Population genetic structure of the goby Stiphodon rutilaureus (Gobiidae) in the New Georgia Group, Solomon Islands

2016 ◽  
Vol 22 (3) ◽  
pp. 281 ◽  
Author(s):  
David T. Boseto ◽  
Sharon J. Furiness Magnuson ◽  
Frank L. Pezold
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Solomon Islands ◽  
Pairwise Comparisons ◽  
The West ◽  
Significant Difference ◽  
Central Regions ◽  
Goby Species ◽  
Mitochondrial Locus ◽  
Management And Conservation

In this study, we use eight microsatellite loci and a mitochondrial locus to investigate the population structure of the amphidromous goby species Stiphodon rutilaureus in the New Georgia Group, Solomon Islands. In total, 206 specimens were collected between June 2010 and August of 2012 on three different trips. The AMOVA results from both types of loci reveal that >95% of variation is contained within populations. Pairwise comparisons reveal non-significant differences between three different regions for the mitochondrial analysis but a significant difference between the west and central regions for the microsatellites. The findings in this study concur with results from previous studies, indicating low or no population structure among populations of amphidromous sicydiine goby species on different islands within an archipelago. This study can provide suggestions for management and conservation of fragile aquatic species.

Conservation and Management of Salmon in the Age of Genomics

2020 ◽  
Vol 8 (1) ◽  
pp. 117-143 ◽  
Author(s):  
Robin S. Waples ◽  
Kerry A. Naish ◽  
Craig R. Primmer
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Evolutionary Ecology ◽  
Natural Populations ◽  
Structure And Function ◽  
Population Assignment ◽  
Genetic Studies ◽  
And Function ◽  
Management And Conservation ◽  
Conservation And Management

Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: ( a) Large increases in the numbers of genetic markers (from dozens to 104–106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and ( b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Population genetic structure of a major reef-building coral species Acropora downingi in northeastern Arabian Peninsula

Coral Reefs ◽  
2021 ◽  
Author(s):  
Felipe Torquato ◽  
Jessica Bouwmeester ◽  
Pedro Range ◽  
Alyssa Marshell ◽  
Mark A. Priest ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Study ◽  
Persian Gulf ◽  
Population Genetic ◽  
Coral Species ◽  
Arabian Peninsula ◽  
Ecological Speciation ◽  
Population Genetic Study ◽  
Sea Of Oman ◽  
Neutral Markers

AbstractCurrent seawater temperatures around the northeastern Arabian Peninsula resemble future global forecasts as temperatures > 35 °C are commonly observed in summer. To provide a more fundamental aim of understanding the structure of wild populations in extreme environmental conditions, we conducted a population genetic study of a widespread, regional endemic table coral species, Acropora downingi, across the northeastern Arabian Peninsula. A total of 63 samples were collected in the southern Arabian/Persian Gulf (Abu Dhabi and Qatar) and the Sea of Oman (northeastern Oman). Using RAD-seq techniques, we described the population structure of A. downingi across the study area. Pairwise G’st and distance-based analyses using neutral markers displayed two distinct genetic clusters: one represented by Arabian/Persian Gulf individuals, and the other by Sea of Oman individuals. Nevertheless, a model-based method applied to the genetic data suggested a panmictic population encompassing both seas. Hypotheses to explain the distinctiveness of phylogeographic subregions in the northeastern Arabian Peninsula rely on either (1) bottleneck events due to successive mass coral bleaching, (2) recent founder effect, (3) ecological speciation due to the large spatial gradients in physical conditions, or (4) the combination of seascape features, ocean circulation and larval traits. Neutral markers indicated a slightly structured population of A. downingi, which exclude the ecological speciation hypothesis. Future studies across a broader range of organisms are required to furnish evidence for existing hypotheses explaining a population structure observed in the study area. Though this is the most thermally tolerant acroporid species worldwide, A. downingi corals in the Arabian/Persian Gulf have undergone major mortality events over the past three decades. Therefore, the present genetic study has important implications for understanding patterns and processes of differentiation in this group, whose populations may be pushed to extinction as the Arabian/Persian Gulf warms.

scholarly journals A multi-approach analysis of the genetic diversity in populations of Astyanax aff. bimaculatus Linnaeus, 1758 (Teleostei: Characidae) from Northeastern Brazil

2008 ◽  
Vol 6 (4) ◽  
pp. 621-630 ◽  
Author(s):  
Vanessa de Carvalho Cayres Pamponet ◽  
Paulo Luiz Souza Carneiro ◽  
Paulo Roberto Antunes de Mello Affonso ◽  
Viviam Souto Miranda ◽  
Juvenal Cordeiro Silva Júnior ◽  
...  
Keyword(s):  
Population Structure ◽  
Human Activities ◽  
Evolutionary History ◽  
Main Channel ◽  
Northeastern Brazil ◽  
Dam Reservoir ◽  
Effective Barrier ◽  
Significant Difference ◽  
Genetic Patterns ◽  
Structure Index

