Genetic impacts of habitat loss on the rare Banded Ironstone Formation endemic Ricinocarpos brevis (Euphorbiaceae)

2019 ◽  
Vol 67 (3) ◽  
pp. 183 ◽  
Author(s):  
Siegfried L. Krauss ◽  
Janet Anthony
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Mining Operations ◽  
Analysis Of Molecular Variance ◽  
Mantel Tests ◽  
Tests Of Association ◽  
Potential Impact

Ricinocarpos brevis (Euphorbiaceae) is a declared rare species currently known from only three Banded Ironstone Formation (BIF) ranges (Perrinvale, Johnston and Windarling Ranges) in the Yilgarn region of Western Australia. The present study assessed the potential impact of proposed mining on genetic diversity within R. brevis. Approximately 30 plants were sampled from each of 14 sites across the known distribution of R. brevis. Genetic variation and its spatial structure was assessed with 144 polymorphic AFLP markers that were generated by two independent primer pairs: M-CTG/P-AC (81 markers) and M-CTA/P-AC (63 markers). Hierarchical spatial genetic structure was assessed by an analysis of molecular variance (AMOVA), Mantel tests of association between genetic- and geographic-distance and ordination. Specific attention was given to the extent of genetic differentiation of the three populations on the Windarling Range W4 deposit, which was proposed for mining operations. Strong genetic differentiation (ΦPT=0.186–0.298) among the three ranges was found. Genetic differentiation of the Johnston Range populations from Windarling and Perrinvale was greater than expected under isolation by distance predictions, suggesting adaptive genetic differentiation driven by site environmental differences, reflected by differences in plant community, substrate and landscape features. In contrast, genetic differentiation among the three Windarling Range regions (W2, W3, W4) was weaker (ΦPT=0.055–0.096). Mean pairwise ΦPT=0.078 for the 10 Windarling sites, which was unchanged with the removal of the W4 populations. In addition, none of the markers scored were unique to the W4 populations. Thus, for this set of markers, the removal of plants on the Windarling Range W4 deposit had little impact on genetic diversity within R. brevis. Strong concordance in results from the independent datasets generated by the two AFLP primer pairs provides overall support for the conclusions drawn.

Genetic diversity and gene flow patterns in two riverine plant species with contrasting life-history traits and distributions across a large inland floodplain

2020 ◽  
Vol 68 (5) ◽  
pp. 384
Author(s):  
William Higgisson ◽  
Dianne Gleeson ◽  
Linda Broadhurst ◽  
Fiona Dyer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Water Resource ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Resource Development ◽  
Water Resource Development ◽  
Floodplain River

Gene flow is a key evolutionary driver of spatial genetic structure, reflecting demographic processes and dispersal mechanisms. Understanding how genetic structure is maintained across a landscape can assist in setting conservation objectives. In Australia, floodplains naturally experience highly variable flooding regimes that structure the vegetation communities. Flooding plays an important role, connecting communities on floodplains and enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is reduced physical and subsequent genetic connections. This study aimed to identify and compare the population structure and dispersal patterns of tangled lignum (Duma florulenta) and river cooba (Acacia stenophylla) across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semiarid Australia. Tangled lignum occurs on floodplains while river cooba occurs along rivers. Leaves were collected from 144 tangled lignum plants across 10 sites and 84 river cooba plants across 6 sites, on the floodplain of the lower and mid Lachlan River, and the Murrumbidgee River, NSW. DNA was extracted and genotyped using DArTseq platforms (double digest RADseq). Genetic diversity was compared with floodplain-river connection frequency, and genetic distance (FST) was compared with river distance, geographic distance and floodplain-river connection frequency between sites. Genetic similarity increased with increasing floodplain-river connection frequency in tangled lignum but not in river cooba. In tangled lignum, sites that experience more frequent flooding had greater genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in tangled lignum, but not in river cooba. The distribution of river cooba along rivers facilitates regular dispersal of seeds via hydrochory regardless of river level, while the dispersal of seeds of tangled lignum between patches is dependent on flooding events. The genetic impact of water resource development may be greater for species which occur on floodplains compared with species along river channels.

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 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 Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhigang Wu ◽  
Xinwei Xu ◽  
Juan Zhang ◽  
Gerhard Wiegleb ◽  
Hongwei Hou
Keyword(s):  
Genetic Diversity ◽  
Tibetan Plateau ◽  
Environmental Factors ◽  
Local Adaptation ◽  
Aquatic Macrophyte ◽  
Spatial Genetic Structure ◽  
Long Distance ◽  
Elevation Gradients ◽  
Mantel Tests ◽  
Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

scholarly journals Landscape structure and the genetic effects of a population collapse

2014 ◽  
Vol 281 (1796) ◽  
pp. 20141798 ◽  
Author(s):  
Serena A. Caplins ◽  
Kimberly J. Gilbert ◽  
Claudia Ciotir ◽  
Jens Roland ◽  
Stephen F. Matter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Landscape Structure ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Genetic Differentiation Of Populations ◽  
Patch Connectivity ◽  
Landscape Genetic ◽  
Independent Effects ◽  
Patterns And Processes

Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift.

scholarly journals Genetic Diversity and Spatial Genetic Structure of Stellaria Holostea Populations from Urban Forest Islands

2014 ◽  
Vol 56 (1) ◽  
pp. 42-53 ◽  
Author(s):  
Maciej Wodkiewicz ◽  
Bożenna Gruszczyńska
Keyword(s):  
Genetic Diversity ◽  
Spatial Organization ◽  
Urban Forest ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Urban Forests ◽  
Clonal Diversity ◽  
Diversity Indices ◽  
Ancient Forest ◽  
Forest Islands

Abstract Stellaria holostea is a clonal herb highly confined to well-established deciduous forests. This study examined whether its genetic diversity and spatial genetic organization in urban forest islands is similar to the values from well-established populations outside urban landscape. We studied four populations in Warsaw and two populations from well preserved forests outside the city. Genetic diversity was greater in populations from well-preserved forests than from forests heavily exploited in the past. High clonal diversity indices indicate that the studied populations did not lose the ability to reproduce sexually. The small populations in urban forests differed from the remaining sites in spatial organization. High overall FST (0.24) and the lack of correlation between genetic and geographic distance between the studied populations indicate limited gene flow. Urban forests may be of great value for conservation of S. holostea and other ancient forest species as they may still harbor substantial genetic variability despite their isolation.

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.

scholarly journals The genetic diversity of Ethiopian barley genotypes in relation to their geographical origin

2021 ◽  
Author(s):  
Surafel Shibru Teklemariam ◽  
Kefyalew Negisho Bayissa ◽  
Andrea Matros ◽  
Klaus Pillen ◽  
Frank Ordon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Geographic Distance ◽  
Snp Array ◽  
Farming Systems ◽  
Mantel Test ◽  
Snp Markers ◽  
Improvement Program ◽  
Climate Conditions ◽  
Breeding Lines

Ethiopia is recognized as a center of diversity for barley, and its landraces are known for the distinct genetic features compared to other barley collections. The genetic diversity of Ethiopian barley likely results from the highly diverse topography, altitude, climate conditions, soil types, and farming systems. To get detailed information on the genetic diversity a panel of 260 accessions, comprising 239 landraces and 21 barley breeding lines, obtained from the Ethiopian biodiversity institute (EBI) and the national barley improvement program, respectively were studied for their genetic diversity using the 50k iSelect single nucleotide polymorphism (SNP) array. A total of 983 highly informative SNP markers were used for structure and diversity analysis. Three genetically distinct clusters were obtained from the structure analysis comprising 80, 71, and 109 accessions, respectively. Analysis of molecular variance (AMOVA) revealed the presence of higher genetic variation (89%) within the clusters than between the clusters (11%), with moderate genetic differentiation (PhiPT=0.11) and adequate gene flow (Nm=2.02). The Mantel test revealed that the genetic distance between accessions is poorly associated with their geographical distance. Despite the observed weak correlation between geographic distance and genetic differentiation, for some regions like Gonder, Jimma, Gamo-Gofa, Shewa, and Welo, more than 50% of the landraces derived from these regions are assigned to one of the three clusters.

Microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri): Is pooling samples safe?

2005 ◽  
Vol 62 (8) ◽  
pp. 1874-1886 ◽  
Author(s):  
Daniel Gomez-Uchida ◽  
Michael A Banks
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Original Data ◽  
Dispersal Distance ◽  
Data Set ◽  
Limited Dispersal ◽  
Composite Samples ◽  
Microsatellite Analyses

By pooling or removing samples of small size, we investigated how results from microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri) were affected. Genotypes from six and seven microsatellite loci from 1206 specimens collected offshore from Washington to California were employed in the analyses. Sample sizes varied greatly among locations (n = 11–114). When adjacent samples of n < 25 were pooled using an absolute genetic distance (FST ≤ 0), the correlation between genetic and geographic distance found in the original data set increased nearly twofold, and overall FST (95% confidence interval) increased from 0.001 (0.000–0.002) to 0.002 (0.001–0.003). Removing samples where n < 25 gave a similar result, yet the correlation increase was smaller. Another pooling strategy based on similarity tests allowed larger sizes in composite samples (n > 100) and further increased the correlation, although this strategy did not raise overall FST. These results indicate that under genetic isolation by distance, excessive pooling might not enhance the overall genetic differentiation among populations. The regression slope in isolation by distance plots was robust throughout all treatments, and its value suggests limited dispersal distance on this species.

scholarly journals Small-scale spatial genetic structure of Asarum sieboldii metapopulation in a valley

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Hyeon Jin Jeong ◽  
Jae Geun Kim
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Forest Understory ◽  
Small Scale ◽  
Low Density ◽  
Stochastic Events

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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