Gene surfing of underdominant alleles promotes formation of hybrid zones

The distribution of genetic diversity over geographic space has long been investigated in population genetics and serves as a useful tool to understand evolution and history of populations. Within some species or across regions of contact between two species, there are instances where there is no apparent ecological determinant of sharp changes in allele frequencies or divergence. To further understand these patterns of spatial genetic structure and potential species divergence, we model the establishment of clines that occur due to the surfing of underdominant alleles during range expansions. We provide analytical approximations for the fixation probability of underdominant alleles at expansion fronts and demonstrate that gene surfing can lead to clines in 1D range expansions. We extend these results to multiple loci via a mixture of analytical theory and individual-based simulations. We study the interaction between the strength of selection against heterozygotes, migration rates, and local recombination rates on the formation of stable hybrid zones. A key result of our study is that clines created by surfing at different loci can attract each other and align after expansion, if they are sufficiently close in space and in terms of recombination distance. Our findings suggest that range expansions can set the stage for parapatric speciation due to the alignment of multiple selective clines, even in the absence of ecologically divergent selection.

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Diaspora in the United States: Chinese and Indians Compared

Journal of Chinese Overseas ◽

10.1163/179325410x526131 ◽

2010 ◽

Vol 6 (2) ◽

pp. 286-310 ◽

Cited By ~ 5

Author(s):

Emily Skop ◽

Wei Li

Keyword(s):

United States ◽

Racial Discrimination ◽

20Th Century ◽

The United States ◽

Foreign Born ◽

Migration Rates ◽

China And India ◽

History Of ◽

Migrant Groups ◽

The U.S

AbstractIn recent years, the migration rates from both China and India to the U.S. have accelerated. Since 2000 more than a third of foreign-born Chinese and 40% of foreign-born Indians have arrived in that country. This paper will document the evolving patterns of immigration from China and India to the U.S. by tracing the history of immigration and racial discrimination, the dramatic transitions that have occurred since the mid-20th century, and the current demographic and socioeconomic profiles of these two migrant groups.

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Phenotypic plasticity promotes balanced polymorphism in periodic environments by a genomic storage effect

10.1101/038497 ◽

2016 ◽

Cited By ~ 1

Author(s):

Davorka Gulisija ◽

Yuseob Kim ◽

Joshua B. Plotkin

Keyword(s):

Phenotypic Plasticity ◽

Large Range ◽

Genetic Model ◽

Effect Sizes ◽

Storage Effect ◽

Recombination Rates ◽

Modifier Locus ◽

Balanced Polymorphism ◽

Analytical Approximations ◽

Varying Environments

Phenotypic plasticity is known to evolve in perturbed habitats, where it alleviates the deleterious effects of selection. But the effects of plasticity on levels of genetic polymorphism, an important precursor to adaptation in temporally varying environments, are unclear. Here we develop a haploid, two-locus population-genetic model to describe the interplay between a plasticity modifier locus and a target locus subject to periodically varying selection. We find that the interplay between these two loci can produce a 'genomic storage effect' that promotes balanced polymorphism over a large range of parameters, in the absence of all other conditions known to maintain genetic variation. The genomic storage effect arises as recombination allows alleles at the two loci to escape more harmful genetic backgrounds and associate in haplotypes that persist until environmental conditions change. Using both Monte Carlo simulations and analytical approximations we quantify the strength of the genomic storage effect across a range of selection pressures, recombination rates, plasticity modifier effect sizes, and environmental periods.

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The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies

10.1101/259135 ◽

2018 ◽

Author(s):

Christelle Fraïsse ◽

Camille Roux ◽

Pierre-Alexandre Gagnaire ◽

Jonathan Romiguier ◽

Nicolas Faivre ◽

...

Keyword(s):

Frequency Spectrum ◽

Approximate Bayesian Computation ◽

Exome Capture ◽

Bayesian Computation ◽

Sampling Strategies ◽

Migration Rates ◽

History Of ◽

Site Frequency Spectrum ◽

Approximate Bayesian ◽

Number Of Individuals

AbstractGenome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

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Fundação Escola Técnica Liberato Salzano Vieira da Cunha: da construção física à constituição de um mito de excelência (1957-1967)

Revista Educação e Emancipação ◽

10.18764/2358-4319.v14n2p375-397 ◽

2021 ◽

Vol 14 (2) ◽

pp. 375

Author(s):

Deise Margô Müller ◽

Luciane Sgarbi S. Grazziotin

Keyword(s):

