Genomic signals of local adaptation and hybridization in Asian white birch

Abstract

Disentangling the numerous processes that affect patterns of genome‐wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing data set for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north‐western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north‐eastern to south‐western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of covariation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7609 SNPs of which 3767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7609 environmentally associated SNPs to estimate the risk of nonadaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.

Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis

“…Moreover, genetic grouping at K = 3 and PCA plots both indicated that the East and South clusters are mixed with the North, Central or West clusters ( Fig. 2 A and D), indicating they are likely introgressed rather than divergent lineages, as for example in white birch ( Nocchi et al., 2023 ), although more evidence is needed. In the East and South clusters located in the HM, which is characterized by deeply dissected landscapes and has created complex genetic structure, geological isolation and hybridization are likely the main factors that have shaped genetic differentiation.…”

“…This region has been suggested to be a site of dynamic flora as numerous species are presently becoming reproductively isolated ( Wu et al., 2022 ). For example, hybridization and young speciation are frequently observed among not only speciose alpine herbs or shrubs, including Gentiana ( Fu et al., 2020 , 2022a ), Saxifraga ( Ebersbach et al., 2020 ) and Rhododendron ( Zheng et al., 2021 ; Ma et al., 2022 ), but also woody species such as Pterocarya ( Wang et al., 2023 ), Populus ( Li et al., 2023 ) and Betula ( Nocchi et al., 2023 ).…”

Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

“…This pattern of population structure is consistent with previous studies in East Asia ( Wu and Wu, 1996 ; Qiu et al ., 2011 , 2017 ; Chen et al ., 2015 ; Ma et al ., 2015 ; Cao et al ., 2016 , 2020 ; Wei et al ., 2016 ). The two genetic clusters within the Sino-Himalayan Forest subkingdom seem to mirror the similar phylogeographic break in many other species ( Meng et al ., 2015 ; Yang et al ., 2017 ; Luo et al ., 2018 ; Wang et al ., 2019 ; Nocchi et al , 2023 ). The level of genetic differentiation among P. macroptera populations is higher than that in other closely related wingnut taxa ( P. stenoptera : 0.067) ( Li et al ., 2018 ).…”

Repeated global adaptation across plant species

“…1 and SI Appendix, Table S1). These datasets included exclusively natural populations and ranged from closely related sister species known to hybridize (50) to species separated by up to 160 million years of evolution (Fig. 1B).…”