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

@article{Sim2016GenomewideSO,
  title={Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate},
  author={Zijian Sim and Jocelyn C Hall and Bill Jex and Troy Hegel and David W. Coltman},
  journal={Molecular Ecology},
  year={2016},
  volume={25}
}
Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice‐free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in… 
Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California
TLDR
The Nebria ingens complex (Coleoptera: Carabidae), a water‐affiliated ground beetle lineage, is used to test how drainage basins are linked to their observed population structure and it is found that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingen complex.
Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest
TLDR
The results for the first time suggest that Yunnan and Sichuan jointly served as two large-scale refugia in eastern Asia in Quaternary glaciations, helping to maintain genetic diversity overall.
Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon
TLDR
It is highlighted how Pleistocene glaciations can drive large-scale intraspecific variation in genomic architecture of northern species as well as evidence of selection on both regions suggests adaptive variation associated with karyotypes.
Management implications of highly resolved hierarchical population genetic structure in thinhorn sheep
TLDR
The results indicate that contemporary patterns of genetic variation can be influenced by events acting over a range of spatial and temporal scales, and thus the importance of interpreting the findings of present-day genetic structure in light of the phylogeographical history of the species in question.
Late Pleistocene origin of the entire circumarctic range of the arctic‐alpine plant Kalmia procumbens
TLDR
It is demonstrated that range‐wide genetic structure in arctic‐alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.
Ancient hybridization patterns between bighorn and thinhorn sheep
TLDR
The results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep, which was probably due to ILS or intermediary secondary contact.
Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon
TLDR
It is highlighted how Pleistocene glaciations can influence large‐scale intraspecific variation in genomic architecture of northern species as well as potential selection on both genomic regions.
The genetic legacy of 50 years of desert bighorn sheep translocations
TLDR
A signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges, is found, and evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep is found.
Identification of winter moth (Operophtera brumata) refugia in North Africa and the Italian Peninsula during the last glacial maximum
TLDR
The results suggest that winter moth populations persisted in at least five Mediterranean LGM refugia, and that outbreaks by winter moth in northwestern Tunisia are not the result of a recent introduction of a nonnative species, but rather are most likely due to land use or environmental changes.
Evolutionary reconstruction supports the presence of a Pleistocene Arctic refugium for a large mammal species
The presence of refugia in the Canadian High Arctic has been subject to debate for decades. We investigated the potential existence of Arctic refugia during the Pleistocene for a large mammal species
...
...

References

SHOWING 1-10 OF 62 REFERENCES
HOT SPOTS OF GENETIC DIVERSITY DESCENDED FROM MULTIPLE PLEISTOCENE REFUGIA IN AN ALPINE UNGULATE
TLDR
Across their range, mountain goats were highly genetically structured and displayed the expected pattern of declining diversity toward the periphery, and Gene flow was high within contiguous mountain ranges, but cross‐assignments paradoxically suggest that long‐distance contemporary dispersal movements are not uncommon.
Species‐wide phylogeography of North American mule deer (Odocoileus hemionus): cryptic glacial refugia and postglacial recolonization
Quaternary climatic oscillations greatly influenced the present‐day population genetic structure of animals and plants. For species with high dispersal and reproductive potential, phylogeographic
Evidence for cryptic glacial refugia from North American mountain sheep mitochondrial DNA
TLDR
These results are the first to demonstrate support for survival of any organism in the latter two refugia of North American mountain sheep Ovis spp, and appear to have conserved a genetic signal that confirms past hybridization of O. dalli and O. canadensis.
Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America
TLDR
The emergent patterns from this review suggest the classic Beringian‐southern refugial paradigm for northwestern North American biota should be refined and highlighted to highlight the ecological and evolutionary consequences of colonization from multiple refugia.
Some genetic consequences of ice ages, and their role in divergence and speciation
The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their
When Cold is Better: Climate-Driven Elevation Shifts Yield Complex Patterns of Diversification and Demography in an Alpine Specialist (American Pika, Ochotona princeps)
TLDR
An ecological niche model of past and future pika distributions highlights the influence of climate on species range and indicates that the distribution of genetic diversity may change dramatically with continued climate warming.
Genetic Evidence for Restricted Dispersal along Continuous Altitudinal Gradients in a Climate Change-Sensitive Mammal: The American Pika
TLDR
Correlative analyses revealed an association between patterns of genetic variation and annual heat-to-moisture ratio, mean annual precipitation, precipitation as snow and mean maximum summer temperature, and changes in climatic regimes forecasted for the region may increase the rate of population extirpation by further reducing dispersal between sites.
Reduced genetic variation in insular northern flying squirrels (Glaucomys sabrinus) along the North Pacific Coast
Nearshore oceanic archipelagos are natural laboratories that could provide valuable insight into the role of evolutionary processes such as founder effects and incipient speciation in biotic
Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls
TLDR
The analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction.
MITOCHONDRIAL PHYLOGEOGRAPHY AND CONSERVATION GENETICS OF WOLVERINE (GULO GULO) OF NORTHWESTERN NORTH AMERICA
TLDR
Conservation plans for these medium-sized carnivores should emphasize maintenance of genetic diversity and recognize that successful dispersal of females between populations may be limited, a finding consistent with male-biased dispersal in wolverines.
...
...