Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species

Adaptive introgression is ubiquitous in animals but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during one year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes, and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after four years (~ 60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically-distinct and reproductively-isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step towards understanding the genome-wide dynamics of speciation-through-introgression.

Download Full-text

Locus-specific introgression in young hybrid swarms: drift dominates selection

10.1101/2020.09.17.300434 ◽

2020 ◽

Cited By ~ 1

Author(s):

S. Eryn McFarlane ◽

Helen V. Senn ◽

Stephanie L. Smith ◽

Josephine M. Pemberton

Keyword(s):

Reproductive Isolation ◽

Policy Implications ◽

Secondary Contact ◽

Hybrid Zones ◽

Policy Makers ◽

Adaptive Introgression ◽

Allelic Replacement ◽

Hybrid Swarms ◽

Genome Wide ◽

Future Work

AbstractClosely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

Download Full-text

Genomic islands of divergence or opportunities for introgression?

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.2414 ◽

2017 ◽

Vol 284 (1850) ◽

pp. 20162414 ◽

Cited By ~ 15

Author(s):

Rachael A. Bay ◽

Kristen Ruegg

Keyword(s):

Gene Flow ◽

Reproductive Isolation ◽

Genomic Islands ◽

Secondary Contact ◽

Catharus Ustulatus ◽

Adaptive Introgression ◽

Evolutionary Forces ◽

Genome Wide ◽

Isolating Mechanisms ◽

Migratory Songbird

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush ( Catharus ustulatus ), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

Download Full-text

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

Scientific Reports ◽

10.1038/s41598-018-34364-0 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 8

Author(s):

Gabriel Costa Monteiro Moreira ◽

Clarissa Boschiero ◽

Aline Silva Mello Cesar ◽

James M. Reecy ◽

Thaís Fernanda Godoy ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Association Studies ◽

Fat Deposition ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Whole Genome ◽

Genome Wide

Download Full-text

Fern speciation and biogeography

Proceedings of the Royal Society of Edinburgh Section B Biological Sciences ◽

10.1017/s0269727000008332 ◽

1985 ◽

Vol 86 ◽

pp. 353-360 ◽

Cited By ~ 5

Author(s):

Rolla Tryon

Keyword(s):

New Species ◽

Parental Species ◽

Local Environment ◽

Limited Range ◽

Ecological Adaptation ◽

Species Selection ◽

Potential Range ◽

Small Range ◽

Extensive Range ◽

Selection Of

SynopsisThe most common kinds of speciation result in new species that initially have a small range. These will develop a limited or an extensive range depending upon the geographic extent of the environment to which they are adapted. A significant element in the extent of the potential range of a new species is the adaptation inherited from the parental species. Selection of a parental species for a local environment at one site can lead to a narrow ecological adaptation and often to a limited potential range. These species are likely to produce derived ones that also have a limited range, and these derivates will increase the regional species endemism and diversity. Selection of a parental species for migration to other sites can lead to a broader ecological adaptation and often to a broad potential range. These species are more likely to produce derived ones that also have an extensive range, and these derivates will increase regional species diversity.

Download Full-text

Detection and characterization of copy number variants based on whole-genome sequencing by DNBSEQ platforms

10.1101/786962 ◽

2019 ◽

Author(s):

Junhua Rao ◽

Lihua Peng ◽

Fang Chen ◽

Hui Jiang ◽

Chunyu Geng ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Copy Number Variants ◽

