T. B. Sackton

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.

Patterns of lineage-specific genome evolution in the brood parasitic black-headed duck (Heteronetta atricapilla)

The paper generates high-quality genomes of the black-headed duck and related species to study lineage-specific evolutionary changes associated with brood parasitism.

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The paper analyzes site frequency spectra across species and finds U-shaped patterns, suggesting that multiple merger coalescent models better fit the data than the standard neutral model.

Sexual Reproduction in Bdelloid Rotifers

The paper shows that bdelloid rotifers, previously thought to be asexual, are facultatively sexual, suggesting sexual reproduction is essential for long-term evolutionary success in eukaryotes.

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.

Immune genes are hotspots of shared positive selection across birds and mammals

The paper identifies immune genes as hotspots of shared positive selection across birds and mammals, showing enrichment for viral immune pathways and pathogen-response genes.

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.