scholarly journals Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1091-1106 ◽  
Author(s):  
Rong Lin Wang ◽  
John Wakeley ◽  
Jody Hey
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Sequence Data ◽  
Sexual Isolation ◽  
Secondary Contact ◽  
Drosophila Pseudoobscura ◽  
Dna Sequence Data ◽  
Principal Finding ◽  
Close Relatives ◽  
Parapatric Speciation

The divergence of Drosophila pseudoobscura and close relatives D. persimilis and D. pseudoobscura bogotana has been studied using comparative DNA sequence data from multiple nuclear loci. New data from the Hsp82 and Adh regions, in conjunction with existing data from Adh and the Period locus, are examined in the light of various models of speciation. The principal finding is that the three loci present very different histories, with Adh indicating large amounts of recent gene flow among the taxa, while little or no gene flow is apparent in the data from the other loci. The data were compared with predictions from several isolation models of divergence. These models include no gene flow, and they were found to be incompatible with the data. Instead the DNA data, taken together with other evidence, seem consistent with divergence models in which natural selection acts against gene flow at some loci more than at others. This family of models includes some sympatric and parapatric speciation models, as well as models of secondary contact and subsequent reinforcement of sexual isolation.

Comparative host–parasite population genetic structures: obligate fly ectoparasites on Galapagos seabirds

Parasitology ◽  
2013 ◽  
Vol 140 (9) ◽  
pp. 1061-1069 ◽  
Author(s):  
IRIS I. LEVIN ◽  
PATRICIA G. PARKER
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Sequence Data ◽  
Population Genetic Study ◽  
Haemosporidian Parasite ◽  
Dna Sequence Data ◽  
Sula Granti ◽  
Breeding Attempt ◽  
Genetic Structures

SUMMARYParasites often have shorter generation times and, in some cases, faster mutation rates than their hosts, which can lead to greater population differentiation in the parasite relative to the host. Here we present a population genetic study of two ectoparasitic flies, Olfersia spinifera and Olfersia aenescens compared with their respective bird hosts, great frigatebirds (Fregata minor) and Nazca boobies (Sula granti). Olfersia spinifera is the vector of a haemosporidian parasite, Haemoproteus iwa, which infects frigatebirds throughout their range. Interestingly, there is no genetic differentiation in the haemosporidian parasite across this range despite strong genetic differentiation between Galapagos frigatebirds and their non-Galapagos conspecifics. It is possible that the broad distribution of this one H. iwa lineage could be facilitated by movement of infected O. spinifera. Therefore, we predicted more gene flow in both fly species compared with the bird hosts. Mitochondrial DNA sequence data from three genes per species indicated that despite marked differences in the genetic structure of the bird hosts, gene flow was very high in both fly species. A likely explanation involves non-breeding movements of hosts, including movement of juveniles, and movement by adult birds whose breeding attempt has failed, although we cannot rule out the possibility that closely related host species may be involved.

scholarly journals Darwin and Genetics

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 757-766 ◽  
Author(s):  
Brian Charlesworth ◽  
Deborah Charlesworth
Keyword(s):  
Natural Selection ◽  
Dna Sequence ◽  
Sequence Data ◽  
Evolutionary Genetics ◽  
Adequate Account ◽  
Dna Sequence Data ◽  
Recent Advances ◽  
Answering Questions

Darwin's theory of natural selection lacked an adequate account of inheritance, making it logically incomplete. We review the interaction between evolution and genetics, showing how, unlike Mendel, Darwin's lack of a model of the mechanism of inheritance left him unable to interpret his own data that showed Mendelian ratios, even though he shared with Mendel a more mathematical and probabilistic outlook than most biologists of his time. Darwin's own “pangenesis” model provided a mechanism for generating ample variability on which selection could act. It involved, however, the inheritance of characters acquired during an organism's life, which Darwin himself knew could not explain some evolutionary situations. Once the particulate basis of genetics was understood, it was seen to allow variation to be passed intact to new generations, and evolution could then be understood as a process of changes in the frequencies of stable variants. Evolutionary genetics subsequently developed as a central part of biology. Darwinian principles now play a greater role in biology than ever before, which we illustrate with some examples of studies of natural selection that use DNA sequence data and with some recent advances in answering questions first asked by Darwin.

scholarly journals Convergent evolution of ‘creepers’ in the Hawaiian honeycreeper radiation

