Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

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Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia

Applied and Environmental Microbiology ◽

10.1128/aem.01594-09 ◽

2010 ◽

Vol 76 (6) ◽

pp. 1946-1954 ◽

Cited By ~ 27

Author(s):

C. C. Linde ◽

J. A. Liles ◽

P. H. Thrall

Keyword(s):

Genetic Diversity ◽

Plant Pathogens ◽

Isolation By Distance ◽

Population Expansion ◽

Alternaria Brassicicola ◽

Evolutionary Potential ◽

Recent Population Expansion ◽

Fungal Plant Pathogens ◽

Cakile Maritima ◽

Founder Populations

ABSTRACT Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions.

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Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

Archives of Polish Fisheries ◽

10.1515/aopf-2016-0010 ◽

2016 ◽

Vol 24 (2) ◽

pp. 85-97 ◽

Cited By ~ 2

Author(s):

Sylvanus A. Nwafili ◽

Tian-Xiang Gao

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Control Region ◽

Haplotype Diversity ◽

Population Expansion ◽

Mitochondrial Control Region ◽

Recent Population Expansion ◽

Base Pair Fragment ◽

Population Structures ◽

High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

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High genetic diversity but no geographical structure of Aedes albopictus populations in Réunion Island

Parasites & Vectors ◽

10.1186/s13071-019-3840-x ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Anne C. Latreille ◽

Pascal Milesi ◽

Hélène Magalon ◽

Patrick Mavingui ◽

Célestine M. Atyame

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Aedes Albopictus ◽

Genetic Variance ◽

Mosquito Control ◽

Isolation By Distance ◽

Virus Transmission ◽

Reunion Island ◽

High Genetic Diversity ◽

Réunion Island

Abstract Background In recent years, the Asian tiger mosquito Aedes albopictus has emerged as a species of major medical concern following its global expansion and involvement in many arbovirus outbreaks. On Réunion Island, Ae. albopictus was responsible for a large chikungunya outbreak in 2005–2006 and more recently an epidemic of dengue which began at the end of 2017 and is still ongoing at the time of writing. This dengue epidemic has seen a high number of human cases in south and west coastal regions, while few cases have been reported in the north and east of the island. To better understand the role of mosquito populations in such spatial patterns of dengue virus transmission in Réunion Island, we examined the genetic diversity and population structure of Ae. albopictus sampled across the island. Results Between November 2016 and March 2017, a total of 564 mosquitoes were collected from 19 locations in three main climatic regions (West, East and Center) of Réunion Island and were genotyped using 16 microsatellite loci. A high genetic diversity was observed with 2–15 alleles per locus and the average number of alleles per population varying between 4.70–5.90. Almost all FIS values were significantly positive and correlated to individual relatedness within populations using a hierarchical clustering approach based on principal components analyses (HCPC). However, the largest part of genetic variance was among individuals within populations (97%) while only 3% of genetic variance was observed among populations within regions. Therefore, no distinguishable population structure or isolation by distance was evidenced, suggesting high rates of gene flow at the island scale. Conclusions Our results show high genetic diversity but no genetic structure of Ae. albopictus populations in Réunion Island thus reflecting frequent movements of mosquitoes between populations probably due to human activity. These data should help in the understanding of Ae. albopictus vector capacity and the design of effective mosquito control strategies.

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Genetic diversity of the lichen-forming alga, Diplosphaera chodatii, in North America and Europe

The Lichenologist ◽

10.1017/s0024282913000510 ◽

2013 ◽

Vol 45 (6) ◽

pp. 799-813 ◽

Cited By ~ 7

Author(s):

Kyle M. FONTAINE ◽

Elfie STOCKER-WÖRGÖTTER ◽

Tom BOOTH ◽

Michele D. PIERCEY-NORMORE

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

North America ◽

Isolation By Distance ◽

Water Level Fluctuations ◽

Free Living ◽

Climatic Zones ◽

Algal Symbiont ◽

Low Levels

AbstractDermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

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Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

10.1101/2020.03.01.971333 ◽

2020 ◽

Author(s):

William S. Pearman ◽

Sarah J. Wells ◽

Olin K. Silander ◽

Nikki E. Freed ◽

James Dale

Keyword(s):

Population Structure ◽

Gene Flow ◽

Population Genetic ◽

Isolation By Distance ◽

Spatial Scales ◽

Population Connectivity ◽

Clear Pattern ◽

Small Spatial Scale ◽

Cook Strait ◽

Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

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Visualizing spatial population structure with estimated effective migration surfaces

10.1101/011809 ◽

2014 ◽

Cited By ~ 5

Author(s):

Desislava Petkova ◽

John Novembre ◽

Matthew Stephens

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Similarity ◽

Large Scale ◽

Genetic Model ◽

Isolation By Distance ◽

Genetic Data ◽

Migration Rates ◽

Spatial Population ◽

Spatial Population Structure

Genetic data often exhibit patterns that are broadly consistent with "isolation by distance" - a phenomenon where genetic similarity tends to decay with geographic distance. In a heterogeneous habitat, decay may occur more quickly in some regions than others: for example, barriers to gene flow can accelerate the genetic differentiation between groups located close in space. We use the concept of "effective migration" to model the relationship between genetics and geography: in this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to quantify and visualize variation in effective migration across the habitat, which can be used to identify potential barriers to gene flow, from geographically indexed large-scale genetic data. Our approach uses a population genetic model to relate underlying migration rates to expected pairwise genetic dissimilarities, and estimates migration rates by matching these expectations to the observed dissimilarities. We illustrate the potential and limitations of our method using simulations and data from elephant, human, and Arabidopsis thaliana populations. The resulting visualizations highlight important features of the spatial population structure that are difficult to discern using existing methods for summarizing genetic variation such as principal components analysis.

