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479 results for “Genome evolution”

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zenodo36/100

Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.

The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.

opencc-by-4.0Oct 2024View details →

dryad36/100

Data from: Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high-latitudes

At high-latitude, climatic shifts hypothetically drove episodes of divergence during isolation in glacial refugia, or ice-free pockets of land that enabled terrestrial species persistence. Upon glacial recession, populations can expand and often come into contact, resulting in admixture between previously isolated groups. To understand how recurrent periods of isolation and contact have impacted evolution at high latitudes, we investigated introgression in the stoat (Mustela erminea), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two temporally isolated introgression events coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~ 200 km south along North America's North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and subsequent introgressive hybridization. Introgression followed by allopatry (e.g., insularization) may contribute to expedited divergence of island taxa experiencing substantial glacial flux.

opencc-zeroDec 2017View details →

zenodo36/100

Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani This repository contains: SNP call data / VCF file Scripts for all processing steps from mapping up to PCA and phylogenetic analyses (script.ts) Scripts for population genomic analyses with LEA and PopGenome (scripts.SE) All script names are self explanatory.

opencc-by-4.0Jun 2021View details →

dryad36/100

Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, Prunus takesimensis Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, P. sargentii distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor. However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of P. takesimensis using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of P. takesimensis, (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor), (3) the geographic origin of P. takesimensis via single introduction from source population of P. sargentii in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species P. takesimsnsis compared to continental progenitor P. sargentii, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.

opencc-zeroAug 2021View details →

dryad36/100

Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution

In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism, and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes that interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes, the sex chromosomes) move through time and space.

opencc-zeroSep 2021View details →

dryad36/100

Data from: Whole-genome phylogenetic reconstruction as a powerful tool to reveal homoplasy and ancient rapid radiation in waterflea evolution

The Supplementary Material (and text) to Van Damme et al., contains 10 Supplementary Figures (Figs S1-S10), 5 Supplementary Tables (Tables S1-S5), Supplementary Materials and Methods (ST1), Supplementary Discussion (ST2) and a complete reference list to the manuscript and supplement (Supplementary References SR1). All Supplementary material and text have been peer-reviewed as part of the manuscript. The supplementary discussion provides an additional framework including the importance of the findings of the phylogenomic study for the interpretation of evolution in the Cladocera.

opencc-zeroOct 2021View details →

dryad36/100

A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha

Background Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species-poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorph fish in general and of electric fish in particular. Results A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A CAFE5 analysis of gene family evolution comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. Conclusions We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appears to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.

opencc-zeroJan 2023View details →

dryad36/100

Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, gene order variability does not predict difficulty in placing certain taxa within molecular phylogenetic studies. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why they do not always fit to the observed patterns without nuisance.

opencc-zeroApr 2023View details →

dryad36/100

Chromosome-level assemblies of the Pieris mannii butterfly genome suggest Z-origin and rapid evolution of the W chromosome

The insect order Lepidoptera (butterflies and moths) represents the largest group of organisms with ZW/ZZ sex determination. While the origin of the Z chromosome predates the evolution of the Lepidoptera, the W chromosomes are considered younger, but their origin is debated. To shed light on the origin of the lepidopteran W, we here produce chromosome-level genome assemblies for the butterfly Pieris mannii, and compare the sex chromosomes within and between P. mannii and its sister species P. rapae. Our analyses clearly indicate a common origin of the W chromosomes of the two Pieris species, and reveal similarity between the Z and W in chromosome sequence and structure. This supports the view that the W in these species originates from Z-autosome fusion rather than from a redundant B chromosome. We further demonstrate the extremely rapid evolution of the W relative to the other chromosomes and argue that this may preclude reliable conclusions about the origins of W chromosomes based on comparisons among distantly related Lepidoptera. Finally, we find that sequence similarity between the Z and W chromosomes is greatest toward the chromosome ends, perhaps reflecting selection for the maintenance of recognition sites essential to chromosome segregation. Our study highlights the utility of long-read sequencing technology for illuminating chromosome evolution.

opencc-zeroJun 2023View details →

dryad36/100

Aquaculture-driven evolution of the salmon louse mtDNA genome

Resistance towards the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000–2002 "pre-resistance") and contemporary (2014–2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000–2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and, that long-distance dispersion of resistance is rapid due to the high level of genetic connectivity that is observed in this species.

opencc-zeroJun 2023View details →

dryad36/100

Data for: Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Co-diversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here we employ dense taxon sampling (520 species) throughout Moraceae and 1,858 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

opencc-zeroJun 2023View details →

dryad36/100

Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)

Owlet moths (Noctuoidea; ~43–45K described species; Nieukerken et al. 2011) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1,234 genes (946.4 kb of nucleotides) obtained from the genome and transcriptome sequences of 76 species representing all six families. Relationships among the families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated to be 74.5 Ma, with most families originating before the end of Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.

opencc-zeroSep 2023View details →

ClinicalTrials.gov36/100

Study of Ibrutinib in Patients With Symptomatic, Previously Untreated Waldenstrom's Macroglobulinemia, and Impact on Tumor Genomic Evolution Using Whole Genome Sequencing

ClinicalTrials.gov study NCT02604511. IPD Sharing: Not stated. Countries: 1. Publications: 3.

restrictedIPD-UNDECIDEDFeb 2026View details →

dryad36/100