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Insight into speciation and adaptation in grouse as revealed by whole genome sequencing
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. (Höglund lab)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
(English)Manuscript (preprint) (Other academic)
Abstract [en]

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. The grouse (subfamily Tetraoninae) constitute an avian lineage whose members inhabit a wide variety of habitats and possess diverse plumage traits and as such offer an interesting case study. Here, we sequence the genomes of 34 individuals comprising three grouse taxa; the willow grouse (Lagopus lagopus lagopus), the red grouse (Lagopus lagopus scoticus) and the rock ptarmigan (Lagopus muta) in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show consistent signs of differential selection across the species. These genes are highly involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics also reveal a strong signal of population expansion acting across the genomes, which is in line with previous demographic studies in these systems. Additionally, we uncover a 3.5Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating the action of uniform selection. The Agouti gene, which is integral in the pigmentation pathway, lies at the 5' start of this region hinting at the conserved development of brown plumage across the three taxa. Together, our results provide a key step in the exploration of grouse speciation and adaptation. 

Keyword [en]
Speciation, adaptation, grouse, Tetraoninae, population genomics, FOXP4, Agouti
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-298415OAI: oai:DiVA.org:uu-298415DiVA: diva2:945908
Available from: 2016-07-04 Created: 2016-07-04 Last updated: 2016-08-26
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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