Nathan L Clark
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View article: Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles
Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles Open
The natural world is full of valuable lessons about genetic adaptation as organisms respond to changing conditions around them. Deciphering these changes is a major goal of evolutionary genetics. Advances have been made through phylogenomi…
View article: Ultra-fast variant effect prediction using biophysical transcription factor binding models
Ultra-fast variant effect prediction using biophysical transcription factor binding models Open
Sequence variation within transcription factor (TF)-binding sites can significantly affect TF–DNA interactions, influencing gene expression and contributing to disease susceptibility or phenotypic traits. Despite recent progress in deep se…
View article: Female membrane proteins regulate postmating ovulation in <i>Drosophila melanogaster</i> by ovulin-dependent and -independent pathways
Female membrane proteins regulate postmating ovulation in <i>Drosophila melanogaster</i> by ovulin-dependent and -independent pathways Open
Ovulation is an intricate process that is essential for reproductive success. In Drosophila melanogaster , ovulation increases after mating. This increase is initiated by the male seminal fluid protein ovulin and is executed by female path…
View article: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies Open
Evolutionary rate covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been em…
View article: Prediction of local convergent shifts in evolutionary rates with <i>phyloConverge</i>
Prediction of local convergent shifts in evolutionary rates with <i>phyloConverge</i> Open
Motivation Convergence analysis can characterize genetic elements underlying morphological adaptations. However, its performance on regulatory elements is limited due to their modular composition of transcription factor motifs, which have …
View article: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors Open
Positive selection is an evolutionary process which increases the frequency of advantageous mutations because they confer a fitness benefit. Inferring the past action of positive selection on protein-coding sequences is fundamental for dec…
View article: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors Open
Positive selection is an evolutionary process which increases the frequency of advantageous mutations because they confer a fitness benefit. Inferring the past action of positive selection on protein-coding sequences is fundamental for dec…
View article: Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies
Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies Open
Synopsis A major goal of research in evolution and genetics is linking genotype to phenotype. This work could be direct, such as determining the genetic basis of a phenotype by leveraging genetic variation or divergence in a developmental,…
View article: Congenital Aphakia Associated With a <scp> <i>GJA8</i> </scp> Pathogenic Variant: A Case Report
Congenital Aphakia Associated With a <span> <i>GJA8</i> </span> Pathogenic Variant: A Case Report Open
Congenital aphakia is a rare eye condition in which the lens fails to form properly. It is typically caused by pathogenic variants within the FOXE3 or HCCS genes; however, it can also be associated with GJA8 pathogenic variants. GJA8 shoul…
View article: ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies
ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies Open
Evolutionary Rate Covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many functional predictions of ERC have been em…
View article: The Shu complex interacts with the replicative helicase to prevent mutations and aberrant recombination
The Shu complex interacts with the replicative helicase to prevent mutations and aberrant recombination Open
Homologous recombination (HR) is important for DNA damage tolerance during replication. The yeast Shu complex, a conserved homologous recombination factor, prevents replication-associated mutagenesis. Here we examine how yeast cells requir…
View article: Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics
Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics Open
Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic re…
View article: Unearthing the secrets of Australia’s most enigmatic and cryptic mammal, the marsupial mole
Unearthing the secrets of Australia’s most enigmatic and cryptic mammal, the marsupial mole Open
The marsupial moles are arguably Australia’s most enigmatic marsupials. Almost indistinguishable from placental (eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome of the southern marsupial mole…
View article: Mammalian retinal specializations for high acuity vision evolve in response to both foraging strategies and morphological constraints
Mammalian retinal specializations for high acuity vision evolve in response to both foraging strategies and morphological constraints Open
Vision is a complex sensory system that requires coordination among cellular and morphological traits, and it remains unclear how functional relationships among traits interact with ecological selective pressures to shape the evolution of …
View article: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors Open
Positive selection is an evolutionary process which increases the frequency of advantageous mutations because they confer a fitness benefit. Inferring the past action of positive selection on protein-coding sequences is fundamental for dec…
View article: RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution Open
Comparative genomics approaches seek to associate molecular evolution with the evolution of phenotypes across a phylogeny. Many of these methods lack the ability to analyze non-ordinal categorical traits with more than two categories. To a…
View article: Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents
Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents Open
It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morpholog…
View article: Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers
Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers Open
Mutations in glycosylation pathways, such as N-linked glycosylation, O-linked glycosylation, and GPI anchor synthesis, lead to Congenital Disorders of Glycosylation (CDG). CDG typically present with seizures, hypotonia, and developmental d…
View article: Mammalian retinal specializations for high acuity vision evolve in response to both foraging strategies and morphological constraints
Mammalian retinal specializations for high acuity vision evolve in response to both foraging strategies and morphological constraints Open
Vision is a complex sensory system that requires coordination among cellular and morphological traits, and it remains unclear how functional relationships among traits interact with ecological selective pressures to shape the evolution of …
View article: Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers
Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers Open
Mutations in glycosylation pathways, such as N-linked glycosylation, O-linked glycosylation, and GPI anchor synthesis, lead to Congenital Disorders of Glycosylation (CDG). CDGs typically present with seizures, hypotonia, and developmental …
View article: Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics Open
Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic re…
View article: Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements
Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements Open
Vocal production learning (“vocal learning”) is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from t…
View article: Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions Open
Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC),…
View article: Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions Open
Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC),…
View article: Reviewer #2 (Public Review): Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Reviewer #2 (Public Review): Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions Open
Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC),…
View article: Reviewer #1 (Public Review): Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Reviewer #1 (Public Review): Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions Open
Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC),…
View article: Author Response: Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions
Author Response: Evolutionary Rate Covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions Open
Co-functional proteins tend to have rates of evolution that covary over time. This correlation between evolutionary rates can be measured over the branches of a phylogenetic tree through methods such as evolutionary rate covariation (ERC),…
View article: RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution Open
Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of a…