scholarly journals Gene Flow Among Populations of the Malaria Vector, Anopheles gambiae, in Mali, West Africa

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 743-750
Author(s):  
Charles Taylor ◽  
Yeya T Touré ◽  
John Carnahan ◽  
Douglas E Norris ◽  
Guimogo Dolo ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Anopheles Gambiae ◽  
Sensu Stricto ◽  
The Other ◽  
Effective Population ◽  
Chromosomal Form ◽  
Migration Rates ◽  
Anopheles Gambiae Complex ◽  
And Migration

Abstract The population structure of the Anopheles gambiae complex is unusual, with several sibling species often occupying a single area and, in one of these species, An. gambiae sensu stricto, as many as three “chromosomal forms” occurring together. The chromosomal forms are thought to be intermediate between populations and species, distinguishable by patterns of chromosome gene arrangements. The extent of reproductive isolation among these forms has been debated. To better characterize this structure we measured effective population size, Ne, and migration rates, m, or their product by both direct and indirect means. Gene flow among villages within each chromosomal form was found to be large (Nem > 40), was intermediate between chromosomal forms (Nem ≈ 3–30), and was low between species (Nem ≈ 0.17–1.3). A recently developed means for distinguishing among certain of the forms using PCR indicated rates of gene flow consistent with those observed using the other genetic markers.

scholarly journals Distinguishing gene flow between malaria parasite populations

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.

scholarly journals Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model

2019 ◽  
Author(s):  
Arun Sethuraman ◽  
Melissa Lynch
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Population Genomics ◽  
Divergence Times ◽  
Effective Population ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Population Sizes ◽  
And Migration ◽  
Erroneous Inferences

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.

Estimating Effective Population Size and Migration Rates From Genetic Samples Over Space and Time

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 429-446 ◽  
Author(s):  
Jinliang Wang ◽  
Michael C Whitlock
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Joint Estimation ◽  
Large Sample Size ◽  
Effective Population ◽  
Likelihood Methods ◽  
Marker Allele ◽  
Migration Rates ◽  
Space And Time ◽  
And Migration

Abstract In the past, moment and likelihood methods have been developed to estimate the effective population size (Ne) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of Ne if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of Ne and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of Ne, respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both Ne and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

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 Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

2020 ◽  
Vol 33 (1) ◽  
pp. 44-59
Author(s):  
Rafael Núñez-Domínguez ◽  
Ricardo E Martínez-Rocha ◽  
Jorge A Hidalgo-Moreno ◽  
Rodolfo Ramírez-Valverde ◽  
José G García-Muñiz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Genetic Management ◽  
Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

Genetic analysis and population structure of the Anopheles gambiae complex from different ecological zones of Burkina Faso

2020 ◽  
Vol 81 ◽  
pp. 104261
Author(s):  
Abdou Azaque Zouré ◽  
Grégoire Noël ◽  
Aboubacar Sombié ◽  
Zéphirin Somda ◽  
Athanase Badolo ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Analysis ◽  
Burkina Faso ◽  
Anopheles Gambiae ◽  
Gambiae Complex ◽  
Ecological Zones ◽  
Anopheles Gambiae Complex

scholarly journals Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4702 ◽  
Author(s):  
Fábio B. Britto ◽  
Anders J. Schmidt ◽  
Adriana M.F. Carvalho ◽  
Carolina C.M.P. Vasconcelos ◽  
Antonia M. Farias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Connectivity ◽  
Brazilian Coast ◽  
Fishery Resource ◽  
Ucides Cordatus ◽  
Migration Rates ◽  
Mangrove Crab ◽  
Key Species

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

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