Duarte-Ribeiro, E. | Search bioRxiv

bioRxiv2026

Whole-genome phylogenomics and synteny resolve a single origin of body-plan asymmetry in flatfishes

Flatfishes display the most dramatic asymmetric body plan in vertebrates, yet whether this rare innovation evolved once (flatfish monophyly, FM) or multiple times (flatfish polyphyly, FP) has remained contentious. A recent genome-wide study supported FP by placing Psettodes, the earliest-diverging flatfish lineage, among symmetric relatives within Carangaria, the clade that also includes billfishes, jacks, mahi-mahi, and barracudas. Subsequent work traced this to base-composition artifacts and inadequate substitution modeling. Here we revisit the question using whole-genome phylogenomic and synteny data from 17 carangarian species spanning flatfishes and carangarian relatives. We contribute three new chromosome-level assemblies, including the first for Psettodes. