Understanding the genetic basis of how species respond to changing environments is essential to the conservation of species. However, the molecular mechanisms of adaptation remain largely unknown for ...long-lived tree species which always have large population sizes, long generation time, and extensive gene flow. Recent advances in landscape genomics can reveal the signals of adaptive selection linking genetic variations and landscape characteristics and therefore have created novel insights into tree conservation strategies. In this review article, we first summarized the methods of landscape genomics used in tree conservation and elucidated the advantages and disadvantages of these methods. We then highlighted the newly developed method "Risk of Non-adaptedness," which can predict the genetic offset or genomic vulnerability of species
allele frequency change under multiple scenarios of climate change. Finally, we provided prospects concerning how our introduced approaches of landscape genomics can assist policymaking and improve the existing conservation strategies for tree species under the ongoing global changes.
Aim: Hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history. Mountain uplifts are known to catalyse species radiation but ...their impact on evolutionarily stable taxa such as many trees remains little understood. The oak Quercus aquifolioides is endemic to yet widely distributed across the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we investigate how the region's Neogene and Quaternary history has driven the species past population dynamics and the resulting extant patterns of intraspecifk diversity. Location: Hengduanshan Biodiversity Hotspot in SW China. Methods: We sampled 58 populations throughout the species range and genotyped a total of 959 individuals at four chloroplast DNA fragments and 11 nuclear microsatellite loci. Phylogenetic reconstructions, molecular dating techniques and ancestral area reconstructions were used in combination with population genetic statistics to infer the biogeographical history of Q. aquifolioides. The phylogeographical study was complemented by a survey of fossil records and a niche modelling exercise. Results: Combined molecular and fossil evidence indicates that Q. aquifolioides descended during the late Miocene from the central Qinghai-Tibet Plateau into Tibet and the western Sichuan Plateau, and from there, into the area of highest endemism in the Hengduan Mountains sensu lato. Great apparent population stability and a haplotype 'radiation' in this area contrasted with marked extinction-recolonization dynamics and reduced population diversity in Tibet. We found evidence for extremely limited seed gene flow but extensive pollen gene flow (global FST: cpDNA = 0.98, nSSR = 0.07) with signals of asymmetric pollen dispersal from the Hengduan Mountains into Tibet. Main conclusion: Our results provide insights of unprecedented detail into the ancient biogeographical history of the Hengduanshan Biodiversity Hotspot, suggesting that past environmental changes in the region may have catalysed radiative diversifications within species much in the same way as among species.
is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant ...taxa, both taxonomically and phylogenetically.
is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of
with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four
cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the
repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the
gene of
compared to two deciduous oak species, and that there had been significant purifying selection on the
gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined
as belonging to sect.
and being closely related to
and
. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus
.
Summary
Ecological character displacement (ECD) refers to a pattern of increased divergence at sites where species ranges overlap caused by competition for resources. Although ECD is believed to be ...common, there are few in‐depth studies that clearly establish its existence, especially in plants.
Thus, we have compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks: Quercus dentata and Quercus aliena. In contrast to previous studies, we define sympatry and allopatry at a local scale, thereby comparing populations that can or cannot directly interact.
Using genetic markers, we found greater genetic divergence between the two oak species growing in mixed stands and inferred that long‐term gene flow has predominantly occurred asymmetrically from the cold‐tolerant species (Q. dentata) to the warm‐demanding later colonizing species (Q. aliena). Analysis of leaf traits revealed greater divergence in mixed than in pure oak stands. This was mostly due to the later colonizing species being characterized by more resource‐conservative traits in the presence of the other species. Controlling for relevant environmental differences did not alter these conclusions.
These results suggest that asymmetric trait divergence can take place where species coexist, possibly due to the imbalance in demographic history of species resulting in asymmetric inter‐specific selection pressures.
