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Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
CNRS, ENTPE, UMR5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.ORCID iD: 0000-0002-8559-5191
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2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 12, p. 2996-3011Article in journal (Refereed) Published
Abstract [en]

Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long‐term persistence of populations, understanding how these processes affect variation over large‐scale geographical gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1,700‐km latitudinal gradient from northern Germany to northern Sweden. Using double digest restriction‐site associated DNA sequencing we obtained 27,590 single nucleotide polymorphisms (SNPs), and identified differentiation outliers and SNPs associated with growing season length. The populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post‐glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern, suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate‐mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019. Vol. 28, no 12, p. 2996-3011
Keywords [en]
adaptive divergence, amphibians, divergent selection, genetic drift, range expansion, small populations
National Category
Evolutionary Biology Ecology
Research subject
Biology with specialization in Animal Ecology
Identifiers
URN: urn:nbn:se:uu:diva-390931DOI: 10.1111/mec.15132ISI: 000475983100005OAI: oai:DiVA.org:uu-390931DiVA, id: diva2:1343210
Available from: 2019-08-15 Created: 2019-08-15 Last updated: 2019-09-09Bibliographically approved
In thesis
1. Population divergence at different spatial scales in a wide-spread amphibian
Open this publication in new window or tab >>Population divergence at different spatial scales in a wide-spread amphibian
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 53
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1841
Keywords
Adaptive divergence, environmental gradients, genomics, life-history, amphibians
National Category
Natural Sciences
Research subject
Biology with specialization in Animal Ecology
Identifiers
urn:nbn:se:uu:diva-391039 (URN)978-91-513-0723-7 (ISBN)
Public defence
2019-09-20, Zootissalen, EBC, Villavägen 9, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2019-08-29 Created: 2019-08-16 Last updated: 2019-09-17Bibliographically approved

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Mörch, Patrik RödinLuquet, EmilienMeyer-Lucht, YvonneRichter Boix, AlexHöglund, JacobLaurila, Anssi

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