Find research datasets worth reusing

opencc-zeroDec 2010View details →

Data from: The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa

The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5 kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of inter-population genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.

opencc-zeroDec 2017View details →

Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.

opencc-zeroMar 2020View details →

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

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 (Zosterops borbonicus) 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 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 is promising to investigate how natural selection and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

opencc-zeroDec 2015View details →

Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.

opencc-zeroJan 2020View details →

Autosomal suppression and fitness costs of an old driving X chromosome in Drosophila testacea

Driving X chromosomes (XDs) are meiotic drivers that bias their own transmission through males by killing Y-bearing gametes. These chromosomes can in theory spread rapidly in populations and cause extinction, but many are found as balanced polymorphisms or as "cryptic" XDs shut down by drive suppressors. The relative likelihood of these outcomes, as well as the evolutionary pathways through which they come about, are not well-understood. An XD was recently discovered in the mycophagous fly, Drosophila testacea, presenting the opportunity to compare this XD with the well-studied XD of its sister species, Drosophila neotestacea. Comparing features of independently evolved XDs in young sister species is a promising avenue towards understanding how XDs and their counter acting forces change over time. In contrast to the XD of D. neotestacea, we find that the XD of D. testacea is old, with its origin predating the radiation of three species: D. testacea, D. neotestacea, and their shared sister species, Drosophila orientacea. Motivated by the suggestion that older XDs should be more deleterious to carriers, we assessed the effect of the XD on both male and female fertility. Unlike what is known from D. neotestacea, we found a strong fitness cost in females homozygous for the XD in D. testacea: a large proportion of homozygous females failed to produce offspring after being housed with males for several days. Our male fertility experiments show that while XD male fertility is lower under sperm depleting conditions, XD males have comparable fertility to males carrying a standard X chromosome under a free mating regime, which may better approximate conditions in wild populations of D. testacea. Lastly, we demonstrate the presence of autosomal suppression of X chromosome drive. Our results provide support for a model of XD evolution where the dynamics of young XDs are governed by fitness consequences in males, whereas in older XD systems, both suppression and fitness consequences in females likely supersede male fitness costs.

opencc-zeroDec 2015View details →

Data from: A genome-wide association study identifies a region strongly associated with symmetrical onychomadesis on chromosome 12 in dogs

Symmetrical onychomadesis causes periodic loss of claws in otherwise healthy dogs. Genome-wide association analysis in 225 Gordon Setters identified a single region associated with symmetrical onychomadesis on chromosome 12 (spanning about 3.3 mb). A meta-analysis including also English Setters indicated that this genomic region predisposes for symmetrical onychomadesis in English Setters as well. The associated region spans most of the major histocompatibility complex and nearly 1 Mb downstream. Like many other autoimmune diseases, associations of symmetrical onychomadesis with DLA class II alleles have been reported. In this study, no associated markers were revealed within any of the DLA-DRB1, -DQA1 or -DQB1 genes, and the odds for symmetrical onychomadesis in the Gordon Setters were much higher, carrying significant single nucleotide polymorphisms compared to the odds of any of the recorded DLA-DRB1/DQA1/DQB1 haplotypes. We noticed that some of the associated DLA haplotypes were different between the English Setters and the Gordon Setters. Interestingly, associated SNP chip markers showed a more consistent pattern of allelic variants related to cases or controls regardless of breed. In conclusion, the associated genetic markers identified in this study hold the potential to aid in selection of breeding animals to reduce the frequency of symmetrical onychomadesis in the dog.

opencc-zeroDec 2018View details →

Data from: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence

Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.

opencc-zeroDec 2013View details →

Data from: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis. - See more at: http://elifesciences.org/content/3/e03318#sthash.Yx6nSY4J.dpuf

opencc-zeroDec 2016View details →

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.

opencc-zeroDec 2014View details →

Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

opennotspecifiedMay 2002View details →

FIGURE 3. Larval polytene chromosomes, IIIS arm. a in Taxonomy and biology of Simulium clarkei Stone & Snoddy (Diptera: Simuliidae), a poorly known black fly of the southeastern United States

FIGURE 3. Larval polytene chromosomes, IIIS arm. a. Simulium emarginatum, Meherrin River, Virginia, showing standard sequence. b. Simulium clarkei, Meherrin River, North Carolina, showing IIIS inversion (brackets) with reversed orientation of 'blister' (bl) and 'capsule' (ca) markers. The centromere is on the left of each chromosome arm.

