scholarly journals Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

2020 ◽  
Author(s):  
Quiterie Haenel ◽  
Krista B. Oke ◽  
Telma G. Laurentino ◽  
Andrew P. Hendry ◽  
Daniel Berner
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Adaptive Divergence ◽  
Entire Genome ◽  
High Dispersal ◽  
A Genome ◽  
Habitat Transition

AbstractHow ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback population pair adapted to contiguous, ecologically different lake and stream habitats. Dense clinal whole-genome sequence data reveal numerous regions fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center co-localizes with the habitat transition. Simulations confirm that such strong reproductive isolation can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from the cline center before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

scholarly journals Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Quiterie Haenel ◽  
Krista B. Oke ◽  
Telma G. Laurentino ◽  
Andrew P. Hendry ◽  
Daniel Berner
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Adaptive Divergence ◽  
Entire Genome ◽  
High Dispersal ◽  
A Genome ◽  
Habitat Transition

AbstractHow ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

scholarly journals Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190548 ◽  
Author(s):  
Yo Y. Yamasaki ◽  
Ryo Kakioka ◽  
Hiroshi Takahashi ◽  
Atsushi Toyoda ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sequence Data ◽  
Continuous Process ◽  
Sympatric Species ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Pungitius Pungitius ◽  
Hybrid Male ◽  
Differential Adaptation

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis , whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis

2019 ◽  
Author(s):  
Thomas Flouris ◽  
Xiyun Jiao ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Mosquito Species ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Important Means

AbstractRecent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

scholarly journals Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Prince Kumar ◽  
Mukesh K. Meghvansi ◽  
D. V. Kamboj
Keyword(s):  
Sequence Data ◽  
Burst Size ◽  
Genomic Analysis ◽  
Dna Helicase ◽  
Shigella Dysenteriae ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Parsimony Method

AbstractShigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.

scholarly journals Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

2020 ◽  
Author(s):  
Lisa Cooper ◽  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
James M Cook ◽  
Konrad Lohse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rain Forest ◽  
Sequence Data ◽  
Dry Forest ◽  
Whole Genome Sequence ◽  
Model Organisms ◽  
Eastern Coast ◽  
Population Divergence ◽  
Fig Wasp ◽  
History Of

AbstractPopulation divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

2020 ◽  
Author(s):  
Erik R Funk ◽  
Garth M Spellman ◽  
Kevin Winker ◽  
Jack J Withrow ◽  
Kristen C Ruegg ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genome Sequence ◽  
Population Genetic ◽  
Approximate Bayesian Computation ◽  
Sequence Data ◽  
Species Group ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Approximate Bayesian

Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.]

scholarly journals Mapping the genetic basis of diabetes mellitus in the Australian Burmese cat (Felis catus)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Georgina Samaha ◽  
Claire M. Wade ◽  
Julia Beatty ◽  
Leslie A. Lyons ◽  
Linda M. Fleeman ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Genome Wide Association Study ◽  
Genetic Model ◽  
Sequence Data ◽  
Pancreatic Beta Cell ◽  
Whole Genome Sequence ◽  
Cell Dysfunction ◽  
Genome Wide ◽  
A Genome ◽  
Pathologic Features

Abstract Diabetes mellitus, a common endocrinopathy affecting domestic cats, shares many clinical and pathologic features with type 2 diabetes in humans. In Australia and Europe, diabetes mellitus is almost four times more common among Burmese cats than in other breeds. As a genetically isolated population, the diabetic Australian Burmese cat provides a spontaneous genetic model for studying diabetes mellitus in humans. Studying complex diseases in pedigreed breeds facilitates tighter control of confounding factors including population stratification, allelic frequencies and environmental heterogeneity. We used the feline SNV array and whole genome sequence data to undertake a genome wide-association study and runs of homozygosity analysis, of a case–control cohort of Australian and European Burmese cats. Our results identified diabetes-associated haplotypes across chromosomes A3, B1 and E1 and selective sweeps across the Burmese breed on chromosomes B1, B3, D1 and D4. The locus on chromosome B1, common to both analyses, revealed coding and splice region variants in candidate genes, ANK1, EPHX2 and LOX2, implicated in diabetes mellitus and lipid dysregulation. Mapping this condition in Burmese cats has revealed a polygenic spectrum, implicating loci linked to pancreatic beta cell dysfunction, lipid dysregulation and insulin resistance in the pathogenesis of diabetes mellitus in the Burmese cat.

