The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi

Hahn, Christoph; Genner, Martin J.; Turner, George F.; Joyce, Domino A.

doi:10.1002/evl3.20

Cited by 28 publications

(28 citation statements)

References 110 publications

(237 reference statements)

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“…Recently, Baalsrud et al 2017 showed that hemoglobin genes have undergone diversifying selection within codfishes (order Gadiformes) and this was influenced by ocean depth. In addition, HBA and HBB genes have shown as candidate genes under selection due to deep water adaptations within cichlid fishes from Lake Malawi (Hahn et al 2017). Coupled with our results it is apparent that water depth can drive selection of hemoglobin genes within different groups of fishes.…”

Section: Hemoglobin Subunit α As a Candidate Gene For Depth Adaptationsupporting

confidence: 82%

Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

Heras

Aguilar

2019

Journal of Heredity

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The genetic underpinnings that contribute to ecological adaptation and speciation are not completely understood, especially within marine ecosystems. These evolutionary processes can be elucidated by studying adaptive radiations, because they provide replicates of divergence within a given environment or time-frame. Marine rockfishes (genus Sebastes) are an adaptive radiation and unique model system for studying adaptive evolution in the marine realm. We investigated molecular evolution associated with ecological (depth) and life history (lifespan) divergence in 2 closely related clades of Sebastes. Brain transcriptomes were sequenced via RNA-Seq from 3 species within the subgenus Pteropodus and a pair of related congeners from the subgenus Sebastosomus in order to identify patterns of adaptive evolution. De novo assemblies from these transcriptomes were used to identify 3867 orthologous clusters, and genes subject to positive selection were identified based on all 5 species, depth, and lifespan. Within all our analyses, we identified hemoglobin subunit α to be under strong positive selection and is associated with the depth of occurrence. In our lifespan analysis we identified immune function genes under positive selection in association with maximum lifespan. This study provides insight on the molecular evolution of rockfishes and these candidate genes may provide a better understanding of how these subgenera radiated within the Northeast Pacific.

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Section: Hemoglobin Subunit α As a Candidate Gene For Depth Adaptationsupporting

confidence: 82%

Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

Heras

Aguilar

2019

Journal of Heredity

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“…Haemoglobin genes in teleost fish are found in two separate chromosomal locations: the minor ‘LA’ cluster and the major ‘MN’ cluster72. The region around the LA cluster has been highlighted by selection scans among four Diplotaxodon species by Hahn et al73, who also noted the similarity of the haemoglobin subunit beta (HBβ) haplotypes between Diplotaxodon and deep benthic species. We confirmed signatures of selection in the two annotated LA cluster haemoglobins.…”

Section: Resultsmentioning

confidence: 99%

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

et al. 2018

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The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.

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“…To do so, the full set of SNPs were used for the construction of 10 covariance matrices using different priors (following Hahn et al .) 107 . The association with genetic variation was tested for three environmental variables known for the lakes under study (environmental predictability, hydroperiod length and salinity) 26 , and two phenotypic variables previously estimated for the genotyped populations (life-history traits: propensity for sex and hatching fraction, Table 5 ) 28 .…”

Section: Methodsmentioning

confidence: 99%

Genomic signatures of local adaptation to the degree of environmental predictability in rotifers

Franch‐Gras

Hahn

García‐Roger

et al. 2018

Sci Rep

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Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.

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The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi

Cited by 28 publications

References 110 publications

Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Genomic signatures of local adaptation to the degree of environmental predictability in rotifers

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