Long‐lived tree species are genetically differentiated and locally adapted with respect to fitness‐related traits, but the genetic basis of local adaptation remains largely unresolved. Recent ...advances in population genetics and landscape genomic analyses enable identification of putative adaptive loci and specific selective pressures acting on local adaptation. Here, we sampled 60 evergreen oak (Quercus aquifolioides) populations throughout the species' range and pool‐sequenced 587 individuals at drought‐stress candidate genes. We analyzed patterns of genetic diversity and differentiation for 381 single nucleotide polymorphisms (SNPs) from 65 candidate genes and eight microsatellites. Outlier loci were identified by genetic differentiation analysis and genome–environment associations. The response pattern of genetic variation to environmental gradient was assessed by linear isolation‐by‐distance/environment tests, redundancy analysis, and nonlinear methods. SNPs and microsatellites revealed two genetic lineages: Tibet and Hengduan Mountains–Western Sichuan Plateau (HDM‐WSP), with reduced genetic diversity in Tibet lineage. More outlier loci were detected in HDM‐WSP lineage than Tibet lineage. Among these, three SNPs in two genes responded to dry season precipitation in the HDM‐WSP lineage but not in Tibet. By contrast, genetic variation in the Tibet lineage was related to geographic distance instead of the environment. Furthermore, risk of nonadaptedness (RONA) analyses suggested HDM‐WSP lineage will have a better capacity to adapt in the predicted future climate compared with the Tibet lineage. We detected genetic imprints consistent with natural selection and molecular adaptation to drought on the Qinghai–Tibet Plateau (QTP) over a range of long‐lived and widely distributed oak species in a changing environment. Our results suggest that different within‐species adaptation processes occur in species occurring in heterogeneous environments.
Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population ...level through phylogeographic analysis. Here we report such a case study on eight putative cypress (Cupressus) species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The analysis involved sequencing three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF) in 371 individuals sampled from populations at 66 localities.
Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure (N(ST) > G(ST), P < 0.05) implied a high correlation between haplotypes/lineages and geographic distribution. Two species, C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity.
It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.
The combination of population and landscape genetics can facilitate the understanding of conservation strategy under the changing climate. Here, we focused on the two most diverse and ecologically ...important evergreen oaks:
and
in Qinghai-Tibetan Plateau (QTP), which is considered as world's biodiversity hotspot. We genotyped 1,657 individuals of 106 populations at 15 nuclear microsatellite loci throughout the species distribution range. Spatial patterns of genetic diversity were identified by mapping the allelic richness (AR) and locally common alleles (LCA) according to the circular neighborhood methodology. Migration routes from QTP were detected by historical gene flow estimation. The response pattern of genetic variation to environmental gradient was assessed by the genotype-environment association (GEA) analysis. The overall genetic structure showed a high level of intra-species genetic divergence of a strong west-east pattern. The West-to-East migration route indicated the complex demographic history of two oak species. We found evidence of isolation by the environment in
-East and
-West lineage but not in
-West and
-East lineage. Furthermore, priority for conservation should be given to populations that retain higher spatial genetic diversity or isolated at the edge of the distribution range. Our findings indicate that knowledge of spatial diversity and migration route can provide valuable information for the conservation of existing populations. This study provides an important guide for species conservation for two oak species by the integration of population and landscape genetic methods.
Abstract The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the ...environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, Taxus cuspidata Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site‐associated DNA sequencing (RAD‐seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD‐seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in T. cuspidata . Outlier detection by F ST outlier analysis and genotype‐environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non‐adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of T. cuspidata under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.
Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such ...as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf‐scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost‐efficient method in terms of time‐consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.
We conducted a comparative analysis to evaluate the accuracy and efficiency of the GMMs and deep learning methods in discriminating two closely related oaks, Q. aliena and Q. dentata, using genetics as a priori classification. We found that deep learning is the most cost‐efficient method in terms of time and cost, whereas GMMs can confirm the leaf shape of admixture individuals and demonstrate the tendency of leaf contraction and expansion. Moreover, we found that the shape of admixture individuals was close to that of Q. dentata, suggesting that oaks retain high levels of fitness variation, with Q. aliena being more favored by selection in leaf morphological traits.
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