scholarly journals Genetic Differentiation and Population Structure of Threatened Prunus africana Kalm. in Western Cameroon Using Molecular Markers

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 446
Author(s):  
Justine G. Nzweundji ◽  
Ulrike Huewe ◽  
Nicolas Niemenak ◽  
Néhémie T. Donfagsiteli ◽  
Klaus Eimert
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Chloroplast Dna ◽  
Isolation By Distance ◽  
Agroforestry System ◽  
Bark Extract ◽  
Medicinal Tree ◽  
Prunus Africana ◽  
Chloroplast Dna Markers

Genetic diversity of species is an important baseline for the domestication process. In Cameroon, Prunus africana, an important and threatened medicinal tree, is among the priority species for domestication. The bark extract has been used to treat various diseases; mainly benign prostatic hyperplasia which affects men above the age of 50. As little is known about the genetic diversity of P. africana in Cameroon, we aimed to determine the genetic diversity and differentiation of several P. africana populations in the western provinces, using sets of chloroplast DNA markers and nuclear microsatellites previously developed for Prunus species. Genetic diversity in the observed populations was considerable and genetic differentiation between populations proved substantial with 21% of the total observed variation detected among populations, revealing a distinct genetic structure among certain populations. However, the lack of correlation between genetic and geographic distances does not support isolation by distance (IBD). The analysis of chloroplast DNA haplotypes revealed no strong phylogeographic component in the genetic structure observed in the western populations of P. africana in Cameroon. The outcome of this study will contribute to improve the genetic characterization of P. africana for its better domestication and conservation in the Cameroon agroforestry system.

scholarly journals Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243999
Author(s):  
Ke-Xin Zhu ◽  
Shan Jiang ◽  
Lei Han ◽  
Ming-Ming Wang ◽  
Xing-Ya Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Management Strategies ◽  
Geographic Distance ◽  
Northern China ◽  
Economic Losses ◽  
Chilo Suppressalis

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

scholarly journals Variation and genetic structure of the endangered Lepus flavigularis (Lagomorpha: Leporidae)

2017 ◽  
Vol 65 (4) ◽  
pp. 1322
Author(s):  
Bárbara Cruz Salazar ◽  
Consuelo Lorenzo ◽  
Eduardo Espinoza Medinilla ◽  
Sergio López
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
San Francisco ◽  
Isolation By Distance ◽  
Santa Cruz ◽  
Management Units ◽  
Lepus Flavigularis ◽  
Santa Maria

Lepus flavigularis, is an endemic and endangered species, with only four populations inhabiting Oaxaca, México: Montecillo Santa Cruz, Aguachil, San Francisco del Mar Viejo and Santa María del Mar. Nevertheless, human activities like poaching and land use changes, and the low genetic diversity detected with mitochondrial DNA and allozymes in previous studies, have supported the urgent need of management strategies for this species, and suggest the definition of management units. For this, it is necessary to study the genetic structure with nuclear genes, due to their inheritance and high polymorphism, therefore, the objective of this study was to examine the variation and genetic structure of L. flavigularis using nuclear microsatellites. We sampled four populations of L. flavigularis and a total of 67 jackrabbits were captured by night sampling during the period of 2001 to 2006. We obtained the genomic DNA by the phenol-chloroform-isoamyl alcohol method. To obtain the diversity and genetic structure, seven microsatellites were amplified using the Polymerase Chain Reaction (PCR); the amplifications were visualized through electrophoresis with 10 % polyacrylamide gels, dyed with ethidium bromide. Genetic diversity was determined using the software GenAlEx v. 6.4, and genetic structure was obtained with ARLEQUIN v. 3.1; null alleles were evaluated using the program Micro-Checker v.2.2.2. Additionally, a Bayesian analysis was performed with software STRUCTURE v. 2.2.3., and the isolation by distance (IBD) was studied using the program PASSAGE v.2.0.11.6. Our results showed that the genetic variation found was low (HO = 0.30, HE = 0.24) when compared to other jackrabbit species. Fixed alleles and moderate levels of genetic differentiation (FST = 0.18, P = 0.001) were detected among populations, indicating the effect of the genetic drift and limited gene flow. Bayesian clustering analysis revealed two groups: (1) jackrabbits from Montecillo Santa Cruz, and (2) individuals living in Aguachil, San Francisco del Mar Viejo and Santa María del Mar. No evidence was found of isolation by distance. It is possible that the geographic barriers present between populations (e.g. lagoons, human settlements), rather than the geographical distance between them, may explain the observed genetic structure. The inbreeding coefficient was negative (FIS = -0.27, P = 0.03), indicating genetic sub-structure in populations. We suggest two management units based on the genetically closer populations, which will help define precise conservation actions in L. flavigularis. This research is the basis for defining translocation of individuals between populations, nevertheless, a more extensive future study, with specific molecular markers for L. flavigularis, is required. In addition, it is necessary to analyze the barriers that limit the gene flow, since it is urgent to reduce the genetic differentiation between populations and increase the genetic diversity of this species. 

