Biology subjects

Mo, Y. K.

Publications and source records attributed to Mo, Y. K..

4 recordsLinked to original sources

bioRxiv2026

Linking genotype to longevity under genealogical discordance in Sebastes rockfishes

AO_SCPLOWBSTRACTC_SCPLOWRockfishes (genus Sebastes) show extreme variation in longevity among closely related species, but the evolutionary history of this young radiation is highly complex. To unpack these relationships and to associate genotypes with phenotypes, we quantified genealogical discordance among 55 Sebastes species and implemented a phyloGWAS framework that incorporates discordant gene histories into genotype-longevity association tests. We found that genealogical discordance is extremely high: the inferred species tree topology differed among several ILS-aware methods, with most internal branches having low concordance factors regardless of which method was used. Nevertheless, some phylogenetic structure was shared by all inferred species trees. We used simulations to assess the statistical properties of phyloGWAS applied to complex traits using different genetic relatedness matrices (GRMs) and under varying levels of discordance. Adding an accurate GRM reduced false positives relative to a model without relatedness, but GRMs only modestly increased power to detect true positives. Using multiple approaches on the Sebastes data, phyloGWAS identified several variants associated with longevity. Our results indicate that extreme genealogical discordance is a core feature of Sebastes evolution and that phyloGWAS can help in connecting genotype to phenotype under these conditions.

evolutionary biology↗

bioRxiv2025

No molecular evidence for Muller's ratchet in mitochondrial genomes

AO_SCPLOWBSTRACTC_SCPLOWMullers ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mitochondria (mtDNA), contrasting the rate of nucleotide substitutions in mitochondrial transfer RNA (tRNA) genes with those in the nuclear genome. However, these studies relied on small datasets that could not control for the higher mutation rate in animal mtDNA. In this study, we re-evaluate evidence for Mullers ratchet with well-annotated mitochondrial and nuclear genomes from three species pairs. Across all three comparisons, mitochondrial tRNA (and protein-coding) genes are evolving under strong constraint, with dt/dS equal to 0.12 in primates, 0.07 in birds, and 0.04 in fruit flies. Compared with nuclear dt/dS, only the fruit fly comparison showed slightly lower constraint in mtDNA. Our results therefore provide evidence for strong, efficacious selection in animal mtDNA, with no ratchet-like accumulation of slightly deleterious mutations.

evolutionary biology↗

bioRxiv2025

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees

Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories that may underlie complex traits. Here, we develop a model and software (Spinney) that explicitly incorporate gene tree heterogeneity into rate estimation. Spinney finds the optimal rate of evolution and ancestral states by jointly maximizing the likelihoods across a set of gene trees. Using simulated data, we compare rate estimates from Spinney with those using the species-tree alone, test Spinneys ability to distinguish true rate variation from spurious signals caused by gene tree discordance, and evaluate ancestral state reconstruction. Spinney consistently produced more accurate rate estimates and reduced incorrect inferences of rate variation. This method therefore provides a flexible framework to integrate gene tree heterogeneity into comparative methods and to produce reliable inferences of quantitative trait evolution, regardless of the source of discordance.

evolutionary biology↗

bioRxiv2022

Updated site concordance factors minimize effects of homoplasy and taxon sampling

MotivationSite concordance factors (sCFs) have become a widely used way to summarize discordance in phylogenomic datasets. However, the original version of sCFs were calculated by sampling a quartet of tip taxa and then applying parsimony-based criteria for discordance. This approach has the potential to be strongly affected by multiple hits at a site (homoplasy), especially when substitution rates are high or taxa are not closely related. ResultsHere, we introduce a new method for calculating site concordance factors. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes of the phylogeny. By sampling from the states at internal nodes adjacent to a given branch, this approach substantially reduces--but does not completely abolish--the effects of homoplasy and taxon sampling. Availability and implementationUpdated sCFs are implemented in IQ-TREE 2.2.2. The software is freely available at https://github.com/iqtree/iqtree2/releases. Contactmoyu@iu.edu

bioinformatics↗