Local adaptation across a climatic gradient despite small effective population size in the rare sapphire rockcress

McKay, John; Bishop, John G.; Lin, Jing-Zhong; Richards, James H.; Sala, Anna; Mitchell‐Olds, Thomas

doi:10.1098/rspb.2001.1715

Cited by 144 publications

(153 citation statements)

References 54 publications

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“…We believe that information from DNA markers together with phenotypic performance and population history may provide reliable guidelines in choosing populations for practical and for conservation purposes. However, setting conservation priorities based exclusively on the diversity of molecular markers might lead to the loss of locally adapted populations [32].…”

Section: The Chicken Ancestor and The Need For Conservationmentioning

confidence: 99%

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Groenen²,

et al. 2003

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-In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of populationspecific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.genetic distance / polymorphism / red jungle fowl / DNA markers / domesticated chicken

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Section: The Chicken Ancestor and The Need For Conservationmentioning

confidence: 99%

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Groenen²,

et al. 2003

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“…In a recent study where desert and Mediterranean plants of Hordeum spontaneum were found to be adapted to their locations and differentiated in phenotypic traits (Volis et al, 2002b), no concordance between quantitative and molecular (allozyme) pairwise genetic distances was detected (Volis et al, 2002a). Several studies in which patterns of quantitative trait variation were strongly associated with climate or distinct habitats also demonstrated a lack of correspondence between molecular and quantitative trait variation patterns (Karhu et al, 1996;Knapp and Rice, 1998;McKay et al, 2001;Steinger et al, 2002). In other studies where genetic subdivisions at quantitative and molecular markers were compared in their relation to geographic subdivision but without tests of local adaptation/ association with environmental parameters, or were compared without any reference to spatial location/ environmental differences, the outcomes varied from a close match (Lagercrantz and Ryman, 1990;Kuittinen et al, 1997;Morgan et al, 2001) to complete disagreement (Podolsky and Holtsford, 1995;Black-Samuelsson et al, 1997;Heaton et al, 1999;Storz, 2002).…”

Section: Introductionmentioning

confidence: 99%

Distinguishing adaptive from nonadaptive genetic differentiation: comparison of QST and FST at two spatial scales

et al. 2005

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Genetic differentiation in 20 hierarchically sampled populations of wild barley was analyzed with quantitative traits, allozymes and Random Amplified Polymorphic DNAs (RAPDs), and compared for three marker types at two hierarchical levels. Regional subdivision for both molecular markers was much lower than for quantitative traits. For both allozymes and RAPDs, most loci exhibited minor or no regional differentiation, and the relatively high overall estimates of the latter were due to several loci with exceptionally high regional differentiation. The allozymeand RAPD-specific patterns of differentiation were concordant in general with one another, but not with quantitative trait differentiation. Divergent selection on quantitative traits inferred from very high regional Q ST was in full agreement with our previous results obtained from a test of local adaptation and multilevel selection analysis. In contrast, most variation in allozyme and RAPD variation was neutral, although several allozyme loci and RAPD markers were exceptional in their levels of regional differentiation. However, it is not possible to answer the question whether these exceptional loci are directly involved in the response to selection pressure or merely linked to the selected loci. The fact that Q ST and F ST did not differ at the population scale, that is, within regions, but differed at the regional scale, for which local adaptation has been previously shown, implies that comparison of the level of subdivision in quantitative traits, as compared with molecular markers, is indicative of adaptive population differentiation only when sampling is carried out at the appropriate scale. Heredity (2005) 95, 466-475.

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“…Local adaptation might be suspected because of the existence of an environmental gradient such as latitude (Toräng et al, 2015) or altitude (Alberto et al, 2011), or because of the existence of several contrasting environments, such as sea and fresh water (DeFaveri and Merilä, 2014). In addition, common garden experiments are also used to study the consequences of local adaptation for conservation (McKay et al, 2001) or even for ecosystem functioning (Bassar et al, 2010). Despite its name, and although it has been used extensively with plants (Linhart and Grant, 1996), this experimental approach can also be applied to a large variety of organisms including fish (Bassar et al, 2010;DeFaveri and Merilä, 2014), invertebrates (Spitze, 1993;Luttikhuizen et al, 2003) and small mammals (Bozinovic et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Common garden experiments in the genomic era: new perspectives and opportunities

Villemereuil¹,

Gaggiotti²,

Mouterde³

et al. 2015

Heredity

291

242

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The study of local adaptation is rendered difficult by many evolutionary confounding phenomena (for example, genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specifically designed to deal with phenotypic plasticity, has a clear role to play in the study of local adaptation, even (if not specifically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efficient, thorough and integrative study of local adaptation. Especially, evidence from genomic (for example, genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits.

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Local adaptation across a climatic gradient despite small effective population size in the rare sapphire rockcress

Cited by 144 publications

References 54 publications

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Distinguishing adaptive from nonadaptive genetic differentiation: comparison of QST and FST at two spatial scales

Common garden experiments in the genomic era: new perspectives and opportunities

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