J. Gatesy

A genomic timescale for placental mammal evolution

This study constructs a genomic timescale for placental mammal evolution using whole genome phylogenies, revealing timing and patterns of ordinal diversification.

Anatomical, ontogenetic, and genomic homologies guide reconstructions of the teeth-to-baleen transition in mysticete whales

This paper reviews phylogenetic, anatomical, and genomic data to reconstruct the teeth-to-baleen transition in mysticete whales, identifying key homologies and evolutionary patterns.

Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses

The paper introduces PCBL, a method to assess gene tree influence in distance-based coalescent analyses, revealing biases that affect phylogenetic inference.

Molecular Evolutionary Analyses of Tooth Genes Support Sequential Loss of Enamel and Teeth in Baleen Whales (Mysticeti)

This study analyzes tooth-related genes in baleen whales to determine the sequence of enamel and tooth loss, finding enamel loss occurred early followed by dentin loss in separate lineages.

Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

This paper evaluates methods for estimating species trees using retroelement insertions, finding that ASTRAL BP and SDPquartets are statistically consistent and accurate, especially in the anomaly zone.

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

This study compares genomic and anatomical features of cetaceans and hippos to determine if aquatic adaptations evolved independently or from a common ancestor.

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

The paper develops a chi-squared quartet-asymmetry test to detect hybridization using retroposon insertion data and applies it to mammalian datasets.

Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’

This paper uses retroposon insertions within a multispecies coalescent framework to analyze ratite phylogeny, finding that retroposon-based species trees show longer branch lengths and are less affected by anomaly zone conditions compared to sequence-based methods.

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

This study identifies genes lost in cetacean ancestors that may have contributed to aquatic adaptations like diving physiology and unihemispheric sleep.

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

This paper introduces partitioned coalescence support (PCS) to analyze phylogenomic conflicts and assess biases in species-tree methods across multiple datasets.