scholarly journals Beyond clines: lineages and haplotype blocks in hybrid zones

2016 ◽  
Author(s):  
Alisa Sedghifar ◽  
Yaniv Brandvain ◽  
Peter Ralph
Keyword(s):  
Hybrid Zone ◽  
Spatial Location ◽  
Hybrid Zones ◽  
Geographic Space ◽  
Trace Back ◽  
Genome Wide ◽  
Genomic Scale ◽  
Dispersal Distances ◽  
Average Block ◽  
Source Of Information

AbstractHybrid zones formed between recently diverged populations offer an opportunity to study the mechanisms underlying reproductive isolation and the process of speciation. Here, we use a combination of analytical theory and explicit forward simulations to describe how selection against hybrid genotypes impacts patterns of introgression across genomic and geographic space. By describing how lineages move across the hybrid zone, in a model without coalescence, we add to modern understanding of how clines form and how parental haplotypes are broken up during introgression. Working with lineages makes it easy to see that clines form in about 1/s generations, where s is the strength of selection against hybrids, and linked clines persist over a genomic scale of 1/T, where T is the age, in generations, of the hybrid zone. Locally disadvantageous alleles tend to exist as small families, whose lineages trace back to the side from which they originated at speed dispersal distances per generation. The lengths of continuous tracts of ancestry provide an additional source of information: blocks of ancestry surrounding incompatibilities can be substantially longer than the genome-wide average block length at the same spatial location, an observation that might be used to identify candidate targets of selection.

scholarly journals Genomic and plumage variation across the controversial Baltimore and Bullock’s oriole hybrid zone

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Jennifer Walsh ◽  
Shawn M Billerman ◽  
Vanya G Rohwer ◽  
Bronwyn G Butcher ◽  
Irby J Lovette
Keyword(s):  
Hybrid Zone ◽  
Distinct Species ◽  
Hybrid Zones ◽  
Reduced Representation ◽  
History Of ◽  
Genomic Scale ◽  
Westward Movement ◽  
Bullock’S Oriole ◽  
Additional Support ◽  
Natural Settings

Abstract Hybrid zones are powerful natural settings for investigating how birds diversify into distinct species. Here we present the first genomic-scale exploration of the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) oriole hybrid zone, which is notable for its long history of study and for its prominence in debates about avian species concepts and species limits. We used a reduced-representation sequencing approach to generate a panel of 3,067 genetic markers for 297 orioles sampled along the Platte River, a natural west-to-east transect across the hybrid zone. We then explored patterns of hybridization and introgression by comparing variation in genomic and plumage traits. We found that hybridization remains prevalent in this area, with nearly all orioles within the hybrid zone showing some degree of genomic mixing, and 41% assigned as recent-generation (F1/F2) hybrids. The center and width of the genomic and plumage gradients are concordant and coincident, supporting our finding that classically scored plumage traits are an accurate predictor of pure vs. hybrid genotypes. We find additional support for previous suggestions that the center of this hybrid zone has moved westward since it was first intensively sampled in the 1950s, but that this westward movement had slowed or ceased by the 1970s. Considered in concert, these results support previous inferences that some form of ongoing selection is counteracting the potential homogenization of these orioles via hybridization, thereby supporting their continued taxonomic separation as distinct species.

scholarly journals Asymmetric introgression reveals the genetic architecture of a plumage trait

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Georgy A. Semenov ◽  
Ethan Linck ◽  
Erik D. Enbody ◽  
Rebecca B. Harris ◽  
David R. Khaydarov ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Hybrid Zone ◽  
Genetic Architecture ◽  
Hybrid Zones ◽  
Partial Dominance ◽  
Sexual Signal ◽  
Asymmetric Introgression ◽  
Genome Wide ◽  
Lineage Divergence ◽  
Wide Population

AbstractGenome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

scholarly journals Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies

2021 ◽  
Author(s):  
Janne Swaegers ◽  
Rosa Ana Sanchez-Guillen ◽  
Pallavi Chauhan ◽  
Maren Wellenreuther ◽  
Bengt Hansson
Keyword(s):  
X Chromosome ◽  
Sex Chromosomes ◽  
Hybrid Zones ◽  
Haldane’S Rule ◽  
Haldane's Rule ◽  
Genome Wide ◽  
Determination System ◽  
Heterogametic Sex ◽  
Sex Determination System ◽  
Genomic Introgression

Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and allow to shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridisation. Moreover, they are thought to contribute to Haldane's rule which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes and (ii) that males are underrepresented among admixed individuals as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data adds to the few studies on species with X0 sex determination system and contradicts the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.

scholarly journals Evidence and Bias: The Case of the Evidential Future in Italian

