Umeå University's logo

umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.ORCID iD: 0000-0001-9225-7521
2020 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, no 2, p. 3803-3817Article in journal (Refereed) Published
Abstract [en]

Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

Place, publisher, year, edition, pages
Oxford University Press, 2020. Vol. 12, no 2, p. 3803-3817
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
URN: urn:nbn:se:umu:diva-169222DOI: 10.1093/gbe/evaa005ISI: 000522862200005Scopus ID: 2-s2.0-85080830244OAI: oai:DiVA.org:umu-169222DiVA, id: diva2:1416980
Funder
Knut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research , RBP14-0040Available from: 2020-03-26 Created: 2020-03-26 Last updated: 2023-03-23Bibliographically approved
In thesis
1. The roles of demography and natural selection in shaping genome-wide variation of Norway spruce
Open this publication in new window or tab >>The roles of demography and natural selection in shaping genome-wide variation of Norway spruce
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the relative contribution of genetic drift, natural selection, and mutation to genetic variation, and quantifying adaptive evolution and the effects of natural selection in species are enduring goals of evolutionary genetics. Norway spruce (Picea abies) is one of the most important conifer species that dominates from both an ecological and economical point of view in many boreal ecosystems. Recently published reference genome of Norway spruce makes it possible to perform population genomic studies to understand the basis of genetic variation and evolutionary effects of natural selection in P. abies by using next-generation sequencing (NGS) data. 

We create an ultra-dense genetic linkage map for Norway spruce using sequence capture data. The consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups (LGs). We also demonstrate, however, that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors. By performing population genetic analyses using the genomic regions anchored to LGs, our genetic linkage map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

In order to understand how different evolutionary forces have shaped patterns of nucleotide diversity in Norway spruce, we perform population genomic analyses using whole-genome resequencing data. We find that genetic diversity is low across a number of populations in spite of a very wide geographic distribution of P. abies. The demographic history of several reoccurring bottlenecks with concomitant decreases in effective population size, the recurrent natural selection (both purifying and positive selection), and the low overall mutation rates seen in conifers, together make contribute to the loss of genome-wide nucleotide diversity in Norway spruce.

We quantify adaptive evolution and the effects of natural selection across the Norway spruce whole genome. The results show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolutionary history of P. abies. We further find a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. The distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicate impact from natural selection to genomic architecture of Norway spruce.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2020. p. 58
Keywords
Norway spruce, whole-genome resequencing, variant calling, genetic linkage map, nucleotide diversity, natural selection
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-174652 (URN)978-91-7855-321-1 (ISBN)978-91-7855-320-4 (ISBN)
Public defence
2020-09-25, KBC huset, Lilla Hörsalen, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2020-09-03 Created: 2020-08-29 Last updated: 2020-09-11Bibliographically approved

Open Access in DiVA

fulltext(1503 kB)186 downloads
File information
File name FULLTEXT01.pdfFile size 1503 kBChecksum SHA-512
663733e080ad317a8452cb6631e1f1334300ed1ea5eb8cf9f09345b75f7f35b49d207513b03dace6285ee28c73d8bb1c9baf52a3f606424175ca0faccbae24c1
Type fulltextMimetype application/pdf

Other links

Publisher's full textScopus

Authority records

Wang, XiBernhardsson, CarolinaIngvarsson, Pär K.

Search in DiVA

By author/editor
Wang, XiBernhardsson, CarolinaIngvarsson, Pär K.
By organisation
Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)
In the same journal
Genome Biology and Evolution
Genetics and Breeding in Agricultural Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 186 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 321 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf