Landscape Genomics in Tree Conservation Under a Changing Environment

Spatially heterogeneous selection and inter-varietal differentiation maintain population structure and local adaptation in a widespread conifer

BACKGROUND

Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir's genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates.

RESULTS

Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas.

CONCLUSIONS

Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.

Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics of Taxus cuspidata

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.

The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China

Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.

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

BACKGROUND AND AIMS

Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios.

METHODS

We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios.

KEY RESULTS

We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations.

CONCLUSIONS

Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.

Identifying genetic variation associated with environmental gradients and drought-tolerance phenotypes in ponderosa pine

As climate changes, understanding the genetic basis of local adaptation in plants becomes an ever more pressing issue. Combining genotype-environment association (GEA) with genotype-phenotype association (GPA) analysis has an exciting potential to uncover the genetic basis of environmental responses. We use these approaches to identify genetic variants linked to local adaptation to drought in Pinus ponderosa. Over 4 million Single Nucleotide Polymorphisms (SNPs) were identified using 223 individuals from across the Sierra Nevada of California. 927,740 (22.3%) SNPs were retained after filtering for proximity to genes and used in our association analyses. We found 1374 associated with five major climate variables, with the largest number (1151) associated with April 1st snowpack. We also conducted a greenhouse study with various drought-tolerance traits measured in first-year seedlings of a subset of the genotyped trees grown in the greenhouse. 796 SNPs were associated with control-condition trait values, while 1149 were associated with responsiveness of these traits to drought. While no individual SNPs were associated with both the environmental variables and the measured traits, several annotated genes were associated with both, particularly those involved in cell wall formation, biotic and abiotic stress responses, and ubiquitination. However, the functions of many of the associated genes have not yet been determined due to the lack of gene annotation information for conifers. Future studies are needed to assess the developmental roles and ecological significance of these unknown genes.

Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables

Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.

Warming appears as the main risk of non-adaptedness for western Mediterranean relict fir forests under expected climate change scenarios

Circum-Mediterranean firs are considered among the most drought-sensitive species to climate change. Understanding the genetic basis of trees' adaptive capacity and intra-specific variability to drought avoidance is mandatory to define conservation measures, thus potentially preventing their extinction. We focus here on Abies pinsapo and Abies marocana, both relict tree species, endemic from south Spain and north Morocco, respectively. A total of 607 samples were collected from eight nuclei: six from Spanish fir and two from Moroccan fir. A genotyping by sequencing technique called double digestion restriction site-associated DNA sequencing (ddRAD-seq) was performed to obtain a genetic matrix based on single-nucleotide polymorphisms (SNPs). This matrix was utilized to study the genetic structure of A. pinsapo populations and to carry out selection signature studies. In order to understand how Spanish fir and Moroccan fir cope with climate change, genotype-environment associations (GEAs) were identified. Further, the vulnerability of these species to climate variations was estimated by the risk of non-adaptedness (RONA). The filtering of the de novo assembly of A. pinsapo provided 3,982 SNPs from 504 out of 509 trees sequenced. Principal component analysis (PCA) genetically separated Grazalema from the rest of the Spanish populations. However, FST values showed significant differences among the sampling points. We found 51 loci potentially under selection. Homolog sequences were found for some proteins related to abiotic stress response, such as dehydration-responsive element binding transcription factor, regulation of abscisic acid signaling, and methylation pathway. A total of 15 associations with 11 different loci were observed in the GEA studies, with the maximum temperature of the warmest month being the variable with the highest number of associated loci. This temperature sensitivity was also supported by the risk of non-adaptedness, which yielded a higher risk for both A. pinsapo and A. marocana under the high emission scenario (Representative Concentration Pathway (RCP) 8.5). This study sheds light on the response to climate change of these two endemic species.

Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation

BACKGROUND

The evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species.

RESULTS

In ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise F_ST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period.

CONCLUSIONS

Our results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (F_ST = 0.036) and all 25,143 SNPs (F_ST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (F_ST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001).

Neutral and adaptive genetic diversity in plants: An overview

Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.

Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F _ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum's range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.

Population and Landscape Genetics Provide Insights Into Species Conservation of Two Evergreen Oaks in Qinghai-Tibet Plateau and Adjacent Regions

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: Quercus aquifolioides and Quercus spinosa 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 Q. aqu-East and Q. spi-West lineage but not in Q. aqu-West and Q. spi-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.