Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, F_ST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, F_ST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.

The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C. lanceolata have lagged significantly behind those of other conifer species due to a lack of suitable markers. To address this issue, we examined 27,666,670 reads from C. lanceolata transcriptome sequences recorded in the SRA database. Assembly produced 35,633 contigs, 1,822 (5.11%) of which contained one or more SSRs. In total, 2,156 SSRs were identified, giving an average SSR density of 68.4 SSRs/Mb. The most common SSR types were tri-SSRs (41.7%), followed by hexa-(29.8%), penta- (12.7%), di-(11.1%) and tetra-(4.7%) SSRs. EST-SSR markers based on the 1,822 SSR-containing contigs were developed using the CMiB pipeline and primer pairs were designed to target 35 loci. Polymorphism was observed in 28 of these loci, for which the number of alleles per locus ranged from 3 to 12 over 16 plus-tree individuals. The observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (F_IS) values for the targeted loci ranged from 0.125 to 0.938, 0.225 to 0.891 and -0.368 to 0.456, respectively. The corres - ponding PIC values ranged from 0.210 to 0.881, with an average of 0.573. Some of these markers have since been used in our ongoing genetic diversity analyses of C. lanceolata. To our knowledge, this is the first analysis of SSRs and EST-SSR markers in C. lanceolata, and the identified EST-SSR markers will be useful in future genetic analyses of C. lanceolata and related species.

Phellodendron has always been of great significance in promoting human health and ecological restoration. However, human activities and climate change have severely affected habitat, population dynamics and sustainable use of Phellodendron. Little is known about the geographical distribution pattern and their responses to climate change of Phellodendron. In order to reveal the impact of climate change on Phellodendron, we conducted a study based on natural distribution data of two species (297 occurrence points), 20 environmental factors, and an optimized MaxEnt model. Our results identified the main environmental factors influencing Phellodendron, predicted their potential geographical distribution, and assessed migration trends under climate change in China. Our analysis showed that Ph. amurense and Ph. chinense have potential suitable habitats of 62.89 × 10⁴ and 70.71 × 10⁴ km², respectively. Temperature and precipitation were found to play an essential role in shaping the present geographical distribution of Phellodendron populations. Based on two future climate scenarios, we forecasted that the potential suitable habitat of Ph. amurense would decrease by 12.52% (SSP245) and increase by 25.28% (SSP585), while Ph. chinense would decline by 19.61% (SSP245) and 15.78% (SSP585) in the late‐21st century. The potential suitable habitats of Ph. amurense and Ph. chinense would shift to northward and westward, respectively. Hydrothermal change was found to be the primary driver of the suitable habitat of Phellodendron populations in the future. We recommend establishing nature reserves for existing Phellodendron populations, especially Ph. chinense. Our study provided a practical framework for the impact of climate change on the suitable habitat of Phellodendron species and guided regional cultivation, long‐term conservation, and sustainable use.

Climate change affects the species spatio‐temporal distribution deeply. However, how climate affects the spatio‐temporal distribution pattern of related species on the large scale remains largely unclear. Here, we selected two closely related species in Taxus genus Taxus chinensis and Taxus mairei to explore their distribution pattern. Four environmental variables were employed to simulate the distribution patterns using the optimized Maxent model. The results showed that the highly suitable area of T. chinensis and T. mairei in current period was 1.616 × 10⁵ km² and 3.093 × 10⁵ km², respectively. The distribution area of T. chinensis was smaller than that of T. mairei in different periods. Comparison of different periods shown that the distribution area of the two species was almost in stasis from LIG to the future periods. Temperature and precipitation were the main climate factors that determined the potential distribution of the two species. The centroids of T. chinensis and T. mairei were in Sichuan and Hunan provinces in current period, respectively. In the future, the centroid migration direction of the two species would shift towards northeast. Our results revealed that the average elevation distribution of T. chinensis was higher than that of T. mairei. This study sheds new insights into the habitat preference and limiting environment factors of the two related species and provides a valuable reference for the conservation of these two threatened species.

Microsatellite markers are widely used in genetic analysis, but the common occurrence of null alleles, is an unfortunate drawback, and one which has not been paid enough attention. In this review, we confirmthe concept of null alleles and their characteristics, detail methods for estimating the frequency of null alleles and discuss potential causes. We also consider the effect of null alleles on genetic studies, such as measurement of population genetic diversity, parentage analysis and assignment tests. The review has a certain reference value for future studies. One main cause of microsatellite null alleles is poor primer annealing due to nucleotide sequence divergence (point mutations or indels) in one or both flanking primers. Microsatellite null alleles are not a natural characteristic of a specific gene, and are essentially different from isozyme null alleles. Although microsatellite null alleles have the characteristics of universality, complexity and invisibility, we can test and estimate their frequency through multiplex approaches, using Hardy-Weinbergequilibrium tests, parent-offspring genotype analysis, and new primer design. Null alleles have significant effects on the results of genetic analysis, potentially decreasing population genetic diversity and increasing genetic differentiation among populations. Moreover, null alleles may decrease the probability of parentage exclusion, even leading to errors or confusion in parentage analysis. Null alleles should be paid more attention and demand caution in future studies. Through a variety of methods, such as locus selection, null alleledata adjustment, and the design of new primers, we can escape the adverse effects of null alleles and achieve greater accuracy in genetic analysis

Taxus is an important genus which is well-known for Taxol. Its genetic analyses were lagged behind those of other conifers due to lack of suitable molecular markers. In this paper, we explored polymorphic loci for Taxus mairei and tested their transferability across species based on 150 EST-SSR loci already developed for Taxus cuspidata previously. The results showed that 103 loci were polymorphic, the number of alleles per locus ranged from 2 to 11 over 16 individuals. The observed heterozygosity (H_o ) and expected heterozygosity (H_e ) varied from 0 to 1 and 0.0625 to 0.891, respectively. The PIC values ranged from 0.11 to 0.754 with an average of 0.453. The average cross-species transferability was 96.07% among 5 species. Most of these loci can be used as universal markers in Taxus genus. The PCA results showed these markers have strong power to identify different species. These markers will be useful for further studies on genetic analysis and conversation of Taxus mairei.