scholarly journals Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

2017 ◽  
Author(s):  
David A. Turissini ◽  
Daniel R. Matute
Keyword(s):  
Genetic Model ◽  
Hidden Markov ◽  
Genetic Material ◽  
Genetic Exchange ◽  
Hybrid Zones ◽  
Ancestral Polymorphism ◽  
Species Pairs ◽  
Genomic Introgression ◽  
Fertile Hybrids ◽  
Drosophila Yakuba

ABSTRACTThe process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.AUTHOR SUMMARYEven though hybridization is thought to be pervasive among animal species, the frequency of introgression, the transfer of genetic material between species, remains largely unknown. In this report we quantify the magnitude and genomic distribution of introgression among three species of Drosophila that encompass the two known stable hybrid zones in this genetic model genus. We obtained whole genome sequences for individuals of the three species across their geographic range (including their hybrid zones) and developed a hidden Markov model-based method to identify patterns of genomic introgression between species. We found that nuclear introgression is rare between both species pairs, suggesting hybrids in nature rarely successfully backcross with parental species. Nevertheless, some D. santomea alleles introgressed into D. yakuba have spread from São Tomé to other islands in the Gulf of Guinea where D. santomea is not found. Our results indicate that in spite of contemporary hybridization between species that produces fertile hybrids, the rates of gene exchange between species are low.

scholarly journals Species-Specific Segregation of Gender-Associated Mitochondrial DNA Types in an Area Where Two Mussel Species (Mytilus edulis and M. trossulus) Hybridize

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1359-1367 ◽  
Author(s):  
Carlos Saavedra ◽  
Donald T Stewart ◽  
Rebecca R Stanwood ◽  
Eleftherios Zouros
Keyword(s):  
Mytilus Edulis ◽  
The Other ◽  
Allozyme Analysis ◽  
Mussel Species ◽  
Species Origin ◽  
Species Pairs ◽  
Nuclear Background ◽  
Species Specific ◽  
Dna Types ◽  
Fertile Hybrids

Abstract In each of the mussel species Mytilus edulis and M. trossulus there exist two types of mtDNA, the F type transmitted through females and the M type transmitted through males. Because the two species produce fertile hybrids in nature, F and M types of one may introgress into the other. We present the results from a survey of a population in which extensive hybridization occurs between these two species. Among specimens classified as “pure” M. edulis or “pure” M. trossulus on the basis of allozyme analysis, we observed no animal that carried the F or the M mitotype of the other species. In most animals of mixed nuclear background, an individual's mtDNA came from the species that contributed the majority of the individual's nuclear genes. Most importantly, the two mtDNA types in post-F1 male hybrids were of the same species origin. We interpret this to mean that there are intrinsic barriers to the exchange of mtDNA between these two species. Because such barriers were not noted in other hybridizing species pairs (many being even less interfertile than M. edulis and M. trossulus), their presence in Mytilus could be another feature of the unusual mtDNA system in this genus.

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 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 THE NET-HMM APPROACH: PHYLOGENETIC NETWORK INFERENCE BY COMBINING MAXIMUM LIKELIHOOD AND HIDDEN MARKOV MODELS

2009 ◽  
Vol 07 (04) ◽  
pp. 625-644 ◽  
Author(s):  
SAGI SNIR ◽  
TAMIR TULLER
Keyword(s):  
Network Inference ◽  
Markov Models ◽  
Hidden Markov ◽  
Bacterial Genome ◽  
Genetic Material ◽  
Phylogenetic Network ◽  
Significance Test ◽  
Amino Acid Sequences ◽  
Phylogenetic Networks ◽  
Significant Mechanism

Horizontal gene transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model, the NET-HMM, for analyzing and modeling phylogenetic networks. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given dataset. Using NET-HMM, we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and three different biological inputs.

scholarly journals Analogous Telesensing Pathways Regulate Mating and Virulence in Two Opportunistic Human Pathogens

mBio ◽  
2010 ◽  
Vol 1 (4) ◽  
Author(s):  
Richard J. Bennett ◽  
Gary M. Dunny
Keyword(s):  
Sex Pheromones ◽  
Genetic Material ◽  
Fungal Species ◽  
Genetic Exchange ◽  
Cell Contact ◽  
Human Pathogens ◽  
Opportunistic Pathogens ◽  
Pheromone Signaling ◽  
Potential Partner ◽  
Mediate Cell

ABSTRACT Telesensing, or probing of the environment by the release of chemical messengers, plays a central role in the sexual programs of microbial organisms. Sex pheromones secreted by mating cells are sensed by potential partner cells and mediate cell-to-cell contact and the subsequent exchange of genetic material. Although the mechanisms used by bacterial and fungal species to promote genetic exchange are distinct, recent studies have uncovered surprising parallels between pheromone signaling in these species. In addition, it is now apparent that pheromone signaling not only controls sexual reproduction and genetic exchange but can also activate expression of potential virulence factors in diverse opportunistic pathogens.

