Matthew W. Hahn
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View article: Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees
Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees Open
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…
View article: Inconsistency of parsimony under the multispecies coalescent
Inconsistency of parsimony under the multispecies coalescent Open
While it is known that parsimony can be statistically inconsistent under certain models of evolution due to high levels of homoplasy, the consistency of parsimony under the multispecies coalescent (MSC) is less well studied. Previous studi…
View article: How sex shapes transcriptome evolution in the songbird brain
How sex shapes transcriptome evolution in the songbird brain Open
Sex differences have captivated scientists for a long time, yet the evolutionary rate of change in sex-biased gene expression has not been directly quantified. To address this issue, we leverage brain gene expression data from male and fem…
View article: Genome‐Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species
Genome‐Wide Adaptation to a Complex Environmental Gradient in a Keystone Phytoplankton Species Open
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 …
View article: IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models Open
IQ-TREE (http://www.iqtree.org) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 signif…
View article: A haplotype‐resolved reference genome of <i>Quercus alba</i> sheds light on the evolutionary history of oaks
A haplotype‐resolved reference genome of <i>Quercus alba</i> sheds light on the evolutionary history of oaks Open
Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. …
View article: Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar
Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar Open
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 b…
View article: Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar
Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar Open
View article: Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction
Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction Open
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 famili…
View article: Low mutation rate but high male-bias in the germline of a short-lived opossum
Low mutation rate but high male-bias in the germline of a short-lived opossum Open
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 stu…
View article: The Meaning and Measure of Concordance Factors in Phylogenomics
The Meaning and Measure of Concordance Factors in Phylogenomics Open
As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci and therefore less sampling …
View article: Distinguishing Between Histories of Speciation and Introgression Using Genomic Data
Distinguishing Between Histories of Speciation and Introgression Using Genomic Data Open
Introgression creates complex, non-bifurcating relationships among species. At individual loci and across the genome, both introgression and incomplete lineage sorting interact to produce a wide range of different gene tree topologies. The…
View article: Inconsistency of parsimony under the multispecies coalescent
Inconsistency of parsimony under the multispecies coalescent Open
While it is known that parsimony can be statistically inconsistent under certain models of evolution due to high levels of homoplasy, the consistency of parsimony under the multispecies coalescent (MSC) is less well studied. Previous studi…
View article: Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas
Genetic polymorphisms associated with adverse pregnancy outcomes in nulliparas Open
Adverse pregnancy outcomes (APOs) affect a large proportion of pregnancies and represent an important cause of morbidity and mortality worldwide. Yet the pathophysiology of APOs is poorly understood, limiting our ability to prevent and tre…
View article: MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees Open
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutiona…
View article: Repeated behavioral evolution is associated with targeted convergence of gene expression in cavity-nesting songbirds
Repeated behavioral evolution is associated with targeted convergence of gene expression in cavity-nesting songbirds Open
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…
View article: A haplotype-resolved reference genome of<i>Quercus alba</i>sheds light on the evolutionary history of oaks
A haplotype-resolved reference genome of<i>Quercus alba</i>sheds light on the evolutionary history of oaks Open
Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. …
View article: A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions
A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions Open
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, r…
View article: The meaning and measure of concordance factors in phylogenomics
The meaning and measure of concordance factors in phylogenomics Open
As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support. Larger datasets have many more sites and many more loci, and therefore less sampling varian…
View article: Data from <i>Selection leads to false inferences of introgression using popular methods</i>
Data from <i>Selection leads to false inferences of introgression using popular methods</i> Open
This includes data associated with the paper Selection leads to false inferences of introgression using popular methods. Data include simulated data files in various formats. Data are further described in the GitHub repository https…
View article: reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting
reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting Open
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 c…
View article: The ‘faulty male’ hypothesis for sex-biased mutation and disease
The ‘faulty male’ hypothesis for sex-biased mutation and disease Open
View article: Selection leads to false inferences of introgression using popular methods
Selection leads to false inferences of introgression using popular methods Open
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 n…
View article: Applications of Machine Learning in Phylogenetics
Applications of Machine Learning in Phylogenetics Open
Machine learning has increasingly been applied to a wide range of questions in phylogeneticinference. Supervised machine learning approaches that rely on simulated training data have beenused to infer tree topologies and branch lengths, to…
View article: Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes
Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes Open
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 …
View article: Phylogenetic inference using generative adversarial networks
Phylogenetic inference using generative adversarial networks Open
Motivation The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Beca…
View article: Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b
Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b Open
Adverse pregnancy outcomes (APOs) are major risk factors for women's health during pregnancy and even in the years after pregnancy. Due to the heterogeneity of APOs, only few genetic associations have been identified. In this report, we co…
View article: Robust inference of historical human generation times
Robust inference of historical human generation times Open
Ragsdale and Thornton (2023) raise concerns about our recent estimates of historical human generation times, concluding that our results were “predominantly driven by nonbiological artifacts.” While we believe these authors have pointed ou…
View article: Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b
Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b Open
Adverse pregnancy outcomes (APOs) are major risk factors for women’s health during pregnancy and even in the years after pregnancy. Due to the heterogeneity of APOs, only few genetic associations have been identified. In this report, we co…
View article: Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance
Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance Open
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating …