Genetic Differentiation Research Articles

Genomic divergence and mutational load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex (B. liuyanii, B. longgangensis, B. masoniana and B. variegata) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between B. liuyanii and B. longgangensis occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of B. masoniana have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park.

Theodore Roosevelt National Park (TRNP) manages a herd of feral horses (Equus caballus) which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient f and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean f of TRNP horses was 0.180, while the mean f for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.

Genetic Structure of Macrophomina phaseolina Populations, the Causal Agent of Sesame Charcoal Rot Disease in Iran

Charcoal rot disease, caused by the fungus <i>Macrophomina phaseolina</i>, is one of the most important diseases of Sesame (<i>Sesamum indicum</i>) all over the world. However, the population biology of <i>M. phaseolina</i> is poorly understood. In this study, <i>M. phaseolina</i> isolates from five different regions of Iran (Khuzestan, Fars, Bushehr, Hormozgan, and Kohgiluyeh & Boyer-Ahmad provinces) (n=200) were analyzed for genetic variation using inter simple sequence repeats marker. In total, 152 unique haplotypes were identified among the 200 <i>M. phaseolina</i> isolates, and gene diversity (H=0.46–0.84) and genotypic diversity were high in each of the regions. The structure analysis clustered five Iranian populations into two distinct groups, the individuals from group 1 were assigned to the Bushehr population and the individuals from Khuzestan, Fars, Hormozgan and Kohgiluyeh & Boyer-Ahmad were aggregated and formed group 2. The results matched with genetic differentiation and gene flow among regions. Analyses of the distribution of gene diversity within and among five Iranian populations were 61% and 39%, respectively. Our results showed that infected seeds are thought to be the dominant mechanism responsible for the spreading of the pathogen in southern parts of Iran. In summary, it is essential to have local quarantine and prevent seed exchanges between geographical populations to restrict the dispersal of pathogen over long distances and provide certified seeds in Iran.

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Wild mustard (Sinapis arvensis L.) is a self-fertilizing weed species that exerts negative impacts on wheat production and herbicides are intensively used to manage it. Cross-fertilization may lead to genetic differentiation in this species. Therefore, this study investigated genetic diversity among wild mustard populations collected from wheat fields across various regions in Türkiye. Genetic variation was evaluated using 5 simple sequence repeat (SSR) markers in populations collected from 30 different locations. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. High genetic variability was recorded among populations within geographic locations. The populations were categorized into two major groups by UPGMA. There was no apparent geographic isolation among tested populations, which displayed a high degree of variability. The primary source of this variability is thought to be the adaptability of wild mustard seeds dispersed through various methods across diverse locations. Despite being a predominantly self-pollinating species, wild mustard may also employ some cross-pollination mechanisms. In conclusion, SSR markers proved useful in determining genetic diversity in outcrossing species, especially where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and intensive use of herbicides.

Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences

Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.

Conservation Challenges Imposed by Evolutionary History and Habitat Suitability Shifts of Endangered Freshwater Mussels under a Global Climate Change Scenario

Climate change and associated shifts in temperature and precipitation patterns have become an increasing concern as drivers of ongoing biodiversity loss. The Mediterranean region is particularly vulnerable, being both a biodiversity hotspot and a region very prone to desertification. Freshwater mussels are amongst the most threatened invertebrate taxa worldwide. Unio tumidiformis is an endemic and endangered species restricted to the southern Iberian Peninsula, living in temporary Mediterranean-type streams. Freshwater mussels need a fish host for successful larval transformation, meaning U. tumidiformis must belong to the genus Squalius. The main objective of this study was to evaluate the vulnerability of U. tumidiformis to climate change, by studying its population genetics and evolutionary history, its current and future habitat suitability, and that of its hosts. Genetic population structure and diversity were assessed using Single-Nucleotide Polymorphisms through Genotyping by Sequencing and used to infer species evolutionary history. The species potential distribution was modeled using an ensemble forecasting approach, and future shifts in habitat suitability were assessed with the projected climate data layers from Worldclim. Most populations showed extreme genetic differentiation (Fst up to 0.745), even from close neighboring ones. Upper Guadiana populations were more diverse and less differentiated. We hypothesize that U. tumidiformis originated in Upper Guadiana and followed the same colonization routes as their hosts with numerous founder effects and bottlenecks. Our results also predicted a reduction of 99% of climatically suitable areas for U. tumidiformis in the Iberian Peninsula until 2040. For the fish hosts, a maximum 42% reduction in suitable areas was estimated throughout the century, with remaining adequate habitats in the north. Our results suggest that difficult conservation options are necessary, prioritizing the preservation of populations, translocations to the northern area of its historical range and stream engineering to increase resilience to droughts.

