Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa

Within the mega-pest lineage of heliothine moths are a number of polyphagous, highly mobile species for which the exchange of adaptive traits through hybridization would affect their properties as pests. The recent invasion of South America by one of the most significant agricultural pests, Helicoverpa armigera, raises concerns for the formation of novel combinations of adaptive genes following hybridization with the closely related Helicoverpa zea. To investigate the propensity for hybridization within the genus Helicoverpa, we carried out whole-genome resequencing of samples from six species, focusing in particular upon H. armigera population structure and its relationship with H. zea. We show that both H. armigera subspecies have greater genetic diversity and effective population sizes than do the other species. We find no signals for gene flow among the six species, other than between H. armigera and H. zea, with nine Brazilian individuals proving to be hybrids of those two species. Eight had largely H. armigera genomes with some introgressed DNA from H. zea scattered throughout. The ninth resembled an F1 hybrid but with stretches of homozygosity for each parental species that reflect previous hybridization. Regions homozygous for H. armigera-derived DNA in this individual included one containing a gustatory receptor and esterase genes previously associated with host range, while another encoded a cytochrome P450 that confers insecticide resistance. Our data point toward the emergence of novel hybrid ecotypes and highlight the importance of monitoring H. armigera genotypes as they spread through the Americas.

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Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone

The Auk ◽

10.1093/auk/ukz015 ◽

2019 ◽

Vol 136 (2) ◽

Author(s):

Joseph D Manthey ◽

Stéphane Boissinot ◽

Robert G Moyle

Keyword(s):

Gene Flow ◽

Contact Zone ◽

Genomic Diversity ◽

Whole Genome ◽

Effective Population ◽

Contact Zones ◽

Population Sizes ◽

Speciation Continuum ◽

Whole Genome Resequencing ◽

Genomic Introgression

Abstract Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall’s Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

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Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

Journal of Heredity ◽

10.1093/jhered/esz029 ◽

2019 ◽

Vol 110 (5) ◽

pp. 587-600

Author(s):

A Millie Burrell ◽

Jeffrey H R Goddard ◽

Paul J Greer ◽

Ryan J Williams ◽

Alan E Pepper

Keyword(s):

Gene Flow ◽

Genetic Connectivity ◽

Effective Population ◽

Evolutionary Potential ◽

Isolated Populations ◽

Long Distance ◽

Population Sizes ◽

History Of ◽

Small Set ◽

Nuclear Microsatellite

Abstract Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

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The formation of avian montane diversity across barriers and along elevational gradients

Nature Communications ◽

10.1038/s41467-021-27858-5 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

José Martín Pujolar ◽

Mozes P. K. Blom ◽

Andrew Hart Reeve ◽

Jonathan D. Kennedy ◽

Petter Zahl Marki ◽

...

Keyword(s):

Gene Flow ◽

Population Differentiation ◽

Bird Species ◽

Geographic Area ◽

Effective Population ◽

Tropical Mountains ◽

Mountainous Regions ◽

Pleistocene Climate ◽

Genome Wide ◽

Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

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Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0311 ◽

2010 ◽

Vol 365 (1543) ◽

pp. 1127-1138 ◽

Cited By ~ 47

Author(s):

Paquita E. A. Hoeck ◽

Jennifer L. Bollmer ◽

Patricia G. Parker ◽

Lukas F. Keller

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population Size ◽

Genetic Drift ◽

Bird Species ◽

Effective Population ◽

Island Size ◽

Island Populations ◽

Population Sizes ◽

Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

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Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

Conservation Genetics ◽

10.1007/s10592-021-01371-0 ◽

2021 ◽

Author(s):

Thomas J. Batter ◽

Joshua P. Bush ◽

Benjamin N. Sacks

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population Expansion ◽

Active Management ◽

Genetic Connectivity ◽

Effective Population ◽

Sex Marker ◽

Cervus Canadensis ◽

Population Sizes ◽

Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

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Genetic Diversity and Population Structure of Zeugodacus Tau Walker (Diptera: Tephritidae) in Southern Thailand

Walailak Journal of Science and Technology (WJST) ◽

10.48048/wjst.2020.7291 ◽

2021 ◽

Vol 18 (4) ◽

Author(s):

Jingyoh ZAELOR ◽

Duangta JULSIRIKUL ◽

Sangvorn KITTHAWEE

Keyword(s):

