@article{hughes_bloom_piller_lang_mayden_2025, title={Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage}, volume={292}, ISSN={["1471-2954"]}, DOI={10.1098/rspb.2024.2101}, abstractNote={Jawless vertebrates once dominated Palaeozoic waters, but just two lineages have persisted to the present day: lampreys and hagfishes. Living lampreys are a relatively small clade, with just over 50 species described, but knowledge of their evolutionary relationships has always been based on either a few mitochondrial genes or a small number of taxa. Biogeographers have noted the disjunct antitropical distribution of living lamprey families. Here, we present a comprehensive phylogenomic analysis of living and fossil lampreys, sampling 36 species with phylogenomic data and 46 in total with genetic data. We present new divergence time estimates based on comprehensive nuclear data and analysis of their diversification dynamics. Our analysis indicates a central role for extreme global warming during the Late Cretaceous Cenomanian–Turonian Boundary Event as a likely cause for the antitropical distribution of living lampreys, and a notable increase in lineage diversification in Northern Hemisphere lampreys during the Miocene corresponding with a period of global cooling.}, number={2038}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Hughes, Lily C. and Bloom, Devin D. and Piller, Kyle R. and Lang, Nicholas and Mayden, Richard L.}, year={2025}, month={Jan} }
 @article{duarte-ribeiro_rosas-puchuri_friedman_woodruff_hughes_carpenter_white_pogonoski_westneat_astarloa_et al._2024, title={Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry}, ISSN={["1546-1718"]}, DOI={10.1038/s41588-024-01784-w}, journal={NATURE GENETICS}, author={Duarte-Ribeiro, Emanuell and Rosas-Puchuri, Ulises and Friedman, Matt and Woodruff, Gavin C. and Hughes, Lily C. and Carpenter, Kent E. and White, William T. and Pogonoski, John J. and Westneat, Mark and Astarloa, Juan Martin Diaz and et al.}, year={2024}, month={May} }
 @article{hughes_nash_white_westneat_2022, title={Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)}, ISSN={["1076-836X"]}, DOI={10.1093/sysbio/syac072}, abstractNote={Abstract
               Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multi-locus studies and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence 1088 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades were largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in a large, economically important groups of coral reef fishes. More broadly, we demonstrate how accounting for sources of biological variability from incomplete lineage sorting and exploring systematic error at conflicting nodes can aid in evaluating alternative phylogenetic hypotheses. [coral reefs; divergence time estimation; exon-capture; fossil calibration; incomplete lineage sorting.]}, journal={SYSTEMATIC BIOLOGY}, author={Hughes, Lily C. and Nash, Chloe M. and White, William T. and Westneat, Mark W.}, year={2022}, month={Nov} }