2019 ◽  
Vol 29 ◽  
pp. 727
Author(s):  
Ilaria Frana ◽  
Paula Menéndez-Benito
Keyword(s):  
Recent Work ◽  
Trace Back ◽  
The Future ◽  
Source Of Information

Evidential markers encode the source of information that an individual (the evidential Origo) has for a proposition. In root declaratives, the Origo is always the speaker (see Korotkova 2016 and references therein). Instead, questions often display interrogative flip: the Origo shifts to the hearer (Garrett 2001; Speas & Tenny 2003, a.o.). While interrogative flip is widely attested across languages, some evidentials have been reported not to flip in questions (see, e.g., San Roque, Floyd & Norcliffe 2017; Bhadra 2017). What determines whether evidentials flip or not? Recent work (Korotkova 2016; Bhadra 2017) has proposed that there is a correlation between lack of flip and bias in questions. This paper contributes to our understanding of the interaction of evidentials and bias by investigating the behaviour of questions with the Italian non-predictive future. We characterize the non-predictive future as an inferential evidential marker (see also Mari 2009; Eckardt & Beltrama forthcoming), and show that lack of flip for the future correlates only with a particular type of bias: a reversal of the default bias associated with negative polar questions (Frana & Rawlins forthcoming). We trace back this pattern to an interaction between the evidential component of the future and the operator that triggers bias reversal.

scholarly journals Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

2018 ◽  
Vol 285 (1874) ◽  
pp. 20172081 ◽  
Author(s):  
Paola Pulido-Santacruz ◽  
Alexandre Aleixo ◽  
Jason T. Weir
Keyword(s):  
Reproductive Isolation ◽  
Amazon Basin ◽  
Species Recognition ◽  
Bird Species ◽  
Hybrid Zones ◽  
Hybrid Index ◽  
Postzygotic Isolation ◽  
Genome Wide ◽  
Species Pairs ◽  
Hybrid Classes

We possess limited understanding of how speciation unfolds in the most species-rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.

scholarly journals Influence of Niche Overlap and Territoriality on Hybridization Between Hermit Warblers and Townsend's Warblers

The Auk ◽  
2000 ◽  
Vol 117 (1) ◽  
pp. 175-183 ◽  
Author(s):  
Scott F. Pearson ◽  
David A. Manuwal
Keyword(s):  
Habitat Use ◽  
Hybrid Zone ◽  
Parental Species ◽  
Niche Overlap ◽  
Habitat Characteristics ◽  
Hybrid Zones ◽  
Parental Fitness ◽  
Habitat Transition ◽  
Habitat Variables ◽  
Washington Cascades

Abstract Hybrid zones between Townsend's Warblers (Dendroica townsendi) and Hermit Warblers (D. occidentalis) in the Pacific Northwest are narrow relative to estimated dispersal distances and appear to be moving, with Townsend's replacing Hermits. We examined whether the habitat-transition and parental-fitness asymmetry models can explain why these zones are narrow and moving by comparing habitat variables associated with warbler territories in the Washington Cascades hybrid zone. Habitat variables did not differ among phenotypes, suggesting that the habitat-transition model cannot explain the narrow and dynamic nature of this hybrid zone. Habitat characteristics of Hermit Warbler territories did not differ inside versus outside the hybrid zone, also suggesting that this zone is not associated with a region of habitat transition. The lack of difference in habitat use could be the result of comparing variables that are not important to pairing success. However, warblers tended to select territories on west-southwest aspects. South aspects in the southern Washington Cascades are dominated by Douglas fir (Pseudotsuga menziesii) and true fir, which is a habitat selected by female warblers when choosing among territories and males. The parental-fitness asymmetry model does not necessarily make predictions about habitat use within the hybrid zone but predicts the superiority of one parental species over the other. However, if significant overlap occurs in habitat use or niche (as in these warblers), then competition between parental species is likely to occur. To determine whether these species compete, we mapped 12 warbler territories and monitored an additional 94 territories throughout the breeding season and found that all males with neighbors compete for and hold exclusive territories. Thus, the pattern of habitat use and territoriality is consistent with the parental-fitness asymmetry model.

scholarly journals Male territorial vocalizations and responses are decoupled in an avian hybrid zone

2008 ◽  
Vol 363 (1505) ◽  
pp. 2879-2889 ◽  
Author(s):  
Paula M den Hartog ◽  
Hans Slabbekoorn ◽  
Carel ten Cate
Keyword(s):  
Hybrid Zone ◽  
Acoustic Signals ◽  
Hybrid Zones ◽  
Natural Hybrid ◽  
Individual Male ◽  
Individual Strategy ◽  
Intraspecific Communication ◽  
Selective Sensitivity ◽  
Species Specific ◽  
Male Signals

