The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Population divergence at different spatial scales in a wide-spread amphibian

To study the distribution of genetic and phenotypic variation in different environments and at different spatial scales is important in order to understand the process of local adaptation and how populations will respond to future climate change. In my thesis I study populations of moor frogs (Rana arvalis) at different spatial scales, first along a 1700 km latitudinal gradient (Paper I, II, IV) and, second, in a system of inter-connected wetlands (III, IV). In Paper I, I present evidence for a major latitudinal break-point in larval life-history traits which is linked to a post glacial contact zone between two lineages that colonized Scandinavia after the last ice age. Using QST-FST comparisons I found divergent selection acting on life-history traits, where a major source of differentiation comes from the two colonization routes. In Paper II I focus on genomic variation, demographic history and selection along the gradient. Using demographic modeling I confirm the proposed demographic history and show historical signatures of gene flow between regions and over the contact zone. In terms of genetic variation showing extreme differentiation as well as associations with growing season length I identify numerous variants under putative divergent selection, some of which have functions relating to immunity and development. I further show that differentiation outlier variation is higher in the north, as compared to neutral variation and variation associated with growing season length, which both decrease with latitude. These patterns are shaped by gene flow over the contact zone and the increased strength of drift at higher latitudes. I reduce the spatial scale in Paper III and characterize larval environments, landscape and geographical distance, to partition their influence on genetic variation. I show that environment explained more of the genetic variation than landscape and geographic distance, indicating that adaptive divergence can persist under high gene flow. Using the environmental variables, I identify genetic variants under putative divergent selection with functions associated with development and immunity. Using data from both scales, QST-FST comparisons and gene-phenotype associations I show in Paper IV that selection on both larval traits aligns across scales, whereas selection on plasticity only aligns in size at metamorphosis. This further connects to the influence of temperature and seasonal time constraints in colder environments. Finally, I find several genetic variants associated with the traits and plasticity at both spatial scales with functions relating to immunity and metamorphosis

Population divergence at different spatial scales in a wide-spread amphibian

To study the distribution of genetic and phenotypic variation in different environments and at different spatial scales is important in order to understand the process of local adaptation and how populations will respond to future climate change. In my thesis I study populations of moor frogs (Rana arvalis) at different spatial scales, first along a 1700 km latitudinal gradient (Paper I, II, IV) and, second, in a system of inter-connected wetlands (III, IV). In Paper I, I present evidence for a major latitudinal break-point in larval life-history traits which is linked to a post glacial contact zone between two lineages that colonized Scandinavia after the last ice age. Using QST-FST comparisons I found divergent selection acting on life-history traits, where a major source of differentiation comes from the two colonization routes. In Paper II I focus on genomic variation, demographic history and selection along the gradient. Using demographic modeling I confirm the proposed demographic history and show historical signatures of gene flow between regions and over the contact zone. In terms of genetic variation showing extreme differentiation as well as associations with growing season length I identify numerous variants under putative divergent selection, some of which have functions relating to immunity and development. I further show that differentiation outlier variation is higher in the north, as compared to neutral variation and variation associated with growing season length, which both decrease with latitude. These patterns are shaped by gene flow over the contact zone and the increased strength of drift at higher latitudes. I reduce the spatial scale in Paper III and characterize larval environments, landscape and geographical distance, to partition their influence on genetic variation. I show that environment explained more of the genetic variation than landscape and geographic distance, indicating that adaptive divergence can persist under high gene flow. Using the environmental variables, I identify genetic variants under putative divergent selection with functions associated with development and immunity. Using data from both scales, QST-FST comparisons and gene-phenotype associations I show in Paper IV that selection on both larval traits aligns across scales, whereas selection on plasticity only aligns in size at metamorphosis. This further connects to the influence of temperature and seasonal time constraints in colder environments. Finally, I find several genetic variants associated with the traits and plasticity at both spatial scales with functions relating to immunity and metamorphosis

Genomic regions of speciation and adaptation among three species of grouse

Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region

batch_1

Final filtered vcf file used for the main analyses

RUN_easySFS

Example command to run easySF

Data from: Postglacial colonization routes coincide with a life history breakpoint along a latitudinal gradient

While adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of postglacial colonization routes in determining phenotypic variation along gradients has received little attention. Here we used a hierarchical QST-FST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life-histories along a 1700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages, however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The QST estimates between the colonization routes were four times higher than FST, indicating a prominent role for natural selection. QST within the colonization routes did not generally differ from FST, but we found temperature-dependent adaptive divergence close to the contact zone. These results indicate that lineage-specific variation can account for much of the adaptive divergence along a latitudinal gradient

denovo_arvalis_noreplic

Script used to run fsc2

Neutral SNP from 13 populations of Rana arvalis

Neutral SNP from 13 populations of Rana arvali

batch_1.summary.sumstats

Stacks summary oupu