Copy Number Variant ◽

Whole Genome ◽

Genome Wide ◽

Wide Range ◽

Distribution Sensitivity ◽

Cnv Detection

AbstractBackgroundNext-generation sequence (NGS) has rapidly developed in past years which makes whole-genome sequencing (WGS) becoming a more cost- and time-efficient choice in wide range of biological researches. We usually focus on some variant detection via WGS data, such as detection of single nucleotide polymorphism (SNP), insertion and deletion (Indel) and copy number variant (CNV), which playing an important role in many human diseases. However, the feasibility of CNV detection based on WGS by DNBSEQ™ platforms was unclear. We systematically analysed the genome-wide CNV detection power of DNBSEQ™ platforms and Illumina platforms on NA12878 with five commonly used tools, respectively.ResultsDNBSEQ™ platforms showed stable ability to detect slighter more CNVs on genome-wide (average 1.24-fold than Illumina platforms). Then, CNVs based on DNBSEQ™ platforms and Illumina platforms were evaluated with two public benchmarks of NA12878, respectively. DNBSEQ™ and Illumina platforms showed similar sensitivities and precisions on both two benchmarks. Further, the difference between tools for CNV detection was analyzed, and indicated the selection of tool for CNV detection could affected the CNV performance, such as count, distribution, sensitivity and precision.ConclusionThe major contribution of this paper is providing a comprehensive guide for CNV detection based on WGS by DNBSEQ™ platforms for the first time.

Download Full-text

Genome-Wide Regulatory Interactions in the Early Stages of Drosophila Speciation

10.36939/ir.202012151547 ◽

2020 ◽

Author(s):

◽

Alwyn Clark Go

Keyword(s):

Reproductive Isolation ◽

Expression Analysis ◽

Regulatory Elements ◽

Specific Expression ◽

Allele Specific Expression ◽

Regulatory Interactions ◽

Early Stages ◽

Genome Wide ◽

Allele Specific ◽

Incomplete Reproductive Isolation

Speciation occurs when reproductive barriers prevent the exchange of genetic information between individuals. A common form of reproductive barrier between species capable of interbreeding is hybrid sterility. Genomic incompatibilities between the divergent genomes of different species contribute to a reduction in hybrid fitness. These incompatibilities continue to accumulate after speciation, therefore, young divergent taxa with incomplete reproductive isolation are important in understating the genetics leading to speciation. Here, I use two Drosophila subspecies pairs. The first is D. willistoni consisting of D. w. willistoni and D. w. winge. The second subspecies pair is D. pseudoobscura, which is composed of D. p. pseudoobscura and D. p. bogotana. Both subspecies pairs are at the early stages of speciation and show incomplete reproductive isolation through unidirectional hybrid male sterility. In this thesis, I performed an exploratory survey of genome-wide expression analysis using RNA-sequencing on D. willistoni and determined the extent of regulatory divergence between the subspecies using allele-specific expression analysis. I found that misexpressed genes showed a degree of tissue specificity and that the sterile male hybrids had a higher proportion of misexpressed genes in the testes relative to the fertile hybrids. The analysis of regulatory divergence between this subspecies pair found a large (66-70%) proportion of genes with conserved regulatory elements. Of the genes showing evidence or regulatory divergence between subspecies, cis-regulatory divergence was more common than other types. In the D. pseudoobscura subspecies pair, I compared sequence and expression divergence and found no support for directional selection driving gene misexpression in their hybrids. Allele-specific expression analysis revealed that compensatory cis-trans mutations partly explained gene misexpression in the hybrids. The remaining hybrid misexpression occurs due to interacting gene networks or possible co-option of cis-regulatory elements by divergent transacting factors. Overall, the results of this thesis highlight the role of regulatory interactions in a hybrid genome and how these interactions could lead to hybrid breakdown by disrupting gene interaction networks.

Download Full-text

Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.2081 ◽

2018 ◽

Vol 285 (1874) ◽

pp. 20172081 ◽

Cited By ~ 31

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.

Download Full-text

BIOM-23. A PILOT STUDY OF WHOLE GENOME SEQUENCING (WGS) OF PLASMA CELL-FREE DNA (cfDNA) FOR ULTRASENSITIVE DETECTION OF TUMOR DNA IN PATIENTS WITH GLIOBLASTOMA (GBM)

Neuro-Oncology ◽

10.1093/neuonc/noab196.054 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi15-vi15

Author(s):

Stephen J Bagley ◽

Jacob Till ◽

Aseel Abdalla ◽

MacLean Nasrallah ◽

Tomer Lauterman ◽

...

