Biology subjects

Peede, D.

Publications and source records attributed to Peede, D..

13 recordsLinked to original sources

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↗

bioRxiv2025

Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis

An estimated one billion people are at risk of acquiring the disease leishmaniasis annually. This disease, among others, is transmitted to humans via sandfly vectors of the family Psychodidae. In the Neotropics, Lutzomyia longipalpis is one of the most common vectors of leishmaniasis, but little is known about its genetics and population structure, hampering control efforts. We generated sex-specific genome assemblies of Lu. longipalpis from Colombia, and examined population genomics of this species. We found that sex accounts for [~]11% of genome-wide variation, primarily driven by differentiation between the sexes in an XY sex chromosome. Analyses of transposable elements indicate that the size difference in the sex chromosome is driven by more transposable elements in the male chromosome. Further, we examined population genomics and structure across the South American continent. We identified significant genetic divergence between Colombian and Brazilian sandflies and population structure within Lu. longipalpis sensu lato samples collected from the same sites in Brazil. These results strongly suggest the presence of multiple, sympatric species within a cryptic species complex, concordant with other published phenotypic evidence. SIGNIFICANCELeishmaniasis has emerged as an important public health issue. Transmission occurs exclusively through Phlebotomine sandflies of the genera Lutzomyia and Phlebotomus, yet our ability to prevent its spread is constrained by limited knowledge of the biological and ecological factors that make these insects effective vectors. In this manuscript, we leverage whole-genome sequencing to investigate the evolutionary forces shaping genetic diversity in Lutzomyia longipalpis, a key vector of leishmaniasis.

genomics↗

bioRxiv2023

The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection

We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30 base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in American populations. Finally, some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. One-Sentence SummaryModern humans and Neanderthals carry a Denisovan variant of the MUC19 gene, which is under positive selection in populations of Indigenous American ancestry.

evolutionary biology↗

bioRxiv2023

Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia

Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism. One-Sentence SummaryAncient interbreeding of East Asian aurochs and cattle suggests management, but leaves no signature in modern eastern breeds.

genomics↗

bioRxiv2022

The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression

The past decade has ushered in a resurgence of studies highlighting the importance of introgression throughout the Tree of Life. Several methods exist for detecting and quantifying introgression on a genomic scale, yet the majority of these methods primarily utilize signals of derived allele sharing between donor and recipient populations. In this study, we exploit the fact that introgression will not only result in derived allele sharing but also the reintroduction of ancestral alleles to derive new estimators of the admixture proportion. Using coalescent simulations, we assess the performance of our new methods and the methods proposed in Lopez Fang et al. 2022 to assess the utility of incorporating shared ancestral variation into genome-wide inferences of introgression. Using coalescent theory, simulations, and applying our methods to human and canid data, we find that methods incorporating ancestral allele sharing are comparable to their derived allele sharing counterparts, in turn providing researchers with the opportunity to utilize more of the genomic signature of introgression.

evolutionary biology↗

bioRxiv2022

Expanding the stdpopsim species catalog, and lessons learned forrealistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

bioinformatics↗

bioRxiv2021

Population structure and introgression among recently differentiated Drosophila melanogaster populations

Despite a century of genetic analysis, the evolutionary history underlying patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. How genetic and phenotypic variation is partitioned across the range of D. melanogaster, particularly in its putative ancestral range in Subtropical Africa, remains unresolved. Here, we assess patterns of population genetic structure, admixture, mate preference, and genetic incompatibility across a global sample, including 174 new accessions from remote regions within Subtropical Africa. While almost all Out of Africa genomes correspond to a single genetic ancestry, different geographic regions within Africa contain multiple ancestries, with substantial cryptic diversity in Subtropical Africa. Admixture between distinct lineages is prevalent across the range, but admixture rates vary between lineages. Female mate choice within Subtropical Africa is highly polymorphic and behavioral types are not monophyletic. The genetic architecture of mate choice is highly polygenic, including loci associated with neurological development, behavior, olfactory perception, and learning. Finally, we discovered that many segregating putative incompatibilities likely evolved during or after expansion out of Africa. This work contributes to our understanding of the evolutionary history of a key model system, and provides insight into the distribution of polymorphic reproductive barriers.

evolutionary biology↗

bioRxiv2021

15 years of introgression studies: quantifying gene flow across Eukaryotes

With the rise of affordable next generation sequencing technology, introgression -- or the exchange of genetic materials between taxa -- is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment on the frequency of introgression in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by providing a meta-analysis of the most comprehensive survey of introgression studies in Eukaryotes to date (724 papers with claims of introgression). We first examined the evidence given to support introgression, and if/how the lines of evidence have changed across time. We then collated a single statistic, Pattersons D, that quantifies the strength of introgression across 123 studies to further assess how taxonomic group, divergence time, and aspects of life history influence introgression. We find three main results. Studies on introgression are much more frequent in plants and mammals than any other taxonomic group. The study of introgression has shifted from a largely qualitative assessment of whether introgression happens, to a focus on when and how much introgression has occurred across taxa. The most often used introgression statistic, Pattersons D, shows several intriguing patterns suggesting introgression reports may be biased by both differences in reporting criteria and sequencing technology, but may also differ across taxonomic systems and throughout the process of speciation. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities, and highlight important areas of future research that can be better assessed once this unified approach is met.

evolutionary biology↗

bioRxiv2020

Widespread introgression across a phylogeny of 155 Drosophila genomes

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across nine monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the nine clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

evolutionary biology↗

bioRxiv2020

Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

evolutionary biology↗

bioRxiv2020

P-elements strengthen reproductive isolation within the Drosophila simulans species complex

Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of reproductive isolation between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that transposable elements can play a role in reproductive isolation and facilitate the process of speciation. IMPACT SUMMARYTransposable elements (TEs) are repetitive genetic units found across the tree of life. They play a fundamental role on the evolution of each species genome. TEs have been implicated in diversification, extinction, and the origin of novelty. However, their potential role in contributing to the maintenance of species boundaries remains largely understudied. Using whole genome sequences, we compared the relative content of TEs across the three species of the Drosophila simulans complex. We find that the presence of one TE, P-element, in D. simulans, and its absence in the sister taxa, differentiates the three species. P-elements (PEs) cause a suite of fitness defects in Drosophila pure-species individuals if their father has PEs but their mother does not, a phenomenon known as hybrid dysgenesis (HD). We thus studied the possibility that PEs enhance isolation between recently-diverged species. In particular, we studied whether the progeny from interspecific crosses were more prone to suffer from HD than pure species. We found that the presence of paternal PEs reduces hybrid female fecundity, mirroring observations of HD described within species. The effect of PEs is stronger in the interspecific hybrids than in pure species. Our results suggest that PEs can strengthen reproductive isolation in well-formed sister species that still hybridize in nature and pose the question of whether other TEs are involved in the formation of species or in their persistence over time.

evolutionary biology↗

bioRxiv2020

Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup

Introgression, 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.

evolutionary biology↗

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↗