scholarly journals Genetic variation and genetic structure within metapopulations of two closely related selfing and outcrossing Zingiber species (Zingiberaceae)

AoB Plants ◽  
2020 ◽  
Author(s):  
Rong Huang ◽  
Zong-Dian Zhang ◽  
Yu Wang ◽  
Ying-Qiang Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Spatial Genetic Structure ◽  
Full Range ◽  
Breeding Systems ◽  
Dispersal Ability ◽  
Phylogenetic Distance ◽  
Plant Populations

Abstract Habitat fragmentation strongly affects the genetic diversity of plant populations, and this has always attracted much research interest. Although numerous studies have investigated the effects of habitat fragmentation on the genetic diversity of plant populations, fewer studies have compared species with contrasting breeding systems while accounting for phylogenetic distance. Here, we compare the levels of genetic diversity and differentiation within and among subpopulations in metapopulations (at fine-scale level) of two closely related Zingiber species, selfing Zingiber corallinum and outcrossing Zingiber nudicarpum. Comparisons of the genetic structure of species from unrelated taxa may be confounded by the effects of correlated ecological traits or/and phylogeny. Thus, we possibly reveal the differences in genetic diversity and spatial distribution of genetic variation within metapopulations that relate to mating systems. Compared to outcrossing Z. nudicarpum, the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity was not different. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum, depending on whether the degree of subpopulation isolation surpass the dispersal ability of pollen and seed. A stronger spatial genetic structure appeared within subpopulations of selfing Z. corallinum potentially due to restricted pollen flow and seed dispersal. In contrast, a weaker genetic structure was apparent in subpopulations of outcrossing Z. nudicarpum most likely caused by extensive pollen movement. Our study shows that high genetic variation can be maintained within metapopulations of selfing Zingiber species, due to increased genetic differentiation intensified primarily by the stochastic force of genetic drift among subpopulations. Therefore, maintenance of natural variability among subpopulations in fragmented areas is key to conserve the full range of genetic diversity of selfing Zingiber species. For outcrossing Zingiber species, maintenance of large populations is an important factor to enhance genetic diversity.

scholarly journals Genetic diversity and structure of Astrocaryum jauari (Mart.) palm in two Amazon river basins

2014 ◽  
Vol 14 (3) ◽  
pp. 166-173 ◽  
Author(s):  
Liliane D. Santos Oliveira ◽  
Santiago L. Ferreyra Ramos ◽  
Maria T. Gomes Lopes ◽  
Gabriel Dequigiovanni ◽  
Elizabeth Ann Veasey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Microsatellite Loci ◽  
Plant Material ◽  
Spatial Genetic Structure ◽  
River Basins ◽  
Genetic Analyses ◽  
Main River ◽  
Genetic Diversity And Structure

Astrocaryum jauari is a non-domesticated palm that is exploited by poachers. Our objective was to investigate the organization of the geneticdiversity and structure of three A. jauari populations. The study was carried out in the state of Amazonas, between the municipalities of Coari and Manaus. Nine microsatellite loci were used for the genetic analyses. High genetic variation was found, with a mean number of alleles per locus varying from 3.9 to 4.4. The average observed heterozygosity, varying from 0.71 to 0.78, was higher than expected. No spatial genetic structure was detected, since only one cluster was observed. Our results indicate a possible dispersion strategy and suggest that conservation measures of this species should focus mainly on the populations found at the end of the main river (Solimões) where most of the plant material originating from the headwaters of the tributaries of this river is concentrated.

scholarly journals Genetic diversity and spatial genetic structure within a population of an aromatic shrub, Lippia origanoides (Verbenaceae), in the Chicamocha Canyon, northeastern Colombia

2008 ◽  
Vol 90 (6) ◽  
pp. 455-465 ◽  
Author(s):  
ADRIANA SUÁREZ G. ◽  
GENIS CASTILLO ◽  
MARIA I. CHACÓN S.
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Diversity Index ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Classical Model ◽  
Issr Markers ◽  
Breeding Systems ◽  
Group Method ◽  
Pair Group

SummaryThe geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86·21%) and quantified using Shannon's diversity index (I=0·453) and the average panmictic heterozygosity (HB=0·484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than ~1·2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

scholarly journals The effects of habitat fragmentation on the genetic structure of wild boar (Sus scrofa) population in Lithuania

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Loreta Griciuvienė ◽  
Žygimantas Janeliūnas ◽  
Vaclovas Jurgelevičius ◽  
Algimantas Paulauskas
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Wild Boar ◽  
Sus Scrofa ◽  
Isolation By Distance ◽  
Wild Boar Population ◽  
Ecological Features

