S. V. Edwards

Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling

The paper introduces an alignment-free method using probabilistic topic modeling to infer genome-wide phylogenies and evaluates its performance on simulated and biological datasets.

Genetic basis and evolution of structural color polymorphism in an Australian songbird

The paper investigates the genetic basis of melanism in white-winged fairywren subspecies, finding that the mainland blue subspecies re-evolved blue plumage from a black ancestor through genetic changes in ASIP and SCUBE2.

PhyloAcc-GT: A Bayesian method for inferringpatterns of substitution rate shifts and associations with binary traits under gene tree discordance

PhyloAcc-GT improves upon PhyloAcc by accounting for gene tree discordance due to incomplete lineage sorting, enhancing accuracy in detecting substitution rate shifts linked to specific lineages.

slimr: An R package for integrating data and tailor-made population genomic simulations over space and time

slimr integrates SLiM 3.0 simulations with R for seamless data analysis and simulation workflows in population genomics.

Evolution of the DAN gene family in vertebrates

This study investigates the evolutionary history of the DAN gene family in vertebrates, revealing its monophyly and identifying new gene lineages and differential loss patterns across species.

De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

This paper presents a high-quality genome assembly of the Northern Cardinal and identifies candidate regulatory regions associated with red plumage coloration and sexual dichromatism.

The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets

This study compares substitution, concatenation, and multispecies coalescent models across 47 phylogenomic datasets, finding the coalescent model performs better.

Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird

This study characterizes the olfactory receptor subgenome and expression in Leachs storm petrels, identifying a large number of intact OR genes and differential expression patterns.

First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis)

The paper uses high-throughput sequencing to assemble the first nuclear genome of the extinct little bush moa and identifies polymorphic microsatellites and candidate genes related to limb development.

Evolutionary dynamics of sex chromosomes of paleognathous birds

This study investigates the evolutionary dynamics of sex chromosomes in paleognathous birds, finding that large non-degenerate regions are retained and that evolutionary rates vary across different genomic regions.

Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

This paper advocates for integrating natural history-derived phenomic data with comparative genomics to better understand the genetic basis of convergent evolution.

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

This paper introduces PhyloAcc, a Bayesian method to detect substitution rate changes in conserved noncoding elements across phylogenies, showing improved accuracy over existing methods in identifying rate shifts associated with convergent phenotypes.

Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone

The paper uses whole-genome data to resolve the phylogeny of flightless birds, finding a resolved topology with rheas as sister to kiwi and emu + cassowary, but also identifies an empirical anomaly zone due to incomplete lineage sorting.

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

This study shows that convergent flightlessness in palaeognathous birds is associated with regulatory changes rather than protein-coding gene evolution.

Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics

The paper introduces conserved non-exonic elements (CNEEs) as a new phylogenomic marker, finding they offer better alignment quality and fewer gaps compared to ultraconserved elements (UCEs) and introns.