A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

@article{Kubota2015AGS,
  title={A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species},
  author={Shosei Kubota and Takaya Iwasaki and Kousuke Hanada and Atsushi J. Nagano and Asao Fujiyama and Atsushi Toyoda and Sumio Sugano and Yutaka Suzuki and Kouki Hikosaka and Motomi Ito and Shin-ichi Morinaga},
  journal={PLoS Genetics},
  year={2015},
  volume={11}
}
Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show… 
Genomic patterns of local adaptation under gene flow in Arabidopsis lyrata.
TLDR
This work uses locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to detect signatures of selection for local adaptation, and estimates patterns of lineage specific differentiation among these populations.
A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a
Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in Arabidopsis lyrata
TLDR
It is suggested that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense were indicated as selected traits in the lowland habitats.
Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives
TLDR
It is concluded that genetic divergence between populations, species and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.
Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
TLDR
It is concluded that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species‐specific.
The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus
TLDR
These analyses point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis to trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.
Plant adaptation and speciation studied by population genomic approaches
TLDR
Recent studies of plants using population genomics are reviewed, covering those focusing on interactions with other organisms, adaptations to local climatic conditions, and the genomic causes and consequences of reproductive isolation.
Population structure and local selection yield high genomic variation in Mimulus guttatus
TLDR
The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM, and many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.
RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway
TLDR
Whether three autotetraploid Cochlearia officinalis ecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions is investigated.
Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation
TLDR
Arabidopsis halleri is introduced and its life history as a perennial model system to study population differentiation and local adaptation and how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms is discussed.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 77 REFERENCES
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils,
Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis)
TLDR
The enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low‐ and high‐altitude populations, suggesting the importance of local adaptation in alpine populations of common voles.
Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
TLDR
Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia, consistent with a process of parallel ecotypic divergence in face of gene flow.
Adaptation to Climate Across the Arabidopsis thaliana Genome
TLDR
A genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana provided a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.
Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
TLDR
Genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps are examined to provide a genomewide perspective on the distribution of adaptive genetic variation innatural plant populations from a highly diverse and heterogeneous alpine environment.
A Map of Local Adaptation in Arabidopsis thaliana
TLDR
Fitness-associated loci exhibited both geographic and climatic signatures of local adaptation, and independent local adaptation by distinct genetic mechanisms may facilitate a flexible evolutionary response to changing environment across a species range.
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
TLDR
The 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47, based on 8.3× dideoxy sequence coverage, is reported, indicating pervasive selection for a smaller genome in this outcrossing species.
DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES
TLDR
A genomic comparison of ecotypes of the prairie sunflower, Helianthus petiolaris, occurring at Great Sand Dunes National Park and Preserve (Colorado), found that selective sweeps were mainly restricted to the dune ecotype and that there was variation across the genome in whether proximity to the nondune population constrained or promoted divergence.
STRONG SELECTION BARRIERS EXPLAIN MICROGEOGRAPHIC ADAPTATION IN WILD SALAMANDER POPULATIONS
TLDR
The results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow, suggesting that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes.
THE GENETIC ARCHITECTURE OF ADAPTATION UNDER MIGRATION–SELECTION BALANCE
TLDR
Analytical approximations and individual‐based simulations are used to explore how genetic architecture evolves when two populations connected by migration experience stabilizing selection toward different optima and find that adaptation with migration tends to result in concentrated genetic architectures with fewer, larger, and more tightly linked divergent alleles.
...
1
2
3
4
5
...