scholarly journals Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup

2020 ◽  
Author(s):  
Antonio Serrato-Capuchina ◽  
Timothy D. Schwochert ◽  
Stephania Zhang ◽  
Baylee Roy ◽  
David Peede ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Flow ◽  
Parental Species ◽  
Cuticular Hydrocarbon ◽  
F1 Hybrids ◽  
Sexual Attractiveness ◽  
Pure Species ◽  
Species Pairs ◽  
Fertile Hybrids ◽  
Drosophila Melanogaster Species Subgroup

ABSTRACTIntrogression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminate how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.

scholarly journals Extensive sympatry and frequent hybridization of ecologically divergent aquatic plants on the Qinghai-Tibetan Plateau

2021 ◽  
Author(s):  
Zhigang Wu ◽  
Zhong Wang ◽  
Dong Xie ◽  
Juan Zhang ◽  
Pengsen Cai ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Aquatic Plants ◽  
Related Species ◽  
Environmental Gradients ◽  
Niche Overlap ◽  
Hybrid Zones ◽  
Limited Information ◽  
Freshwater Biodiversity ◽  
Genetic Incompatibility ◽  
Species Pairs

Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa across an altitudinal gradient. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants in alpines. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to inconsistences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.

BIOSYSTEMATICS OF PISSODES GERMAR (COLEOPTERA: CURCULIONIDAE): FEEDING PREFERENCE AND BREEDING SITE SPECIFICITY OF P. STROBI AND P. APPROXIMATUS

1983 ◽  
Vol 115 (12) ◽  
pp. 1627-1636 ◽  
Author(s):  
Thomas W. Phillips ◽  
Gerald N. Lanier
Keyword(s):  
Field Tests ◽  
Breeding Site ◽  
Sympatric Species ◽  
Feeding Preference ◽  
White Pine ◽  
Breeding Sites ◽  
Pissodes Strobi ◽  
Species Pairs ◽  
Males And Females ◽  
Fertile Hybrids

AbstractPissodes strobi (Peck) and P. approximatus Hopkins are sibling species that can produce fertile hybrids in the laboratory, but in nature they are isolated by differences in their breeding habits. In a laboratory assay for feeding preference, these species exhibited similar patterns of acceptance of most conifer hosts in the fall, but differed distinctly in their preferences for certain conifers in the spring. Both species had high levels of feeding on white spruce in the fall and spring tests, hut these data apparently do not reflect host preference in nature. In field tests, P. strobi males and females confined on 1-year-old terminal leaders of eastern white pine (their usual breeding sites) produced abundant progeny, whereas P. approximatus pairs confined on leaders produced few progeny. Mixed species pairs were successful in killing and breeding in white pine leaders when the females were P. strobi, but not when the females were P. approximatus. Laboratory-reared hybrids were unsuccessful when forced to breed in leaders. When confined on red pine bolts (the usual breeding sites of P. approximatus), P. strobi and hybrids produced substantially fewer progeny than did P. approximatus. Breeding site separation provides compelling evidence of reproductive isolation between these sympatric species.

scholarly journals Genetic exchange and the origin of adaptations: prokaryotes to primates

2008 ◽  
Vol 363 (1505) ◽  
pp. 2813-2820 ◽  
Author(s):  
Michael L Arnold ◽  
Yuval Sapir ◽  
Noland H Martin
Keyword(s):  
Gene Transfer ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
De Novo ◽  
Genetic Material ◽  
Introgressive Hybridization ◽  
Genetic Exchange ◽  
Viral Recombination ◽  
Adaptive Trait

Data supporting the occurrence of adaptive trait transfer (i.e. the transfer of genes and thus the phenotype of an adaptive trait through viral recombination, lateral gene transfer or introgressive hybridization) are provided in this review. Specifically, we discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi, plants and animals. Each of these examples reflects the same consequence, namely that the transfer of genetic material, through whatever mechanism, may result in adaptive evolution. In particular, each of the events discussed has been inferred to impact adaptations to novel environmental settings in the recipient lineage.

scholarly journals A Hidden Markov Model for Investigating Recent Positive Selection through Haplotype Structure

2014 ◽  
Author(s):  
Hua Chen ◽  
Jody Hey ◽  
Montgomery Slatkin
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Positive Selection ◽  
Genetic Model ◽  
Hidden Markov ◽  
Large Data ◽  
Data Sets ◽  
Recent Positive Selection ◽  
A Genome ◽  
Wide Range

Recent positive selection can increase the frequency of an advantageous mutant rapidly enough that a relatively long ancestral haplotype will be remained intact around it. We present a hidden Markov model (HMM) to identify such haplotype structures. With HMM identified haplotype structures, a population genetic model for the extent of ancestral haplotypes is then adopted for parameter inference of the selection intensity and the allele age. Simulations show that this method can detect selection under a wide range of conditions and has higher power than the existing frequency spectrum-based method. In addition, it provides good estimate of the selection coefficients and allele ages for strong selection. The method analyzes large data sets in a reasonable amount of running time. This method is applied to HapMap III data for a genome scan, and identifies a list of candidate regions putatively under recent positive selection. It is also applied to several genes known to be under recent positive selection, including the LCT, KITLG and TYRP1 genes in Northern Europeans, and OCA2 in East Asians, to estimate their allele ages and selection coefficients.

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