Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago

Cui, Rongfeng; Tyers, Alexandra M.; Malubhoy, Z. J.; Wisotsky, Sadie; Valdesalici, Stefano; Henriette, Elvina; Pond, Sergei L. Kosakovsky; Valenzano, Dario Riccardo

doi:10.1111/mec.15982

Cited by 12 publications

(12 citation statements)

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“…We resequenced the whole genomes of 70 M. polymorpha plants from 55 sites on the island of Hawaii with a 29.6-fold mean sequencing coverage (Fig 1A). The 55 sites covered the environmental range of the habitats on the island, spanning 15-2,373 m in altitude, 9˚C -23˚C in mean annual air temperature, 486-6,379 mm in annual precipitation, and from <100 to over 250,000 years old in substrate age.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, it is possible that a reduction in N e found around 5 Mya was associated with the introduction into the Hawaiian Archipelago through long-distance dispersal. Considering that long-distance dispersal does not always result in a temporal reduction in N e [54,55], the ecological windows open to the ancestral populations of the species was likely to be small. The immigration could rely on a rare dispersal vector, such as jet stream [56,57], and/or only a fraction of immigrants survived on new environments [58].…”

Section: Divergence and Admixture Historymentioning

confidence: 99%

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Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

et al. 2022

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Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments. The continuous M. polymorpha forest stands on the island of Hawaii were differentiated into three genetic clusters, each of which grows in a distinctive environment and includes substantial genetic and phenotypic diversity. The three genetic clusters showed signatures of selection in genomic regions encompassing genes relevant to environmental adaptations, including genes associated with light utilization, oxidative stress, and leaf senescence, which are likely associated with the ecological differentiation of the species. Our demographic modeling suggested that the glaberrima cluster in wet environments maintained a relatively large population size and two clusters split: polymorpha in the subalpine zone and incana in dry and hot conditions. This ecological divergence possibly began before the species colonized the island of Hawaii. Interestingly, the three clusters recovered genetic connectivity coincidentally with a recent population bottleneck, in line with the weak reproductive isolation observed in the species. This study highlights that the degree of genetic differentiation between ecologically-diverged populations can vary depending on the strength of natural selection in the very early phases of speciation.

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Section: Resultsmentioning

confidence: 99%

Section: Divergence and Admixture Historymentioning

confidence: 99%

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

et al. 2022

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“…GVCFs (Method 1.7 in Data S1) were first converted to msmc format using the vcfAllSiteParser.py script followed by generate_multihetsep.py. We ran two joined MSMC analyses with 10 males or females, setting the initial rho/mu to 1 (Cui et al., 2021). Thirty bootstrap replicates were generated by randomly cutting the input data into 5 Mb blocks and rearranging their order.…”

Section: Methodsmentioning

confidence: 99%

“…We constructed a timed phylogeny and estimated the per-year mutation rate of B. taipingensis, other sciaenids and representative teleost fishes combining UPhO v.2021-07-12 (Ballesteros & Hormiga, 2016), IQTree 2.1.3 (Nguyen et al, 2015), MCMCTree 4.9j (dos Reis & Yang, 2011;Yang & Rannala, 2006) and RAxML 8.2.12 (Stamatakis, 2006) as previously described (Method 1.6 in Data S1; Cui et al, 2019Cui et al, , 2021.…”

Section: Timed Tree Reconstructionmentioning

confidence: 99%

Phased genome assemblies reveal haplotype‐specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae)

Cui,

Wu,

Yan

et al. 2024

Molecular Ecology

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While haplotype‐specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed‐haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame‐shifting variants as the most deleterious type, followed by mutations in the 5′‐UTR, 3′‐UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high‐impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter‐haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype‐resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.

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“…TreeMix was run with 0–10 migration edges in five iterations (at ‐k value 1000). The function optM was used to determine the optimum number of migration edges (using the approach of Cui et al, 2021; Fitak, 2021; Senczuk et al, 2021) from the output files from TreeMix, using both the linear modelling and SiZer (Sonderegger et al, 2009) methods. To further investigate admixture patterns among populations, we used the f 3 population test of treeness (Reich et al, 2009) in the program Threepop as implemented in the TreeMix package.…”

Section: Methodsmentioning

confidence: 99%

Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex

Rutherford,

Rossetto,

Bragg

et al. 2023

American J of Botany

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PremiseSpecies delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take account of complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar ‘species’ within the eucalypts.MethodsMultiple populations of each recognized scribbly gum species were sampled over a wide region across climates and genome‐wide scans used to resolve species boundaries.Key resultsWe found that none of the taxa were completely diverged, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time blurring species boundaries.ConclusionsOur results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that the use of high throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and support it as a standard practice for disentangling species complexes.This article is protected by copyright. All rights reserved.

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Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago

Cited by 12 publications

References 59 publications

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

Phased genome assemblies reveal haplotype‐specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae)

Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex

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