scholarly journals Genetic Divergence of Two Sitobion avenae Biotypes on Barley and Wheat in China

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 117
Author(s):  
Da Wang ◽  
Xiaoqin Shi ◽  
Deguang Liu ◽  
Yujing Yang ◽  
Zheming Shang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Host Plant ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Critical Role ◽  
Geographic Distance ◽  
Sitobion Avenae ◽  
Insect Populations

Host plant affinity and geographic distance can play critical roles in the genetic divergence of insect herbivores and evolution of insect biotypes, but their relative importance in the divergence of insect populations is still poorly understood. We used microsatellite markers to test the effects of host plant species and geographic distance on divergence of two biotypes of the English grain aphid, Sitobion avenae (Fabricius). We found that clones of S. avenae from western provinces (i.e., Xinjiang, Gansu, Qinghai and Shaanxi) had significantly higher genetic diversity than those from eastern provinces (i.e., Anhui, Henan, Hubei, Zhejiang and Jiangsu), suggesting their differentiation between both areas. Based on genetic diversity and distance estimates, biotype 1 clones of eastern provinces showed high genetic divergence from those of western provinces in many cases. Western clones of S. avenae also showed higher genetic divergence among themselves than eastern clones. The Mantel test identified a significant isolation-by-distance (IBD) effect among different geographic populations of S. avenae, providing additional evidence for a critical role of geography in the genetic structure of both S. avenae biotypes. Genetic differentiation (i.e., FST) between the two biotypes was low in all provinces except Shaanxi. Surprisingly, in our analyses of molecular variance, non-significant genetic differentiation between both biotypes or between barley and wheat clones of S. avenae was identified, showing little contribution of host-plant associated differentiation to the divergence of both biotypes in this aphid. Thus, it is highly likely that the divergence of the two S. avenae biotypes involved more geographic isolation and selection of some form than host plant affinity. Our study can provide insights into understanding of genetic structure of insect populations and the divergence of insect biotypes.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8304 ◽  
Author(s):  
Biao Xiong ◽  
Limei Zhang ◽  
Shubin Dong ◽  
Zhixiang Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Sex Ratios ◽  
Mainland China ◽  
Small Sample ◽  
Chloroplast Microsatellites ◽  
Wild Populations ◽  
Haplotype Networks ◽  
Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

scholarly journals Diverging Genetic Structure of Coexisting Populations of the Black Storm-Petrel and the Least Storm-Petrel in the Gulf of California

2020 ◽  
Vol 13 ◽  
pp. 194008292094917
Author(s):  
Misael D. Mancilla-Morales ◽  
Santiago Romero-Fernández ◽  
Araceli Contreras-Rodríguez ◽  
José J. Flores-Martínez ◽  
Víctor Sánchez-Cordero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Mate Selection ◽  
Gulf Of California ◽  
Population Genetic ◽  
Life Histories ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Storm Petrel

