Biology subjects

Hahn, M. W.

Publications and source records attributed to Hahn, M. W..

At least 19 recordsLinked to original sources

bioRxiv2026

Estimating de novo mutation rates using parent-offspring pairs

Existing pedigree approaches to identifying de novo mutations (DNMs) require at least two parents and a single offspring, limiting applicability. Here, we introduce OOPS (Only One Parent Sequencing), a framework for detecting DNMs using only a single parent-offspring pair. OOPS uses short-read data from the parent and both short and long-read data from the offspring to reconstruct haplotypes in the child, one of which can then be assigned to the sequenced parent. We show that candidate de novo mutations from the assigned haplotype can be identified, allowing for estimation of the mutation rate. To demonstrate the accuracy of OOPS, we apply it to a human pedigree in which mutations have also been identified using standard trio-based approaches. OOPS achieves comparable accuracy to trio-based pipelines and recovers consistent mutation rate estimates. By removing the requirement for complete trio sequencing, OOPS expands mutation rate estimation to a wider range of settings.

genomics↗

bioRxiv2026

New approaches to detecting and characterizing introgression in large species trees

Many current phylogeny-based methods to detect introgression use samples of species-quartets to detect asymmetries in gene tree frequencies. While this has proven to be an accurate and robust approach, applying it to larger species trees often means having to test dozens to hundreds of quartets across a tree. Furthermore, any single introgression event can have effects on multiple quartets--with no principled way to determine the number of unique events from a set of quartets--and the direction of introgression cannot always be determined from quartet comparisons alone. Here, we present a new approach to detecting introgression using the frequency with which more distantly related clades are attached to one another among a set of gene trees. Testing for introgression between pairs of branches is straightforward using these discordant attachment frequencies. We further show that the direction of introgression can be inferred between any pair of branches separated by at least two internal branches of the species tree, and that theoretical expectations of gene tree frequencies under introgression can be used to accurately determine the number of independent times genes have been exchanged. Application of these methods to data from cichlids and Drosophila demonstrate the power of the new approaches. The DAFT software package is available from: https://github.com/smishra677/DAFT/

evolutionary biology↗

bioRxiv2026

Linking genotype to longevity under genealogical discordance in Sebastes rockfishes

AO_SCPLOWBSTRACTC_SCPLOWRockfishes (genus Sebastes) show extreme variation in longevity among closely related species, but the evolutionary history of this young radiation is highly complex. To unpack these relationships and to associate genotypes with phenotypes, we quantified genealogical discordance among 55 Sebastes species and implemented a phyloGWAS framework that incorporates discordant gene histories into genotype-longevity association tests. We found that genealogical discordance is extremely high: the inferred species tree topology differed among several ILS-aware methods, with most internal branches having low concordance factors regardless of which method was used. Nevertheless, some phylogenetic structure was shared by all inferred species trees. We used simulations to assess the statistical properties of phyloGWAS applied to complex traits using different genetic relatedness matrices (GRMs) and under varying levels of discordance. Adding an accurate GRM reduced false positives relative to a model without relatedness, but GRMs only modestly increased power to detect true positives. Using multiple approaches on the Sebastes data, phyloGWAS identified several variants associated with longevity. Our results indicate that extreme genealogical discordance is a core feature of Sebastes evolution and that phyloGWAS can help in connecting genotype to phenotype under these conditions.

evolutionary biology↗

bioRxiv2026

Ancestry-specific performance of variant effect predictors in clinical variant classification