A core area of speciation research concerns the coevolution of species-specific signals and the selective sensitivity to such signals. Signals and responses to them should be tuned to each other, to be effective in intraspecific communication. Hybrid zones are ideal to study the presence of such ‘behavioural coupling’ and the mechanisms governing it, and this has rarely been done. Our study examines acoustic signals of males and their response to them in the context of territorial interactions in a natural hybrid zone between two dove species, Streptopelia vinacea and Streptopelia capicola . Male signals are important in hybrid zone dynamics as they are essential for territory establishment, which is crucial for successful reproduction. We tested whether the response of individual male hybrids is linked to how similar their own signal is to the playback signal. We did not find evidence for behavioural coupling. The combined evidence from the low level of response to hybrid and heterospecific signals outside the hybrid zone and a lack of coupling within the hybrid zone suggests that perceptual learning may explain our results. Learning to respond to locally abundant signals may be the best individual strategy and is likely to contribute to the maintenance of a hybrid zone.

scholarly journals Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

2016 ◽  
Vol 283 (1843) ◽  
pp. 20161380 ◽  
Author(s):  
Ryan P. Kovach ◽  
Brian K. Hand ◽  
Paul A. Hohenlohe ◽  
Ted F. Cosart ◽  
Matthew C. Boyer ◽  
...  
Keyword(s):  
Invasive Species ◽  
Rainbow Trout ◽  
Natural Populations ◽  
Cutthroat Trout ◽  
Field Studies ◽  
Selective Advantage ◽  
Hybrid Zones ◽  
Introduced Fish ◽  
Westslope Cutthroat Trout ◽  
Genome Wide

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

scholarly journals Genome-wide analysis of DNA turnover and gene expression in stationary-phase Saccharomyces cerevisiae

Microbiology ◽  
2010 ◽  
Vol 156 (6) ◽  
pp. 1758-1771 ◽  
Author(s):  
A. de Morgan ◽  
L. Brodsky ◽  
Y. Ronin ◽  
E. Nevo ◽  
A. Korol ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Stationary Phase ◽  
Dna Synthesis ◽  
Exponential Phase ◽  
Yeast Cells ◽  
Genome Wide ◽  
Dna Turnover ◽  
Genomic Scale ◽  
Dna Maintenance

Exponential-phase yeast cells readily enter stationary phase when transferred to fresh, carbon-deficient medium, and can remain fully viable for up to several months. It is known that stationary-phase prokaryotic cells may still synthesize substantial amounts of DNA. Although the basis of this phenomenon remains unclear, this DNA synthesis may be the result of DNA maintenance and repair, recombination, and stress-induced transposition of mobile elements, which may occur in the absence of DNA replication. To the best of our knowledge, the existence of DNA turnover in stationary-phase unicellular eukaryotes remains largely unstudied. By performing cDNA-spotted (i.e. ORF) microarray analysis of stationary cultures of a haploid Saccharomyces cerevisiae strain, we demonstrated on a genomic scale the localization of a DNA-turnover marker [5-bromo-2′-deoxyuridine (BrdU); an analogue of thymidine], indicative of DNA synthesis in discrete, multiple sites across the genome. Exponential-phase cells on the other hand, exhibited a uniform, total genomic DNA synthesis pattern, possibly the result of DNA replication. Interestingly, BrdU-labelled sites exhibited a significant overlap with highly expressed features. We also found that the distribution among chromosomes of BrdU-labelled and expressed features deviates from random distribution; this was also observed for the overlapping set. Ty1 retrotransposon genes were also found to be labelled with BrdU, evidence for transposition during stationary phase; however, they were not significantly expressed. We discuss the relevance and possible connection of these results to DNA repair, mutation and related phenomena in higher eukaryotes.

scholarly journals Copy number variation of the putative speciation genes in the European house mouse hybrid zone

2021 ◽  
Author(s):  
Alexey Yanchukov ◽  
Zusana Hiadlovska ◽  
Zeljka Pezer ◽  
Milos Macholan ◽  
Jaroslav Pialek ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
House Mouse ◽  
Hybrid Zone ◽  
Copy Number ◽  
Digital Pcr ◽  
Gene Copy ◽  
Ancestral Population ◽  
Hybrid Zones ◽  
Interaction Sites ◽  
Number Variation

Hybrid zones have long been described as "windows on the evolutionary process", and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculus and Mus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e. musculus or domesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al., in prep.). The copy numbers of five genes were clearly associated with the prevalence of either musculus or domesticus genomes across the hybrid zone. In three cases, the highest and/or outlying levels of association were observed at or very close to the annotated positions of the respective gene amplicons, demonstrating the power of our approach in confirming the reference locations of copy number variants. Notably, several other reference locations were recognized as positive outliers in the association with particular CNV genes, possibly representing the extra gene copies and/or their epistatic interaction sites.

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