Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

@article{Hohenlohe2010PopulationGO,
  title={Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags},
  author={Paul A Hohenlohe and Susan Bassham and Paul D. Etter and Nicholas Stiffler and Eric A. Johnson and William A. Cresko},
  journal={PLoS Genetics},
  year={2010},
  volume={6}
}
Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals… 

Figures and Tables from this paper

Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations
TLDR
It is concluded that natural selection has maintained this variation over geological timescales and that the same alleles the authors observe in freshwater stickleback today are the same as those under selection in ancient, now-extinct freshwater habitats.
Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
TLDR
The findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations.
Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations
TLDR
The genomic variation that is involved in recent and rapid local adaptation in stickleback has therefore been evolving throughout the 15‐million‐year history since the two species lineages split, demonstrating how selection on ecological timescales is a result of genome evolution over geological timescale, and vice versa.
Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions
TLDR
Analysis of striking parallel morphological divergences of parapatric stream–lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada emphasizes the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.
Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss
TLDR
High-throughput genotyping for the economically and culturally important salmonid Oncorhynchus mykiss suggests an important adaptive role for immune-related functions and presents a large genomic resource for future studies.
Predictable genome‐wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish
TLDR
This study uses multiple populations of threespine stickleback fish adapted to two different types of derived freshwater habitats—basic and acidic lakes on the island of North Uist, Outer Hebrides, Scotland—and the present‐day proxy of their marine ancestor to reveal striking genome‐wide determinism in both the loci involved in parallel divergence, and in the direction in which alleles at these loci have been selected.
Genomics of adaptation revealed in threespine stickleback
TLDR
The main model organism is the threespine stickleback fish and it is demonstrated that the repeated occurrence of similar stream phenotypes are, in this particular system, better explained by an evolutionary scenario of 'ecological vicariance' rather than repeated parallel divergence.
The Population Genomics of Parallel Adaptation: Lessons from Threespine Stickleback
TLDR
This work reviews results and assess alternative modes for the genetic basis of parallel phenotypic adaptation in threespine stickleback in terms of the genetic architecture of the traits and the source of adaptive variation across populations.
Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes
TLDR
Dense genetic maps demonstrate that the interaction between selection and population structure may impact large stretches of the stickleback genome, and advance the understanding of how the structuring of populations across geography influences the outcomes of selection, and how the recombination landscape broadens the genomic reach of selection.
Genetic variation in the acorn barnacle from allozymes to population genomics.
TLDR
A survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 213 REFERENCES
New genomic tools for molecular studies of evolutionary change in threespine sticklebacks
TLDR
A number of genomic and genetic tools should make it possible to identify the molecular basis of many different evolutionary traits in stickleback, and to begin to answer longstanding questions about the numbers and types of mutations that control the appearance of new morphological, physiological, and behavioral traits during vertebrate evolution.
The genetic architecture of divergence between threespine stickleback species
TLDR
A genome-wide linkage map is developed for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago.
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
TLDR
A population genetic analysis of Drosophila simulans is presented based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba, to suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophile genome.
Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling
Recombinational Landscape and Population Genomics of Caenorhabditis elegans
TLDR
Despite the low population, effective recombination rate and extensive linkage disequilibrium among chromosomes, which are techniques that account for background levels of genomic similarity, permit association mapping in wild C. elegans strains.
Hitchhiking Mapping Reveals a Candidate Genomic Region for Natural Selection in Three-Spined Stickleback Chromosome VIII
TLDR
The results suggest that the narrow interval around locus Stn90 has likely been under directional selection, but the region contains several predicted genes, each of which can be the actual targets of selection.
Rapid genetic divergence in postglacial populations of threespine stickleback (Gasterosteus aculeatus): the role of habitat type, drainage and geographical proximity
TLDR
The utility of hypervariable microsatellites for detecting recent population divergences and the danger of operating at temporal or spatial scales which are beyond their resolution are demonstrated.
Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations.
TLDR
Rapid and repeated armor loss in Alaskan stickleback populations appears to be occurring through the fixation of large-effect variants in the same genes, implicating the same Mendelian armor reduction genes.
Identifying footprints of directional and balancing selection in marine and freshwater three‐spined stickleback (Gasterosteus aculeatus) populations
TLDR
To identify targets of natural selection in the three‐spined stickleback genome, 103 microsatellite and two indel markers including expressed sequence tags and quantitative trait loci (QTL)‐associated loci, were genotyped in four freshwater and three marine populations and indicated that a high proportion of loci might be affected by balancing selection and a lower proportion by directional selection.
Intraspecific Systematics of Gasterosteus Aculeatus Populations: Implications for Behavioral Ecology
TLDR
The phylogeny of threespine stickleback populations and the use of phylogenetic information to analyze causation of pelvic girdle variation among populations are reviewed and criteria for selection of populations and behavioral traits for comparative studies are discussed.
...
1
2
3
4
5
...