Predicting the effects of genetic variants and assessing prediction performance are key computational tasks in genomic medicine. It has been shown that well-calibrated variant effect predictors can be reliably used as evidence towards establishing pathogenicity (or benignity) of missense variants, thereby rendering these variants suitable for use in (or exclusion from) the genetic diagnosis of rare Mendelian conditions. However, most predictors have been trained or calibrated on data that may not be sufficiently representative to lead to similar performance across all genetic ancestries. This raises questions about the responsible deployment of these tools to improve human health. To better understand the utility of computational predictors, we set out to assess their ancestry-specific performance in terms of accuracy and evidence strength according to the ACMG/AMP guidelines. First, we determined that the expected count of rare variants in an individuals genome and the allele frequency distribution of these variants are the key confounders when evaluating a predictors performance across different genetic ancestries. Second, we found that a predictors accuracy itself inversely correlates with the allele frequency of the rare variant. After stratifying according to allele frequency, we show that established methods for predicting the pathogenicity of missense variants have comparable performance levels across major ancestry groups. Our results therefore support the wide deployment of such models in the context of genetic diagnosis and related applications.

bioinformatics↗

bioRxiv2026

Distribution of Gene Tree Topologies with Duplication, Loss, and Coalescence

MotivationMany methods can be used to infer the number and timing of gene duplication and loss events from gene trees. Most such reconciliation methods use a model of gene duplication that does not include the coalescent process, or that restricts it in important ways. As a result, changes to tree topologies due to coalescence will incur a cost of extra duplications and losses using these methods, events that did not actually occur. ResultsHere, we present results from the multispecies coalescent with duplication and loss (MSC-DL) model, which allows for the unrestricted interaction between duplication, loss, and coalescence. Theoretical results show that even histories with only a single duplication event can lead to many more trees than are normally considered: for a species tree with 2 tips, 9 trees are possible, while with 6 tips, more than 19 million trees are possible; adding even a single loss almost doubles the number of possible topologies. The probabilities of different topologies and their branch lengths under the MSC-DL for trees with two species are calculated exactly, and we provide an approach for calculating such probabilities on larger trees. These results have important implications for the accuracy of reconciliation methods, ortholog identification methods, and our understanding of evolutionary histories of duplication and loss. Supplementary InformationSupplementary materials are available at https://github.com/smishra677/Distribution-of-Gene-Tree-Topologies-with-Duplication-Loss-and-Coalescence.

evolutionary biology↗

bioRxiv2025

No molecular evidence for Muller's ratchet in mitochondrial genomes

AO_SCPLOWBSTRACTC_SCPLOWMullers ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mitochondria (mtDNA), contrasting the rate of nucleotide substitutions in mitochondrial transfer RNA (tRNA) genes with those in the nuclear genome. However, these studies relied on small datasets that could not control for the higher mutation rate in animal mtDNA. In this study, we re-evaluate evidence for Mullers ratchet with well-annotated mitochondrial and nuclear genomes from three species pairs. Across all three comparisons, mitochondrial tRNA (and protein-coding) genes are evolving under strong constraint, with dt/dS equal to 0.12 in primates, 0.07 in birds, and 0.04 in fruit flies. Compared with nuclear dt/dS, only the fruit fly comparison showed slightly lower constraint in mtDNA. Our results therefore provide evidence for strong, efficacious selection in animal mtDNA, with no ratchet-like accumulation of slightly deleterious mutations.

evolutionary biology↗

bioRxiv2025

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees

Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories that may underlie complex traits. Here, we develop a model and software (Spinney) that explicitly incorporate gene tree heterogeneity into rate estimation. Spinney finds the optimal rate of evolution and ancestral states by jointly maximizing the likelihoods across a set of gene trees. Using simulated data, we compare rate estimates from Spinney with those using the species-tree alone, test Spinneys ability to distinguish true rate variation from spurious signals caused by gene tree discordance, and evaluate ancestral state reconstruction. Spinney consistently produced more accurate rate estimates and reduced incorrect inferences of rate variation. This method therefore provides a flexible framework to integrate gene tree heterogeneity into comparative methods and to produce reliable inferences of quantitative trait evolution, regardless of the source of discordance.