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Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

mBio ◽

10.1128/mbio.02361-19 ◽

2019 ◽

Vol 10 (5) ◽

Cited By ~ 1

Author(s):

Alexander B. Chase ◽

Philip Arevalo ◽

Eoin L. Brodie ◽

Martin F. Polz ◽

Ulas Karaoz ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Isolation By Distance ◽

Dispersal Limitation ◽

Genomic Diversity ◽

Gene Content ◽

Microbial Populations ◽

Free Living ◽

Phylogenetic Structure ◽

Isolation By Environment

ABSTRACT For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance). IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.

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Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow, and fine-scale population structure in northern Dolly Varden (Salvelinus malma malma) in Canada

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2015-0016 ◽

2015 ◽

Vol 72 (10) ◽

pp. 1477-1493 ◽

Cited By ~ 17

Author(s):

Les N. Harris ◽

Robert Bajno ◽

Colin P. Gallagher ◽

Itsuro Koizumi ◽

Lucy K. Johnson ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Life History ◽

Gene Flow ◽

Isolation By Distance ◽

Dolly Varden ◽

Salvelinus Malma ◽

Dolly Varden Salvelinus Malma ◽

Northern Dolly Varden ◽

Population Demographic

The northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in northern Dolly Varden from the western Canadian Arctic to resolve landscape and life-history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls, with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other, while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized, and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic, and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.

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Dispersal patterns and population structure of Aedes albopictus (Diptera: Culicidae) in three different climatic regions of China

10.21203/rs.3.rs-38761/v3 ◽

2020 ◽

Author(s):

Jian Gao ◽

Hengduan Zhang ◽

Xiaoxia Guo ◽

Dan Xing ◽

YanDe Dong ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Environmental Factors ◽

Aedes Albopictus ◽

Population Expansion ◽

The Other ◽

Tropical Region ◽

Dispersal Patterns ◽

Climatic Regions ◽

The Mean

Abstract Background:Aedes albopictus is an indigenous primary vector for Dengue and Zika viruses in China. Compared with its insecticide resistance, biology, and vector competence, little is known about its genetic variation, which corresponds to environmental variations. Thus, the present study examines how Ae. albopictus varies among different climatic regions in China and deciphers its potential dispersal patterns.Methods:The genetic variation and population structure of 17 Ae. albopictus populations collected from three climatic regions of China were investigated with 11 microsatellite loci and the mitochondrial coxI gene.Results:Of 44 isolated microsatellite markers, 11 pairs were chosen for genotyping analysis and had an average PIC value of 0.713, representing high polymorphism. The number of alleles was high in each population, with the ne value increasing from the temperate region (3.876) to the tropical region (4.144). Twenty-five coxI haplotypes were detected, and the highest diversity was observed in the tropical region. The mean Ho value (ca. 0.557) of all the regions was significantly lower than the mean He value (ca. 0.684), with nearly all populations significantly departing from HWE and displaying significant population expansion (p-value < 0.05). Two genetically isolated groups and three haplotype clades were evaluated via STRUCTURE and haplotype phylogenetic analyses, and the tropical populations were significantly isolated from those in the other regions. Most genetic variation in Ae. albopictus was detected within populations and individuals at 31.40% and 63.04%, respectively, via the AMOVA test, and a relatively significant positive correlation was observed among only the temperate populations via IBD analysis (R2 = 0.6614, p = 0.048). Recent dispersions were observed among different Ae. albopictus populations, and four major migration trends with high gene flow (Nm>0.4) were reconstructed between the tropical region and the other two regions. Environmental factors, especially temperature and rainfall, may be the leading causes of genetic diversity in different climatic regions.Conclusions:Continuous dispersion contributes to the genetic communication of Ae. albopictus populations across different climatic regions, and environmental factors, especially temperature and rainfall, may be the leading causes of genetic variation.

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Complex population structure of the Atlantic puffin revealed by whole genome analyses

10.1101/2020.11.05.351874 ◽

2020 ◽

Author(s):

Oliver Kersten ◽

Bastiaan Star ◽

Deborah M. Leigh ◽

Tycho Anker-Nilssen ◽

Hallvard Strøm ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Isolation By Distance ◽

Spatial Scales ◽

Secondary Contact ◽

Whole Genome ◽

Genome Data ◽

Complex Population ◽

Genome Analyses ◽

Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

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