Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves

@article{Schweizer2016TargetedCA,
  title={Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves},
  author={Rena M. Schweizer and Jacqueline A. Robinson and Ryan J. Harrigan and Pedro Silva and Marco Galverni and Marco Musiani and Richard E. Green and John Novembre and Robert K. Wayne},
  journal={Molecular Ecology},
  year={2016},
  volume={25}
}
In an era of ever‐increasing amounts of whole‐genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array‐based genome scans is uncertain. We previously performed a SNP array‐based genome scan to identify candidate genes under selection in six distinct grey wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1‐kb… 
Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species
TLDR
Assessment of adaptive genomic variation within a nonmodel plant species, the narrow‐leaf hopbush, shows that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline.
Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows
TLDR
High‐density genomewide genetic data collected across an extensive range of temperate, arid and tropical climates, in Australian populations that were introduced from Europe 150 years ago is analysed to identify putative loci subject to selection across these varied climates.
Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
TLDR
A multiplexed, sequence capture assay for red foxes provides a template to assess immunogenetic variation in wildlife disease systems and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies.
The evolutionary history of grey wolf Y chromosomes
TLDR
The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago, and the disputed origin of a recently founded population of Scandinavian wolves is addressed.
Environmental correlates of genetic variation in the invasive and largely panmictic European starling in North America
TLDR
This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.
Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium
TLDR
Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations, and methodological considerations for population genomics studies that aim to use novel genomic approaches on non-model systems are provided.
Environmental correlates of genetic variation in the invasive European starling in North America
TLDR
This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world‐wide local adaptation in these highly dispersive and invasive birds.
Broad Concordance in the Spatial Distribution of Adaptive and Neutral Genetic Variation across an Elevational Gradient in Deer Mice
TLDR
Exome-wide population genomic analysis on deer mice sampled along an elevational gradient of nearly 4000 m of vertical relief found that a large proportion of the exome has experienced a history of altitude-related selection, suggesting new hypotheses about the genetic basis of physiological adaptation to high-altitude, and the spatial distribution of adaptive genetic variation along environmental gradients.
Conservation genomics illuminates the adaptive uniqueness of North American gray wolves
TLDR
It is recommended that future conservation efforts should provide full protection for distinct ecotypes, support scientifically rigorous definitions of historical range to inform restoration, and enhance the legal status of admixed populations.
Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations
TLDR
The results suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se, and that the interplay between gene flow and selection was stronger towards the northern peripheries.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 175 REFERENCES
Genetic subdivision and candidate genes under selection in North American grey wolves
TLDR
It is shown that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan, likely reflecting high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome.
Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
TLDR
This study is the first to demonstrate the efficiency of large‐scale targeted resequencing for a nonmodel species with such a large and unsequenced genome, suggesting changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein‐coding mutations.
Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing data sets.
TLDR
It is found that putative targets of selection were highly significantly enriched in genic and nonsynonymous single nucleotide polymorphisms, and that DIND was more powerful than iHS in the context of small sample sizes, low-quality genotype calling, or poor coverage.
Localizing Recent Adaptive Evolution in the Human Genome
TLDR
It is found that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.
A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids.
TLDR
It is found that these enigmatic canids are highly admixed varieties derived from gray wolves and coyotes, respectively, and divergent genomic history suggests that they do not have a shared recent ancestry as proposed by previous researchers.
Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication
TLDR
It is shown that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data.
Classic Selective Sweeps Revealed by Massive Sequencing in Cattle
TLDR
This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to identify specific regions targeted by selection during speciation, domestication and breed formation of cattle.
Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication
TLDR
It is argued that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
Genome-wide signatures of population bottlenecks and diversifying selection in European wolves
TLDR
The results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population.
Genome-wide detection and characterization of positive selection in human populations
TLDR
‘Long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are developed.
...
1
2
3
4
5
...