scholarly journals Structural genomic variation leads to unexpected genetic differentiation in Lake Tanganyika’s sardines

2019 ◽  
Author(s):  
Julian Junker ◽  
Jessica A. Rick ◽  
Peter B. McIntyre ◽  
Ismael Kimirei ◽  
Emmanuel A. Sweke ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Evolutionary Biology ◽  
Lake Tanganyika ◽  
Isolation By Distance ◽  
Genomic Variation ◽  
Population Declines ◽  
Structural Genomic ◽  
Important Species ◽  
Lake Kivu

AbstractIdentifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika’s two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal unexpected differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion in L. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.

scholarly journals Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Hydrobiologia ◽  
2020 ◽  
Author(s):  
Ruben Alexander Pettersen ◽  
Claudia Junge ◽  
Kjartan Østbye ◽  
Tor Atle Mo ◽  
Leif Asbjørn Vøllestad
Keyword(s):  
Genetic Structure ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Genetic Structuring ◽  
Thymallus Thymallus ◽  
Homing Behavior ◽  
Genetic Population ◽  
Monogenean Parasite ◽  
European Grayling ◽  
Genetic Clusters

Abstract Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.

scholarly journals Birds are islands for parasites

2014 ◽  
Vol 10 (8) ◽  
pp. 20140255 ◽  
Author(s):  
Jennifer A. H. Koop ◽  
Karen E. DeMatteo ◽  
Patricia G. Parker ◽  
Noah K. Whiteman
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Island Populations ◽  
Louse Species ◽  
Parasite Populations

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host–parasite populations. We found that island populations of the Galápagos hawk ( Buteo galapagoensis ) and a parasitic feather louse species ( Degeeriella regalis ) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se , suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.

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 Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

2020 ◽  
Vol 29 (17) ◽  
pp. 3277-3298 ◽  
Author(s):  
Julian Junker ◽  
Jessica A. Rick ◽  
Peter B. McIntyre ◽  
Ismael Kimirei ◽  
Emmanuel A. Sweke ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genomic Variation ◽  
Structural Genomic

scholarly journals Genetic Structure of Cronartium ribicola Populations in Eastern Canada

1999 ◽  
Vol 89 (10) ◽  
pp. 915-919 ◽  
Author(s):  
K. Et-touil ◽  
L. Bernier ◽  
J. Beaulieu ◽  
J. A. Bérubé ◽  
A. Hopkin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Distribution Systems ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Cronartium Ribicola ◽  
Eastern Canada ◽  
Long Distance ◽  
Evolutionary Forces

The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (Ht = 0.386) was present within populations (Hw = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (Fst = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA φst = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

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 Incipient signs of genetic differentiation among African elephant populations in fragmenting miombo ecosystems in south-western Tanzania

2017 ◽  
Author(s):  
Alex L. Lobora ◽  
Cuthbert L. Nahonyo ◽  
Linus K. Munishi ◽  
Tim Caro ◽  
Charles Foley ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Loss Of Heterozygosity ◽  
Isolation By Distance ◽  
Age Classes ◽  
Illegal Hunting ◽  
Genetic Structure Of Populations ◽  
Elephant Population ◽  
Genetic Substructure ◽  
Western Tanzania

AbstractHabitat fragmentation plays a major role in the reduction of genetic diversity among wildlife populations. The African savannah elephant population of the Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania, comprises one of the world’s largest remaining elephant populations, but is increasingly threatened by loss of connectivity and poaching for ivory. We investigate whether there are incipient signs of genetic isolation (loss of heterozygosity) within the younger cohort as a result of habitat loss between the two ecosystems. To investigate the genetic structure of populations, we compared the genotypes for 11 microsatellite loci in the western (n = 81 individuals from Katavi-Rukwa), central (n = 36 individuals from Lukwati and Piti), and eastern populations (n = 193, individuals from Ruaha-Rungwa). We found evidence of significant genetic differentiation among the three populations, but the levels were low, suggesting recent divergence. Furthermore, we identified weak isolation by distance, suggesting higher gene flow among nearer individuals with samples within 50km of each other being more genetically similar to one another than beyond. Although sample sizes were small, a further analysis of genetic differences across populations and in separate age classes revealed evidence of increasing genetic structure among younger age classes across the landscape. In a long-lived species with overlapping generations, it takes a long time to develop genetic substructure even when there are substantial obstacles to migration. Thus, in these recently fragmented populations, inbreeding (and the loss of heterozygosity) may be less of an immediate concern than demography (the loss of adults due to illegal hunting).

scholarly journals Variation and genetic structure of the endangered Lepus flavigularis (Lagomorpha: Leporidae)

