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94 results for “gene islands”
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations
<p>Invasive alien species continue to threaten global biodiversity. CRISPR-based gene drives, which can theoretically spread through populations despite imparting a fitness cost, could be used to suppress or eradicate pest populations. We develop an individual-based, spatially explicit, stochastic model to simulate the ability of CRISPR-based homing and X-chromosome shredding drives to eradicate populations of invasive mice (Mus muculus) from islands. Using the model, we explore the interactive effect of the efficiency of the drive constructs and the spatial ecology of the target population on the outcome of a gene-drive release. We also consider the impact of polyandrous mating and sperm competition, which could compromise the efficacy of some gene-drive strategies. Our results show that both drive strategies could be used to eradicate large populations of mice. Whereas parameters related to drive efficiency and demography strongly influence drive performance, we find that sperm competition following polyandrous mating is unlikely to impact the outcome of an eradication effort substantially. Assumptions regarding the spatial ecology of mice influenced the probability of and time required for eradication, with short-range dispersal capabilities and limited mate-search areas producing `chase' dynamics across the island characterised by cycles of local extinction and recolonization by mice. We also show that highly efficient drives are not always optimal, when dispersal capabilities are low, rapid local population supression around the introduction sites can cause loss of the gene drive before it can spread to the entire island. We conclude that, although the design of efficient gene drives is undoubtedly critical, accurate data on the spatial ecology of target species is critical for predicting the result of a gene-drive release.</p>
Data from: Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
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Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations
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Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility
Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species we identified genomic islands of high differentiation (FST) and of high divergence (Dxy), and we analyzed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.
Highland islands: assessing gene flow among populations of an aquatic highland endemic
<p>A variety of hierarchical gene flow models have been proposed to explain the distribution of genetic variation in aquatic environments. These models, including the Stream Hierarchy (SH), Death Valley (DV), Headwater (HW), and Widespread Gene flow (WG) models, provide testable hypotheses that focus on the degree of within-basin or within-stream network connectivity and an organism's dispersal abilities. We tested these models using <em>Tlaloc hildebrandi</em> (Profundulidae, Cyprinodontiformes), a freshwater fish endemic to the highlands of the Grijalva and Usumacinta River basins in southern Mexico. Data from ultraconserved elements (UCEs) showed that although <em>T. hildebrandi</em> was recovered as monophyletic, the sub-basins were not. We generated single nucleotide polymorphisms from the UCEs to analyse the data in a population genetic framework. These results differed between analyses such that two (STRUCTURE analysis) or three (DAPC analysis) genetic groupings were recovered. Overall, the results of this study provide support for the SH model. Some individuals from the Jataté sub-basin, however, conformed to the HW model, due to historical connections among headwater streams and rivers of the Jataté and Amarillo–Chenalhó clades/clusters. The greatest degree of gene flow has occurred from the Grijlava to the Usumacinta basins, two geographically proximate basins that have been hypothesized to have had previous connections.</p>
Dataset for "Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island"
<p>HawaiiPopulation_Raw.bcf.gz</p> <p>- Unfiltered SNP + INDEL VCF file for Hawaii Island Metrosideros</p> <p> </p> <p>HawaiiPopulation_FILTERED_SNP.bcf.gz</p> <p>- Filtered SNP VCF for Hawaii Island Metrosideros</p> <p> </p> <p>Population_WithOutgroup_Raw.vcf.gz</p> <p>- Unfiltered SNP + INDEL VCF file used in analysis that grouped G<sub>H1</sub>, G<sub>H2</sub>, N subpopulation with the outgroup samples.</p> <p> </p> <p>Population_WithOutgroup_FILTERED_SNP.vcf.gz</p> <p>- Filtered SNP VCF file used in analysis that grouped G<sub>H1</sub>, G<sub>H2</sub>, N subpopulation with the outgroup samples.</p> <p> </p> <p>Population_WithOutgroup.geno.gz</p> <p>- Genotype file generated from the genomic_general from S. Martin and used as input for Dxy and Fst window analysis</p> <p> </p> <p>Popgene_stat*</p> <p>- 5, 10, and 50 kbp windows of calculating pi, Dxy, Fst, Omega, Hscan, and H12 statistics </p> <p> </p> <p>GPHOCS_INPUT.txt</p> <p>- Input data file for GPhoCS analysis</p> <p> </p> <p>GPHOCS_control_*</p> <p>- GPhoCS control file</p> <p> </p> <p>DADI_INPUT*</p> <p>- Input 2D-SFS file for dadi analysis</p>
Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility
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Highland islands: assessing gene flow among populations of an aquatic highland endemic
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Data from: Speciation with gene flow in an island endemic hummingbird
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Giant island mice exhibit widespread gene expression changes in key metabolic organs
Abstract Island populations repeatedly evolve extreme body sizes, but the genomic basis of this pattern remains largely unknown. To understand how organisms on islands evolve gigantism, we compared genome-wide patterns of gene expression in Gough Island mice, the largest wild house mice in the world, and mainland mice from the WSB/EiJ wild-derived inbred strain. We used RNASeq to quantify differential gene expression in three key metabolic organs: gonadal adipose depot, hypothalamus and liver. Between 4,000 and 8,800 genes were significantly differentially expressed across the evaluated organs, representing between 20 and 50% of detected transcripts, with 20% or more of differentially expressed transcripts in each organ exhibiting expression fold changes of at least 2X. A minimum of 73 candidate genes for extreme size evolution, including Irs1 and Lrp1, were identified by considering differential expression jointly with other data sets: (i) genomic positions of published quantitative trait loci for body weight and growth rate; (ii) whole genome sequencing of 16 wild-caught Gough Island mice that revealed fixed single nucleotide differences between the strains; (iii) publicly available tissue-specific regulatory elements. Additionally, patterns of differential expression across three time points in the liver revealed that Arid5b potentially regulates hundreds of genes. Functional enrichment analyses pointed to cell cycling, mitochondrial function, signaling pathways, inflammatory response, and nutrient metabolism as potential causes of weight accumulation in Gough Island mice. Collectively, our results indicate that extensive gene regulatory evolution in metabolic organs accompanied the rapid evolution of gigantism during the short time house mice have inhabited Gough Island.