Характеристика микрогаплотипа гена FADS2 у коренного населения Сибири

Our study of the FADS2 gene polymorphism in the indigenous populations of Siberia resulted in finding a microhaplotype of 150 nucleotides in length, represented by various combinations of polymorphism variants in four loci (rs174609, rs174610, rs174611, rs74771917). By these loci, 5 microhaplotype variants were identifie d in the studied populations of the northeastern (Chukchi, Koryak, Even) and southeastern (Buryat) parts of Siberia, the effective numbe r of which (Ae) varies from 2.16 in Buryats to 3.89 in Koryaks. Heterozygosity values in the populations vary from 0.624 in Buryats to 0.805 in Evens. The analysis of genetic differentiation showed highly authentic differences between the northern and southern populations of Siberia's eastern part in the distribution of the FADS2 gene microhaplotype variants. Thus, this microhaplotype has a sufficiently high informativity for detecting genetic differences between Siberian indigenous populations and can, therefore, be used in panels of markers designed for genetic identification at the population and individual level.

Molecular Genetic Diversity of Manioc (Manihot esculenta Crantz) Using Simple Sequence Repeated Markers (SSR) in the Kara Region of Togo

Cassava (Manihot esculenta Crantz), a plant of the future, is one of the main crops with high genetic potential. Therefore, the knowledge of its genetic variability would be of great importance for its effective use in genetic improvement programs. The objective of this work was to characterize the genetic diversity of cassava cultivars present in the Kara region of Togo. Thus, a total of 91 cassava leaf samples collected in the 7 prefectures of the Kara region were analyzed using 7 pairs of SSR microsatellite primers. Fifty-three alleles were detected with an average of 7.57 alleles per locus. The polymorphic information content ranged from 0.63 to 0.83 with an average of 0.74, indicating a high level of marker polymorphism. Molecular analysis of variance revealed that the majority of variability occurred within individuals and accounted for 99 % of the total variation between individuals. Weak genetic differentiation (Fst=0.011) was also observed between populations. The genetic structuring model based on the Neighbour-Joining algorithm method divided the individuals into 6 groups independently of local names. These results indicate the presence of high genetic resource variability in the studied populations. Therefore, it would be important to implement management strategies to better conserve cassava genetic resources and to facilitate the identification of successful cultivars.

Growth performance and selection signatures revealed by whole-genome resequencing in genetically selected grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is a highly productive freshwater fish species that is widely cultivated worldwide, contributing substantial economic value to the aquaculture industry annually. Recently, a breeding program for grass carp has progressed to the fourth generation (F4) after four consecutive generations of family selection. To further assess the growth performance of the genetically selected grass carp F4, a 90-day consecutive growth comparison experiment was conducted between the selected population and a wild base population. The results showed that the selected grass carp F4 had better growth performance. Whole-genome resequencing of both wild and selected populations of grass carp yielded a total of 4,354,416 high-quality single nucleotide polymorphisms (SNPs). Parameters of genetic diversity including observed heterozygosity (Ho), expected heterozygosity (He), nucleotide diversity (π), and polymorphic information content (PIC) were slightly decreased in the selected population compared to the wild population. The fixation index (Fst) indicated a low level of genetic differentiation (Fst = 0.021). Selection signatures analysis identified a total of 173 candidate selected regions with a cumulative size of 23.75 Mb, and 912 candidate genes including igf-1r, igfbp-2, igfbp-5 and itga6. This study provides valuable insights into the growth performance and the genetic basis of selection signatures in the process of grass carp selective breeding, and offers guidance for future breeding programs.

Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China.

Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12-5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47-4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11-2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae.

Elevational and climatic gradients shape the genetic structure of a typical Tibetan loach Triplophysa stenura (Cypriniformes: Nemacheilidae)

Species resilience to diversified environments largely depends on their genetic diversity. Disentangling the respective roles of multiple landscape factors on population genetic variation could help us interpret the adaptive mechanism of species to environments, which is a central issue in evolutionary biology and biodiversity conservation. Herein, a typical Tibetan loach Triplophysa stenura was selected as study object to perform landscape genetics analyses inferred from mitochondrial cytochrome b gene sequences. Based on extensive sample collection, a total of 377 individuals from 20 sites in the Yarlung Tsangpo River were included in the analyses and results of genetic diversity assessment demonstrated relatively high haplotype diversity and low nucleotide diversity for most geographic populations. Genetic diversity pattern analysis proved that both haplotype and nucleotide diversity were greater in higher, colder and drier areas, which was consistent with the central-marginal hypothesis for this plateau hinterland-originated species. Degree of genetic differentiation among geographic populations varied from low level to extremely high level, with genetic variation coming mainly from within populations. Elevational and climatic divergences were detected to be principally responsible for the formation of population genetic structure of this species, coinciding with the isolation-by-environment model. On this basis, we put forward some applicable proposals that the marginal populations with relatively low elevations deserved more attentions in designing conservation scheme and those genetically differentiated populations should be treated as separate conservation units. In the context of global climate change and intensifying human activity, a sound genetic resources monitoring along elevational or climatic gradient is pivotal to develop future conservation interventions.

