Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis

Abstract

The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

Effects of landscapes and range expansion on population structure and local adaptation

“…Wind-pollinated conifers are generally characterized by low population differentiation at nuclear markers, even across large geographical distances (Alberto et al, 2013). The more widely distributed and montane parental species P. tabuliformis and P. yunnanesis accord well with this expectation, with estimates of F ST ranging from 0.023 to 0.086 (Ma et al, 2006;Wang et al, 2011;Gao et al, 2012;Xia et al, 2018). By contrast, P. densata possesses substantial spatial genetic structure, similar to other plants inhabiting the QTP (Geng et al, 2009;Qiu et al, 2011;Wen et al, 2014).…”

Landscape genomics predicts climate change‐related genetic offset for the widespread Platycladus orientalis (Cupressaceae)

“…Mantel r = .4079 p = .004 (Xia et al, 2018). This signature of IBE can be produced by genetic adaptation to local environments (Nachman & Payseur, 2012;Wang & Bradburd, 2014).…”

“…China (Xia et al, 2018). In addition, human activities also contributed to the fragmentation of P. orientalis.…”

Neutral and Climate-Driven Adaptive Processes Contribute to Explain Population Variation in Resin Duct Traits in a Mediterranean Pine Species

“…It is noteworthy that most studies aiming to assess the adaptive value of quantitative traits by testing the existence of environmental gradients have failed to differentiate neutral from adaptive variation. Accounting for the neutral population genetic structure can, however, considerably change the interpretation of clinal patterns (Xia et al, 2018;López-Goldar et al, 2019).…”