evolutionary biology↗

bioRxiv2025

How sex shapes transcriptome evolution in the songbird brain

Sex differences have long captivated scientists, yet the evolutionary rate of change in sex-biased gene expression has not been directly quantified. To address this issue, we introduce new options in CAGEE (Computational Analysis of Gene Expression Evolution), specifically unbounded Brownian motion and variable evolutionary rates among genes. We applied these features to brain transcriptomes of ten songbird species, half of which convergently evolved obligate cavity-nesting, an element of reproductive ecology linked to sex-specific changes in competitive behavior. We find that the degree of sex-bias - measured as male:female expression ratio for each gene - evolves twice as fast on the Z chromosome versus autosomes, but Z gene expression does not evolve at different rates among sexes. Most Z-linked genes are male-biased in their expression, but not all. These sex-balanced genes are not skewed in their rate of evolution, contrary to the hypothesis that some genes experience selection for balance and consequently evolve more slowly. Finally, the degree of sex-bias in gene expression evolves more quickly along obligate-cavity nesting lineages, suggesting that sex-specific selection may shape the evolution of brain sex differences, or lack thereof. Together, these results provide new insights into the interplay between sex and gene expression evolution.

evolutionary biology↗

bioRxiv2025

Estimating recombination using only the allele frequency spectrum

Standard methods for estimating the population recombination parameter,{rho} , are dependent on sampling individual genotypes and calculating various types of disequilibria. However, recent machine learning (ML) approaches to estimating recombination have used pooled sequencing data, which does not sample individual genotypes and cannot be used to calculate disequilibria beyond the length of a single sequence read. Motivated by these results, this study examines the "black box" of such ML methods to understand what signals are being used to infer recombination rates. We find that it is indeed possible to estimate recombination solely using the allele frequency spectrum, and we provide a genealogical interpretation of these results. We further show that even a simplified representation of the allele frequency spectrum can be used to estimate recombination. We demonstrate the accuracy of such inferences using both simulations and data from humans. These results offer a new way to understand the effects of recombination on patterns of sequence data, as well as providing an example of how the internal workings of ML methods can give insight into biological processes. Article SummaryMachine learning methods are becoming more common, offering powerful approaches to study the natural world. We investigated a popular machine learning method to see how it worked, discovering that it was exploiting data (the allele frequency spectrum) to estimate genetic recombination rates that had not been considered before. Our study demonstrates that this approach is indeed quite powerful, opening up new avenues of research. The work also demonstrates that looking inside machine learning models can sometimes teach us novel things about nature.

evolutionary biology↗

bioRxiv2024

Unprecedented female mutation bias in aye-ayes

Every mammal studied to date has been found to have a male mutation bias: male parents transmit more de novo mutations to offspring than female parents, contributing increasingly more mutations with age. Although male-biased mutation has been studied for more than 75 years, its causes are still debated. One obstacle to understanding this pattern is its near universality--without variation in mutation bias, it is difficult to find an underlying cause. Here, we present new data on multiple pedigrees from two primate species: aye-ayes (Daubentonia madagascarensis), a member of the strepsirrhine primates, and olive baboons (Papio anubis). In stark contrast to the pattern found across mammals, we find a much larger effect of maternal age than paternal age on mutation rates in the aye-aye. In addition, older aye-aye mothers transmit substantially more mutations than older fathers. We carry out both computational and experimental validation of our results, contrasting them with results from baboons and other primates using the same methodologies. Further, we analyze a set of DNA repair and replication genes to identify candidate mutations that may be responsible for the change in mutation bias observed in aye-ayes. Our results demonstrate that mutation bias is not an immutable trait, but rather one that can evolve between closely related species. Further work on aye-ayes (and possibly other lemuriform primates) should help to explain the molecular basis for sex-biased mutation.

evolutionary biology↗

bioRxiv2024

Using paralogs for phylogenetic inference mitigates the effects of long-branch attraction

