title: Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing.
abstract: The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes.
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.|State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China.
authors.forename: Guangpeng
authors.initials: G
authors.lastname: Ren
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.|Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Rubén G
authors.initials: RG
authors.lastname: Mateo
authors.affiliation: State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China.
authors.forename: Jianquan
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Suchan
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Nadir
authors.initials: N
authors.lastname: Alvarez
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.|Institute of Earth Surface Dynamics, Geopolis, University of Lausanne, 1015, Lausanne, Switzerland.
authors.forename: Antoine
authors.initials: A
authors.lastname: Guisan
authors.affiliation: Department of Systematic and Evolutionary Botany and Botanic Garden, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
authors.forename: Elena
authors.initials: E
authors.lastname: Conti
authors.affiliation: Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
mesh_terms: D002980:Climate; D017753:Ecosystem; D014644:Genetic Variation; D023281:Genomics; D005843:Geography; D008957:Models, Genetic; D005810:Multigene Family; D011157:Population Dynamics; D031825:Primula / Q000235:genetics*; D025341:Principal Component Analysis; D011336:Probability; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA; D013045:Species Specificity
keywords: Himalayas; Quaternary climatic changes; demography; isolation by distance; phylogeography; population structure; restriction site-associated DNA sequencing (RADseq)