Few reports are available about the ichthyofauna of typical semi-arid rivers, although the regional diversity has been constantly threatened by human activities, mainly related to impoundment and construction of dams. The goal of the present work was to evaluate using different methods, the population genetic structure of a characin fish, Astyanax aff. bimaculatus, widespread throughout hydrographic basins of Bahia, Northeastern Brazil. Morphological (meristic and morphometric data), cytogenetic (karyotype and Ag-NOR), and molecular (RAPD and SPAR) analyses were carried out in specimens collected upstream and downstream of Pedra Dam, in the main channel of Contas River (Contas River Basin), and in the Mineiro stream, which belongs to the adjacent Recôncavo Sul basin. Few external differences were detected among populations, where the individuals collected upstream of Pedra Dam were slightly larger than the others. Cytogenetic data also showed a similar karyotypic pattern (2n=50; 6m+28sm+12st+4a; FN= 96) and NORs located on the short arms of up to two chromosome pairs, with numerical inter- and intra-populational variation. Nonetheless, RAPD and SPAR analyses differentiated reliably the three populations, revealing striking differences in the allele frequencies among the localities studied and a significant difference in population structure index (Fst=0.1868, P<0.0001). The differences between populations within a same river were as significant as those between distinct hydrographic basins, indicating that the dam/reservoir represents an effective barrier to gene flow. Additionally, environmental peculiarities from each locality are also believed to influence the genetic patterns detected herein. On the other hand, the similarity between samples from Contas River and Recôncavo Sul basins could be related to a common evolutionary history, since both basins are geographically close to each other. Finally, the present study shows that a multi-approach analysis is particularly useful in identifying the population structure of widely distributed species and to evaluate the impacts of human activities on natural fish populations.

scholarly journals A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009665
Author(s):  
Olivier François ◽  
Clément Gain
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Population Genetic ◽  
Principal Component ◽  
Large Data ◽  
Population Subdivision ◽  
Adaptive Genetic Variation ◽  
Genomic Locus ◽  
Inbreeding Coefficients ◽  
Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

scholarly journals Dynamic genetic diversity and population structure of Coreius guichenoti

ZooKeys ◽  
2021 ◽  
Vol 1055 ◽  
pp. 135-148
Author(s):  
Dongqi Liu ◽  
Feng Lan ◽  
Sicai Xie ◽  
Yi Diao ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Yangtze River ◽  
Fish Passage ◽  
The Yangtze River ◽  
Artificial Breeding ◽  
Significant Difference ◽  
High Elevations

To investigate the genetic effects on the population of Coreius guichenoti of dam constructions in the upper reaches of the Yangtze River, we analyzed the genetic diversity and population structure of 12 populations collected in 2009 and 2019 using mitochondrial DNA (mtDNA) control regions. There was no significant difference in genetic diversity between 2009 and 2019 (P &gt; 0.05), but the population structure tended to become stronger. Genetic differentiation (FST) among five populations (LX, BB, YB, SF and JA) collected in 2009 was not significant (P &gt; 0.05). However, some populations collected in 2019 were significantly differentiated (P &lt; 0.05), indicating that the population structure has undergone change. A correlation analysis showed that the genetic diversity of the seven populations collected in 2019 was significantly negatively correlated with geographical height (r = −0.808, P = 0.028), indicating that the populations at high elevations were more vulnerable than those at low elevations. In order to prevent the further decrease of genetic diversity and population resources, some conservation and restoration suggestions, such as fish passage and artificial breeding, are put forward.

Evidence supporting panmixia in Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic

2014 ◽  
Vol 71 (5) ◽  
pp. 763-774 ◽  
Author(s):  
Denis Roy ◽  
David C. Hardie ◽  
Margaret A. Treble ◽  
James D. Reist ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Conservation Strategies ◽  
Greenland Halibut ◽  
Northwest Atlantic ◽  
Population Genetic Differentiation ◽  
Conservation Implications ◽  
Greenland Halibut Reinhardtius Hippoglossoides ◽  
Reinhardtius Hippoglossoides ◽  
Species Specific

Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.

Population genetic structure of wild boars in the West Balkan region

2012 ◽  
Vol 48 (8) ◽  
pp. 859-863 ◽  
Author(s):  
N. Velickovic ◽  
M. Djan ◽  
D. Obreht ◽  
Lj. Vapa
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
The West ◽  
Wild Boars ◽  
Balkan Region

Punk in Russia: From the “Declassed Elements” to the Class Struggle

2021 ◽  
Author(s):  
Ivan Gololobov
Keyword(s):  
Soviet Union ◽  
Social Engagement ◽  
Initial Conditions ◽  
Russian Society ◽  
Political Commitment ◽  
Political Movement ◽  
The West ◽  
The Soviet Union ◽  
Significant Difference ◽  
The Right

This chapter discusses the evolution of punk in Russia since its inception at the end of the 1970s. It pays particular attention to the changing perception of class belonging and the political engagement of the punk scene in Russia. Whereas in the West punk was a political movement closely associated with its working-class background, in the Soviet Union it emerged as a protest of middle-class intellectuals fighting for the right to be different and to stand out from the uniformed workers’ and peasants’ collective. This defined the particular stand of early Russian punk toward the genre’s social engagement and political appeal. Working-classness and political commitment—initial conditions of punk identity in the West—became something early Russian punk was positioned against. The dramatic transformation of Russian society over the following decades inevitably affected the cultural ideology of Russian punk, and from the 1990s onward it had to find its place and defend its significant difference amid the realities of “wild” neoliberal capitalism. The chapter shows how in Russia punk evolved from being a highly individualistic and apolitical practice to one of the most radical and politically committed scenes, closely affiliated with other struggles on the Left.

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