Effect of Human Disturbance on Genetic Structure of Rare and Endangered Paphiopedilum micranthum Implied the Habitat Status

Seven populations of Paphiopedilum micranthum from Southeast China were used to assess the influence of human disturbance on genetic structure through analysis with sequence-related amplified polymorphism technology. The results indicated that there was high genetic diversity at species level ( p = 81.25%; I = 0.3709) and a significantly higher differentiation level compared to that those of other outcrossing orchid species, and that moderately disturbed populations sustained higher genetic diversity indexes than the natural populations. This study revealed that human disturbance and population size did not significantly affect the populations’ genetic diversity but aggravated their differentiation. This may suggest that the habitat had a much greater influence on genetic variation.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽

10.3390/f11040469 ◽

2020 ◽

Vol 11 (4) ◽

pp. 469 ◽

Cited By ~ 1

Author(s):

Yanwen Deng ◽

Tingting Liu ◽

Yuqing Xie ◽

Yaqing Wei ◽

Zicai Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Human Disturbance ◽

Haplotype Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

High Genetic Diversity ◽

Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

eLife ◽

10.7554/elife.47091 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 8

Author(s):

Anna-Liisa Laine ◽

Benoit Barrès ◽

Elina Numminen ◽

Jukka P Siren

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Fungal Pathogen ◽

Population Genetic ◽

Reproductive Strategies ◽

Natural Populations ◽

Pathogen Population ◽

To Come ◽

Pathogen Populations

Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.

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High Genetic Diversity and Insignificant Interspecific Differentiation inOpisthopappusShih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China

The Scientific World JOURNAL ◽

10.1155/2013/275753 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Rongmin Guo ◽

Lihua Zhou ◽

Hongbo Zhao ◽

Fadi Chen

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Species Level ◽

Endangered Plants ◽

High Genetic Diversity ◽

Fragmented Distribution ◽

Polymorphic Bands ◽

Genetic Structures ◽

Different Levels

OpisthopappusShih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely,O. taihangensis(Ling) Shih andO. longilobusShih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR) to analyze the genetic diversity and genetic structure from different levels (genus, species, and population) in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB) of up to 90.91% at genus level. At species level, bothO. taihangensis(PPB=90.12%,H=0.1842, andI=0.289) andO. longilobus(PPB=95.21%,H=0.2226, andI=0.3542) have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation inO. longilobus(84.95%) was higher than that inO. taihangensis(80.45%). A certain genetic differentiation among populations inO. taihangensiswas found (Gst=0.2740,Φst=0.196) and genetic differentiation inO. longilobuswas very small (Gst=0.1034,Φst=0.151). Gene flow in different degrees (Nm=1.325and 4.336, resp.) and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst=0.0453) between species and the clustering result based on the genetic distance showed that interspecific differentiation betweenO. taihangensisandO. longilobuswas not significant and could occur lately.

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Diversity and genetic structure in natural populations of Geonoma schottiana Mart (arecaceae): implications for conservation

CERNE ◽

10.1590/s0104-77602011000200006 ◽

2011 ◽

Vol 17 (2) ◽

pp. 195-201 ◽

Cited By ~ 2

Author(s):

Mirian de Sousa Silva ◽

Fábio de Almeida Vieira ◽

Dulcinéia de Carvalho

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Natural Populations ◽

Diversity Indices ◽

Tropical Species ◽

High Genetic Diversity ◽

Minas Gerais State ◽

Isozyme Loci ◽

Important Food Source

Geonoma schottiana is an underbrush palm which is found in high densities in tropical forests. This species is known for having an asynchronous fruit producing pattern, over all seasons of the year, thus being an important food source for frugivores. This work aims to determine the diversity and spatial genetic structure of two natural populations, referred to as MC I and MC II, of which 60 individuals were sampled, in Poço Bonito Biological Reserve, Lavras, Minas Gerais state. Results of 10 polymorphic isozyme loci indicated a high genetic diversity for the species (Ĥe= 0.428 and Ĥo = 0.570), with an mean number of alleles per locus of 2.0. Estimates of Cockerham's coancestry coefficients indicated an absence of intrapopulation (<img border=0 width=28 height=24 src="../../../../../../img/revistas/cerne/v17n2/a06car02.jpg" > or = -0.343) and interpopulation inbreeding (<img border=0 width=26 height=26 src="../../../../../../img/revistas/cerne/v17n2/a06car01.jpg" > or = -0.161), suggesting that on average populations are not endogamous. A high genetic divergence was found between populations (<img border=0 width=26 height=27 src="../../../../../../img/revistas/cerne/v17n2/a06car03.jpg"> = 13.5%), in comparison to most tropical species (<5%). Consequently, the estimated historical gene flow was low (<img border=0 width=26 height=27 src="../../../../../../img/revistas/cerne/v17n2/a06car04.jpg">m = 0.40). The analysis of spatial distribution of G. schottiana genotypes in MCI revealed a random distribution of genotypes. The high genetic diversity indices found suggest that the populations in question favor in situ genetic conservation, consequently favoring the conservation of riparian environments.

