Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

Strasburg, Jared L.; Kane, Nolan C.; Raduski, Andrew R.; Bonin, Aurélie; Michelmore, Richard W.; Rieseberg, Loren H.

doi:10.1093/molbev/msq270

Cited by 93 publications

(118 citation statements)

References 69 publications

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“…Unlike the natural populations, the adaptive loci are likely to more severely affect the Ne estimates, especially on LG2, in which roughly two-fold differences were found between 95%-CI-loci estimation (NeLG2 = 10053) and total-loci estimation (NeLG2 = 5597). The severe influence of adaptive loci on larger-Ne population (LG2) than small-Ne population (LG1) is consistent with a case of sunflowers that the adaptive divergence is positively correlated with the Ne of the species with large Ne but not of the species with small Ne [57]. The dramatically different estimates of adaptive divergence on larger-Ne population could be due to the easier accumulation of adaptive variations between high-differentiated lineages, which have higher Ne estimates [57].…”

Section: Ne Of Reforested Populations and Ne Reduction Of Biased Sampsupporting

confidence: 83%

Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management

Huang

et al. 2015

Forests

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Effective population size (Ne) is a crucial metric for evaluating the current status of genetic diversity and conservation management. Population of Kandelia obovata, a mangrove species that is patchily distributed along the estuaries off Southeastern China, is genetically structured. Here, we applied skyline analyses to infer the demographic history of K. obovata based on Amplified Fragment Length Polymorphisms (AFLP) data. Congruent trends of population growth rate among populations, but concurrent change in Ne estimates, were inferred in all populations. The recent rapid habitat expansion explains the high census population size but small Ne of populations in Northern Taiwan. Our study also revealed lower Ne of reforested populations than their sources. In silico demographic analyses simulate the small or biased sampling of seedlings for reforestation and revealed over 90% and 99% Ne reduction when only 1/2 and 1/10 samples were collected, respectively. These results emphasize the importance of a comprehensive sampling of OPEN ACCESSForests 2015, 6 1440 seeds for restoration. Overall, this study rendered, not only the current Ne of K. obovata populations, but also indicates the importance of Ne estimation on restoration.

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Section: Ne Of Reforested Populations and Ne Reduction Of Biased Sampsupporting

confidence: 83%

Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management

Huang

et al. 2015

Forests

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“…This is the first report of this quantity on a genome-wide scale for a conifer (but see Eckert et al 2013), which will add to the emerging literature of adaptive amino acid evolution estimates for plant species (Gossmann et al 2010;Slotte et al 2010;Strasburg et al 2011). In addition, a suite of 31 outliers with respect to summaries of the site-frequency spectrum was also identified after accounting for a simple demographic null model (see Table S10).…”

Section: Evolutionary Genetics Of Gene Regions Underlying Phenotypic mentioning

confidence: 85%

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

et al. 2013

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A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for .7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the .1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.A primary goal of population and quantitative genetics is to understand the genetic architecture of ecologically relevant traits (Stinchcombe and Hoekstra 2008; Barrett and Hoekstra 2011;Neale and Kremer 2011). A primary step on the path to this goal is to link genetic with phenotypic variation, either through linkage mapping of quantitative trait loci using pedigrees or through linkage disequilibrium mapping in natural populations (Lander and Schork 1994), with the latter currently being the most utilized. A multitude of studies ranging across a diverse set of taxa have discovered myriad genotype-phenotype correlations (Hindorff et al. 2009;Ingvarsson and Street 2011;Neale and Kremer 2011). Each discovered variant, however, often explains only a small fraction of the heritable phenotypic variance, thus being consistent with a polygenic model for the genetic architecture of complex traits (Lynch and Walsh 1998). Concomitant with the discovery of these associations are population genomic scans documenting deviations from expectations derived using the neutral theory (Nielsen 2005). Such scans have also discovered large numbers of loci putatively underlying phenotypic traits in many different taxa (e.g., Pollinger et al. 2005;Pritchard et al. 2010;Hufford et al. 2012), but in this case the link between genotype and phenotype is not explicit. A natural question thus arises about how much overlap exists between the lists gen...

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“…In contrast, weakly underdominant rearrangements can go to fixation more easily via drift, but are expected to have minimal effects on gene flow. In this case, however, the drift-based establishment of even weakly underdominant rearrangements is improbable due to the occurrence of sporophytic self-incompatibility (resulting in obligate outcrossing) and large effective population sizes in wild Helianthus species (Strasburg et al 2011). …”

Section: Discussionmentioning

confidence: 99%

Chromosomal Evolution and Patterns of Introgression inHelianthus

et al. 2014

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Knowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodones Dune sunflower (H. niveus ssp. tephrodes) genomes and compared them to a consensus map of cultivated sunflower (H. annuus) to identify chromosomal rearrangements between species. The genetic maps of H. argophyllus and H. niveus ssp. tephrodes included 17 linkage groups each and spanned 1337 and 1478 cM, respectively. Comparative analyses revealed greater divergence between H. annuus and H. niveus ssp. tephrodes (13 inverted segments, 18 translocated segments) than between H. annuus and H. argophyllus (10 inverted segments, 8 translocated segments), consistent with their known phylogenetic relationships. Marker order was conserved across much of the genome, with 83 and 64% of the H. argophyllus and H. niveus ssp. tephrodes genomes, respectively, being syntenic with H. annuus. Population genomic analyses between H. annuus and H. argophyllus, which are sympatric across a portion of the natural range of H. annuus, revealed significantly elevated genetic structure in rearranged portions of the genome, indicating that such rearrangements are associated with restricted gene flow between these two species.C HROMOSOMAL rearrangements are of considerable interest because they are often associated with barriers to gene flow between related species, either due to their direct effects on the fitness of heterozygotes or through the indirect effects of genic barriers embedded within them (White 1978;Barton and Bengtsson 1986;Rieseberg et al. 1995bRieseberg et al. , 1999Rieseberg 2001;Navarro and Barton 2003;Kirkpatrick and Barton 2006; reviewed in Faria and Navarro 2010;Gimenez et al. 2012). As such, detailed information on karyotypic differences between species provides insight into the nature of reproductive isolation and, more pragmatically, informs attempts to introgress beneficial alleles from wild species into crop gene pools (Chetelat and Meglic 2000;Foulongne et al. 2003;Dirlewanger et al. 2004). An improved understanding of synteny across species can also facilitate the identification and localization of functionally important genes in a taxon of interest through the extrapolation of gene order from model species (e.g., Choi et al. 2004;Dilbirligi et al. 2006).The genus Helianthus, which is composed of 49 species native to the Americas (Timme et al. 2007) and includes cultivated sunflower (Helianthus annuus L.; 2n = 2x = 34; hereafter referred to as ANN), has emerged as a model for genetic studies of adaptation, hybridization, and speciation (Rieseberg et al. 1995a,b;Lai et al. 2005;Reagon and Snow 2006;Massinga et al. 2009;Gutierrez et al. 2010;Vekemans 2010;Roumet et al. 2013). Insight into the nature and extent of reproductive barriers within Helianthus will ...

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Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

Cited by 93 publications

References 69 publications

Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management

Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

Chromosomal Evolution and Patterns of Introgression inHelianthus

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