Matthew W. Pennell

Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

Unicellular and Multicellular Modes of Selection Impose Distinct Constraints on Cellular Phenotype Evolution

This study uses a geometric model to show that selection on cellular phenotypes in unicellular and multicellular organisms imposes different constraints on the evolution of differentiation from a shared genome.

Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci

The paper shows that avian immunoglobulin loci use gene conversion instead of V(D)J recombination, with rapid evolution of inversions that generate pseudogenes as donors for antibody diversity.

PlantCAD2: a DNA foundation model for interpreting genomes across flowering plants

PlantCAD2 is a DNA foundation model pre-trained on 65 angiosperm genomes, showing improved performance in evolutionary conservation and chromatin accessible region prediction compared to existing models.

Characterizing and mitigating confounding by unreplicated evolutionary events in phylogenetic regression

This paper introduces a method to reduce false positives in phylogenetic regression by incorporating eigenvectors of the phylogenetic variance-covariance matrix and presents a new R package for visualization.

Disruption of a CCR5-like immunoglobulin gene is linked to plague susceptibility in black-footed ferrets

The paper identifies a disrupted CCR5-like immunoglobulin gene in black-footed ferrets linked to increased susceptibility to plague caused by Yersinia pestis.

Phenotypic complexity makes the molecular basis of evolutionary convergence predictable

The paper shows that phenotypic complexity determines whether convergent evolution leads to molecular convergence, using simulations of regulatory gene expression.

Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix

This paper introduces a method using genetic relatedness matrices to control genetic confounding in observational studies, showing improved performance over existing approaches in smaller datasets.

Collective behavior drives diversification across the tree of ray-finned fishes

The paper quantifies collective movement phenotypes in ray-finned fishes using machine learning and finds it correlates with predation pressure, diet, and increased diversification rates.

Discovery of additional ancient genome duplications in yeasts

The paper discovers three novel ancient whole genome duplications in Saccharomycotina yeasts, suggesting WGD may be more common in fungi than previously thought.

Interspecific divergence of gene expression biophysics driven by both evolutionary systems drift and strong selective constraints on bursting rate

This study estimates biophysical parameters of gene expression in multiple vertebrate species and finds coordinated evolution under evolutionary systems drift and additional constraints on transcriptional bursting.

GeneCAD: Plant Genome Annotation with a DNA Foundation Model

GeneCAD improves gene annotation in plant genomes using a DNA foundation model, achieving higher accuracy than existing tools across diverse species.

The Untapped Potential of Tree Size in Reconstructing Evolutionary and Epidemiological Dynamics

This paper explores the use of tree size in phylodynamic inference, showing it provides additional insights for diversification questions not captured by shape or branch lengths alone.

Comparative analysis of mammalian adaptive immune loci revealed spectacular divergence and common genetic patterns

The paper compares IG/TR loci across 44 mammalian species, finding correlations in gene counts, structural patterns linked to population bottlenecks, and haplotype diversity suggesting limited recombination potential.

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

The paper investigates the relationship between gene family expansions and metabolic traits in yeasts, finding that keystone gene families drive multiple metabolic innovations.

Genetic and selective constraints on the optimization of gene product diversity

The paper develops a mathematical model to predict isoform abundance distributions across species and genes, finding that factors beyond selection, like population size and cis-acting loci, significantly influence evolutionary outcomes.

Complete sequencing of ape genomes

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

How developmental constraints shape the evolution of repeated structures

The paper introduces a model linking developmental constraints to the evolution of repeated structures, showing how structural features of gene regulatory networks influence divergence and fitness under selection.

Phylogenetic analysis reveals how selection and mutation shape the coevolution of mRNA and protein abundances

This study uses a phylogenetic model to analyze multi-species data and finds that protein abundances are under strong stabilizing selection, while mRNA abundances adapt more quickly due to mutational opportunity.

Evaluating methods for B-cell clonal family assignment

This study evaluates methods for assigning B-cell sequences to clonal families, finding that SCOPer-H performs best but requires a reference genome, while mPTP shows promise for non-model organisms.

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

This paper unifies statistical genetics and phylogenetics by developing a general model for genetic covariance, showing how GWAS and phylogenetic regression are special cases and demonstrating improved association testing through shared methodology.

Assessing Assembly Errors in Immunoglobulin Loci: A Comprehensive Evaluation of Long-read Genome Assemblies Across Vertebrates

The paper evaluates long-read genome assemblies of immunoglobulin loci across 74 vertebrates, identifies assembly errors, and demonstrates methods to correct them using a new pipeline called CloseRead.