Insights into the aridification history of Central Asian Mountains and international conservation strategy from the endangered wild apple tree

Abstract

Aim Evolutionary processes of mountain plants in arid lands remain poorly understood. Here, we investigate population genomics of the endangered wild apple tree to interpret the effects of long‐term aridification on plant diversification and demographical history in Central Asian Mountains. Location The Tianshan Mountains, spanning north‐western China, Kazakhstan, Kyrgyzstan and Tajikistan. Taxon Malus sieversii (Rosaceae) Methods Using genome‐wide single nucleotide polymorphisms, we assessed genetic diversity and genetic structure of 15 populations across the species' range. Demographical history was simulated with approximate Bayesian computation and species distribution modelling. We used a general linear model to identify key environmental factors affecting population genetic diversity and structure. Results We separated the 15 populations into three groups: the eastern group of western Junggar Mountains in China; the central group of the Ili Valley, the Talas Alatau Mountains in Kazakhstan and Kyrgyzstan; and the western group of Tajikistan and the Dzungarian Alatau in Kazakhstan. Central populations had higher genetic diversity and effective population size than eastern and western populations. The three groups split at the late Miocene and subsequently experienced extensive admixture. We detected a significant pattern of isolation by distance, but not isolation by environment, among these populations. Population genetic diversity was significantly associated with longitudinal and current environmental gradients. Main conclusions Long‐term aridification promoted distribution fragmentation and plant lineage divergence of relict broad‐leaved forests in Central Asian Mountains. Both geographical isolation and environmental heterogeneity shaped spatial patterns in genetic variation among M. sieversii populations. To maintain genetic integrity, we propose the establishment of an international network for the conservation of this endangered wild apple tree.

Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China

“…Geographical isolation and environmental heterogeneity are considered to be the crucial drivers of allopatric variance (Evans et al, 2014 ; Jiang et al, 2018 ; Binks et al, 2019 ). A geographic barrier not only facilitates the local adaptation of populations but also can lead to the evolution of populations with unique genetic characteristic (Barnes et al, 2002 ; Zhang et al, 2020 ). Our results reveal distinct differentiation between P. euphratica populations of the NX and SX clades, suggesting that the Tianshan Mountains may limit gene flow between the two clades and that the differences in local environments and the long period of isolation facilitated their allopatric divergence.…”

“…To examine the relationships between genetic diversity at the population level and geographical factors, as well as environmental factors according to a previous study (Zhang et al, 2020 ), the genetic diversity of each population was represented by expected heterozygosity ( H e ). Latitude and longitude were considered to be the main geographical factors affecting the P. euphratica and P. pruinosa populations.…”

“…The protection of Populus forests in northwestern China is an extremely urgent issue. One effective strategy for protection of a plant species is to identify priority protection areas or conservation units (Zhang et al, 2020 ). Assessing the genetic variations in Populus populations would be beneficial for the conservation and utilization of the genetic resources of these species and could provide useful basic data on Populus germplasm to facilitate breeding.…”

“…The development of molecular markers at the whole-genome level is becoming increasingly accurate and efficient (Verma et al, 2015 ). Genome-wide single nucleotide polymorphism (SNP) markers are widely used to assess the genotypes and genetic relationships of various populations (Lu et al, 2020 ; Zhang et al, 2020 ). Genotyping-in-Thousands by sequencing (GT-seq) has proven to be an efficient SNP genotyping technology (Campbell et al, 2015 ) and has been widely applied in many fields of research (Bootsma et al, 2020 ; McKinney et al, 2020 ; Powell and Campbell, 2020 ; Schmidt et al, 2020 ).…”

Current biogeographical roles of the Kunlun Mountains

“…Some studies have recently demonstrated that the ecosystem of the QTP experienced a significant shift at the Paleogene/Neogene boundary (Deng et al, 2019 ) and that the Kunlun Mountains have reached their present height over the last 17 Ma (Pan, 2000 ; Sun et al, 2015 ). The arid climate of Central Asia appeared in the late Miocene, with an origin time of 5.3 Ma (i.e., 5.23–5.38 Ma), and multiple climate fluctuations have occurred since the early Pliocene, especially the Quaternary (Huang et al, 2015 ; Zhang et al, 2021 ; Zhang & Sun, 2011 ). Hence, the Kunlun Mountains did not rise to their present elevation in the early Pliocene (5.3 Ma).…”