Abstract Background Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of Lithuania’s wild boar population have not yet been thoroughly studied. The purposes of this study were to investigate the genetic diversity of S. scrofa and assess the effects of habitat fragmentation on the population structure of wild boar in Lithuania. A total of 96 S. scrofa individuals collected from different regions of Lithuania were genotyped using fifteen microsatellite loci. Results The microsatellite analysis of the wild boars indicated high levels of genetic diversity within the population. Microsatellite markers showed evidence of a single panmictic wild boar population in Lithuania according to STRUCTURE’s highest average likelihood, which was K = 1. This was supported by pairwise Fst values and AMOVA, which indicated no differentiation between the four sampling areas. The results of the Mantel test revealed a weak isolation by distance and geographic diversity gradients that persisted between locations. Motorway fencing and heavy traffic were not an effective barrier to wild boar movement. Conclusions There was limited evidence of population genetic structure among the wild boar, supporting the presence of a single population across the study area and indicating that there may be no barriers hindering wild boar dispersal across the landscape. The widespread wild boar population in Lithuania, the high level of genetic variation observed within subpopulations, and the low level of variation identified between subpopulations suggest migration and gene flow between locations. The results of this study should provide valuable information in future for understanding and comparing the detailed structure of wild boar population in Lithuania following the outbreak of African swine fever.

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

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.

scholarly journals Potential effects of life history on demographic genetic structure in stage-structured plant populations

2021 ◽  
Author(s):  
Yoichi Tsuzuki ◽  
Takenori Takada ◽  
Masashi Ohara
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Life History ◽  
Genetic Structure ◽  
Temporal Dynamics ◽  
Structured Populations ◽  
Plant Populations ◽  
Expected Heterozygosity ◽  
Neutral Locus ◽  
Two Indices

Standing genetic variation, or genetic diversity, is a source of adaptive evolution, and is crucial for long-term population persistence under environmental changes. One empirical method to predict the temporal dynamics of standing genetic variation in age- or stage-structured populations is to compare genetic diversity and composition among age/stage classes. The resultant within-population genetic structure, sometimes referred to as demographic genetic structure, has been regarded as a proxy of potential genetic changes that accompany sequential generation turnover. However, especially in stage-structured plant populations, individuals in more juvenile stages do not necessarily represent future populations, as they might die, stop growing, or retrogress over the course of life history. How demographic genetic structure is subjected to life history and whether it is a good proxy of temporal genetic dynamics had remained unclear. Here, we developed a matrix model which well describes temporal dynamics of expected heterozygosity, a common proxy of genetic diversity, for a neutral locus in stage-structured populations under equilibrium assumption. Based on the model, two indices of demographic genetic structure were formulated: relative ratio of expected heterozygosity and genetic differentiation among stage classes. We found that the two indices were largely determined by stable stage distribution and population size, and that they did not show clear correlations with the change rate of genetic diversity, indicating that inferring future genetic diversity from demographic genetic structure conventionally is misleading. Our study facilitates reliable interpretation on empirical demographic genetic data.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals Spatial genetic structure of the sea sandwort (<i>Honckenya peploides</i>) on Surtsey: an immigrant's journey

2014 ◽  
Vol 11 (22) ◽  
pp. 6495-6507 ◽  
Author(s):  
S. H. Árnason ◽  
Ǽ. Th. Thórsson ◽  
B. Magnússon ◽  
M. Philipp ◽  
H. Adsersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Early Stage ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Rapid Expansion ◽  
Aflp Markers ◽  
Plant Colonization ◽  
Southern Coast ◽  
Binary Matrix

Abstract. Sea sandwort (Honckenya peploides) was one of the first plants to successfully colonize and reproduce on the volcanic island Surtsey, formed in 1963 off the southern coast of Iceland. Using amplified fragment length polymorphic (AFLP) markers, we examined levels of genetic variation and differentiation among populations of H. peploides on Surtsey in relation to populations on the nearby island Heimaey and from the southern coast of Iceland. Selected populations from Denmark and Greenland were used for comparison. In addition, we tested whether the effects of isolation by distance could be seen in the Surtsey populations. Using two primer combinations, we obtained 173 AFLP markers from a total of 347 plant samples. The resulting binary matrix was then analysed statistically. The main results include the following: (i) Surtsey had the highest proportion of polymorphic markers as well as a comparatively high genetic diversity (55.5% proportion of polymorphic loci, PLP; 0.1974 HE) and Denmark the lowest (31.8% PLP; 0.132 HE), indicating rapid expansion during an early stage of population establishment on Surtsey and/or multiple origins of immigrants; (ii) the total genetic differentiation (FST) among Surtsey (0.0714) and Heimaey (0.055) populations was less than half of that found among the mainland populations in Iceland (0.1747), indicating substantial gene flow on the islands; (iii) most of the genetic variation (79%, p < 0.001) was found within localities, possibly due to the outcrossing and subdioecious nature of the species; (iv) a significant genetic distance was found within Surtsey, among sites, and this appeared to correlate with the age of plant colonization; and (v) the genetic structure analysis indicated multiple colonization episodes on Surtsey, whereby H. peploides most likely immigrated from the nearby island of Heimaey and directly from the southern coast of Iceland.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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

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.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

Sign in / Sign up

Export Citation Format

Share Document