FIGURE 4 in Chromosomal and morphological taxonomy of larvae of Simulium (Gomphostilbia) (Diptera: Simuliidae) in Thailand

FIGURE 4. Photographs of postgenal clefts of Simulium species in subgenus Gomphostilbia. A, Simulium asakoae. B, S. gombakense. C, S. sheilae. D, S. dentistylum. E, S. sp. nr. sheilae. F, S. sp. A.

FIGURE 3 in Chromosomal and morphological taxonomy of larvae of Simulium (Gomphostilbia) (Diptera: Simuliidae) in Thailand

FIGURE 3. Photographs of gill filaments of Simulium species in subgenus Gomphostilbia. A, Simulium angulistylum. B, S. sp. A. C, S. novemarticulatum. D, S. siamense. E, S. sheilae. F, S. sp. nr. sheilae.

FIGURE 2 in Chromosomal and morphological taxonomy of larvae of Simulium (Gomphostilbia) (Diptera: Simuliidae) in Thailand

FIGURE 2. Photographs of setae on abdominal cuticle of Simulium species in subgenus Gomphostilbia. A, Simulium angulistylum. B, S. decuplum. C, S. dentistylum. D, S. siamense. E, S. sp. A. F, S. asakoae. G, S. sheilae. H, S. sp. nr. sheilae. I, S. novemarticulatum. J, S. sp. B.

FIGURE 1 in Chromosomal and morphological taxonomy of larvae of Simulium (Gomphostilbia) (Diptera: Simuliidae) in Thailand

FIGURE 1. Idiograms of chromosome arm IIS for 12 Simulium species in subgenus Gomphostilbia from Khao Yai National Park, showing relative locations of Ce, centromere; RB, ring of Balbiani; Bu, bulge; Sh, shoestring. A, Simulium angulistylum. B, S. decuplum. C, S. dentistylum. D, S. gombakense. E, S. siamense. F, S. sp. A. G, S. asakoae. H, S. sheilae. I, S. sp. nr. sheilae. J, S. novemarticulatum. K, S. sp. B. L, S. sp. C.

FIGURES 10A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)

FIGURES 10A–E. Leiobunum hiraiwai, penis, ventral view (left) and tip of penis, lateral view (right), Kinki race. Localities: A. Mt Hoko (14). B. Kisokomakôgen (15). C. Mt Ontake (17). D. Narai (18). E. Mt Kokuzô (19). Numerals in parentheses denote code numbers of localities given in Fig. 7.

FIGURES 1A–L in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)

FIGURES 1A–L. Leiobunum hiraiwai (Sato & Suzuki). A–B. Eye tubercle of male, lateral view. C–F. Genital operculum (C–D male, E–F female). G–H. Labrum of female, lateral view. IK. Chelicera of male, mesal view. L. Body of female, dorsal view. Localities (numerals in parentheses denote code numbers given in Fig. 7): A. Mt Bunagatake (10 — Kinki race). B, J. Mt Utsukushigahara (42 — Utsukushigahara race). C. Mt Hyônosen (8 — Kinki race). D, K. Mt Amagi (40 — Izu race). E, G, L. Kisokomakôgen (15 — Kinki race). F, H. Togakushi (50 — Western Kantô race). I. Mt Hiko (2 — KyushuHiroshima race).

FIGURE 18 in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)

FIGURE 18. Diagrams illustrating the possible evolution of the races in Leiobunum hiraiwai. Details in the text.

FIGURES 5A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)

FIGURES 5A–E. Male karyotypes of Leiobunum hiraiwai. Races: A. KyushuHiroshima race. B–C. Kinki race. D–E. Intermediate populations. Localities: A. Mt Hikosan (2n = 18). B. Mt Bunagatake (2n = 20). C. Tsuetsukitôge Pass (2n = 20). D. Todai (2n = 20). E. Mt Nyûgasa (2n = 20).

FIGURES 6A–E in Geographic variation of chromosomes and somatic morphology in the Japanese polymorphic species Leiobunum hiraiwai (Arachnida: Opiliones: Sclerosomatidae)

FIGURES 6A–E. Male karyotypes of Leiobunum hiraiwai. Races: A. Kamikôchi race. B–C. Utsukushigaraha race. D. Western Kantô race. E. Izu race. Localities: A. Ariake Spa (2n = 20). B. Mt Utsukushigahara (2n = 20). C. Kowashimizu, 1630 m alt., Mt Kirigamine (2n = 20). D. Mt BushûMitake (2n = 22). E. Mt Amagi (2n = 22).