Single cell and bulk RNA expression analyses identify enhanced hexosamine biosynthetic pathway and O-GlcNAcylation in acute myeloid leukemia blasts and stem cells.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults with an overall poor prognosis and high relapse rate. Multiple factors including genetic abnormalities, differentiation defects and altered cellular metabolism contribute to AML development and progression. Though the roles of oxidative phosphorylation and glycolysis are defined in AML, the role of the hexosamine biosynthetic pathway (HBP), which regulates the O-GlcNAcylation of cytoplasmic and nuclear proteins, remains poorly defined. We studied the expression of the key enzymes involved in the HBP in AML blasts and stem cells by RNA sequencing at the single-cell and bulk level. We performed flow cytometry to study OGT protein expression and global O-GlcNAcylation. We studied the functional effects of inhibiting O-GlcNAcylation on transcriptional activation in AML cells by Western blotting and real time PCR and on cell cycle by flow cytometry. We found higher expression levels of the key enzymes in the HBP in AML as compared to healthy donors in whole blood. We observed elevated O-GlcNAc Transferase (OGT) and O-GlcNAcase (OGA) expression in AML stem and bulk cells as compared to normal hematopoietic stem and progenitor cells (HSPCs). We also found that both AML bulk cells and stem cells show significantly enhanced OGT protein expression and global O-GlcNAcylation as compared to normal HSPCs, validating our in silico findings. Gene set analysis showed substantial enrichment of the NF-κB pathway in AML cells expressing high OGT levels. Inhibition of O-GlcNAcylation decreased NF-κB nuclear translocation and the expression of selected NF-κB-dependent genes controlling cell cycle. It also blocked cell cycle progression suggesting a link between enhanced O-GlcNAcylation and NF-κB activation in AML cell survival and proliferation. Our study suggests the HBP may prove a potential target, alone or in combination with other therapeutic approaches, to impact both AML blasts and stem cells. Moreover, as insufficient targeting of AML stem cells by traditional chemotherapy is thought to lead to relapse, blocking HBP and O-GlcNAcylation in AML stem cells may represent a novel promising target to control relapse.

Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae).

The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.

Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters.

Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and S. beltoni. S. beltoni has only recently been described based, most notably, on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified three narrow peaks along the genome with highly differentiated SNPs. These regions harbor six genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.

Genomic and common garden data reveal significant genetic differentiation in the endangered San Fernando Valley spineflower Chorizanthe parryi var. fernandina

AbstractSan Fernando Valley spineflower (Chorizanthe parryi var. fernandina [S. Watson] Jeps.) (Polygonaceae) is an herbaceous annual plant, endemic to California, and until rediscovered in 1999 had been thought to be extinct for almost seven decades. Historically documented at 10 locations, it currently persists at 2, separated by approximately 27 km. State listed as endangered, a description of its genetic diversity and structure is of conservation interest. After determining a lack of variation in ploidy, we examined genetic variation from samples within both populations: a common garden study for potentially adaptive genetic variation in selected growth and phenological traits and analysis of single nucleotide polymorphisms identified through restriction-site associated DNA sequencing. Both measures indicated that this highly restricted taxon nevertheless harbors substantial levels of genetic diversity and has significant between- and within-population genetic structure. Combining approaches from population genomics and common garden studies provided more insight into the patterns and basis of genetic diversity than is typical for studies of non-model species. Although local adaptation was not specifically studied (i.e., via reciprocal transplant studies), the differences determined from these two independent lines of evidence indicate that mixing gene pools between populations is not recommended at this time. Further, with significant differences revealed among subpopulations, we caution against mixing genotypes across subpopulations for the most part, and without much more evidence that this would not pose a risk of outbreeding depression. The importance of supporting pollinator health and diversity is highlighted. With genetic diversity—particularly with an annual species—being dynamic, fluctuating with the usual processes and with contributions from the soil seedbank, we recommend periodic resampling to monitor genetic diversity and structure. Climate change is anticipated to contribute to this variability.

Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan

Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.

Morphological, genetic and ecological divergence in near-cryptic bryophyte species widespread in the Holarctic: the Dicranum acutifolium complex (Dicranales) revisited in the Alps.