Estimations on the influence of evolutionary and ecological forces as drivers of population gene diversity and genetic structure have been performed on a growing number of colonial seabirds, but many remain poorly studied. In particular, the population genetic structure of storm-petrels (Hydrobatidae) has been evaluated in only a few of the 24 recognized species. We assessed the genetic diversity and population structure of the Black Storm-Petrel ( Hydrobates melania) and the Least Storm-Petrel ( Hydrobates microsoma) in the Gulf of California. The two species were selected because they are pelagic seabirds with comparable ecological traits and breeding grounds. Recent threats such as introduced species of predators and human disturbance have resulted in a decline of many insular vertebrate populations in this region and affected many different aspects of their life histories (ranging from reproductive success to mate selection), with a concomitant loss of genetic diversity. To elucidate to what extent the population genetic structure occurs in H. melania and H. microsoma, we used 719 base pairs from the mitochondrial cytochrome oxidase c subunit I gene. The evaluation of their molecular diversity, genetic structure, and gene flow were performed through diversity indices, analyses of molecular and spatial variance, and isolation by distance (IBD) across sampling sites, respectively. The population genetic structure (via AMOVA and SAMOVA) and isolation by distance (pairwise p-distances and FST/1– FST (using ΦST) were inferred for H. microsoma. However, for H. melania evidence was inconclusive. We discuss explanations leading to divergent population genetic structure signatures in these species, and the consequences for their conservation.

Seed Adaptive Traits of Fagus sylvatica Populations in Northeastern Greece

2020 ◽  
Vol 66 (4) ◽  
pp. 403-415
Author(s):  
Georgios Varsamis ◽  
Theodora Merou ◽  
Ioannis Takos ◽  
Chrisovalantis Malesios ◽  
Apostolos Manolis ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Chloroplast Dna ◽  
Fagus Sylvatica ◽  
Environmental Conditions ◽  
Dna Markers ◽  
Spatial Scales ◽  
Adaptation Strategies ◽  
Adaptive Traits ◽  
Chloroplast Dna Markers

Abstract Fagus sylvatica in Europe is expected to be severely affected by the ongoing climate change. In this article, seed adaptive traits, in terms of morphology and germination, of F. sylvatica populations of different postglacial lineage and intrapopulation genetic diversity were evaluated. Eight plots from two geographical provenances, Evros and Drama, were selected. Provenance shaped both morphology and germination patterns, but the effect was more pronounced on germination. Seeds from Drama were larger and heavier than those from Evros but exhibited a higher degree of dormancy and slower germination. High among-plots variability on morphology and germination was also observed, especially in Evros. This higher variability was consistent with the higher level of genetic diversity observed at genomic and chloroplast DNA markers at small or larger spatial scales from previous published studies on the same plots. Results suggested the existence of different seed adaptation strategies, mainly between provenances, as a result of possible adaptation to different environmental conditions, whereas a possible influence of a generally complex pattern of admixture between different beech subspecies and postglacial lineages could not be excluded.

Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers

2018 ◽  
Vol 66 (6) ◽  
pp. 335
Author(s):  
T. Pan ◽  
P. Yan ◽  
M. Yang ◽  
H. Wang ◽  
I. Ali ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Yangtze River ◽  
The Yangtze River ◽  
Geographic Scale ◽  
Widespread Species ◽  
Bufo Gargarizans ◽  
Toad Bufo

Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.

scholarly journals Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

2020 ◽  
Author(s):  
Godfrey Kinyori Wagutu ◽  
Xiangrong Fan ◽  
Wenlong Fu ◽  
Wei Li ◽  
Yuanyuan Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Landscape Heterogeneity ◽  
Maximum Temperature ◽  
Zizania Latifolia ◽  
Precipitation Seasonality ◽  
Isolation By Environment

AbstractGlobal aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Øpt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

scholarly journals A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

2021 ◽  
Author(s):  
Souta Nakajima ◽  
Masanao Sueyoshi ◽  
Shun K. Hirota ◽  
Nobuo Ishiyama ◽  
Ayumi Matsuo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Low Temperature ◽  
Genetic Differentiation ◽  
Water Temperature ◽  
Sampling Design ◽  
Cold Water ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Sampling Strategy ◽  
Genotyping By Sequencing

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.

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