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.
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.
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
.
The combination of ocean warming and acidification as a result of increasing atmospheric carbon dioxide (CO2) is considered to be a significant threat to calcifying organisms and their activities on ...coral reefs. How these global changes impact the important roles of decalcifying organisms (bioeroders) in the regulation of carbonate budgets, however, is less understood. To address this important question, the effects of a range of past, present and future CO2 emission scenarios (temperature + acidification) on the excavating sponge Cliona orientalis Thiele, 1900 were explored over 12 weeks in early summer on the southern Great Barrier Reef. C. orientalis is a widely distributed bioeroder on many reefs, and hosts symbiotic dinoflagellates of the genus Symbiodinium. Our results showed that biomass production and bioerosion rates of C. orientalis were similar under a pre‐industrial scenario and a present day (control) scenario. Symbiodinium population density in the sponge tissue was the highest under the pre‐industrial scenario, and decreased towards the two future scenarios with sponge replicates under the ‘business‐as‐usual’ CO2 emission scenario exhibiting strong bleaching. Despite these changes, biomass production and the ability of the sponge to erode coral carbonate materials both increased under the future scenarios. Our study suggests that C. orientalis will likely grow faster and have higher bioerosion rates in a high CO2 future than at present, even with significant bleaching. Assuming that our findings hold for excavating sponges in general, increased sponge biomass coupled with accelerated bioerosion may push coral reefs towards net erosion and negative carbonate budgets in the future.
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.
A new multi-layer irrotational Boussinesq-type model is proposed for both linear and nonlinear surface water waves over mildly sloping seabeds. The model is formulated in terms of computational ...horizontal and vertical velocity components within each layer and satisfies exact kinematic and dynamic free-surface conditions as well as kinematic seabed conditions. Using a Stokes-type expansion, a theoretical analysis of the new multi-layer model is carried out to examine both linear and nonlinear properties, including wave celerity, velocity profiles, shoaling amplitude, second- and third-order transfer functions and amplitude dispersion. The dispersive coefficients in the governing equations are determined by optimizing the linear celerity or linear velocity profiles. For example, the four-layer model shows extremely high accuracy and is applicable up to
$kh=667$
–800 (where
$k$
is the wavenumber and
$h$
is a typical water depth) with a 1 % error in wave phase celerity, and up to
$kh=352$
–423 with a 1 % error in the linear velocity components. The super- and subharmonic transfer functions are extremely accurate up to
$kh=300$
(1 % error), the third-order harmonics and amplitude dispersion are accurate up to
$kh=477$
(1 % error), and the shoaling property is optimized to cover the range of
$0<kh<300$
, which presents a 0.06 % tolerance error in shoaling amplitude. The high-accuracy nature of the model increases its suitability for simulating random wave propagation from extremely deep to shallow waters over mildly sloping topographies. The model is implemented numerically on a non-staggered grid via a composite fourth-order Adams–Bashforth–Moulton time integration. The numerical results show good agreement with both the analytical solutions and experimental data.
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.
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