There is mounting evidence that reproductively isolated, but morphologically weakly differentiated species (so-called cryptic species) represent a substantial part of biological diversity, especially in bryophytes. We assessed the evolutionary history and ecological differentiation of a species pair, Dicranum brevifolium and D. septentrionale, which have overlapping ranges in the Holarctic. Despite their morphological similarity, we found similar genetic differentiation as between morphologically well-differentiated Dicranum species. Moreover, we detected gene tree discordance between plastid and nuclear markers, but neither of the two datasets resolved the two as sister species. The signal in trnL-trnF better reflects the morphological and ecological affinities and indicates a close relationship while ITS sequence data resolved the two taxa as phylogenetically distantly related. The discordance is probably unrelated to the ecological differentiation of D. septentrionale to colonise subneutral to alkaline substrates (vs. acidic in D. brevifolium), because this ability is rare in the genus and shared with D. acutifolium. This taxon is the closest relative of D. septentrionale according to the trnL-trnF data and does not share the discordance in ITS. We furthermore demonstrate that beside D. acutifolium, both D. septentrionale and D. brevifolium occur in the Alps but D. brevifolium is most likely rarer. Based on morphological analyses including factor analysis for mixed data of 45 traits we suggest treating the latter two as near-cryptic species and we recommend verifying morphological determinations molecularly.

SSR Marker–Based Genetic Diversity and Relationship Analyses of Stephania tetrandra S. Moore

AbstractStephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations.

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

Karst tiankengs in China are globally significant locations for studying ecological environments and plant diversity. However, there are few reports on how the unique geographical environment of tiankengs affects plant genetic diversity and genetic structure. This study used Hyper-seq gene sequencing technology to develop large-scale genomic SNPs of Manglietia aromatica, both within and outside the tiankengs. Its aim was to investigate the impact of tiankengs on the genetic diversity and genetic structure of the M. aromatica population. The analysis results indicate that the genetic diversity of the populations within the tiankeng (π = 0.2044) is higher than that of the populations outside of it (π = 0.1671), indicating that the tiankengs have a positive impact on species diversity. The genetic differentiation coefficient (FST) between the populations inside and outside the tiankeng was 0.0534 and the FST values of populations within the tiankeng were 0.077, 0.082, and 0.141, meaning that the genetic variation in the tiankengs is very high. The genetic similarity outside the tiankengs is also very high, indicating that the tiankengs are effectively preserving the genetic diversity of M. aromatica. Furthermore, the gene introgression analysis results gave no proof of gene flow between the three tiankeng populations. This suggests that the tiankengs not only protect species diversity, but also hinder gene flow between populations to some extent. However, this hindrance may gradually subside with the evolution of the tiankengs. The genetic structure analysis revealed that the M. aromatica population in Guangxi, China, can be classified into three subpopulations. The first is the tiankeng subpopulation, including all the populations in tiankengs. The second subpopulation consists of populations surrounding the tiankengs. These two subpopulations are distributed in Leye County in northwestern Guangxi, China, and are very close to each other. The third is the Huanjiang subpopulation, which is located far away from the tiankengs. Considering the direction of gene flow and genetic structure, it is speculated that the populations in the tiankengs evolved from the populations near the pit mouth. This study confirms that the tiankengs are shelters and provide a suitable habitat for the endangered plant M. aromatica, because its genetic diversity is well conserved and the species is well adapted to the habitat within the tiankengs.

Genetic structure and diversity of semi-captive populations: the anomalous case of the Asian elephant

AbstractWild species living in captivity are subject to loss of genetic diversity, inbreeding depression, and differentiation among populations. Only very few species have been under human care for centuries but have not been selectively bred, have free-ranging movements most of the time, and retain porous barriers to gene flow between wild and captive populations. Such captive populations are expected to retain high levels of genetic diversity and anthropogenic factors should result in a limited genetic differentiation from wild populations. Asian elephants have been trained and used by humans for at least 4000 years as war animals, mounts of kings and draught animals. In Myanmar and Laos, elephants are still being used for hauling timber in the forest while retaining traditional management practices including seasonal release, free mating and movement. However, habitat fragmentation, isolation and reduced gene flows are threatening both semi-captive and wild pools. We genotyped 167 semi-captive elephants from Laos and Myanmar using a panel of 11 microsatellite loci to estimate the genetic diversity and population structure. We found that elephants of both countries presented high levels of genetic diversity and a low degree of inbreeding, if any. This agrees with the expected high level of genetic diversity in semi-captive populations. We found a weak differentiation along a geographical gradient from southern Laos to northern Myanmar but no differentiation between wild-caught and captive-born pools. The potential value for conservation of a large population of semi-captive elephants has been recognized but the conservation community has yet to fully explore the potential role semi-captive elephants could play in maintaining gene flows.