Traditionally, the inference of species trees has relied on orthologs, or genes related through speciation events, to the exclusion of paralogs, or genes related through duplication events. This has led to a focus on using only gene families with a single gene-copy per species, as these families are likely to be composed of orthologs. However, recent work has demonstrated that phylogenetic inference using paralogs is both accurate and allows researchers to take advantage of more data. Here, we investigate a case in which using larger gene families actually increases accuracy compared to using single-copy genes alone. Long-branch attraction is a phenomenon in which taxa with long branches may be incorrectly inferred as sister taxa due to homoplasy. The most common solution to long-branch attraction is to increase taxon sampling to break up long branches. Sampling additional taxa is not always feasible, possibly due to extinction or limited access to high-quality DNA. We propose the use of larger gene families with additional gene copies to break up long branches. Using simulations, we demonstrate that using larger gene families mitigates the impacts of long-branch attraction across large regions of parameter space, especially when either maximum parsimony or maximum likelihood with a misspecified substitution model is used for inference. We also analyze data from Chelicerates, with a focus on assessing support for a sister relationship between scorpions and pseudoscorpions. Previous work has suggested that the failure to recover this relationship is due to long-branch attraction between pseudoscorpions and other lineages. Using data from larger gene families increases support for a clade uniting scorpions and pseudoscorpions, although other resolutions of this relationship continue to have higher support. Together, this work highlights the potential utility of larger gene families in phylogenetic inference.

evolutionary biology↗

bioRxiv2024

Low mutation rate but high male-bias in the germline of a short-lived opossum

Age and sex have been found to be important determinants of the mutation rate per generation in mammals, but the mechanisms underlying these factors are still unclear. One approach to distinguishing between alternative mechanisms is to study species that reproduce at very young ages, as competing hypotheses make different predictions about patterns of mutation in these organisms. Here, we study the germline mutation rate in the gray short-tailed opossum, Monodelphis domestica, a laboratory model species that becomes reproductively mature at less than six months of age. Whole-genome sequencing of 22 trios reveals the lowest mutation rate per generation found in mammals thus far (0.26 x 10-8 per base pair per generation at an average parental age of 313 days), which is expected given their early reproduction. We also examine the mutation spectrum and find fewer mutations at CpG sites in opossums than in humans, consistent with the lower CpG content in the opossum genome. We observe that two-thirds of mutations are inherited from the male parent in opossums, slightly lower than the degree of male bias observed in organisms that reproduce at much older ages. Nevertheless, the very young age at reproduction in opossums suggests that ongoing spermatogonial divisions in males after puberty are not the primary driver of the observed male mutation bias. These findings contribute to a growing body of evidence that the differences between male and female germline mutation may arise from mechanisms other than cell division post-puberty. Article SummaryThis study investigates the germline mutation rate in the gray short-tailed opossum, a marsupial with early reproductive maturity. By sequencing 22 families, we report the lowest mutation rate recorded in mammals but a typical male mutation bias. These findings add to growing evidence that challenges the traditional view that continuing cell division is the primary driver of male-biased mutations. Instead, the study suggests that alternative mechanisms, such as differences in DNA repair, may influence sex-specific mutation rates.

evolutionary biology↗

bioRxiv2024

Phylotranscriptomics reveals convergent behavioral evolution associated with shared and unique mechanisms in cavity-nesting songbirds

Uncovering the genomic bases of phenotypic adaptation is a major goal in biology, but this has been hard to achieve for complex behavioral traits. Here, we leverage the repeated, independent evolution of obligate cavity-nesting in birds to test the hypothesis that pressure to compete for a limited breeding resource has facilitated convergent evolution in behavior, hormones, and gene expression. We used an integrative approach, combining aggression assays in the field, testosterone measures, and transcriptome-wide analyses of the brain in wild-captured females and males. Our experimental design compared species pairs across five avian families, each including one obligate cavity-nesting species and a related species with a more flexible nest strategy. We find behavioral convergence, with higher levels of territorial aggression in obligate cavity-nesters, particularly among females. Across species, levels of testosterone in circulation were not associated with nest strategy, nor aggression. Phylogenetic analyses of individual genes and co-regulated gene networks revealed more shared patterns of brain gene expression than expected by drift, but the scope of convergent gene expression evolution was limited to a small percent of the genome. When comparing our results to other studies that did not use phylogenetic methods, we suggest that accounting for shared evolutionary history may reduce the number of genes inferred as convergently evolving. Altogether, we find that behavioral convergence in response to shared ecological pressures is associated with largely independent gene expression evolution across different avian families, punctuated by a narrow set of convergently evolving genes.