De Novo ◽

History Of Education ◽

Educational Institutions ◽

Education History ◽

Technical School ◽

Geographic Space ◽

Methodological Choices ◽

History Of ◽

The City ◽

Physical Construction

Este estudo tem viés historiográfico e o objeto de análise é a Fundação Escola Técnica Liberato Salzano Vieira da Cunha localizada no município de Novo Hamburgo/RS. Tem o objetivo de explicitar as escolhas metodológicas que viabilizam a produção historiográfica vinculada à temática da História das Instituições de Ensino. Ao se investigar a gênese do processo de implantação de uma escola técnica, em determinado tempo e lugar, foi possível compreender a construção de um discurso de excelência de ensino em tal instituição e o envolvimento desse discurso com as políticas públicas de educação vigentes no período estudado, articuladas às características regionais do espaço geográfico em que a escola está localizada.Palavras chave: Metodologia de Pesquisa. Ensino Técnico Profissionalizante. História da Educação. História das Instituições de Ensino.Liberato Salzano Vieira da Cunha Technical School: from the physical construction to the constitution of a myth of excellence (1957-1967)ABSTRACTThis historiographical study relates to the History of Educational Institutions, and its object of analysis is the Liberato Salzano Vieira da Cunha Technical School, located in the city of Novo Hamburgo/RS. It aims at revealing the methodological choices that enable historiographical production in past times. Investigating the genesis of the process of implantation of a technical school, in a certain time and place, enabled understanding about the construction of a discourse of educational excellence in this institution, as well as the involvement of this discourse with educational public policies in effect in the period studied, articulated to the regional characteristics of the geographic space in which the school is located.Keywords: Research Methodology. Technical Professional Secondary Education. History of Education. History of Educational Institutions.Fundación Escuela Técnica Liberato Salzano Vieira da Cunha: de la construcción física hasta la constitución de un mito de excelencia (1957 - 1967)RESUMENEste estudio tiene un carácter historiográfico y el objeto del análisis es la Fundación Escuela Técnica Liberato Salzano Vieira da Cunha, situada en la ciudad de Novo Hamburgo/RS. Tiene el objetivo de explicitar las opciones metodológicas que hacen posible la producción historiográfica vinculada a la temática de la Historia de las Instituciones de Educación. Investigando el origen del proceso de implantación de una escuela técnica, en determinado tiempo y lugar, fue posible entender la construcción de un discurso de excelencia de enseñanza en tal institución y el envolvimiento de ese discurso con las políticas públicas de educación vigentes en el período estudiado, articuladas a las características regionales del espacio geográfico donde se localiza la escuela.Palabras clave: Metodología de investigación. Enseñanza técnica profesional. Historia de la Educación. Historia de las Instituciones de Educación.

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Divide mobility controls knickpoint migration on the Roan Plateau

10.5194/egusphere-egu2020-11177 ◽

2020 ◽

Author(s):

Wolfgang Schwanghart ◽

Dirk Scherler

Keyword(s):

Colorado River ◽

Drainage Area ◽

Lagrangian Model ◽

Drainage Network ◽

Migration Rates ◽

Tectonic History ◽

Area Loss ◽

Temporal Aspects ◽

History Of ◽

River Profiles

<p>Knickpoints in longitudinal river profiles provide proxies for the climatic and tectonic history of active mountains. The analysis of river profiles commonly relies on the assumption that drainage network configurations are stable. Here we show that this assumption must made cautiously if changes in contributing area are fast relative to knickpoint migration rates. We study the Parachute Creek basin in the Roan Plateau, Colorado, United States. Low spatial variations in climate and erosional efficiency permit us to reveal and quantify drainage-area loss that occurred in one of the subbasins where observed knickpoint locations are farther upstream than predicted by a model that takes present-day drainage areas into account. We developed a Lagrangian model of knickpoint migration which enables us to study the kinematic links between drainage area loss and knickpoint migration and that provides us with constraints on the temporal aspects of area loss. Modelled onset and amount of area loss are consistent with cliff retreat rates along the margin of the Roan Plateau inferred from the incisional history of the upper Colorado River.</p>

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A maladaptive combination of traits contributes to the maintenance of a stable hybrid zone between two divergent species of Drosophila

10.1101/138388 ◽

2017 ◽

Cited By ~ 3

Author(s):

Brandon S. Cooper ◽

Alisa Sedghifar ◽

W. Thurston Nash ◽

Aaron A. Comeault ◽

Daniel R. Matute

Keyword(s):

Gene Flow ◽

Hybrid Zone ◽

Hybrid Zones ◽

Hybrid Male ◽

Open Habitat ◽

Preferred Habitat ◽

Species Overlap ◽

Agricultural Areas ◽

Stable Hybrid ◽

Advanced Generation

ABSTRACTGeographical areas where two species come into contact and hybridize serve as natural laboratories for assessing mechanisms that limit gene flow between species. The ranges of about half of all closely related Drosophila species overlap, and the genomes of several pairs reveal signatures of past introgression. However, only two contemporary hybrid zones have been characterized in the genus, and both are recently diverged sister species (D. simulans-D. sechellia, Ks = 0.05; D. yakuba-D. santomea, Ks = 0.048). Here we present evidence of a new hybrid zone, and the ecological mechanisms that maintain it, between two highly divergent Drosophila species (Ks = 0.11). On the island of Bioko in west Africa, D. teissieri occupies mostly forests, D. yakuba occupies mostly open agricultural areas, and recently, we discovered that hybrids between these species occur near the interface of these habitats. Genome sequencing revealed that all field-sampled hybrids are F1 progeny of D. yakuba females and D. teissieri males. We found no evidence for either advanced-generation hybrids or F1 hybrids produced by D. teissieri females and D.yakuba males. The lack of advanced-generation hybrids on Bioko is consistent with mark-recapture and laboratory experiments that we conducted, which indicate hybrids have a maladaptive combination of traits. Like D. yakuba, hybrids behaviorally prefer open habitat that is relatively warm and dry, but like D. teissieri, hybrids have low desiccation tolerance, which we predict leaves them physiologically ill-equipped to cope with their preferred habitat. These observations are consistent with recent findings of limited introgression in the D. yakuba clade and identify an ecological mechanism for limiting gene flow between D. yakuba and D. teissieri; namely, selection against hybrids that we have documented, in combination with hybrid male sterility, contributes to the maintenance of this narrow (~30m), stable hybrid zone centered on the forest-open habitat ecotone. Our results show how a deleterious combination of parental traits can result in unfit or maladapted hybrids.

