Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

Abstract

Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168-13,092 years ago and ending 1584-3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale.

Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi

“…Low measure of allelic richness and private allelic richness indicate that the adaptive potential of a population is likely to be diminished (McLaughlin et al 2002;Oubory et al 2010). Nevertheless, previous work found ecologically relevant local adaptation in R. oldhamii populations (Hsieh et al 2013). In the present study, species in the subgenus Tsutsusi displayed a reduced level of expected heterozygosity (69.1 %) and a much lower level of observed allelic richness (40.5 %) compared with species in the R. pseudochrysanthum complex (Hymenanthes subgenus).…”

“…Genetic data of 95 samples from four populations of R. oldhamii in this study was also used in a previous published paper (Hsieh et al 2013). For each primer pair, the 5′-end forward primer was labeled with a 6-carboxyfluorescein, hexachloro-fluorescein, or tetramethyl-6-carboxyrhodamine fluorescent tag.…”

“…Moreover, variation partitioning showed 36.46 % of variation was attributed to pure environment in contrast to 3.02 % attributed to pure geography, and cumulative adjusted R 2 value near 0.40 explained by environmental predictors (Tables 3 and 4). R. oldhamii is distributed across a large geographic area and was found to have increasing environmental heterogeneity, which may have reduced the homogenizing effect of gene flow between populations, favoring genetic divergence by local adaptation (Hsieh et al 2013); thus, IBE has a stronger influence on speciation than IBD in comparison between R. oldhamii and R. rubropilosum. This is likely due to the fact that R. oldhamii is a species distributed in warm, humid forest understory environments and R. rubropilosum, particularly R. rubropilosum var.…”

The effect of long-term historical habitat fragmentation on genetic diversity of the relictual conifer Calocedrus macrolepis (Cupressaceae) in China

“…MIGRATE-N estimates the long-term effective population size (N e ) of each population group as parameter h (that is, 4N e l, where l is the mutation rate per site). MIGRATE-N also estimates the bi-directional M among population groups and among populations within a region (M = m/l, where m is the immigration rate per generation) (Hsieh et al 2013). The Markov Chain settings consisted of ten short and three long chains per run, with an increment of 20.…”

Phylogeography of Quercus glauca (Fagaceae), a dominant tree of East Asian subtropical evergreen forests, based on three chloroplast DNA interspace sequences

“…These multiple refugia have been proposed as hotspots for biodiversity conservation. However, phylogeographic studies conducted on plant species in this region are limited, and most were restricted to either narrow geographical regions (e.g., Japanese-Taiwan archipelagos; Hsieh et al 2013;Kono et al 2012;Nakamura et al 2010) or focused on endangered species with few populations (Chou et al 2011;Gao et al 2007;Gong et al 2008b;Wang et al 2009). Recent phylogeographic studies on two sympatric beeches (Fagus lucida and Fagus longipetiolata) in subtropical China (Zhang et al 2013) and on the Tertiary genus Cercidiphyllum (Qi et al 2012) in warm-temperate deciduous forests of East Asia suggest that pre-Quaternary events (at the Miocene/Pliocene boundary) are associated with the early divergence of the species and haplotypes of both genera.…”