Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data

Capturing diversity: Split systems and circular approximations for conservation

We investigated the implications of employing a circular approximation of split systems in the calculation of maximum diversity subsets of a set of taxa in a conservation biology context where diversity is measured using Split System Diversity (SSD). We conducted a comparative analysis between the maximum SSD score and the maximum SSD set(s) of size k, efficiently determined using a circular approximation, and the true results obtained through brute-force search based on the original data. Through experimentation on simulated datasets and SNP data across 50 Atlantic Salmon populations, our findings demonstrate that employing a circular approximation can lead to the generation of an incorrect max-SSD set(s). We built a graph-based split system whose circular approximation led to a max-SSD set of size k=4 that was less than the true max-SSD set by 17.6%. This discrepancy increased to 25% for k=11 when we used a hypergraph-based split system. The same comparison on the Atlantic salmon dataset revealed a mere 1% difference. However, noteworthy disparities emerged in the population composition between the two sets. These findings underscore the importance of assessing the suitability of circular approximations in conservation biology systems. Caution is advised when relying solely on circular approximations to determine sets of maximum diversity, and careful consideration of the data characteristics is crucial for accurate results in conservation biology applications.

Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

Whether ex situ populations constructed in the limited nursery resources of botanical gardens can preserve enough genetic diversity of endangered plants in the wild remains uncertain. Here, a case study was conducted with Camellia tunghinensis, which is one of the species with the lowest natural distribution area in the sect. Chrysantha (golden camellia) of the family Theaceae. We investigated the genetic diversity and population structure of 229 samples from wild and ex situ populations using genotyping by sequencing (GBS). Core germplasm was constructed from these samples. The results showed that wild C. tunghinensis exhibited high genetic diversity, with observed heterozygosity of 0.257-0.293 and expected heterozygosity of 0.247-0.262. Compared with wild populations, the genetic diversity of ex situ populations established by transplanting wild seedlings was close to or even higher. However, the genetic diversity of those established by seed or cuttings of a few superior trees was lower. The Admixture analysis revealed that the structure of the ex situ populations derived from seeds and cuttings was relatively simple compared with the ex situ populations derived from transplanted wild seedlings and wild populations. These results suggested that direct transplanting of wild seedlings was more conducive to preserving the genetic diversity of endangered plants in the wild. In addition, wild populations demonstrated a small differentiation (mean F ST = 0.044) among themselves, possibly due to long-term and frequent gene flow between the wild populations. In contrast, moderate differentiation (mean F ST > 0.05) was detected among ex situ populations and between ex situ and wild populations. This may be the combined result of the absence of gene flow pathways and strong selection pressure in various ex situ environments. Finally, 77 core germplasms were extracted from 229, likely representing the genetic diversity of C. tunghinensis. This study provides future strategies for the ex situ conservation and management of the golden camellia species and other rare and endangered plants.

Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum

BACKGROUND

Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.

METHODS

In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.

RESULTS

The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization.

CONCLUSIONS

Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.

Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook)

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4^th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4^th cycle breeding population was high with nucleotide diversity (P_i ) of 0.003, and H_o and H_e of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (F_st < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.

Changes in demography and geographic distribution in the weeping pinyon pine (Pinus pinceana) during the Pleistocene

Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying ecological communities. Here, we try to identify the processes underlying the demographic history of P. pinceana and characterize its genetic diversity using 3100 SNPs from genotyping by sequencing 90 adult individuals from 10 natural populations covering the species' entire geographic distribution. We inferred its population history and contrasted possible demographic scenarios of divergence that modeled the genetic diversity present in this restricted pinyon pine; in support, the past distribution was reconstructed using climate from the Last Glacial Maximum (LGM, 22 kya). We inferred that P. pinceana diverged into two lineages ~2.49 Ma (95% CI 3.28-1.62), colonizing two regions: the Sierra Madre Oriental (SMO) and the Chihuahuan Desert (ChD). Our results of population genomic analyses reveal the presence of heterozygous SNPs in all populations. In addition, low migration rates across regions are probably related to glacial-interglacial cycles, followed by the gradual aridification of the Chihuahuan Desert during the Holocene.

