A method for the estimation of gene flow parameters from a population structure caused by restricted gene flow and genetic drift

1987 ◽  
Vol 73 (5) ◽  
pp. 724-736 ◽  
Author(s):  
H. Van Dijk
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Drift ◽  
Restricted Gene Flow ◽  
Flow Parameters

scholarly journals Adaptive divergence in resistance to herbivores inDatura stramonium

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1411 ◽  
Author(s):  
Guillermo Castillo ◽  
Pedro L. Valverde ◽  
Laura L. Cruz ◽  
Johnattan Hernández-Cumplido ◽  
Guadalupe Andraca-Gómez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
Datura Stramonium ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Trichome Density ◽  
Phenotypic Differentiation ◽  
Phenotypic Resistance ◽  
Resistance Traits

Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations ofDatura stramonium, we compared the degree of phenotypic differentiation (PST) of leaf resistance traits (trichome density, atropine and scopolamine concentration) against neutral genetic differentiation (FST) at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher thanFSTacross the range of trait heritability values. In contrast, genetic differentiation in trichome density was different fromFSTonly when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits inD. stramonium.

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 variability in Indian populations of banana corm weevil [Cosmopolites sordidus (Coleoptera: Curculionidae)] assessed by RAPDs and AFLPs

2017 ◽  
Vol 37 (03) ◽  
pp. 149-162 ◽  
Author(s):  
Sweta Kumari U. Yadav ◽  
Jyotsna Singh ◽  
B. Padmanaban ◽  
Lalitha Sunil Kumar
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Hot Spot ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Distance ◽  
Mantel Test ◽  
Cosmopolites Sordidus ◽  
Restricted Gene Flow ◽  
Control And Management ◽  
Economic Pest

AbstractCosmopolites sordidus(Germar), commonly known as banana corm weevil, is an important economic pest in Asia that can cause severe yield loss depending upon the stage at which infestation occurs. In spite of its economic importance, little is known about the population structure of this pest in India. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) were used to characterize the population genetic structure ofC. sordiduscollected from five hot spot locations in India. Nineteen RAPD primers and five selective AFLP primer combinations generated 147 and 304 amplification products, respectively. UPGMA dendrograms generated with both marker systems failed to reveal populations clustered based on geographic distance, which was confirmed by the Mantel test, which did not show a strong correlation between genetic distance and geographic distance. Values of indices of genetic identity showed that the populations were closely related. Though the gene flow estimate (Nm) between the populations was 0.469, suggesting restricted gene flow, the populations are not genetically distinct. These observations suggest that the range expansion of this banana pest in India has taken place through transport of infested corms and plant material, resulting in genetically close populations that are geographically distinct. These results provide important information on the population structure of this pest in India, which will aid in designing suitable strategies for its control and management, especially with respect to insecticide resistance.

scholarly journals Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus)

2009 ◽  
Vol 9 (1) ◽  
pp. 297 ◽  
Author(s):  
Sebastian Steinfartz ◽  
Scott Glaberman ◽  
Deborah Lanterbecq ◽  
Michael A Russello ◽  
Sabrina Rosa ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Restricted Gene Flow ◽  
Amblyrhynchus Cristatus ◽  
Marine Iguanas

scholarly journals Genetic population structure of Gyrodactylus thymalli (Monogenea) in a large Norwegian river system

Parasitology ◽  
2015 ◽  
Vol 142 (14) ◽  
pp. 1693-1702 ◽  
Author(s):  
RUBEN ALEXANDER PETTERSEN ◽  
TOR ATLE MO ◽  
HAAKON HANSEN ◽  
LEIF ASBJØRN VØLLESTAD
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Gene Flow ◽  
Haplotype Diversity ◽  
River System ◽  
Genetic Population Structure ◽  
Restricted Gene Flow ◽  
Upstream Migration ◽  
Genetic Population ◽  
Long Time

