Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Wang, Le; Wan, Zi Yi; Lim, Huan Sein; Yue, Gen Hua

doi:10.1111/mec.13714

Cited by 40 publications

(47 citation statements)

References 112 publications

(122 reference statements)

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“…Recent studies exploring the distribution of genomic islands have also advanced the idea that islands arise from neutral processes without a major contribution from divergent selection (Campagna et al . 2015; Wang et al . 2016) and the results of our model identify the scenarios where this is particularly likely to be the case.…”

Section: Discussionmentioning

confidence: 99%

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The multiple population genetic and demographic routes to islands of genomic divergence

Quilodrán

Ruegg

Sendell‐Price

et al. 2019

Preprint

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1 1 1. The way that organisms diverge into reproductively isolated species is a major question in 1 2 biology. The recent accumulation of genomic data provides promising opportunities to 1 3 understand the genomic landscape of divergence, which describes the distribution of 1 4 differences across genomes. Genomic areas of unusually high differentiation have been called 1 5 genomic islands of divergence. Their formation has been attributed to a variety of 1 6 mechanisms, but a prominent hypothesis is that they result from divergent selection over a 1 7 small portion of the genome, with surrounding areas homogenised by gene flow. Such islands 1 8 have often been interpreted as being associated with divergence with gene flow. However 1 9other mechanisms related to genetic architecture and population history can also contribute to 2 0 the formation of genomic islands of divergence. 2 1 2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes 2 2 under the complex and nuanced conditions that are found in natural systems. Here, we 2 3 develop an individual-based simulation to explore the dynamics of diverging genomes under 2 4 various scenarios of gene flow, selection and genotype-phenotype maps. 2 5 3. Our modelling results are consistent with empirical observations demonstrating the formation 2 6of genomic islands under genetic isolation. Importantly, we have quantified the range of 2 7 conditions that produce genomic islands. We demonstrate that the initial level of genetic 2 8 diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene 2 9 flow are all important factors that can influence the formation of genomic islands. Because the 3 0 accumulation of genomic differentiation over time tends to erode the signal of genomic 3 1 islands, genomic islands are more likely to be observed in recently divergent taxa, although 3 2 not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene 3 3 flow primarily slows the swamping of islands of divergence with time. 3 44. By using this framework, further studies may explore the relative influence of particular suites 3 5 of events that contribute to the emergence of genomic islands under sympatric, parapatric and 3 6 allopatric conditions. This approach represents a novel tool to explore quantitative 3 7 expectations of the speciation process, and should prove useful in elucidating past and 3 8 projecting future genomic evolution of any taxa. 3 9 4 0

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Section: Discussionmentioning

confidence: 99%

“…Some studies document a small number of very prominent islands (e.g. Turner, Hahn & Nuzhdin 2005; Wang et al . 2016), however finding multiple islands of low relief is also common (e.g.…”

Section: Discussionmentioning

confidence: 99%

The multiple population genetic and demographic routes to islands of genomic divergence

Quilodrán

Ruegg

Sendell‐Price

et al. 2019

Preprint

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“…As revealed in our previous studies using GBS, construction of genetic maps was achievable [32, 35]. Here, we adapted not only much stricter filtering criteria for SNP genotyping, but also more data control processes so as to generate high confidence genetic maps.…”

Section: Discussionmentioning

confidence: 99%

Construction of high-resolution recombination maps in Asian seabass

et al. 2017

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BackgroundA high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing.ResultsA high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males.ConclusionsThese high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.

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“…Interestingly, if extinction does not occur, drift in small isolated groups can produce, or contribute to, genetic and phenotypic divergence, possibly leading to speciation (12,13).…”

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Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

Benazzo

Trucchi

Cahill

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

159

132

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Survival and divergence in a small group: the extraordinary genomic history of the endangered Apennine brown bear stragglers 2 AbstractAbout 100 km east of Rome, in the Central Apennine mountains, a critically endangered population of approximately fifty brown bears live in complete isolation. Mating outside this population is prevented by several hundred kilometers of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. First, we found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In Central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show non-random peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles a) can be an important driver of divergence in isolation, b) can be tolerated when balancing selection prevents random loss of variation at important genes and c) is followed by or results directly in favorable behavioral changes. SignificanceA small and relict population of brown bears lives in complete isolation in the Italian Apennine mountains, providing a unique opportunity to study the impact of drift and selection on the genomes of a large endangered mammal and to reconstruct the phenotypic consequences and the conservation implications of such evolutionary processes. The Apennine bear is highly inbred and harbors very low genomic variation. Several deleterious mutations have been accumulated by drift. We found evidence that this is a consequence of habitat fragmentation in the Neolithic, when human expansion and land clearance shrank its habitat, and that retention of variation at immune system and olfactory receptor genes, as well as changes in diet and behavior, prevented the extinction of the Apennine bear.

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Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Cited by 40 publications

References 112 publications

The multiple population genetic and demographic routes to islands of genomic divergence

The multiple population genetic and demographic routes to islands of genomic divergence

Construction of high-resolution recombination maps in Asian seabass

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

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