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Looking into the past: the reaction of three grouse species to climate change over the last million years using whole genome sequences
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. (Höglund lab)
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland & deCODE Genetics/Amgen, Reykjavik, Iceland.
The Icelandic Institute of Natural History, Borgir v. Nordurslod, Akureyri 600, Iceland & Department of Natural Resource Sciences, University of Akureyri, Borgir vid Nordurslod, Akureyri 600, Iceland & Biomedical Center, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, 570-580 p.Article in journal (Refereed) Published
Abstract [en]

Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying PSMC signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne. Our results highlight the usefulness of the PSMC approach in investigating species’ reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.

Place, publisher, year, edition, pages
2016. Vol. 25, no 2, 570-580 p.
Keyword [en]
climate change, effective population size, pairwise sequentially Markovian coalescent, Pleistocene, Tetraoninae
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-295467DOI: 10.1111/mec.13496ISI: 000369530000010PubMedID: 26607571OAI: oai:DiVA.org:uu-295467DiVA: diva2:933803
Available from: 2016-06-07 Created: 2016-06-07 Last updated: 2016-08-26Bibliographically approved
In thesis
1. Inferring demographic history and speciation of grouse using whole genome sequences
Open this publication in new window or tab >>Inferring demographic history and speciation of grouse using whole genome sequences
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability.

I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse.

Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 49 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1391
Keyword
Demographic history, speciation, effective population size, adaptation, willow grouse, red grouse, black grouse, rock ptarmigan, Tetraoninae, conservation genetics, climate change, PSMC, species distribution modelling, FOXP4, Agouti
National Category
Evolutionary Biology Ecology Genetics
Identifiers
urn:nbn:se:uu:diva-299926 (URN)978-91-554-9627-2 (ISBN)
External cooperation:
Public defence
2016-09-16, Lindahlssalen, EBC (Evolutionary Biology Center), Norbyvägen 18B, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2016-08-24 Created: 2016-07-29 Last updated: 2016-08-26

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