A bird’s white-eye view on avian sex chromosome evolution

Leroy, Thibault; Anselmetti, Yoann; Tilak, Marie‐Ka; Bérard, Sèverine; Csukonyi, Laura; Gabrielli, Maëva; Scornavacca, Céline; Milá, Borja; Thébaud, Christophe

doi:10.1101/505610

Cited by 22 publications

(35 citation statements)

References 139 publications

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“…However, we did not find any evidence for strong bottlenecks or abrupt changes in population sizes, making faster accumulation of divergent alleles in recently established populations unlikely. Moreover, another recent study on Z. borbonicus has also shown that there is weak support for a fast‐Z effect in the clade to which this species belongs (Leroy et al, 2019). Another mechanism that might lead to stronger differentiation at Z‐linked loci is female‐biased dispersal, which is frequent in passerine birds (Greenwood, 1980).…”

Section: Discussionmentioning

confidence: 99%

“…Autosomes ( Recent studies revealed the existence of neo-sex chromosomes in Sylvioidea, to which Zosteropidae belong (Pala et al, 2012), and their existence was recently confirmed in the Reunion grey whiteeye (Leroy et al, 2019). These neo-sex chromosomes emerged from the fusion of Z and W chromosomes with the first 10 Mb of chromosome 4A.…”

Section: F-statistics % Of Variance Explainedmentioning

confidence: 99%

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Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage

et al. 2020

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Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome‐wide markers to investigate the diversification of the Reunion grey white‐eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping‐by‐sequencing and pooled RAD‐seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z‐linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

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Section: Discussionmentioning

confidence: 99%

Section: F-statistics % Of Variance Explainedmentioning

confidence: 99%

Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage

et al. 2020

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“…Mb. For comparison, the silvereye assembly had a scaffold N50 length of 3.581 Mb and a contig N50 length of 41.7 kb (Cornetti et al 2015), and the Mascarene grey white-eye had a scaffold N50 length of 1.763 Mb and a contig N50 length of 20.9 kb (Leroy et al 2019).…”

Section: Resultsmentioning

confidence: 99%

“…The phenotypic diversity in Zosterops is mostly conserved to a small body size and yellow-greenish colour patterns, even though aberrant phenotypes exist for some (mostly island endemic) taxa. With a lack of reference genomes available for this species and family as a whole, recent studies, such as on the silvereye (Zosterops lateralis, Cornetti et al 2015) or the Mascarene grey white-eye (Z. borbonicus, Leroy et al 2019) have demonstrated the relevance of generating genomic resources for this group of birds.…”

Section: Introductionmentioning

confidence: 99%

Genome Report:De novogenome assembly and annotation for the Taita white-eye (Zosterops silvanus)

Engler

Lawrie

Gansemans

et al. 2020

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The Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest.With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a 'great speciator'. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

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“…The pipeline developed by [111] was used to compute Tajima's π estimator of nucleotide diversity and the GC content over non-overlapping 10-kb windows. Then we concatenated the gene into different classes according to their length and compute πN and πS over 4 mb windows, which allows circumventing the problem associated to low πs values.…”

Section: Measuring Gc Content Non-synonynous and Synonymous Diversitymentioning

confidence: 99%

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Rougemont

Moore

Leroy

et al. 2019

Preprint

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Understanding the impacts of current human activities on within-species genetic variation requires a thorough description of the historical factors that have shaped the genomic and geographical distribution of nucleotide diversity. Past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential under the nearly neutral theory. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncoryhnchus kisutch) to address three issues. First, we demonstrate that a single glacial refugium is the source of the majority of present-day genetic diversity, with minor but detectable inputs from secondary micro-refugia. We propose a scenario whereby several ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Following this expansion, we identify particular populations having undergone continuous declines in population size (Ne). Second, we combine multiple evidence from demographic modelling, analysis of recombination landscape, and genome-wide landscape of diversity to demonstrate that selection at linked sites and Hill-Robertson interference played a major role in shaping genetic diversity across the Coho salmon genome. Third, we demonstrate that this demographic history generated subtle differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations. Taken together, we found considerable support for the joint contributions of demographic history and linked selection in the load of deleterious mutations. We suggest that these inferences should be better integrated in conservation genetics of managed fish species which currently focuses largely on within-population adaptation. Author SummaryReconstruction of a species' past demographic history from genome-wide data allows understanding how historical factors interact with intrinsic genomic properties to shape the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing and whole genome sequence data with demographic modelling to address these issues in the Coho salmon, a Pacific salmon species with rapidly declining census size in some parts of its range, notably in the south. Our demographic reconstructions indicate a linear decrease in genetic diversity towards the north of the species range, supporting the hypothesis of a major southern refugia for the Coho salmon and a northern route of postglacial recolonization. Accordingly, the number of candidate deleterious homozygous derived mutations was higher in northern populations. Demographic modelling also suggested the existence of cryptic refugia that may have been missed with the use of simpler summary statistics. We further showed that the species' genome was shaped by linked selection and biased gene conv...

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A bird’s white-eye view on avian sex chromosome evolution

Cited by 22 publications

References 139 publications

Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage

Differential divergence in autosomes and sex chromosomes is associated with intra‐island diversification at a very small spatial scale in a songbird lineage

Genome Report:De novogenome assembly and annotation for the Taita white-eye (Zosterops silvanus)

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

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