scholarly journals Population genomics of two congeneric Palaearctic shorebirds reveals differential impacts of Quaternary climate oscillations across habitats types

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hui Zhen Tan ◽  
Elize Ying Xin Ng ◽  
Qian Tang ◽  
Gary A. Allport ◽  
Justin J. F. J. Jansen ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Habitat Preferences ◽  
Ecological Factors ◽  
Past Research ◽  
Glacial Refugia ◽  
Biogeographic Patterns ◽  
Quaternary Climate

AbstractIntracontinental biotic divisions across the vast Palaearctic region are not well-characterized. Past research has revealed patterns ranging from a lack of population structure to deep divergences along varied lines of separation. Here we compared biogeographic patterns of two Palaearctic shorebirds with different habitat preferences, Whimbrel (Numenius phaeopus) and Eurasian curlew (N. arquata). Using genome-wide markers from populations across the Palaearctic, we applied a multitude of population genomic and phylogenomic approaches to elucidate population structure. Most importantly, we tested for isolation by distance and visualized barriers and corridors to gene flow. We found shallow Palaearctic population structure in subpolar bog and tundra-breeding whimbrels, consistent with other species breeding at a similarly high latitude, indicating connectivity across the tundra belt, both presently and during southward shifts in periods of global cooling. In contrast, the temperate grassland-breeding Eurasian curlew emerged in three distinct clades corresponding to glacial refugia. Barriers to gene flow coincided with areas of topographic relief in the central Palaearctic for whimbrels and further east for Eurasian curlews. Our findings highlight the interplay of historic and ecological factors in influencing present-day population structure of Palaearctic biota.

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

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

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.

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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

2013 ◽  
Vol 45 (6) ◽  
pp. 799-813 ◽  
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.

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

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.

scholarly journals Spatial Genetic Structure of the Insect-Vectored Conifer Pathogen Leptographium wageneri Suggests Long Distance Gene Flow Among Douglas-fir Plantations in Western Oregon

2021 ◽  
Vol 4 ◽  
Author(s):  
Patrick I. Bennett ◽  
Javier F. Tabima ◽  
Anna L. Leon ◽  
John Browning ◽  
Michael J. Wingfield ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Bark Beetles ◽  
Population Genomics ◽  
Spatial Genetic Structure ◽  
Douglas Fir ◽  
Insect Vector ◽  
Long Distance ◽  
Tree Disease ◽  
Genetic Clustering

Many fungi in the Ophiostomatales are vectored by bark beetles that introduce these fungi directly into their tree hosts. Most of these fungal associates have little effect on their hosts, but some can cause serious diseases. One such fungus, Leptographium wageneri, causes an economically and ecologically important tree disease known as black stain root disease (BSRD). For this study, 159 full genome sequences of L. wageneri were analyzed using a population genomics approach to investigate the epidemiology, dispersal capabilities, and reproductive biology of this fungus. Analyses were performed with SNP haplotypes from 155 isolates of L. wageneri var. pseudotsugae collected in 16 Douglas-fir stands in Oregon and 4 isolates of L. wageneri var. wageneri collected in pinyon pine stands in southern California. These two host-specific varieties appear to be evolutionarily divergent, likely due a combination of factors such as host differentiation and geographic isolation. We analyzed gene flow and population structure within and among Douglas-fir plantations in western Oregon to infer the relative importance of local vs. long distance dispersal in structuring populations of L. wageneri var. pseudotsugae. Long-distance gene flow has occurred between Douglas-fir plantations, contributing to diversity and population structure within stands, and likely reflecting the behavior of an important insect vector. Genetic clustering analyses revealed the presence of unique local clusters within stands and plantations in addition to those common among multiple stands or plantations. Although populations of L. wageneri var. pseudotsugae are primarily asexual, two mating types were present in many stands, suggesting that recombination is at least possible and may contribute to genetic diversity.

scholarly journals Visualizing spatial population structure with estimated effective migration surfaces

2014 ◽  
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.

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

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
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.

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

2015 ◽  
Vol 72 (10) ◽  
pp. 1477-1493 ◽  
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.

scholarly journals Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

2020 ◽  
Author(s):  
Pamela Vega-Polo ◽  
Maria M. Cobo ◽  
Andrea Argudo ◽  
Bernardo Gutierrez ◽  
Jennifer Rowntree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Anthropogenic Activities ◽  
Conservation Status ◽  
Ecological Factors ◽  
Andean Region ◽  
Key Factor ◽  
Distance Model

AbstractThe Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 homologous SSR markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE=0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated to the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystems as a whole.

Sign in / Sign up

Export Citation Format

Share Document