2008 ◽  
Vol 5 (2) ◽  
pp. 221-224 ◽  
Author(s):  
Dawn M Reding ◽  
Jeffrey T Foster ◽  
Helen F James ◽  
H. Douglas Pratt ◽  
Robert C Fleischer
Keyword(s):  
Natural Selection ◽  
Adaptive Radiation ◽  
Phylogenetic Relationships ◽  
Convergent Evolution ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Evolutionary Patterns ◽  
Dna Sequence Data ◽  
Hawaiian Honeycreepers ◽  
Mtdna Introgression

Natural selection plays a fundamental role in the ecological theory of adaptive radiation. A prediction of this theory is the convergent evolution of traits in lineages experiencing similar environments. The Hawaiian honeycreepers are a spectacular example of adaptive radiation and may demonstrate convergence, but uncertainty about phylogenetic relationships within the group has made it difficult to assess such evolutionary patterns. We examine the phylogenetic relationships of the Hawaii creeper ( Oreomystis mana ), a bird that in a suite of morphological, ecological and behavioural traits closely resembles the Kauai creeper ( Oreomystis bairdi ), but whose mitochondrial DNA (mtDNA) and osteology suggest a relationship with the amakihis ( Hemignathus in part) and akepas ( Loxops ). We analysed nuclear DNA sequence data from 11 relevant honeycreeper taxa and one outgroup to test whether the character contradiction results from historical hybridization and mtDNA introgression, or convergent evolution. We found no evidence of past hybridization, a phenomenon that remains undocumented in Hawaiian honeycreepers, and confirmed mtDNA and osteological evidence that the Hawaii creeper is most closely related to the amakihis and akepas. Thus, the morphological, ecological and behavioural similarities between the evolutionarily distant Hawaii and Kauai creepers represent an extreme example of convergent evolution and demonstrate how natural selection can lead to repeatable evolutionary outcomes.

scholarly journals Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

2019 ◽  
Author(s):  
Katharine L Korunes ◽  
Carlos A Machado ◽  
Mohamed AF Noor
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Drosophila Pseudoobscura ◽  
Ancestral Polymorphism ◽  
Chromosomal Inversions ◽  
History Of ◽  
Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

scholarly journals An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

2019 ◽  
Author(s):  
Aaron J. Stern ◽  
Peter R. Wilton ◽  
Rasmus Nielsen
Keyword(s):  
Natural Selection ◽  
Allele Frequency ◽  
Dna Sequence ◽  
Importance Sampling ◽  
Likelihood Function ◽  
Sequence Data ◽  
Lactase Persistence ◽  
Selection Coefficient ◽  
Dna Sequence Data ◽  
Full Likelihood

AbstractMost current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. The method treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, under various demographic models and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1.Author summaryCurrent methods to study natural selection using modern population genomic data are limited in their power and flexibility. Here, we present a new method to infer natural selection that builds on recent methodological advances in estimating genome-wide genealogies. By using importance sampling we are able to efficiently estimate the likelihood function of the selection coefficient. We show our method improves power to test for selection over competing methods across a diverse range of scenarios, and also accurately infers the selection coefficient. We also demonstrate a novel capability of our model, using it to infer the allele’s frequency over time. We validate these results with a study of a lactase persistence SNP in Europeans, and also study a set of 11 pigmentation-associated variants.

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 Early history of Neanderthals and Denisovans

2017 ◽  
Vol 114 (37) ◽  
pp. 9859-9863 ◽  
Author(s):  
Alan R. Rogers ◽  
Ryan J. Bohlender ◽  
Chad D. Huff
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Early History ◽  
Middle Pleistocene ◽  
Dna Sequence Data ◽  
The Past ◽  
History Of

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

scholarly journals Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

2021 ◽  
Author(s):  
Vanina Tonzo ◽  
AdriÀ Bellvert ◽  
Joaquín Ortego
Keyword(s):  
Gene Flow ◽  
Biological Diversity ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Secondary Contact ◽  
Lineage Sorting ◽  
Glacial Cycles ◽  
Reciprocal Monophyly ◽  
Geometric Morphometric

AbstractInferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression. In this study, we combined high throughput sequence data (ddRADseq), geometric morphometric information, and novel phylogenetic inference methods that explicitly account for gene flow to infer the evolutionary relationships and the timing and mode of diversification in a complex of Ibero-Maghrebian montane grasshoppers of the subgenus Dreuxius (genus Omocestus). Our analyses supported the phenotypic distinctiveness of most sister taxa, two events of historical introgression involving lineages at different stages of the diversification continuum, and the recent Pleistocene origin (< 1 Ma) of the complex. Phylogenetic analyses did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting overseas migration between the two continents during the Pleistocene. Collectively, these results indicate that periods of isolation and secondary contact linked to Pleistocene glacial cycles likely contributed to both allopatric speciation and post divergence gene flow in the complex. This study exemplifies how the integration of multiple lines of evidence can help to reconstruct complex histories of reticulated evolution and highlights the important role of Quaternary climatic oscillations as a diversification engine in the Ibero-Maghrebian biodiversity hotspot.

scholarly journals Lack of Spatial Genetic Structure Among Nesting and Wintering King Eiders

The Condor ◽  
2004 ◽  
Vol 106 (2) ◽  
pp. 229-240 ◽  
Author(s):  
John M. Pearce ◽  
Sandra L. Talbot ◽  
Barbara J. Pierson ◽  
Margaret R. Petersen ◽  
Kim T. Scribner ◽  
...  
Keyword(s):  
Gene Flow ◽  
North America ◽  
Sequence Data ◽  
Spatial Genetic Structure ◽  
Haplotype Frequency ◽  
Gene Frequencies ◽  
Dna Sequence Data ◽  
Somateria Spectabilis ◽  
Breeding Populations ◽  
Wintering Areas

Abstract The King Eider (Somateria spectabilis) has been delineated into two broadly distributed breeding populations in North America (the western and eastern Arctic) on the basis of banding data and their use of widely separated Pacific and Atlantic wintering areas. Little is known about the level of gene flow between these two populations. Also unknown is whether behavioral patterns common among migratory waterfowl, such as site fidelity to wintering areas and pair formation at these sites, have existed for sufficient time to create a population structure defined by philopatry to wintering rather than to nesting locations. We used six nuclear microsatellite DNA loci and cytochrome b mitochondrial DNA sequence data to estimate the extent of spatial genetic differentiation among nesting and wintering areas of King Eiders across North America and adjacent regions. Estimates of interpopulation variance in microsatellite allele and mtDNA haplotype frequency were both low and nonsignificant based on samples from three wintering and four nesting areas. Results from nested clade analysis, mismatch distributions, and coalescent-based analyses suggest historical population growth and gene flow that collectively may have homogenized gene frequencies. The presence of several unique mtDNA haplotypes among birds wintering near Greenland suggests that gene flow may now be more limited between the western and eastern Arctic, which is consistent with banding data. Ausencia de Estructura Genética Espacial entre Áreas de Nidificación e Invernada en Somateria spectabilis Resumen. Con base en datos de anillamiento y en el uso de áreas de invernada separadas en el Pacífico y el Atlántico, la especie Somateria spectabilis ha sido separada en dos poblaciones reproductivas de amplia distribución en Norte América (las del Ártico este y oeste). Se conoce poco sobre los niveles de flujo génico entre estas dos poblaciones. También se desconoce si patrones de comportamiento comunes entre aves acuáticas migratorias, como la fidelidad a los sitios de invernada y la formación de parejas en dichos sitios, han existido por suficiente tiempo como para crear estructura poblacional definida por la filopatría a las áreas de invernada en lugar de a las áreas de nidificación. Utilizamos seis loci nucleares de ADN microsatelital y secuencias del gen mitocondrial citocromo b para estimar el grado de diferenciación genética espacial entre áreas de nidificación e invernada de S. spectabilis a través de Norte América y regiones adyacentes. Los estimados de la varianza interpoblacional en la frecuencia de alelos de microsatélites y de haplotipos de ADNmt fueron bajos y no significativos con base en muestras de tres áreas de invernada y cuatro de nidificación. Los resultados de un análisis de clados anidados, de las distribuciones “mismatch” y de análisis basados en coalescencia sugieren la existencia de crecimiento poblacional histórico y flujo génico, eventos que colectivamente podrían haber homogeneizado las frecuencias génicas. La presencia de varios haplotipos exclusivos entre aves que invernan cerca de Groenlandia sugiere que el flujo génico podría ser ahora más limitado entre el Ártico oeste y este, lo que es consistente con los datos de anillamiento.

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