scholarly journals Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11425
Author(s):  
Sofia G. Seabra ◽  
Ana S.B. Rodrigues ◽  
Sara E. Silva ◽  
Ana Carina Neto ◽  
Francisco Pina-Martins ◽  
...  
Keyword(s):  
Gene Flow ◽  
Western Europe ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Plant Diseases ◽  
Morphological Data ◽  
Philaenus Spumarius ◽  
Mitochondrial Coi ◽  
Temperature And Precipitation ◽  
Genome Wide

Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.

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.

Gene flow within the M evolutionary lineage ofApis mellifera: role of the Pyrenees, isolation by distance and post-glacial re-colonization routes in the western Europe

Apidologie ◽  
2007 ◽  
Vol 38 (2) ◽  
pp. 141-155 ◽  
Author(s):  
Irati Miguel ◽  
Mikel Iriondo ◽  
Lionel Garnery ◽  
Walter S. Sheppard ◽  
Andone Estonba
Keyword(s):  
Gene Flow ◽  
Western Europe ◽  
Isolation By Distance ◽  
Colonization Routes ◽  
Evolutionary Lineage

scholarly journals The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis)

2020 ◽  
Vol 10 (9) ◽  
pp. 3147-3163
Author(s):  
Ashley T Sendell-Price ◽  
Kristen C Ruegg ◽  
Eric C Anderson ◽  
Claudio S Quilodrán ◽  
Benjamin M Van Doren ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
A Priori ◽  
Genomic Islands ◽  
Zosterops Lateralis ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Speciation Continuum ◽  
Genomic Patterns

Abstract Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.

scholarly journals Estimating barriers to gene flow from distorted isolation by distance patterns

2017 ◽  
Author(s):  
Harald Ringbauer ◽  
Alexander Kolesnikov ◽  
David Field ◽  
Nicholas H. Barton
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Covariance Structure ◽  
Simulated Data ◽  
Flower Color ◽  
Two Dimensions ◽  
Genome Wide ◽  
Linear Barrier ◽  
Wide Range ◽  
Classical Pattern

ABSTRACTIn continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.

scholarly journals Climate tolerances of Philaenus spumarius should be considered in risk assessment of disease outbreaks related to Xylella fastidiosa

2021 ◽  
Author(s):  
M. Godefroid ◽  
M. Morente ◽  
T. Schartel ◽  
D. Cornara ◽  
A. Purcell ◽  
...  
Keyword(s):  
Mediterranean Basin ◽  
Western Europe ◽  
Xylella Fastidiosa ◽  
Disease Outbreaks ◽  
Mediterranean Area ◽  
Plant Diseases ◽  
Distribution Models ◽  
Philaenus Spumarius ◽  
Southern Mediterranean ◽  
The Mediterranean

AbstractThe bacterium Xylella fastidiosa (Xf) is an invasive insect-borne pathogen, which causes lethal diseases to important crops including olives, citrus, almonds and grapes as well as numerous forest, ornamental, and uncultivated plants. Outbreaks of Xf-related plant diseases are currently occurring in the Mediterranean region, causing substantial losses to various agricultural sectors. Several models have recently been published to identify which regions are at highest risk in Europe; however, such models did not consider the insect vectors, which constitute the key driver of short-range Xf spread. We fitted bioclimatic species distribution models to depict the macroclimatic preferences of the meadow spittlebug Philaenus spumarius L. (1978) (Hemiptera: Aphrophoridae), the major epidemiologically relevant vector currently responsible for Xf spread in the Europe. Many regions of Western Europe and Mediterranean basin are predicted by models as highly climatically suitable for this vector, including all regions where severe Xf have occurred so far. Conversely, the driest and warmest areas of the Mediterranean basin are predicted as little suitable for P. spumarius. Models forecast that agricultural-important parts of the southern Mediterranean area might experience a substantial decrease in climatic suitability for P. spumarius by the period 2040–2060. Areas predicted as highly suitable just for the bacterium but not optimal for this vector are apparently still free of severe Xf outbreaks, suggesting that climate tolerances of P. spumarius might partly explain the current spatial pattern of Xf outbreaks in Europe and should always be considered in further risk assessments.

scholarly journals Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

2015 ◽  
Author(s):  
Jason Munshi-South ◽  
Christine P Zolnik ◽  
Stephen E Harris
Keyword(s):  
Population Genomics ◽  
Isolation By Distance ◽  
Impervious Surface ◽  
Snp Markers ◽  
Environment Modeling ◽  
Evolutionary Potential ◽  
Animal Populations ◽  
Genome Wide ◽  
Isolation By Environment ◽  
White Footed Mouse

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genome-wide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genome-wide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genome-wide variation was estimated as a proxy for evolutionary potential using more than 10,000 SNP markers generated by ddRAD-Seq. We found that genome-wide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genome-wide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genome-wide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

scholarly journals Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of two Candidula sister species

2021 ◽  
Vol 376 (1825) ◽  
Author(s):  
Luis J. Chueca ◽  
Tilman Schell ◽  
Markus Pfenninger
Keyword(s):  
Gene Flow ◽  
Western Europe ◽  
Population Genomics ◽  
Land Snail ◽  
Historical Demography ◽  
Land Snails ◽  
Whole Genome ◽  
Sequencing Data ◽  
Climatic Fluctuations ◽  
Population Distributions

Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula . Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

scholarly journals First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

2017 ◽  
Author(s):  
Jessica L. Allen ◽  
Sean K. McKenzie ◽  
Robin S. Sleith ◽  
S. Elizabeth Alter
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Distribution Models ◽  
Extrinsic Factors ◽  
Biogeographic Patterns ◽  
Ecological Requirements ◽  
Genome Wide ◽  
Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.

scholarly journals Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations

2019 ◽  
Vol 36 (9) ◽  
pp. 1849-1861 ◽  
Author(s):  
Mário Vicente ◽  
Mattias Jakobsson ◽  
Peter Ebbesen ◽  
Carina M Schlebusch
Keyword(s):  
Gene Flow ◽  
Southern Africa ◽  
Isolation By Distance ◽  
Hunter Gatherers ◽  
Data Set ◽  
Genome Wide ◽  
Distance Model ◽  
Comprehensive Picture ◽  
Genome Wide Data ◽  
The Impact

Abstract Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as “Khoe-San” populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx’a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.

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.

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