Dataset Information

Divergence-Based Introgression Polarization.

ABSTRACT: Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.

SUBMITTER: Forsythe ES

PROVIDER: S-EPMC7197497 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Divergence-Based Introgression Polarization.

Forsythe Evan S ES Sloan Daniel B DB Beilstein Mark A MA

Genome biology and evolution 20200401 4

Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and ...[more]

PMID: 32219392

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Project description:Abstract A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages (“ghost introgression”). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference‐based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re‐evaluating the evolutionary independency of cryptic lineages, the group‐wise diverged single‐nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta. Previous population genetics study revealed a sympatric cryptic lineage of Cycas revoluta in Taiwan. By detecting the SNP outliers and annotating its functions of lineages sympatric and allopatric to the cryptic lineage, plus approximate Bayesian computation model selection, this article provided a mechanism of the sympatric cryptic lineage divergence by ghost introgression.

Dataset Information

Divergence-Based Introgression Polarization.

Publications

Divergence-Based Introgression Polarization.

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