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Association between spatial genetic variation and potential distribution in tree fern Alsophila gigantea (Cyatheaceae) in Hainan Island, China

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49312407 ◽

2021 ◽

Vol 49 (3) ◽

pp. 12407

Author(s):

Ting WANG ◽

Zhen WANG ◽

Shufeng LI ◽

Zhanming YING ◽

Xiaoxian RUAN ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Spatial Genetic Structure ◽

Geographic Distance ◽

Population Level ◽

Hainan Island ◽

Mantel Test ◽

High Genetic Diversity ◽

Spatial Genetic Variation

Spatial genetic variation involves spatial genetic structure (SGS) and genetic diversity is important genetic features of plants. We first evaluated spatial genetic structure (SGS) and genetic diversity among four populations of Alsophila gigantea from Hainan Island, China, using inter-simple sequence repeat (ISSR) markers. Significant but weak FSGS was found in A. gigantea. High genetic diversity was identified at the species level and the population level. AMOVA analysis revealed a low level of genetic differentiation among the four populations with high gene flow. Mantel test showed no significant correlation between genetic distance and geographic distance. It was found that association between annual mean temperature and annual precipitation with FSGS. Combined with these spatial genetic variation, abundant precipitation and suitable temperature create a stable environment for A. gigantea in Hainan Island, which allows the fern to expand rapidly during the LGM. These results further emphasized the role of outcrossing, and history and environmental factors in the evolution of A. gigantea. This study also provided new insights on in local adaptation of A. gigantea to environmental fluctuations, and available genetic data to enhance the conservation for relict tree ferns.

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Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

Biodiversity Science ◽

10.3724/sp.j.1003.2013.09098 ◽

2014 ◽

Vol 21 (5) ◽

pp. 601-609

Author(s):

Wang Deyun ◽

Peng Jie ◽

Chen Yajing ◽

Lü Guosheng ◽

Zhang Xiaoping ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Endangered Species ◽

Rare And Endangered Species ◽

Rare And Endangered

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Population genetic structure and dispersal of Pinus occidentalis in the Dominican Republic by chloroplastic SSR with implications for its conservation, management, and reforestation

Canadian Journal of Forest Research ◽

10.1139/cjfr-2021-0282 ◽

2021 ◽

Author(s):

Luis E. Rodríguez de Francisco ◽

Rosanna Carreras-De León ◽

Rafael M. Navarro Cerrillo ◽

Liz A. Paulino-Gervacio ◽

María-Dolores Rey ◽

...

Keyword(s):

Genetic Structure ◽

Dominican Republic ◽

Population Genetic Structure ◽

Population Genetic ◽

Conservation Management ◽

Natural Populations ◽

Limited Information ◽

High Genetic Diversity ◽

The Impact ◽

Pinus Occidentalis

Pinus occidentalis is the dominant species of forest ecosystems in the Dominican Republic, located between 200 and 3000 meters above sea level, with extensive and overexploited natural populations. However, over the years, various restoration plans have been performed, which could affect the genetic structure of P. occidentalis. Despite being the species with the highest occurrence in the Dominican forests, there is no existing information on genetic structure and molecular characterization among natural populations with limited information on both phenological and productive characterization. In this study, the genetic structure, diversity, and gene flow of the five P. occidentalis natural populations of the Dominican Republic were determined using microsatellite markers. A total of 145 individuals were genotyped with eight polymorphic chloroplastic microsatellites, producing an average of 41 haplotypes with high genetic diversity across populations (HE = 0.90). Significant population genetic structure was found between populations (FST = 0.123). These results reflect the impact of reforestation programs on natural populations and diluting the natural genetic signature. Analysis of population genetic data is, therefore, crucial for the breeding and conservation programs of P. occidentalis in the country.

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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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Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.618380 ◽

2021 ◽

Vol 9 ◽

Author(s):

Heather R. Kates ◽

Fernando López Anido ◽

Guillermo Sánchez-de la Vega ◽

Luis E. Eguiarte ◽

Pamela S. Soltis ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gene Flow ◽

Genetic Structure ◽

Morphological Diversity ◽

Cucurbita Maxima ◽

Wild Progenitor ◽

Breeding Potential ◽

Trait Improvement ◽

Wild Progenitors

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

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