SUMMARYThe extent of geographic genetic variation is the result of several processes such as mutation, gene flow, selection and drift. Processes that structure the populations of parasite species are often directly linked to the processes that influence the host. Here, we investigate the genetic population structure of the ectoparasite Gyrodactylus thymalli Žitňan, 1960 (Monogenea) collected from grayling (Thymallus thymallus L.) throughout the river Glomma, the largest watercourse in Norway. Parts of the mitochondrial dehydrogenase subunit 5 (NADH 5) and cytochrome oxidase I (COI) genes from 309 G. thymalli were analysed to study the genetic variation and investigated the geographical distribution of parasite haplotypes. Three main clusters of haplotypes dominated the three distinct geographic parts of the river system; one cluster dominated in the western main stem of the river, one in the eastern and one in the lower part. There was a positive correlation between pairwise genetic distance and hydrographic distance. The results indicate restricted gene flow between sub-populations of G. thymalli, most likely due to barriers that limit upstream migration of infected grayling. More than 80% of the populations had private haplotypes, also indicating long-time isolation of sub-populations. According to a molecular clock calibration, much of the haplotype diversity of G. thymalli in the river Glomma has developed after the last glaciation.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN SELECTED BEEF BREEDS

AGROFOR ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Kristína LEHOCKÁ ◽  
Radovan KASARDA ◽  
Barbora OLŠANSKÁ ◽  
Nina MORAVČÍKOVÁ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Beef Cattle ◽  
Genetic Drift ◽  
High Linkage Disequilibrium ◽  
Snp Markers ◽  
Data Set ◽  
Population Structure Analysis ◽  
Red Angus

The aim of the study was to estimate genetic drift and gene flow related to population structure and genetic diversity in selected beef cattle. For the evaluation of the genetic drift and gene flow among analysed populations, the Bayesian Population Structure Analysis and software Treemix were used. The genetic analysis included two cattle breeds bred in Slovakia (Charolais and Limousine). In addition to the Limousine and Charolais breeds, other beef cattle (Angus N = 90, Belgian Blue N = 4, Blonde d'Aquitaine N= 5, Hereford N = 98 and Red Angus N = 15) were analysed. The 50k Bead chip was used; the dataset consisted of 34,834 SNPs. To avoid detection bias, SNPs with high linkage disequilibrium (r2 = 0.05) were pruned from the database; the final data set consisted of 296 animals and 2,539 SNP markers. Our results reflected four modes of gene flow between Angus, Red Angus, Charolais, Limousine and Hereford. Analysed breeds were not confirmed to influence genetic make-up of Belgian Blue and Blonde d'Aquitaine populations. All migration edges reached weight values below 0.2. The only two migration edges higher in weight was observed, first between the ancestor of Limousine breed into Blond d'Aquitaine, and second among historical ancestor of Hereford breed into Red Angus. Our results reflect that the donor population has made a significant contribution to the recipient population.

Population structure of the Patagonian toothfish around Heard, McDonald and Macquarie Islands

2002 ◽  
Vol 14 (4) ◽  
pp. 364-373 ◽  
Author(s):  
SHARON A. APPLEYARD ◽  
ROBERT D. WARD ◽  
RICHARD WILLIAMS
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Heterogeneity ◽  
Restricted Gene Flow ◽  
Effective Population ◽  
Significant Differentiation ◽  
Macquarie Island ◽  
Male Dispersal ◽  
Patagonian Toothfish

Two mitochondrial DNA regions and seven microsatellite loci were examined in Patagonian toothfish from three locations in the Southern Ocean (Macquarie Island, five collections; Heard and McDonald Islands, four collections; Shag Rocks/South Georgia area, one collection). Striking mtDNA heterogeneity was detected between the three fishing locations (FST=0.445, P<0.001), but spatial and temporal collections within the same location were not significantly different. No significant overall microsatellite differentiation between the three locations was apparent (FST=−0.009, P=0.785). However, some individual loci showed small but significant differentiation, which in each case was attributable to between rather than within-location differentiation. Greater differentiation of mtDNA can, in principle, be explained either by female philopatry and male dispersal, or by its greater sensitivity to changes in effective population size. The latter seems more likely as tagging indicates that toothfish is generally a sedentary species. The genetic heterogeneity between the three locations indicates restricted gene flow, with the fish at each location comprising independent units. Depletion in one location is therefore unlikely to be quickly replaced by immigration from another.

scholarly journals Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago

2008 ◽  
Vol 363 (1506) ◽  
pp. 3083-3096 ◽  
Author(s):  
Hans Peter Comes ◽  
Andreas Tribsch ◽  
Christiane Bittkau
Keyword(s):  
Gene Flow ◽  
Continental Shelf ◽  
Genetic Drift ◽  
Spatial Scales ◽  
Population Level ◽  
Minor Role ◽  
Restricted Gene Flow ◽  
Sea Levels ◽  
Rising Sea Levels ◽  
A Minor

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times ( ca <5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the Aegean Nigella arvensis complex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of Aegean Nigella , as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in Aegean Nigella have so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant species.

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