A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

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.

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A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

Heredity ◽

10.1038/s41437-021-00468-z ◽

2021 ◽

Author(s):

Souta Nakajima ◽

Masanao Sueyoshi ◽

Shun K. Hirota ◽

Nobuo Ishiyama ◽

Ayumi Matsuo ◽

...

Keyword(s):

Genetic Structure ◽

Water Temperature ◽

Sampling Design ◽

Cold Water

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Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽

10.1371/journal.pone.0243999 ◽

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.

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Genetic Divergence of Two Sitobion avenae Biotypes on Barley and Wheat in China

Insects ◽

10.3390/insects11020117 ◽

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.

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Plant-associate interactions and diversification across trophic levels

10.1101/2021.07.29.454357 ◽

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

Bulletin of Entomological Research ◽

10.1017/s0007485309990538 ◽

2010 ◽

Vol 100 (5) ◽

pp. 521-527 ◽

Cited By ~ 9

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.

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Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America

The Condor ◽

10.1093/condor/duz036 ◽

2019 ◽

Vol 121 (3) ◽

Cited By ~ 1

Author(s):

Iva Popovic ◽

David P L Toews ◽

Carson C Keever ◽

C Toby St. Clair ◽

Blake A Barbaree ◽

...

Keyword(s):

Genetic Structure ◽

Isolation By Distance ◽

Spatial Scales ◽

River Estuary ◽

Genotyping By Sequencing ◽

Genomic Diversity ◽

Nucleotide Polymorphisms ◽

Migratory Connectivity ◽

Calidris Alpina ◽

The Pacific

Abstract Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at 2 spatial scales (within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at 3 locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin within the FRE, Sacramento Valley (California), and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis. A small proportion of the total genotypic variance (R2 =0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.

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Genetic structure of marginal populations of white spruce (Piceaglauca) at its northern limit of distribution in Nouveau-Québec

Canadian Journal of Forest Research ◽

10.1139/x89-211 ◽

1989 ◽

Vol 19 (11) ◽

pp. 1371-1379 ◽

Cited By ~ 29

Author(s):

Monique Tremblay ◽

Jean-Pierre Simon

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Geographic Distance ◽

White Spruce ◽

Gene Exchange ◽

Northern Limit ◽

Marginal Populations ◽

Subarctic Region ◽

Hardy Weinberg Equilibrium ◽

Or Gene

The genetic structure of six marginal populations of white spruce (Piceaglauca (Moench) Voss) located at Richmond Gulf in the subarctic region of Nouveau-Québec, and one southern population located at Kuujjuaraapik (Poste-de-la-Baleine) were analyzed by acrylamide gel electrophoresis for seven enzyme systems. The analysis of 27 loci disclosed an average polymorphism of 76.2% and a level of heterozygosity of 0.319. Data based on Wright's; statistics: indicated a deficiency of heterozygotes for 60% of the loci, as calculated from the Hardy–Weinberg equilibrium. These results, coupled with the very low percentage of filled seeds in cones of all populations, suggest that a certain level of inbreeding or gene exchange among near-neighbour relatives influences the genetic structure of these populations. The genetic differentiation among populations is relatively high for a conifer [Formula: see text] and is not correlated with geographic distance. The age of trees, covering a period of 400 years affected by climatic changes, does not contribute to the genetic differentiation of the populations.

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

10.1101/574665 ◽

2019 ◽

Cited By ~ 1

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.

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

Australian Journal of Botany ◽

10.1071/bt20074 ◽

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.

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