Search results for " Genomics"

Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

2018

This work was supported by the Academy of Finland to AH (projects 132619 and 267244) and to MK (projects 268214 and 272927) and NERC (UK) funding to MGR (grants NE/E015255/1 and NE/J020818/1) and PhD studentship to DJP (NE/I528634/1). The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species. We use branch tests to identify genes showing accelerated divergence in contrasts between col…

Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits.

2016

Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species - the great tit Parus major - at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km), u…

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

2017

Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic…

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations.

2017

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population str…

Is homoploid hybrid speciation that rare? An empiricist’s view

2017

Is homoploid hybrid speciation that rare? An empiricist’s view

Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

2021

Significance Both theory and experiments suggest that fishing can drive the evolution of an earlier maturation age. However, determining whether changes in the wild are the result of fisheries-induced evolution has been difficult. Temporal, genome-wide datasets can directly reveal responses to selection. Here, we investigate the genomes of two wild Atlantic cod populations from samples that pre- and postdate periods of intensive fishing. Although phenotypic changes suggest fisheries-induced evolution, we do not find evidence for any strong genomic change or loss of genetic diversity. While evolution could have occurred through undetectable frequency changes at many loci, the irreversible lo…

Plant genes involved in arbuscular mycorrhiza formation and functioning

2002

Knowledge about that part of the plant genome involved in the establishment and functioning of the arbuscular mycorrhizal (AM) symbiosis is important for the basic understanding of this symbiosis. It is also essential for a ‘genes to the field’ approach based on the identification and exploitation of genes that could be central to developing sustainable plant production systems in the future.

2021

Abstract The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, …

Selection for Robustness in Mutagenized RNA Viruses

2007

Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we experimentally validate this hypothesis, dubbed the ‘‘survival of the flattest,’’ using two populations of the vesicular stomatitis RNA virus. Characterization of fitness distributions and genetic variability indicated that one population showed a higher replication rate, whereas the other was more robust to mut…

Establishing laboratory cultures and performing ecological and evolutionary experiments with the emerging model speciesChironomus riparius

2019

Chironomus riparius is a well‐established model organism in various fields such as ecotoxicology and ecology, and therefore, environmental preferences, ecological interactions and metabolic traits are well‐studied. With the recent publication of a high‐quality draft genome, as well as different population genetic parameters such as mutation and recombination rate, the species can be used as an alternative to the Drosophila models in experimental population genomics or molecular ecology. To facilitate access to this promising experimental model species for a wider range of researchers, we describe experimental methods to first create and sustain long‐term cultures of C. riparius and then use…