Brant C. Faircloth

This paper introduces a deep learning method that integrates genomic and trait data to improve species delimitation in complex speciation scenarios.

The paper assembles and annotates a genome for a Chilean Tigriopus copepod population, suggesting it may represent a novel species based on divergence and morphology.

The paper examines thermal tolerance and its plasticity in copepods across populations, finding that higher heat tolerance correlates with stable peptidase expression, while plasticity is linked to chitin and ECM gene expression changes.

The paper examines genetic differentiation and hybridization in three closely related bird taxa at contact zones using RADSeq data, finding weak genetic differentiation and evidence of introgressive hybridization in one zone.

This study examines how heat stress adaptation in copepods involves both genetic and plastic responses, showing shared molecular mechanisms across populations.

This study evaluates methods for inferring large-scale avian phylogenies, finding that fast tree search approaches balance computational efficiency and accuracy.

The paper compares phylogenomic methods using a well-resolved bird species tree, finding that ML concatenation performs best, while METAL shows promise with large datasets.

The paper presents a highly contiguous reference genome for Northern Bobwhite using HiRise assembly and HiC libraries, improving contiguity and completeness compared to existing genomes.

Adapterama II introduces a flexible and cost-effective method for amplicon sequencing on Illumina platforms using fusion primers and quadruple indexing.

The paper introduces a low-cost, highly multiplexed RADseq library preparation method called 2RAD/3RAD, which improves efficiency and compatibility with sequencing platforms.

The paper introduces dual-indexing systems to reduce NGS start-up, buy-in, and sample preparation costs by enabling combinatorial indexing of Illumina libraries.

The paper designs and tests RNA baits to capture phylogenetically informative loci in anthozoans, successfully resolving evolutionary relationships across multiple taxa.