scholarly journals Comprehensive genomic analysis of Vibrio cholerae from three outbreaks in Uganda, 2014 - 2016

2019 ◽  
Author(s):  
Ivan Sserwadda ◽  
Dickson Aruhomukama ◽  
Gerald Mboowa
Keyword(s):  
Sequence Data ◽  
Response Regulator ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Type Iv Secretion ◽  
Whole Genome Sequence ◽  
Isomerase Activity ◽  
Type Iv ◽  
Antimicrobial Resistance Genes ◽  
Integrative And Conjugative Element

Abstract Objective: This study aimed at providing a comprehensive genomic analysis of whole-genome sequence data obtained from V. cholerae isolates from different outbreaks in Uganda using bioinformatics approaches. Results :The ten sequenced strains of V. cholerae were found to carry virulence-associated genes MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, rstR, Type IV secretion system genes, T6SS genes vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD; alsR; the flagella-mediated cytotoxin gene, makA; Type IV pilus genes tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D, IlpA, and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified were VSP-1, VSP-2, VPI-1, and VPI-2. Antimicrobial resistance genes identified in the strains included strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9. The strains also contained genes of the VC1786 integrative and conjugative element. SNP-based phylogenetic analysis revealed 218 shared SNPs in the strains, of these, 98 were missense. Gene enrichment analysis of the 98 SNPs revealed enrichment in genes that mediate transmembrane-signaling activity, peptidyl-prolyl cis-trans isomerase activity, and phosphorelay response regulator activity.

scholarly journals Phylogenetic, population genetic, and morphological analyses reveal evidence for one species of Eastern Indigo Snake (Drymarchon couperi)

2018 ◽  
Author(s):  
Brian Folt ◽  
Javan Bauder ◽  
Stephen Spear ◽  
Dirk Stevenson ◽  
Michelle Hoffman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Nuclear Gene ◽  
Large Species ◽  
High Dispersal ◽  
Contemporary Gene Flow ◽  
Eastern Indigo Snake

AbstractAccurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized that Drymarchon couperi is two species. Here, we use diverse approaches to test the two-species hypothesis for D. couperi. Our analyses reveal that (1) phylogenetic reconstruction in previous studies was based entirely on variance of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant population admixture and nuclear gene flow between mitochondrial lineages, and (3) morphological analyses recover a single diagnosable species. Our results are inconsistent with the two-species hypothesis, thus we reject it and formally place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.

scholarly journals Distinguishing gene flow between malaria parasite populations

PLoS Genetics ◽  
2021 ◽  
Vol 17 (12) ◽  
pp. e1009335
Author(s):  
Tyler S. Brown ◽  
Olufunmilayo Arogbokun ◽  
Caroline O. Buckee ◽  
Hsiao-Han Chang
Keyword(s):  
Gene Flow ◽  
Malaria Parasite ◽  
Sequence Data ◽  
Spatial Scales ◽  
Population Level ◽  
Whole Genome Sequence ◽  
Surveillance Studies ◽  
Migration Rates ◽  
Mobility Data ◽  
Parasite Populations

Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report examines the use of population-level summaries of genetic divergence (FST) and relatedness (identity-by-descent) to distinguish levels of gene flow between malaria populations, focused on field-relevant questions about data size, sampling, and interpretability of observations from genomic surveillance studies. To do this, we use P. falciparum whole genome sequence data and simulated sequence data approximating malaria populations evolving under different current and historical epidemiological conditions. We employ mobile-phone associated mobility data to estimate parasite migration rates over different spatial scales and use this to inform our analysis. This analysis underscores the complementary nature of divergence- and relatedness-based metrics for distinguishing gene flow over different temporal and spatial scales and characterizes the data requirements for using these metrics in different contexts. Our results have implications for the design and implementation of malaria genomic surveillance studies.

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