Search results for "Divergence"
showing 10 items of 257 documents
Fossorial but widespread: the phylogeography of the common spadefoot toad (Pelobates fuscus), and the role of the Po Valley as a major source of gene…
2007
International audience; Pelobates fuscus is a fossorial amphibian that inhabits much of the European plain areas. To unveil traces of expansion and contraction events of the species' range, we sequenced 702 bp of the mitochondrial cytochrome b gene. To infer the population history we applied phylogeographical methods, such as nested clade phylogeographical analysis (NCPA), and used summary statistics to analyse population structure under a neutral model of evolution. Populations were assigned to different drainage systems and we tested hypotheses of explicit refugial models using information from analysis of molecular variance, nucleotide diversity, effective population size estimation, NCP…
“A cleaner break”: Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta)
2020
Abstract Capture and long‐distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat…
Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana
2020
Funding: UK Natural Environment Research Council (Grant Number(s): NE/L501852/1, NE/P000592/1); Academy of Finland (GrantNumber(s): 267244, 268214, 322980), Ella ja Georg Ehrnroothin Säätiö. Detecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here, we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and tested for signatures of cold adaptation in population genomic divergence. We…
Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout
2018
Brown trout (Salmo trutta) exhibit highly diverse life histories varying from resident, slow-growing, and early maturing to migratory, fast-growing, and late maturing, even within single watersheds. We sampled 11 locations within the transboundary Finnish–Russian River Koutajoki watershed to evaluate genomic differences among mainstem and headwater sites, of which some are isolated by migration barriers. Restriction site associated sequencing (RADSeq) revealed that the most headwater localities supported unique, isolated populations with generally lower heterozygosity compared with the mainstem populations. The sampled migratory adults in the three main stems showed signals of admixture de…
Neither Diplectanum nor specific: a dramatic twist to the taxonomic framework of Diplectanum (Monogenea: Diplectanidae).
2019
The taxonomy of the genus Diplectanum has been exclusively based on morphological features, with 28 nominal species parasitic on perciform fishes recognised. We used molecular data, to our knowledge for the first time, to evaluate the taxonomic framework of Diplectanum, infer the relationships amongst species attributed to this genus, re-assess the degree of host specificity and explore the population genetic structure of Diplectanum spp. parasitising Mediterranean sciaenids, which are potential target fish species for aquaculture diversification in the region. A minimum of 10 specimens of Diplectanum spp. were sequenced per host species (Argyrosomus regius, Sciaena umbra, Umbrina canariens…
"Islands of divergence" in the Atlantic cod genome represent polymorphic chromosomal rearrangements
2016
- In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at “genomic islands of divergence,” resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod (Gadus morhua) within geographically fine-scaled coastal areas. The “genomic islands” extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were id…
Prioritizing covariates in the planning of future studies in the meta-analytic framework
2016
Science can be seen as a sequential process where each new study augments evidence to the existing knowledge. To have the best prospects to make an impact in this process, a new study should be designed optimally taking into account the previous studies and other prior information. We propose a formal approach for the covariate prioritization, i.e., the decision about the covariates to be measured in a new study. The decision criteria can be based on conditional power, change of the p-value, change in lower confidence limit, Kullback-Leibler divergence, Bayes factors, Bayesian false discovery rate or difference between prior and posterior expectation. The criteria can be also used for decis…
Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation
2019
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis…
Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
2017
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long…
Graph-based network analysis of transcriptional regulation pattern divergence in duplicated yeast gene pairs
2019
The genome and interactome of Saccharomyces cerevisiae have been characterized extensively over the course of the past few decades. However, despite many insights gained over the years, both functional studies and evolutionary analyses continue to reveal many complexities and confounding factors in the construction of reliable transcriptional regulatory network models. We present here a graph-based technique for comparing transcriptional regulatory networks based on network motif similarity for gene pairs. We construct interaction graphs for duplicated transcription factor pairs traceable to the ancestral whole-genome duplication as well as other paralogues in Saccharomyces cerevisiae. We c…