2017 ◽  
Vol 65 (4) ◽  
pp. 1322
Author(s):  
Bárbara Cruz Salazar ◽  
Consuelo Lorenzo ◽  
Eduardo Espinoza Medinilla ◽  
Sergio López
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
San Francisco ◽  
Isolation By Distance ◽  
Santa Cruz ◽  
Management Units ◽  
Lepus Flavigularis ◽  
Santa Maria

Lepus flavigularis, is an endemic and endangered species, with only four populations inhabiting Oaxaca, México: Montecillo Santa Cruz, Aguachil, San Francisco del Mar Viejo and Santa María del Mar. Nevertheless, human activities like poaching and land use changes, and the low genetic diversity detected with mitochondrial DNA and allozymes in previous studies, have supported the urgent need of management strategies for this species, and suggest the definition of management units. For this, it is necessary to study the genetic structure with nuclear genes, due to their inheritance and high polymorphism, therefore, the objective of this study was to examine the variation and genetic structure of L. flavigularis using nuclear microsatellites. We sampled four populations of L. flavigularis and a total of 67 jackrabbits were captured by night sampling during the period of 2001 to 2006. We obtained the genomic DNA by the phenol-chloroform-isoamyl alcohol method. To obtain the diversity and genetic structure, seven microsatellites were amplified using the Polymerase Chain Reaction (PCR); the amplifications were visualized through electrophoresis with 10 % polyacrylamide gels, dyed with ethidium bromide. Genetic diversity was determined using the software GenAlEx v. 6.4, and genetic structure was obtained with ARLEQUIN v. 3.1; null alleles were evaluated using the program Micro-Checker v.2.2.2. Additionally, a Bayesian analysis was performed with software STRUCTURE v. 2.2.3., and the isolation by distance (IBD) was studied using the program PASSAGE v.2.0.11.6. Our results showed that the genetic variation found was low (HO = 0.30, HE = 0.24) when compared to other jackrabbit species. Fixed alleles and moderate levels of genetic differentiation (FST = 0.18, P = 0.001) were detected among populations, indicating the effect of the genetic drift and limited gene flow. Bayesian clustering analysis revealed two groups: (1) jackrabbits from Montecillo Santa Cruz, and (2) individuals living in Aguachil, San Francisco del Mar Viejo and Santa María del Mar. No evidence was found of isolation by distance. It is possible that the geographic barriers present between populations (e.g. lagoons, human settlements), rather than the geographical distance between them, may explain the observed genetic structure. The inbreeding coefficient was negative (FIS = -0.27, P = 0.03), indicating genetic sub-structure in populations. We suggest two management units based on the genetically closer populations, which will help define precise conservation actions in L. flavigularis. This research is the basis for defining translocation of individuals between populations, nevertheless, a more extensive future study, with specific molecular markers for L. flavigularis, is required. In addition, it is necessary to analyze the barriers that limit the gene flow, since it is urgent to reduce the genetic differentiation between populations and increase the genetic diversity of this species. 

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.

Genetic structure of the introduced heaven tree (Ailanthus altissima) in Japan: evidence for two distinct origins with limited admixture

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 133-139 ◽  
Author(s):  
Hiroyuki Kurokochi ◽  
Yoko Saito ◽  
Yuji Ide
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Invasive Plant ◽  
Isolation By Distance ◽  
Ailanthus Altissima ◽  
Nuclear Markers ◽  
Distance Analysis ◽  
Nuclear Microsatellite ◽  
Geographical Genetic Structure ◽  
Future Management

The heaven tree, Ailanthus altissima (Mill.) Swingle, was intentionally introduced from China to many temperate areas globally, where it has become successfully established. Here, we investigated the patterns of genetic differentiation between introduced Japanese A. altissima populations using both plastid and nuclear microsatellite markers. Three hundred and eighty-eight trees were sampled from six planted and 12 naturalized populations. Two distinct chloroplastic haplotypes were observed, which allowed us to separate two groups of trees, H1 and H3, containing 128 and 260 trees, respectively. Nine nuclear genetic microsatellites revealed 17.7 alleles per locus on average. These data did not indicate significant isolation-by-distance. Analysis of molecular variance showed the absence of genetic differentiation between the planted and naturalized populations. In contrast, the two groups defined according to the chloroplastic haplotypes (H1 and H3) were differentiated. STRUCTURE analysis showed that, within each haplotype group, most trees were strictly assigned to one cluster, with the exception of a few (ca. 30) trees. Our results indicate that (1) geographical genetic structure was weak, with high genetic variation among populations; (2) a congruent signal was revealed by chloroplastic and nuclear markers, indicating two distinct provenances; and (3) admixture between the two lineages has occurred, but remains limited. Several other invasive plant species have already been reported to exhibit similar trends; hence, future management of A. altissima might be required in Japan.

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