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

Abstract

Ecological speciation has long been noted as a central topic in the field of evolutionary biology, and investigation into the relative importance of ecological and geographical factors is becoming increasingly emphasized. We surveyed genetic variation of 277 samples from 25 populations of nine Rhododendron species within Tsutsusi subgenus in Taiwan using simple sequence repeats of expressed sequence tags. Bayesian clustering revealed four genetic lineages: (1) the Rhododendron simsii, Rhododendron kanehirai, and Rhododendron nakaharae lineage (lineage 1); (2) the R h o d o d e n d ro n l o n g i p e r u l a t u m , R h o d o d e n d ro n breviperulatum, and Rhododendron noriakianum lineage (lineage 2); (3) the Rhododendron rubropilosum lineage (lineage 3); and (4) the Rhododendron oldhamii lineage (lineage 4).Asymmetric introgressions were found from lineage 3 into lineages 1 and 2 (introgressed lineages). Genetic admixture of non-R. oldhamii species was also revealed by a neighborjoining tree. Variation partitioning showed that environment explained much larger portions of genetic variation than geography between non-introgressed lineages (i.e., between R. oldhamii and other lineages). However, the Mantel and partial Mantel tests and the multiple matrix regression with randomization found that isolation-by-distance played a more important role than isolation-by-environment (IBE) in contributing to genetic variation in most between lineage comparisons. Nevertheless, strong IBE was found when compared between non-introgressed lineages of R. oldhamii and R. rubropilosum, suggesting post-speciation ecological divergence. Several environmental variables, including annual mean temperature, aspect, isothermality, seasonal precipitation, slope, and soil pH, could be important ecological drivers involved in reproductive isolation between R. oldhamii and non-R. oldhamii species within the Tsutsusi subgenus.

Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence

“…While genetic differentiation between subpopulations was best explained by consideration of geographical distance alone, as found in many other plants (Diniz‐Filho et al, 2013; Sexton et al, 2014; Durka et al, 2017), environmental distance played a major role in explaining epigenetic differentiation. This result is consistent with unrelatedness of genetic and epigenetic differentiation found here and in other plants (Li et al, 2008; Paun et al, 2010; Huang et al, 2015) and suggests that genetic and epigenetic spatial patterns in H. foetidus reflected contrasting causal processes. It must be stressed, however, that both genetic and epigenetic variation exemplified combined scenarios where IBD and IBE simultaneously applied.…”

“…The subpopulations studied were differentiated genetically and epigenetically. The F st values computed from epigenetic markers doubled those for genetic ones, which suggests greater epigenetic than genetic differentiation as frequently found in other plants (Lira‐Medeiros et al, 2010; Richards et al, 2012; Zhao et al, 2014; Huang et al, 2015). Under strict IBD, all neutral genomic markers are expected to display identical F st ; hence, heterogeneous F st values for different markers would provide evidence that systematic pressures have affected some but not others (Lewontin and Krakauer, 1973).…”

“…Results of this study agree with the prediction that spatial epigenetic structure is likely to conform frequently to IBE (Herrera et al, 2016). Correlations between environmental factors and epigenetic characteristics of plant populations have often been reported (Lira‐Medeiros et al, 2010; Schulz et al, 2014; Huang et al, 2015; Foust et al, 2016; Keller et al, 2016), but these studies generally did not explicitly address the spatial component of the epigenome–environment relationship as done here. Despite their correlative nature, simultaneous spatial analyses of epigenetic, genetic, and environmental variation between populations are useful to evaluate the emerging, but still insufficiently documented notion that local environmental features can drive epigenetic differentiation of plant populations (Schulz et al, 2014; Foust et al, 2016; Wilschut et al, 2016).…”

“…These studies advanced the hypothesis that spatial epigenetic structure can conform to IBE, even when genetic variation does not, if environmental differences between populations are more important than geographical distances as predictors of epigenetic differentiation (Herrera and Bazaga, 2016; Herrera et al, 2016). To our knowledge, however, the possibility that epigenetic variation between populations conforms to IBE has been not explicitly tested (but see Schulz et al, 2014; Huang et al, 2015). Since local adaptation is accepted as a major process causing IBE (Orsini et al, 2013; Wang and Bradburd, 2014), the current dearth of information on epigenetic IBE is hindering progress in understanding the possible adaptive value of epigenetic responses to environmental variation.…”

Postglacial range expansion and the role of ecological factors in driving adaptive evolution of Musa basjoo var. formosana

“…formosana was comparable to that of M. balbisiana , another wild banana species, occurred in China (average H E  = 0.241) 61 . Patterns of genetic variation in contemporary populations of a species are influenced by the historical processes that shaped the distribution of a species 1, 2 , by the landscape ecological properties 11, 62 , and by life history traits 63 . High levels of H E in M. basjoo var.…”