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations
<p>Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large-small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush-warbler<i> Horornis ruficapilla</i>, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of inter-island gene flow in archipelagos as the study of island biogeography progresses into the genomic era.</p>
Data from: Spatial variation in climate mediates gene flow across an island archipelago
High levels of gene flow among partially isolated populations can overwhelm selection and limit local adaptation. This process, known as "gene swamping," can homogenize genetic diversity among populations and reduce the capacity of a species to withstand rapid environmental change. We studied brown anole lizards (Anolis sagrei) distributed across seven islands in The Bahamas. We used microsatellite markers to estimate gene flow among islands and then examined the correlation between thermal performance and island temperature. The thermal optimum for sprint performance was correlated with both mean and maximum island temperature whereas performance breadth was not correlated with any measure of temperature variation. Gene flow between islands decreased as the difference between mean island temperatures increased, even when those islands were adjacent to one another. These data suggest that phenotypic variation is the result of either 1) local genetic adaptation with selection against immigrants maintaining variation in the thermal optimum, 2) irreversible forms of adaptive plasticity such that immigrants have reduced fitness, or 3) an interaction between fixed genetic differences and plasticity. In general, the patterns of gene flow we observed suggest that local thermal environments represent important ecological filters that can mediate gene flow on relatively fine geographic scales.
Data from: Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands
Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and inter-population gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely-related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multi-locus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, E. formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the south-east Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.
Data from: Hybridization and barriers to gene flow in an island bird radiation
While reinforcement may play a role in all major modes of speciation, relatively little is known about the timescale over which species hybridize without evolving complete reproductive isolation. Birds have high potential for hybridization, and islands provide simple settings for uncovering speciation and hybridization patterns. Here we develop a phylogenetic hypothesis for a phenotypically-diverse radiation of finch-like weaver-birds (Foudia) endemic to the western Indian Ocean islands. We find that unlike Darwin's finches, each island-endemic Foudia population is a monophyletic entity for which speciation can be considered complete. In explaining the only exceptions – mismatches between taxonomy, mitochondrial and nuclear data – phylogenetic and coalescent methods support introgressive hybridization rather than incomplete lineage sorting. Human introductions of known timing of one island-endemic species, to all surrounding archipelagos provide two fortuitous experiments; (1) population sampling at known times in recent evolutionary history, (2) bringing allopatric lineages of an island radiation into secondary contact. Our results put a minimum time bound on introgression (235 years), and support hybridization between species in natural close contact (parapatry), but not between those in natural allopatry brought into contact by human introduction. Time in allopatry, rather than in sympatry, appears key in the reproductive isolation of Foudia species.
Data from: The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica
Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a tree species (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance
Data from: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Background and Aims: Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Methods: Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Key Results: Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). Conclusions: The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations.
Building an eDNA surveillance toolkit for invasive rodents on islands: Can we detect wild-type and gene drive Mus musculus?
<p>R code, data, and qPCR efficiencies for experiments related to this paper.</p>
Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.
FIGURE 3 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 3. Phylogeography of Gongylomorphus skinks in Mauritius based on 1102bp of combined mtDNA sequence data. Lower-case letters refer to collection localities in Fig. 1 and Table 1. Haplotype networks are drawn with the areas of circles proportional to number of individuals observed; dots represent unobserved haplotypes, and lines between them each represent a single nucleotide substitution. Filled circles represent samples collected from extant populations, and open circles samples from extinct ones.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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