scholarly journals Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8550 ◽  
Author(s):  
Kaho H. Tisthammer ◽  
Zac H. Forsman ◽  
Robert J. Toonen ◽  
Robert H. Richmond
Keyword(s):  
Genetic Structure ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
High Stress ◽  
Single Location ◽  
Isolation By Environment ◽  
Porites Lobata ◽  
Significant Genetic Structure ◽  
Contrasting Habitats

We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats.

scholarly journals Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

2019 ◽  
Author(s):  
Kaho H. Tisthammer ◽  
Zac H. Forsman ◽  
Robert J. Toonen ◽  
Robert H. Richmond
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
High Stress ◽  
Disruptive Selection ◽  
Single Location ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Significant Genetic Structure ◽  
Contrasting Habitats

ABSTRACTWe examined genetic structure in the lobe coralPorites lobataamong pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oʻahu and Maui, Hawai‘i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVAFST= 0.04 ∼ 0.19,P< 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST∼ 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041∼0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

scholarly journals Genetic divergence correlates with the contemporary landscape in populations of Slimy Salamander (Plethodon glutinosus) species complex across the lower Piedmont and Coastal Plain of the southeastern United States

2018 ◽  
Vol 96 (11) ◽  
pp. 1244-1254 ◽  
Author(s):  
Walter H. Smith ◽  
Jessica A. Wooten ◽  
Carlos D. Camp ◽  
Dirk J. Stevenson ◽  
John B. Jensen ◽  
...  
Keyword(s):  
South Carolina ◽  
Genetic Distance ◽  
Principal Components ◽  
Coastal Plain ◽  
Genetic Divergence ◽  
Species Complex ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Plethodon Glutinosus ◽  
Isolation By Environment

A primary goal of landscape genetics is to elucidate factors associated with genetic structure among populations. Among the important patterns identified have been isolation by distance (IBD), isolation by barrier (IBB), and isolation by environment (IBE). We tested hypotheses relating each of these possible patterns to genetic divergence in the Slimy Salamander (Plethodon glutinosus (Green, 1818)) species complex across the lower Piedmont and Coastal Plain of Georgia, USA, and adjacent areas of South Carolina, USA. We sequenced 2148 total bp, including three regions of the mitochondrial genome and a nuclear intron, and related genetic distance to GIS-derived surrogate variables representing possible IBD (geographic distance), IBE (principal components of 19 climate variables, watershed, and normalized difference vegetation index (NDVI)), and IBB (streams of fourth order and higher). Multiple matrix regression with randomization analysis indicated significant relationships between genetic distance and two principal components of climate, as well as NDVI. These results support roles for environment (IBE) in helping to drive genetic divergence in this group of salamanders. The absence of a significant influence of IBD and IBB was surprising. It is possible that the signal effects of geographic distance and barriers on genetic divergence may have been erased by more recent responses to the environment.

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.

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.

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 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.

Population genetic structure and secondary endosymbionts of Q Bemisia tabaci (Hemiptera: Aleyrodidae) from Greece

2012 ◽  
Vol 102 (3) ◽  
pp. 353-365 ◽  
Author(s):  
A. Tsagkarakou ◽  
L. Mouton ◽  
J.B. Kristoffersen ◽  
E. Dokianakis ◽  
M. Grispou ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Bemisia Tabaci ◽  
Molecular Diversity ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Cultivated Plants ◽  
High Frequencies ◽  
Genetic Groups ◽  
Aegean Islands

AbstractWe investigated the molecular diversity of the major agricultural pest Bemisia tabaci and of its associated secondary endosymbionts in Greece. Analyzing mitochondrial DNA, we found that the Q1 (=Q west) is predominant. We used eight microsatellite polymorphic markers to study the genetic structure of 37 populations from mainland and insular Greece, collected on different host species from outdoor and protected crops as well as from non-cultivated plants. In some cases, gene flow was found to be low even between populations separated by just a few kilometres. Bayesian analysis identified two main genetic groups, the first encompassing populations from south Crete and the second composed of populations from north Crete, two other Aegean islands and mainland Greece. Genetic differentiation was not correlated with different host plant species or habitat, or greenhouse versus open environment populations. Gene flow significantly decreased with geographic distance, but no isolation by distance existed when only the samples from mainland Greece or only the samples from Crete were considered. The secondary symbionts Wolbachia and Hamiltonella were present at high frequencies while Arsenophonus, Cardinium and Rickettsia were absent from Greek populations. Multilocus sequence typing of Wolbachia identified two Wolbachia strains. These two strains were found together in most of the populations studied but never in the same host individual. Their role on the observed population structure is discussed.

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 Plant-associate interactions and diversification across trophic levels

2021 ◽  
Author(s):  
Jeremy B Yoder ◽  
Albert Dang ◽  
Caitlin MacGregor ◽  
Mikhail Plaza
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Species Interactions ◽  
Host Plants ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Trophic Levels ◽  
Population Structures ◽  
Genetic Structures ◽  
Antagonistic Interactions

Interactions between species are widely understood to have promoted the diversification of life on earth, but how interactions spur the the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled published genetic data for host plants and intimately associated herbivores, parasites, and mutualists. We first tested whether host and associate population structures were correlated --- an indication of associates locally adapting to hosts --- and tested for confounding correlations with geographic distance or climate variation. We used Bayesian multiple regression to estimate the effect of host plant genetic differentiation on associate genetic differentiation over and above the confounding effects of geography and climate. We found that plant and associate genetic structures are indeed often congruent, but isolation by distance and by climate are also common. Multiple regressions established that the effect of host plants on associates is robust to accounting for geographic distance and climate. Finally, associate genetic structure was significantly explained by plant genetic structure more often in antagonistic interactions than in mutualistic ones. This supports a key prediction of coevolutionary theory, that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions promote diversity via the effect of hosts' geographic distribution on mutualists' dispersal.

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