation in six riverine fish species

Molecular Ecology ◽

10.1111/mec.16317 ◽

2021 ◽

Author(s):

Yue Shi ◽

Kristen L. Bouska ◽

Garrett J. McKinney ◽

William Dokai ◽

Andrew Bartels ◽

...

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Fish Species ◽

Genomic Architecture ◽

Riverine Fish

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Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim revealed by reduced representation sequencing

10.21203/rs.3.rs-19749/v1 ◽

2020 ◽

Author(s):

Cheng Jin ◽

Huixia Kao ◽

Shubin Dong

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Industrial Development ◽

High Quality ◽

Reduced Representation ◽

Rare And Endangered ◽

Reduced Representation Sequencing

Abstract BackgroundStudying population genetic structure and gene flow of plant populations and their influence factors is crucial in field of conservation biology, especially rare and endangered plants. Tetraena mongolica Maxim (TM), belong to Zygophyllaceae family, a rare and endangered plant with narrow distribution. Due to excessive logging, urban expansion, industrial development and development of the scenic spot in the last decades, has caused habitat fragments and decline.ResultsIn this study, the genetic diversity, the population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found existing TM populations have moderate levels of genetic diversity, very low genetic differentiation and high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups, Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. The migration model indicated that the gene flow is more of an north to south migration pattern in history.ConclusionsOur study demonstrate that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. For recommendations of conservation management, all 8 populations should be protected as a whole population, rather than just those in the core area of TM nature reserve, especially the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

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Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing

BMC Plant Biology ◽

10.1186/s12870-020-02594-y ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Jin Cheng ◽

Huixia Kao ◽

Shubin Dong

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Reduced Representation ◽

Rare And Endangered ◽

Reduced Representation Sequencing

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Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim revealed by reduced representation sequencing

10.21203/rs.3.rs-19749/v2 ◽

2020 ◽

Author(s):

Cheng Jin ◽

Huixia Kao ◽

Shubin Dong

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Endangered Plants ◽

High Quality ◽

Reduced Representation ◽

Rare And Endangered ◽

Reduced Representation Sequencing

Abstract Background: Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. Results: In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity , and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of an north to south migration pattern in history. Conclusions: This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve, In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

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Local adaptation and the evolution of inversions on sex chromosomes and autosomes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0423 ◽

2018 ◽

Vol 373 (1757) ◽

pp. 20170423 ◽

Cited By ~ 12

Author(s):

Tim Connallon ◽

Colin Olito ◽

Ludovic Dutoit ◽

Homa Papoli ◽

Filip Ruzicka ◽

...

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Evolutionary Dynamics ◽

Deleterious Mutation ◽

Local Selection ◽

Theoretical Predictions ◽

Elevated Rate ◽

Genomic Regions ◽

Spatially Varying ◽

Spatially Varying Selection

Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.

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