Comparison of genetic diversity between ancient and common populations of Docynia delavayi (Franch.) Schneid

Docynia delavayi (Franch.) Schneid. (D. delavayi), is a wild fruit tree which combines edible, medicinal, ecological and ornamental uses. In this study, ancient and common populations of D. delavayi were examined for genetic diversity and structure using SSR markers. As a result, a total of 136 alleles were detected at 18 SSR loci, with the mean of 7.56 alleles. The value of Na, Ne, I, He and Nm of the ancient populations were lower than those of the common populations except for Ho and Fst. It indicates that the genetic diversity of the common populations is higher than that in ancient populations. The genetic differences between ancient populations were slightly greater than those between common populations, which demonstrated less gene flow between ancient populations. According to the analysis of molecular variance (AMOVA), the genetic variation within the common population was greater than that in the ancient population, indicating that there was a higher genetic diversity within the common population. Also, the clustering heatmap results are partially consistent with the principal coordinate analysis (PCoA) results. Moreover, the mantel test showed an extremely significant correlation between genetic and geography distance (r = 0.214, p < 0.0001). Based on this work, we proposed strategies for protecting, which offers a theoretical basis for their effective utilization and conservation of D. delavayi ancient tree resources.

Population structure in Quercus suber L. revealed by nuclear microsatellite markers

Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.

Strong Genetic Structure Observed in Primulina danxiaensis, a Small Herb Endemic to Mount Danxia With Extremely Small Populations

Danxia landform occurring sporadically in southern China is a unique type of petrographic geomorphology. It has nurtured about 400 rare or threatened plant and animal species, whose diversity, endemism, and conservation have called increasing scientific and public attentions. Among them, Primulina danxiaensis (W. B. Liao, S. S. Lin, and R. J. Shen) W. B. Liao and K. F. Chung is a tiny perennial grass species recorded only in Mount Danxia, a natural World Heritage Site as part of China’s Danxia. In this study, restriction site-associated DNA sequencing (RAD-seq) was performed to investigate genetic diversity among these 12 populations of P. danxiaensis. A total of 432,041 variant sites were detected in 84,779 loci across 94 samples. The expected heterozygosity (H_E) ranged from 0.017 to 0.139. Bottleneck signals were detected in most populations, Tajima’s D tests showed that most loci could be under recent positive selection, and one of the six positively selected loci identified by BayeScan was annotated as tRNA^Glu, which may contribute to the species’ adaptation to shady environment. STRUCTURE analysis and phylogenetic tree showed that the 12 populations of P. danxiaensis could be divided into four gene pools (clades) corresponding to their geographic locations, and significant correlation was observed between genetic and geographic distances. Our study demonstrated that P. danxiaensis maintained a middle level of genetic diversity and strong population structure; geographic distance could be an important factor limiting gene flow among populations of P. danxiaensis, which were only sporadically recorded in Mount Danxia.

Effects of arbuscular mycorrhizal fungi on the nitrogen distribution in endangered Torreya jackii under nitrogen limitation

Arbuscular mycorrhizal fungi regulated the distribution of nitrogen in the leaves, thereby facilitating the adaptation of the endangered plant Torreya jackii to a low-nitrogen environment. Rhizophagus irregularis was inoculated into sterilized soil to investigate its impact on the distribution ratio of leaf nitrogen in cell wall proteins, cell membrane proteins, water-soluble proteins, and photosynthetic systems which includes the carboxylation system (P_C), energy metabolism (P_B), and light-harvesting system in the endangered species Torreya jackii. The results showed that R. irregularis reduced the specific leaf weight and the distribution ratio of nitrogen in cell wall proteins in the leaves of T. jackii, whereas it enhanced the distribution ratio of nitrogen in cell membrane proteins and water-soluble proteins. R. irregularis enabled more nitrogen uptake for growth by decreasing the distribution of nitrogen to the structural substances. At low-nitrogen levels, inoculation with R. irregularis improved the plant height (18.78 ~ 36.04%), shoot dry weight (50.53 ~ 64.33%), total dry weight (42.86 ~ 52.82%), maximal net photosynthetic rate (P_max) (16.83 ~ 20.11%), photosynthetic nitrogen use efficiency (PNUE) (40.01 ~ 43.14%), P_C (33.56 ~ 38.59%) and P_B (29.08 ~ 34.02%). However, it did not substantially affect the leaf nitrogen content per unit area or the leaf nitrogen content per unit mass. Moreover, P_max exhibited a significant positive correlation with P_C and P_B, and all three parameters showed a significant positive correlation with the PNUE, thereby revealing that R. irregularis increased the photosynthetic capacity and PNUE of T. jackii through boosting P_C and P_B.

Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species

Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.

Genetics and Improvement of Forest Trees

Forest tree improvement has mainly been implemented to enhance the productivity of artificial forests [...]