The population genetics of the fundamental cytotype-shift in invasive Centaurea stoebe s.l.: genetic diversity, genetic differentiation and small-scale genetic structure differ between cytotypes but not between ranges

Abstract Background Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short seed dispersal distance by ants as their seed distributor. It is known that many flowers of A. sieboldii depend on self-fertilization. Because these characteristics can affect negatively in genetic structure, investigating habitat structure and assessment of genetic structure is needed. A total of 27 individuals in a valley were sampled for measuring genetic diversity, genetic distance, and genetic differentiation by RAPD-PCR. Results The habitat areas of A. sieboldii metapopulation were relatively small (3.78~33.60 m2) and population density was very low (five to seven individuals in 20×20 m quadrat). The habitat of A. sieboldii was a very shady (relative light intensity = 0.9%) and mature forest with a high evenness value (J = 0.81~0.99) and a low dominance value (D = 0.19~0.28). The total genetic diversity of A. sieboldii was quite high (h = 0.338, I = 0.506). A total of 33 band loci were observed in five selected primers, and 31 band loci (94%) were polymorphic. However, genetic differentiation along the valley was highly progressed (Gst = 0.548, Nm = 0.412). The average genetic distance between subpopulations was 0.387. The results of AMOVA showed 52.77% of variance occurs among populations, which is evidence of population structuring. Conclusions It is expected that a small-scale founder effect had occurred, an individual spread far from the original subpopulation formed a new subpopulation. However, geographical distance between individuals would have been far and genetic flow occurred only within each subpopulation because of the low density of population. This made significant genetic distance between the original and new population by distance. Although genetic diversity of A. sieboldii metapopulation is not as low as concerned, the subpopulation of A. sieboldii can disappear by stochastic events due to small subpopulation size and low density of population. To prevent genetic isolation and to enhance the stable population size, conservative efforts such as increasing the size of each subpopulation or the connection between subpopulations are needed.

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

10.21203/rs.3.rs-779119/v1 ◽

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.

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

Australian Journal of Zoology ◽

10.1071/zo18059 ◽

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.

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Spectrum of genetic diversity and networks of clonal organisms

Journal of The Royal Society Interface ◽

10.1098/rsif.2007.0230 ◽

2007 ◽

Vol 4 (17) ◽

pp. 1093-1102 ◽

Cited By ~ 56

Author(s):

Alejandro F Rozenfeld ◽

Sophie Arnaud-Haond ◽

Emilio Hernández-García ◽

Víctor M Eguíluz ◽

Manuel A Matías ◽

...

Keyword(s):

Genetic Diversity ◽

Population Genetics ◽

Genetic Structure ◽

Small World ◽

Clonal Plants ◽

Posidonia Oceanica ◽

Genetic Distances ◽

Wide Range ◽

Clonal Organisms ◽

Genetic Structure And Diversity

Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations were examined using a combination of new tools to analyse microsatellite data in the marine angiosperm Posidonia oceanica . These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a ‘small-world’ topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in subfamilies of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.

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

10.1101/2020.05.29.124685 ◽

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.

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The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

10.21203/rs.3.rs-640424/v1 ◽

2021 ◽

Author(s):

Yuan Li ◽

Fangrui Lou ◽

Hai Li ◽

Rui Wang ◽

Zizi Cai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Expansion ◽

Nucleotide Polymorphisms ◽

Stress Reactions ◽

Long Distance ◽

Evolutionary Mechanisms ◽

Inflammatory Reactions ◽

Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

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Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

Frontiers in Genetics ◽

10.3389/fgene.2021.705337 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shumiao Zhang ◽

Chao Li ◽

Yiping Li ◽

Qi Chen ◽

Defu Hu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Size ◽

Population Genomics ◽

Distribution Area ◽

History Of ◽

Père David’S Deer ◽

Free Ranging ◽

Elaphurus Davidianus

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

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Different Habitats Show Similar Genetic Structure of Bunias orientalis L. (Brassicaceae)in Lithuania

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4129186 ◽

2013 ◽

Vol 41 (2) ◽

pp. 396 ◽

Cited By ~ 5

Author(s):

Jolanta PATAMSYTĖ ◽

Tatjana ČĖSNIENĖ ◽

Donatas NAUGŽEMYS ◽

Violeta KLEIZAITĖ ◽

Virginija TUNAITIENĖ ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Genetic Difference ◽

Habitat Type ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Baltic Countries ◽

Bunias Orientalis ◽

The Impact

We studied genetic diversity within and among populations of warty cabbage (Bunias orientalis L.), which is an alien species in Lithuania and other Baltic countries. In Lithuania, this weed colonises two main types of habitats: railway/roadsides and meadows on riversides. The aim of this study was to assess the genetic structure of invasive populations of B. orientalis in Lithuania and consider the impact of diverse habitats on the partitioning of genetic diversity using inter-simple sequence repeat (ISSR) markers. An analysis of molecular variance (AMOVA) carried out on the basis of ISSR showed that there is high genetic differentiation (46%) among populations of B. orientalis, which is probably caused by the founder effect and limited gene flow. However, we observed no impact of habitat on the genetic difference among populations. Similar levels of ISSR polymorphic loci were observed in riverside (P = 31.67%) and railway/roadsides (P = 30.51%) populations. UPGMA cluster analysis and principal coordinate analysis (PCoA) also did not show grouping of studied populations according to habitat type. High genetic differentiation among populations, as indicated by ISSR markers, confirm multiple independent introductions of this species in Lithuania.

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Genetic Diversity and Population Genetic Structure of Erythrophleum fordii Oliv., an Endangered Rosewood Species in South China

Forests ◽

10.3390/f9100636 ◽

2018 ◽

Vol 9 (10) ◽

pp. 636 ◽

Cited By ~ 3

Author(s):

Jing Tan ◽

Zhi-Gang Zhao ◽

Jun-Jie Guo ◽

Chun-Sheng Wang ◽

Jie Zeng

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Endangered Species ◽

Genetic Differentiation ◽

South China ◽

Population Genetic Structure ◽

Population Genetic ◽

The Mean ◽

Erythrophleum Fordii ◽

Private Alleles

Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. FIS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (FST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.

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Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters

Scientific Reports ◽

10.1038/s41598-021-94257-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kean Chong Lim ◽

Amy Yee-Hui Then ◽

Alison Kim Shan Wee ◽

Ahemad Sade ◽

Richard Rumpet ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Fishery Management ◽

Peninsular Malaysia ◽

Fine Scale ◽

Nadh Dehydrogenase Subunit 2 ◽

Bamboo Shark

AbstractThe demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.

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