evolutionary biology↗

bioRxiv2024

A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

O_LIWhite oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. C_LIO_LIWe report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. C_LIO_LIOur genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus. Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). C_LIO_LIThe white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade. C_LI

genomics↗

bioRxiv2024

A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions

Whole genome duplications (WGDs) can be a key event in evolution, playing a role in both adaptation and speciation. While WGDs are common throughout the history of plants, only a few examples have been proposed in metazoans. Among these, recent proposals of WGD events in Chelicerates, the group of Arthropods that includes horseshoe crabs, ticks, scorpions, and spiders, include several rounds in the history of horseshoe crabs, with an additional WGD proposed in the ancestor of spiders and scorpions. However, many of these inferences are based on evidence from only a small portion of the genome (in particular, the Hox gene cluster); therefore, genome-wide inferences with broader species sampling may give a clearer picture of WGDs in this clade. Here, we investigate signals of WGD in Chelicerates using whole genomes from 17 species. We employ multiple methods to look for these signals, including gene tree analysis of thousands of gene families, comparisons of synteny, and signals of divergence among within-species paralogs. We test several scenarios of WGD in Chelicerates using multiple species trees as a backbone for all hypotheses. While we do find support for at least one WGD in the ancestral horseshoe crab lineage, we find no evidence for a WGD in the history of spiders and scorpions using any genome-scale method. This study not only sheds light on genome evolution and phylogenetics within Chelicerates, but also demonstrates how a combination of comparative methods can be used to investigate signals of ancient WGDs.

evolutionary biology↗

bioRxiv2023

reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting

Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizontal transfer), ignoring effects of the coalescent process, including incomplete lineage sorting (ILS). Here, we present a new heuristic algorithm for carrying out reconciliation that accurately accounts for ILS by treating it as a series of nearest neighbor interchange (NNI) events. For discordant branches of the gene tree identified by last common ancestor (LCA) mapping, our algorithm recursively chooses the optimal history by comparing the cost of duplication and loss to the cost of NNI and loss. We demonstrate the accuracy of our new method, which we call reconcILS, using a new simulation engine (dupcoal) that generates gene trees produced by the interaction of duplication, loss, and ILS under the MSC-DL model. Despite being a heuristic method, reconcILS is much more accurate than models that ignore ILS, and at least as accurate or better than leading methods that can model ILS, while also able to handle much larger datasets. We demonstrate the use of reconcILS by applying it to a dataset of 23 primate genomes, highlighting its accuracy compared to standard methods in the presence of large amounts of ILS.

bioinformatics↗

bioRxiv2023

Selection leads to false inferences of introgression using popular methods

Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g., of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum (SFS). Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed. Article SummaryDetecting migration between closely related populations is a central objective in many evolutionary biology studies. However, popular methods for detecting migration assume a simplified model of evolution. Here, we evaluate the impacts of biologically realistic natural selection, recombination, and mutation on three methods for detecting migration. We find that biological complexity leads to false inferences of migration, suggesting that results should be interpreted with caution and that new methods are needed to make robust inferences of migration across empirical systems.

evolutionary biology↗

bioRxiv2023

Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics data with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8,000 years in one of the worlds largest brackish water bodies: the colonization of the Baltic Sea by the marine diatom Skeletonema marinoi. To this end, we used a novel approach for protist population genomics, combining target capture of the entire nuclear genome with pooled sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified >3,000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient availability. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation, and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient is a major factor driving local adaptation of S. marinoi. Altogether, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterized by a multitude of environmental gradients, is driven by intricate changes in diverse metabolic pathways and functions.

microbiology↗