Peede, D. | Search bioRxiv

bioRxiv2026

Joint ancestry inference reveals the landscape of archaic introgression in admixed populations

Studying the evolutionary history of archaic segments in recently admixed individuals requires inferring both continental and archaic ancestry in admixed genomes. Here, we present TRACTINATOR, the first deep-learning method for simultaneous inference of continental and archaic ancestry in admixed human genomes. The model combines SNP sequences, population allele-frequency information, and S* statistics to improve both inference tasks. By learning relationships between haplotypes and population allele frequencies, TRACTINATOR can generalize across genomic regions and even across different genomic datasets. We train our model using both real and synthetic data, and show that augmenting with synthetic data improves accuracy for both continental and archaic ancestry inference. Finally, we apply TRACTINATOR to admixed Latin American populations from the 1,000 Genomes Project, revealing how archaic ancestry is distributed within chromosomal segments of African, European and Indigenous American ancestry in Latin American individuals. For candidates of adaptive introgression, we also infer whether the archaic haplotype was introduced via European or Indigenous American ancestors.

bioinformatics↗

bioRxiv2018

Recent invasion of P transposable element into Drosophila yakuba

Transposable elements (TEs) are self-replicating genetic units that are common across prokaryotes and eukaryotes. They have been implicated in the origin of new molecular functions and in some cases, new phenotypes. Yet, the processes that lead to their evolution and how they enter the genome of their hosts remain largely underexplored. The P-element is one of the most well-known TEs in Eukaryotes, due to its rapid expansion in Drosophila melanogaster in the 1960s and its faster invasion of D. simulans, despite its fitness consequences in both species. Here, we describe a recent invasion of P-elements into Drosophila yakuba. Overall, PEs were found in D. yakuba with no PEs detected across its sister species, D. teissieri and D. santomea. These findings are surprising due the lack of a genetic bridge between D. yakuba and other Drosophila that harbor PEs, implicating a horizontal gene transfer mechanism similar to the one that gave rise to the invasion of PEs in D. melanogaster and D. simulans. We also report that the presence of these PEs causes a mild hybrid dysgenesis phenomenon; namely they cause a reduction in female reproductive potential (lower number of ovaries and ovarioles), but only at 29{degrees}C and not at 23{degrees}C. Given the ability of PEs to cross species boundaries and the fact that both D. santomea and D. teissieri have the ability to produce fertile progeny with D. yakuba, the yakuba species complex provides an opportunity to study PE spread through vertical transmission.\n\nARTICLE SUMMARYP-elements (PEs) are transposons found in Neotropical Drosophila species. PEs have previously invaded two African Drosophila species where they rapidly increased in population frequency and fixed. We found that PEs invaded the genome of D. yakuba, an African species. In just 8 years, the frequency of the PEs increased from 0% to 18% but then decreased to 2%. This turnover shows that PE invasions can be transient. We found no evidence of full PEs in D. yakuba sister species, D. santomea and D. teissieri. PEs in this species complex can reveal the interplay between transposable elements and hybridization in nature.

evolutionary biology↗