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

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.

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Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

10.1101/485904 ◽

2018 ◽

Cited By ~ 1

Author(s):

Gang Li ◽

Henrique V. Figueiro ◽

Eduardo Eizirik ◽

William J. Murphy

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Phylogenetic Signal ◽

Selective Sweeps ◽

A Genome ◽

Chromosome Recombination ◽

History Of ◽

Lineage Divergence ◽

Recurrent Patterns ◽

Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

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Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

10.1101/2020.02.21.959205 ◽

2020 ◽

Author(s):

Lisa Cooper ◽

Lynsey Bunnefeld ◽

Jack Hearn ◽

James M Cook ◽

Konrad Lohse ◽

...

Keyword(s):

Gene Flow ◽

Rain Forest ◽

Sequence Data ◽

Dry Forest ◽

Whole Genome Sequence ◽

Model Organisms ◽

Eastern Coast ◽

Population Divergence ◽

Fig Wasp ◽

History Of

AbstractPopulation divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

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Early history of Neanderthals and Denisovans

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1706426114 ◽

2017 ◽

Vol 114 (37) ◽

pp. 9859-9863 ◽

Cited By ~ 41

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.

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Complex introgression history of the erato-sara clade of Heliconius butterflies

10.1101/2021.02.10.430600 ◽

2021 ◽

Author(s):

Yuttapong Thawornwattana ◽

Fernando A. Seixas ◽

Ziheng Yang ◽

James Mallet

Keyword(s):

Gene Flow ◽

Genomic Sequence ◽

Sequence Data ◽

Whole Genome Sequence ◽

Hybrid Origin ◽

Ancestral Population ◽

Ancestral Gene ◽

Species Phylogeny ◽

Full Likelihood ◽

History Of

AbstractIntrogression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.

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The Y-chromosome clarifies the evolutionary history of Sus scrofa by large-scale deep genome sequencing

10.1101/126060 ◽

2017 ◽

Author(s):

Huashui Ai ◽

Jun Ren ◽

Junwu Ma ◽

Zhiyan Zhang ◽

Wanbo Li ◽

...

Keyword(s):

Gene Flow ◽

Y Chromosome ◽

Sus Scrofa ◽

Evolutionary History ◽

Large Scale ◽

Divergence Time ◽

Chromosome Y ◽

Wild Boars ◽

History Of ◽

Ancient Gene

AbstractThe genetics and evolution of sex chromosomes are largely distinct from autosomes and mitochondrial DNA (mtDNA). The Y chromosome offers unique genetic perspective on male-line inheritance. Here, we uncover novel evolutionary history of Sus scrofa based on 205 high-quality genomes from worldwide-distributed different wild boars and domestic pig breeds. We find that only two haplotypes exist in the distal and proximal blocks of at least 7.7 Mb on chromosome Y in pigs across European and Asian continents. And the times of most recent common ancestors (TMRCA) within both haplotypes, approximately 0.14 and 0.10 million years, are far smaller than their divergence time of around 1.07 million years. What’s more, the relationship between Sumatran and Eurasian continent Sus scrofa is much closer than that we knew before. And surprisingly, European pigs share the same haplotype with many Chinese pigs, which is not consistent with their deep splitting status on autosome and mtDNA. Further analyses show that the haplotype in Chinese pigs was likely introduced from European wild boars via ancient gene flow before pig domestication about 24k years ago. Low mutation rates and no recombination in the distal and proximal blocks on chromosome Y help us detect this male-driven ancient gene flow. Taken together, our results update the knowledge of pig demography and evolution, and might shed insight into the genetics and evolution studies on chromosome Y in other mammals.

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