Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Li, Chengyin; Sun, Ye; Huang, Hongwen; Cannon, Charles H.

doi:10.1038/hdy.2014.58

Cited by 27 publications

(24 citation statements)

References 36 publications

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“…Our results revealed a pattern of genetic divergence similar to that shown in Castanopsis fargesii [34]. The authors proposed that the rapid and dramatic uplift of the western Yunnan-Guizhou plateau and the eastern Wuyi Mountains had a huge impact on the molecular differentiation of the subtropical broad-leaved tree species in China.…”

Section: Genetic Structure Analysis Of T Ciliatasupporting

confidence: 77%

Genetic diversity and population structure ofToona ciliatarevealed by simple sequence repeat markers

Zhan

Hui

et al. 2019

Biotechnology & Biotechnological Equipment

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Toona ciliata (Meliaceae) is a rare, fast-growing commercial tree species that produces red timber with beautiful grains. It used to be widely distributed in the past, but few natural forests exist in the field now. Here, we tested 12 nuclear microsatellite markers derived from 551 individuals of 29 populations in China, and investigated the genetic diversity and population structure in T. ciliata. Our results revealed 146 alleles obtained from all of the populations studied here, with an average polymorphic information content of 0.723. The populations could be divided into two major genetic lineages using STRUTURE analysis: 14 and 15 populations from different provinces clustered in Western and Eastern genetic lineages, respectively. The genetic differentiation among the two genetic lineages was 28%. The genetic diversity of the Western lineage was higher than that of the Eastern lineage. Moreover, a Mantel test of the relationship between genetic and geographic distances revealed significantly positive correlations both among all 29 populations and within the Eastern genetic lineage, whereas there was no significant correlation in the Western genetic lineage. Therefore, in the conservation strategy of T. ciliatare sources, the two genetic lineages should be treated independently. To the best of our knowledge, these data are the first detailed characterization of the genetic structure and diversity of T. ciliata populations using nuclear microsatellite markers. The obtained results lay the foundation for preservation of the T. ciliata germplasm resources and support further artificial breeding efforts.

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Section: Genetic Structure Analysis Of T Ciliatasupporting

confidence: 77%

Genetic diversity and population structure ofToona ciliatarevealed by simple sequence repeat markers

Zhan

Hui

et al. 2019

Biotechnology & Biotechnological Equipment

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“…Castanopsis carlesii is distributed over a large geographical range throughout subtropical China, and substantial differences in characteristics of precipitation and temperature were obvious across this area (Li et al . ).…”

Section: Discussionmentioning

confidence: 97%

“…This is also confirmed by the DIY ABC analysis that suggested the existence of recurrent gene flow between these varieties. Widespread and abundant gene flow has been revealed in natural populations of other Castanopsis species, maintaining high diversity while diversifying selection was acting on specific genomic regions (Li et al 2014). Differential adaptation to natural environment can drive phenotypic divergence of population, and simulations showed that even weak selection for local adaptations could cause highly divergent clades geographically localized (Irwin 2012).…”

Section: Adaptation and Divergence With Gene Flowmentioning

confidence: 99%

“…Differential adaptation to natural environment can drive phenotypic divergence of population, and simulations showed that even weak selection for local adaptations could cause highly divergent clades geographically localized (Irwin 2012). Castanopsis carlesii is distributed over a large geographical range throughout subtropical China, and substantial differences in characteristics of precipitation and temperature were obvious across this area (Li et al 2014).…”

Section: Adaptation and Divergence With Gene Flowmentioning

confidence: 99%

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Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)

2016

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Local adaptation to different environments has the potential to maintain divergence between populations despite recurrent gene flow and is an important driver for generating biological diversity. In this study, we investigate the role of adaptation in the maintenance of two parapatric varieties of a forest tree. We used sequence variation of chloroplastic DNA and restriction site-associated DNA to investigate the genetic structure of two varieties of Castanopsis carlesii in subtropical China and relate it to climatic variation. We used niche reconstruction methods to investigate niche differentiation between the two varieties and to estimate the past distribution of this species. A deep divergence was observed between the two varieties, but evidence of introgression and genetic admixture was detected in two phenotypically and geographically intermediate populations. Niche reconstruction suggests that the distribution of the two varieties was disjunct during periods of global cooling and that the two varieties occupy significantly different niches. The genetic structure was mainly driven by environmental factors, and 13 outlier loci under divergent selection were correlated with climatic variation. These results suggest that the two varieties evolved in allopatry and came back into secondary contact after the last glacial maximum and that they are an evolutionary example of divergence maintained by climatic selection despite recurrent gene flow.

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“…Although microsatellites are frequently presumed to be neutral because they are not transcribed or translated, they can be linked to functional genes under selection (e.g. Vasemagi et al 2005;Li et al 2014) or may be involved in DNA folding (Li et al 2002). SNPs can be influenced by either neutral or adaptive genetic processes and can represent functional, coding regions of the genome, which on the one hand are under purifying selection to avoid deleterious changes and on the other under positive selection for advantageous changes.…”

Section: Introductionmentioning

confidence: 99%

Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

Elbers

Clostio

Taylor

2016

Molecular Ecology Resources

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Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus – a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP dataset (16 tortoises from 4 populations sequenced at 17,901 SNPs) to two microsatellite datasets, a full dataset of 101 tortoises and a partial dataset of 16 tortoises previously genotyped at 10 microsatellites. For the full microsatellite dataset, observed heterozygosity, expected heterozygosity, and FST were correlated between SNPs and microsatellites; however, allelic richness was not. The same was true for the partial microsatellite dataset, except that allelic richness, but not observed heterozygosity, was correlated. The number of clusters estimated by Structure differed for each dataset (SNPs = 2; partial microsatellite = 3; full microsatellite = 4). PCA showed four clusters for all datasets. More than 800 SNPs were needed to correlate with allelic richness, observed heterozygosity, and expected heterozygosity, but only 100 were needed for FST. The number of SNPs typically obtained from NGS far exceeds the number needed to correlate with microsatellite parameter estimates. Our study illustrates that diversity, FST, and PCA results from microsatellites can mirror those obtained with SNPs. These results may be generally applicable to small populations, a defining feature of endangered and threatened species, because theory predicts that genetic drift will tend to outweigh selection in small populations.

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Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

Cited by 27 publications

References 36 publications

Genetic diversity and population structure ofToona ciliatarevealed by simple sequence repeat markers

Genetic diversity and population structure ofToona ciliatarevealed by simple sequence repeat markers

Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)

Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

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