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77 results for “chromosomal differentiation”
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
<p>When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (<em>Zonotrichia atricapilla</em>) and the white-crowned sparrow (<em>Zonotrichia leucophrys</em>) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of <em>Z. leucophrys</em>. The two <em>Z. leucophrys</em> subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species <em>Z. leucophrys</em> and <em>Z. atricapilla</em> show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between <em>Z. atricapilla</em> and <em>Z. leucophrys</em> appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.</p>
Data from: Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry
<p>Abstract: When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) <em>Fragaria chiloensis</em> plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a <em>Harbinger</em> transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.</p> <p>Repository content: data (sequence alignments, phylogenetic trees, genome assembly, and vcf files) and scripts associated with the manuscript "Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry"</p>
Figure 2 in New insights into the chromosomal differentiation patterns among cichlids from Africa and Madagascar
Figure 2. – Karyotypes of Malagasy and African cichlids after conventional fluorescence in situ hybridization counterstained with DAPI (blue). m/sm pairs are separated on the first line of each karyotype. The 18S rRNA probed chromosomes are shown (red). Scale bar = 5 µm.
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
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A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae
<p>European flat oyster (<em>Ostrea edulis</em>) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite <em>Bonamia ostreae</em>. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with <em>B. ostreae</em> exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long-term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs hatchery) when using neutral markers, and to bonamiosis status (NV vs LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier datasets showed high genetic divergence (FST > 0.25) unlike neutral loci (FST not ≠ 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE-C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE-C8. A range of relevant immune functions were specifically enriched among genes annotated on OE-C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker-assisted selection could be applied to breed resilient strains of <em>O. edulis</em> to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following <em>B. ostreae</em> infection is demonstrated.</p>
Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)
<p>We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing data to discover SNPs in Rio Grande silvery minnow samples of known and unknown sex; and we produced two contig level genomes from<span> Nanopore long-read sequencing. </span><span>Raw NextRAD was aligned to each of the genomes. </span><span>Subsequent SNP calling and filtering were repeated independently to obtain two datasets, one using the female genome as reference (female-referenced dataset) and another using the male genome (male-referenced dataset). The SNP calling identified 4.46 M raw variants in female-referenced dataset and of these 16,714 biallelic SNPs were retained after all filtering steps. For this set of SNPs, the average depth of coverage for the retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for the retained 53 males (ranging from 18.93 to 65.56). When using the male genome as reference we obtained 3.77 M raw variants and 17,920 biallelic SNPs. In this case the average depth of coverage for the same 64 females was 36.01 (ranging from 8.99 to 87.34) and for the same 53 males was 33.36 (ranging from 19.23 to 66.27).</span></p>
Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)
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A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae
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Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals
Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z-chromosome (females are heterogametic, ZW). We tested for elevated Z-differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal Anas gracilis and the dichromatic chestnut teal A. castanea. Despite prominent morphological differences, these two species are genetically indistinguishable at both mitochondrial DNA (mean ΦST < 0.0001) and 17 autosomal loci (mean ΦST = 0.0056). However, we detected elevated Z-differentiation (mean ΦST = 0.281) and tentative evidence of an island of differentiation on the Z-chromosome. This elevated differentiation was explained by a high frequency of derived alleles in chestnut teal that were absent in grey teal, which parallels independent evidence for a gain in dichromatism from a monochromatic ancestor. Coalescent estimates of demographic history and simulations indicated that the elevated Z-differentiation was unlikely to be explained by neutral processes, but instead supported a role of divergent selection. We discuss evidence for models of speciation with gene flow versus adaptive divergence in the absence of gene flow and find that both hypotheses are plausible explanations of the data. Overall, these teal have the weakest background differentiation documented to date for a species showing a large Z-effect, and they are an excellent model species for studying speciation genomics and the evolution of sexual dichromatism.
Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
Linking intraspecific and interspecific divergence is an important challenge in speciation research. X chromosomes are expected to evolve faster than autosomes and disproportionately contribute to reproductive barriers, and comparing genetic variation on X and autosomal markers within and between species can elucidate evolutionary processes that shape genome variation. We performed RADseq on a 16-population transect of two closely-related Australian cricket species, Teleogryllus commodus and T. oceanicus, covering allopatry and sympatry. This classic study system for sexual selection provides a rare exception to Haldane's rule, as hybrid females are sterile. We found no evidence of recent introgression, despite the fact that the species co-exist in overlapping habitats in the wild and interbreed in the laboratory. Putative X-linked loci showed greater differentiation between species compared to autosomal loci. However, population differentiation within species was unexpectedly lower on X-linked markers than autosomal markers, and relative X-to-autosomal genetic diversity was inflated above neutral expectations. Populations of both species showed genomic signatures of recent population expansions, but these were not strong enough to account for the inflated X/A diversity. Instead, most of the excess polymorphism on the X could better be explained by sex-biased processes that increase the relative effective population size of the X, such as interspecific variation in the strength of sexual selection among males. Taken together, the opposing patterns of diversity and differentiation at X versus autosomal loci implicate a greater role for sex-linked genes in maintaining species boundaries in this system.
Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana
With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North American songbird, using next-generation sequencing. Additionally, we reassess previous phylogeographic studies within the group. Based on ~30 million sequencing reads and more than 16 000 single-nucleotide polymorphisms in 41 individuals, we identified a strong positive relationship between genetic differentiation and chromosome size, with a negative relationship between genetic diversity and chromosome size. A combination of selection and drift may explain these patterns, although we found no evidence for selection. Because the observed genomic patterns are very similar between widespread, allopatric clades, it is unlikely that selective pressures would be so similar across such different ecological conditions. Alternatively, the accumulation of fixed differences between lineages and loss of genetic variation within lineages due to genetic drift alone may explain the observed patterns. Due to relatively higher recombination rates on smaller chromosomes, larger chromosomes would, on average, accumulate fixed differences between lineages and lose genetic variation within lineages faster, leading to the patterns observed here in C. americana.
Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
<p>Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (<i>Zosterops borbonicus</i>) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic 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 SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal 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 <i>TYRP1</i>, 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 is promising to investigate how natural selection and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.</p>
Data from: Dmrt1 polymorphism and sex-chromosome differentiation in Rana temporaria
Sex-determination mechanisms vary both within and among populations of common frogs, opening opportunities to investigate the molecular pathways and ultimate causes shaping their evolution. We investigated the association between sex-chromosome differentiation (as assayed from microsatellites) and polymorphism at the candidate sex-determining gene Dmrt1 in two Alpine populations. Both populations harboured a diversity of X-linked and Y-linked Dmrt1 haplotypes. Some males had fixed male-specific alleles at all markers ("differentiated" Y chromosomes), others only at Dmrt1 ("proto-" Y chromosomes), while still others were genetically indistinguishable from females (undifferentiated X chromosomes). Besides these XX males, we also found rare XY females. The several Dmrt1 Y haplotypes differed in the probability of association with a differentiated Y chromosome, which we interpret as a result of differences in the masculinizing effects of alleles at the sex-determining locus. From our results, the polymorphism in sex-chromosome differentiation and its association with Dmrt1, previously inferred from Swedish populations, are not just idiosyncratic features of peripheral populations, but also characterize highly diverged populations in the central range. This implies that an apparently unstable pattern has been maintained over long evolutionary times.
Data from: Sex-chromosome differentiation and 'sex races' in the common frog (Rana temporaria)
Sex-chromosome differentiation was recently shown to vary among common frog populations in Fennoscandia, suggesting a trend of increased differentiation with latitude. By rearing families from two contrasted populations (respectively, from northern and southern Sweden), we show this disparity to stem from differences in sex-determination mechanisms rather than in XY-recombination patterns. Offspring from the northern population display equal sex ratios at metamorphosis, with phenotypic sexes that correlate strongly with paternal LG2 haplotypes (the sex chromosome); accordingly, Y haplotypes are markedly differentiated, with male-specific alleles and depressed diversity testifying to their smaller effective population size. In the southern population, by contrast, a majority of juveniles present ovaries at metamorphosis; only later in development do sex ratios return to equilibrium. Even at these later stages, phenotypic sexes correlate only mildly with paternal LG2 haplotypes; accordingly, there are no recognizable Y haplotypes. These distinct patterns of gonadal development fit the concept of 'sex races' proposed in the 1930s, with our two populations assigned to the 'differentiated' and 'semi-differentiated' races, respectively. Our results support the suggestion that 'sex races' differ in the genetic versus epigenetic components of sex determination. Analysing populations from the 'undifferentiated race' with high-density genetic maps should help to further test this hypothesis.
Data from: Sex-chromosome differentiation parallels post-glacial range expansion in European tree frogs (Hyla arborea).
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Data from: Sex-chromosome differentiation and ‘sex races’ in the common frog (Rana temporaria)
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Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes
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Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana
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Phylogeography, more than elevation, accounts for sex-chromosome differentiation in Swiss populations of the common frog (Rana temporaria)
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Data from: Geographic variation in sex-chromosome differentiation in the common frog (Rana temporaria)
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