Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

2016 ◽  
Vol 25 (15) ◽  
pp. 3696-3705 ◽  
Author(s):  
Zijian Sim ◽  
Jocelyn C. Hall ◽  
Bill Jex ◽  
Troy M. Hegel ◽  
David W. Coltman
Keyword(s):  
Glacial Refugia ◽  
Genome Wide ◽  
Postglacial Recolonization

scholarly journals Genomics of end-Pleistocene population replacement in a small mammal

2018 ◽  
Vol 285 (1872) ◽  
pp. 20172624 ◽  
Author(s):  
Petr Kotlík ◽  
Silvia Marková ◽  
Mateusz Konczal ◽  
Wiesław Babik ◽  
Jeremy B. Searle
Keyword(s):  
Small Mammals ◽  
Bank Vole ◽  
Glacial Refugia ◽  
European Population ◽  
Population History ◽  
Clethrionomys Glareolus ◽  
Autosomal Snps ◽  
Genome Wide ◽  
Northern Territories ◽  
Approximate Bayesian

Current species distributions at high latitudes are the product of expansion from glacial refugia into previously uninhabitable areas at the end of the last glaciation. The traditional view of postglacial colonization is that southern populations expanded their ranges into unoccupied northern territories. Recent findings on mitochondrial DNA (mtDNA) of British small mammals have challenged this simple colonization scenario by demonstrating a more complex genetic turnover in Britain during the Pleistocene–Holocene transition where one mtDNA clade of each species was replaced by another mtDNA clade of the same species. Here, we provide evidence from one of those small mammals, the bank vole ( Clethrionomys glareolus ), that the replacement was genome-wide. Using more than 10 000 autosomal SNPs we found that similar to mtDNA, bank vole genomes in Britain form two (north and south) clusters which admix. Therefore, the genome of the original postglacial colonists (the northern cluster) was probably replaced by another wave of migration from a different continental European population (the southern cluster), and we gained support for this by modelling with approximate Bayesian computation. This finding emphasizes the importance of analysis of genome-wide diversity within species under changing climate in creating opportunities for sophisticated testing of population history scenarios.

scholarly journals Genome‐wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree

2015 ◽  
Vol 207 (3) ◽  
pp. 723-734 ◽  
Author(s):  
Kai N. Stölting ◽  
Margot Paris ◽  
Cécile Meier ◽  
Berthold Heinze ◽  
Stefano Castiglione ◽  
...  
Keyword(s):  
Forest Tree ◽  
Populus Alba ◽  
Genome Wide ◽  
Postglacial Recolonization ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dunja Lukić ◽  
Tom Pinceel ◽  
Federico Marrone ◽  
Monika Mioduchowska ◽  
Csaba F. Vad ◽  
...  
Keyword(s):  
Glacial Refugia ◽  
Temporary Ponds ◽  
Secondary Contact ◽  
Glacial Cycles ◽  
Long Distance ◽  
Mitochondrial Coi ◽  
Postglacial Recolonization ◽  
History Of ◽  
Suitable Habitats ◽  
Glacial Periods

AbstractPleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.

Species-wide phylogeography of North American mule deer (Odocoileus hemionus): cryptic glacial refugia and postglacial recolonization

2009 ◽  
Vol 18 (8) ◽  
pp. 1730-1745 ◽  
Author(s):  
EMILY K. LATCH ◽  
JAMES R. HEFFELFINGER ◽  
JENNIFER A. FIKE ◽  
OLIN E. RHODES Jr
Keyword(s):  
North American ◽  
Mule Deer ◽  
Odocoileus Hemionus ◽  
Glacial Refugia ◽  
Postglacial Recolonization

Genetic subdivision, glacial refugia and postglacial recolonization in the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela)

2000 ◽  
Vol 9 (6) ◽  
pp. 771-781 ◽  
Author(s):  
J. Alexandrino ◽  
E. Froufe ◽  
J. W. Arntzen ◽  
N. Ferrand
Keyword(s):  
Glacial Refugia ◽  
Genetic Subdivision ◽  
Postglacial Recolonization ◽  
Chioglossa Lusitanica

Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant modelArabidopsis arenosa

2016 ◽  
Vol 25 (16) ◽  
pp. 3929-3949 ◽  
Author(s):  
Filip Kolář ◽  
Gabriela Fuxová ◽  
Eliška Záveská ◽  
Atsushi J. Nagano ◽  
Lucie Hyklová ◽  
...  
Keyword(s):  
Glacial Refugia ◽  
Niche Divergence ◽  
Genome Wide

scholarly journals Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

2021 ◽  
Author(s):  
Matthew Osmond ◽  
Graham Coop
Keyword(s):  
Isolation By Distance ◽  
Glacial Refugia ◽  
Approximate Model ◽  
Long Distance ◽  
Population Movements ◽  
Continuous Space ◽  
Amount Of Information ◽  
Branching Brownian Motion ◽  
High Dispersal ◽  
Genome Wide

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation by distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, up till recently, not been computational feasible. Here we capitalize on important recent advances in gene-genealogy reconstruction and develop methods to use thousands of trees to estimate time-varying per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to the 1001 Genomes dataset of over one thousand Arabidopsis thaliana genomes sampled across a wide geographic extent. We detect a very high dispersal rate in the recent past, especially longitudinally, and use inferred ancestor locations to visualize many examples of recent long-distance dispersal and admixture. We also use inferred ancestor locations to identify the origin and ancestry of the North American expansion and to depict alternative geographic ancestries stemming from multiple glacial refugia. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

scholarly journals Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

2021 ◽  
Author(s):  
Carolina Osuna-Mascaro ◽  
Rafael Rubio de Casas ◽  
Jose M Gomez ◽  
Joao Loureiro ◽  
Silvia Castro ◽  
...  
Keyword(s):  
Glacial Refugia ◽  
Plant Evolution ◽  
Glacial Refugium ◽  
Major Influence ◽  
Species Complexes ◽  
Genome Wide ◽  
Brassicaceae Species ◽  
Genomic Analyses ◽  
Genomic Regions ◽  
Hybridization And Introgression

Background and Aims: Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes. Methods: We combined flow cytometry, transcriptomic and genomic analyses, and pollen-tube growth assays to investigate the consequences of polyploidization, hybridization, and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2Myr, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization, and introgression. Key Results: Our results support a scenario of widespread hybridization involving both extant and ghost taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, likely of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as prezygotic barriers appeared weak in many cases. Conclusions: The evolution of Erysimum spp. has been determined by hybridization to a large extent. The adaptive value of such genomic exchanges remains unclear, but our results indicate the importance of hybridization for plant diversification across evolutionary scales.

scholarly journals Genome‐wide SNP data reveal improved evidence for Antarctic glacial refugia and dispersal of terrestrial invertebrates

2019 ◽  
Vol 28 (22) ◽  
pp. 4941-4957 ◽  
Author(s):  
Angela McGaughran ◽  
Aleks Terauds ◽  
Peter Convey ◽  
Ceridwen I. Fraser
Keyword(s):  
Glacial Refugia ◽  
Terrestrial Invertebrates ◽  
Snp Data ◽  
Genome Wide
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