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Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences

eLife ◽

10.7554/elife.36317 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 40

Author(s):

Fanny Pouyet ◽

Simon Aeschbacher ◽

Alexandre Thiéry ◽

Laurent Excoffier

Keyword(s):

Gene Conversion ◽

Purifying Selection ◽

Genomic Diversity ◽

Background Selection ◽

Recombination Rates ◽

Biased Gene Conversion ◽

Synonymous Sites ◽

History Of ◽

Demographic Inference ◽

Genomic Regions

Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.

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Recombination and Gene Flux Caused by Gene Conversion and Crossing Over in Inversion Heterokaryotypes

Genetics ◽

10.1093/genetics/146.2.695 ◽

1997 ◽

Vol 146 (2) ◽

pp. 695-709 ◽

Cited By ~ 11

Author(s):

Arcadio Navarro ◽

Esther Betrán ◽

Antonio Barbadilla ◽

Alfredo Ruiz

Keyword(s):

Gene Conversion ◽

Poisson Model ◽

Distal Segment ◽

Crossing Over ◽

Recombination Rates ◽

Dna Variation ◽

Inverted Segment ◽

Variation Patterns ◽

History Of ◽

Counting Model

A theoretical analysis of the effects of inversions on recombination and gene flux between arrangements caused by gene conversion and crossing over was carried out. Two different mathematical models of recombination were used: the Poisson model (without interference) and the Counting model (with interference). The main results are as follows. (1) Recombination and gene flux are highly site-dependent both inside and outside the inverted regions. (2) Crossing over overwhelms gene conversion as a cause of gene flux in large inversions, while conversion becomes relatively significant in short inversions and in regions around the breakpoints. (3) Under the Counting model the recombination rate between two markers depends strongly on the position of the markers along the inverted segment. Two equally spaced markers in the central part of the inverted segment have less recombination than if they are in a more extreme position. (4) Inversions affect recombination rates in the uninverted regions of the chromosome. Recombination increases in the distal segment and decreases in the proximal segment. These results provide an explanation for a number of observations reported in the literature. Because inversions are ubiquitous in the evolutionary history of many Drosophila species, the effects of inversions on recombination are expected to influence DNA variation patterns.

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Divide mobility controls knickpoint migration on the Roan Plateau (Colorado, USA)

Geology ◽

10.1130/g47054.1 ◽

2020 ◽

Vol 48 (7) ◽

pp. 698-702 ◽

Cited By ~ 1

Author(s):

Wolfgang Schwanghart ◽

Dirk Scherler

Keyword(s):

Colorado River ◽

Drainage Area ◽

Lagrangian Model ◽

Stream Power ◽

Migration Rates ◽

Tectonic History ◽

Area Loss ◽

Temporal Aspects ◽

History Of ◽

River Profiles

Abstract Knickpoints in longitudinal river profiles are proxies for the climatic and tectonic history of active mountains. The analysis of river profiles commonly relies on the assumption that drainage network configurations are stable. Here, we show that this assumption must be made cautiously if changes in contributing area are fast relative to knickpoint migration rates. We studied the Parachute Creek basin in the Roan Plateau, Colorado, United States, where knickpoint retreat occurs in horizontally uniform lithology so that drainage area is the sole governing variable. In this basin, we identified an anomalous catchment in the degree to which a stream power–based model predicted knickpoint locations. The catchment is experiencing area loss as the plateau edge is eroded by cliff migration in proximity to the Colorado River. Model predictions improve if the plateau edge is assumed to have migrated over the time scale of knickpoint retreat. Finally, a Lagrangian model of knickpoint migration enabled us to study the kinematic links between drainage area loss and knickpoint migration and offered constraints on the temporal aspects of area loss. Modeled onset and amount of area loss are consistent with cliff retreat rates along the margin of the Roan Plateau inferred from the incisional history of the upper Colorado River.

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Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa167 ◽

2020 ◽

Vol 132 (1) ◽

pp. 161-173

Author(s):

Camila D Ritter ◽

Laís A Coelho ◽

João Mg Capurucho ◽

Sergio H Borges ◽

Cíntia Cornelius ◽

...

Keyword(s):

Population Structure ◽

Bird Species ◽

Population History ◽

Sister Species ◽

White Sand ◽

Migration Rates ◽

History Of ◽

The Last Glacial Maximum ◽

Vegetation Patches ◽

The Last Glacial

Abstract Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.

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