Population Structure ◽

Gene Flow ◽

Fruit Fly ◽

Haplotype Network ◽

Single Strand Conformation Polymorphism ◽

Fruit Flies ◽

Effective Population ◽

Bottleneck Effect ◽

Southern Thailand ◽

Population Sizes

The population structure of a fruit fly, Zeugodacus tau, was studied by a Single-Strand Conformation Polymorphism (SSCP) technique. Twenty haplotypes of Cytochrome Oxidase unit I (COI) sequence were found in flies collected from Southern Thailand. The phylogenetic tree and haplotype network revealed gene flow across a large geographic range. With the aid of winds, their gene flow diminished population structure. The population size of Z. tau in Southern Thailand seemed to be large and stable, but the other populations in some locations had experienced a bottleneck effect, leading to local genetic differentiation. Fruit flies from the eastern areas had large effective population sizes, whereas the populations from other areas were smaller. This pattern matched the ecological niche centroid model, in which fruit flies disperse from high population areas to lower ones.

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Distinguishing gene flow between malaria parasite populations

10.1101/2021.01.08.425858 ◽

2021 ◽

Author(s):

Tyler Steven Brown ◽

Aimee R. Taylor ◽

Olufunmilayo Arogbokun ◽

Caroline O. Buckee ◽

Hsiao-Han Chang

Keyword(s):

Gene Flow ◽

Malaria Parasite ◽

Sequence Data ◽

Simulated Data ◽

Whole Genome Sequence ◽

Effective Population ◽

Migration Rates ◽

Population Sizes ◽

And Migration ◽

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 evaluates numerically the ability to distinguish different levels of gene flow between malaria populations, using different amounts of real and simulated data, where data are simulated using parameters that approximate different epidemiological conditions. Specifically, using Plasmodium falciparum whole genome sequence data and sequence data simulated for a metapopulation with different migration rates and effective population sizes, we compare two estimators of gene flow, explore the number of genetic markers and number of individuals required to reliably rank highly connected locations, and describe how these thresholds change given different effective population sizes and migration rates. Our results have implications for the design and implementation of malaria genomic surveillance efforts.

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Analysis of coyote mitochondrial DNA genotype frequencies: estimation of the effective number of alleles.

Genetics ◽

10.1093/genetics/128.2.405 ◽

1991 ◽

Vol 128 (2) ◽

pp. 405-416 ◽

Cited By ~ 2

Author(s):

N Lehman ◽

R K Wayne

Keyword(s):

Mitochondrial Dna ◽

Geographic Location ◽

Monte Carlo Sampling ◽

Effective Population ◽

Mobile Species ◽

Genotype Frequencies ◽

Site Survey ◽

Population Sizes ◽

High Gene ◽

Mitochondrial Dna Genotype

Abstract A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.

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Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

PLoS ONE ◽

10.1371/journal.pone.0259124 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0259124

Author(s):

Damian C. Lettoof ◽

Vicki A. Thomson ◽

Jari Cornelis ◽

Philip W. Bateman ◽

Fabien Aubret ◽

...

Keyword(s):

Gene Flow ◽

Genetic Drift ◽

Urban Areas ◽

Population Genomics ◽

Genomic Structure ◽

Genomic Diversity ◽

Effective Population ◽

Population Genomic ◽

Population Sizes ◽

Urban Matrix

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

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Distribution of gene tree histories under the coalescent model with gene flow

10.1101/023937 ◽

2015 ◽

Author(s):

Yuan Tian ◽

Laura Kubatko

Keyword(s):

Gene Flow ◽

Maximum Likelihood ◽

Gene Tree ◽

Species Tree ◽

Tree Topology ◽

Effective Population ◽

Sequence Alignments ◽

Data Set ◽

Coalescent Model ◽

Population Sizes

We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed to analyze multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The model is formulated using a Markov chain representation, which allows use of matrix exponentiation to compute analytical expressions for the probability density of gene tree genealogies. The gene tree history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and gene tree histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the gene tree history distribution may identify the species tree and associated parameters. Thus, the gene tree history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015) to demonstrate the usefulness of our method for the analysis of empirical data. Key words: coalescent, gene flow, migration, hybridization, gene tree, topology, history, maximum likelihood, speciation.

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