Keyword(s):

Pilot Study ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tumor Tissue ◽

Methylation Status ◽

Tumor Burden ◽

Whole Genome ◽

Newly Diagnosed ◽

Genome Wide ◽

Tumor Dna

Abstract BACKGROUND Plasma circulating tumor DNA (ctDNA) is rarely detectable by traditional methods in patients with GBM. As a result, unlike in lung and other cancers, serial next generation sequencing of ctDNA for monitoring GBM tumor burden has been challenging. In light of the low tumor fraction (TF) of DNA fragments in GBM patient plasma and the urgent need to improve upon MRI for tracking GBM tumor burden, we conducted a pilot study in patients with newly diagnosed GBM using the C2 intelligence platform (C2i Genomics), which leverages genome-wide mutational integration for highly sensitive ctDNA detection. METHODS Plasma was collected pre- and post-operatively in patients with newly diagnosed GBM undergoing surgical resection/biopsy. cfDNA was extracted, quantified, and analyzed for fragment size. Genomic DNA (gDNA) was extracted from matched tumor tissue. Whole genome sequencing (WGS) was performed on both gDNA and cfDNA. A specific copy number alteration (CNA) compendium was created for each patient to generate a readout of TF (Zviran, Nat Medicine 2020). We assessed the association between TF at post-operative day 1 (a surrogate for residual disease) and OS, adjusting for other prognostic factors using Cox regression. RESULTS 37 patients were enrolled. For samples with high tumor fraction (n=5), a statistically significant (p< 1e-4) correlation between CNA profiles of tumor tissue and plasma samples was observed. Post-operative TF above the median value was associated with inferior OS (median 7.7 vs. 19.3 months, p=0.019). This association persisted after adjusting for age, O6-methylguanine-DNA methyltransferase methylation status, extent of resection, and performance status (adjusted HR 2.5, 95% CI 1.1-5.6, p=0.03). CONCLUSION Genome-wide mutational integration enables ultra-sensitive detection of ctDNA in GBM patient plasma. Post-operative TF measured by the C2i test is independently associated with OS in newly diagnosed GBM, providing the foundation to evaluate this technology for personalized prognostication and disease monitoring.

Download Full-text

Candidate Predisposition Variants in Kaposi Sarcoma as Detected by Whole-Genome Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz337 ◽

2019 ◽

Vol 6 (10) ◽

Author(s):

Sanni J Rinne ◽

Lauri J Sipilä ◽

Päivi Sulo ◽

Emmanuelle Jouanguy ◽

Vivien Béziat ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Kaposi Sarcoma ◽

The Other ◽

Whole Genome ◽

Genome Wide ◽

Starting Point ◽

Familial Clustering ◽

Iranian Family ◽

Classic Kaposi Sarcoma

Abstract Familial clustering of classic Kaposi sarcoma (CKS) is rare with, approximately 100 families reported to date. We studied 2 consanguineous families, 1 Iranian and 1 Israeli, with multiple cases of adult CKS and without overt underlying immunodeficiency. We performed genome-wide linkage analysis and whole-genome sequencing to discover the putative genetic cause for predisposition. A 9-kb homozygous intronic deletion in RP11-259O2.1 in the Iranian family and 2 homozygous variants, 1 in SCUBE2 and the other in CDHR5, in the Israeli family were identified as possible candidates. The presented variants provide a robust starting point for validation in independent samples.

Download Full-text

Multi-locus interactions and the build-up of reproductive isolation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0543 ◽

2020 ◽

Vol 375 (1806) ◽

pp. 20190543 ◽

Cited By ~ 2

Author(s):

I. Satokangas ◽

S. H. Martin ◽

H. Helanterä ◽

J. Saramäki ◽

J. Kulmuni

Keyword(s):

Reproductive Isolation ◽

Empirical Work ◽

Hybrid Fitness ◽

Epistatic Interactions ◽

Genome Scans ◽

Theoretical Approaches ◽

Genome Wide ◽

Experimental Approaches ◽

Polymorphism Data

All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Download Full-text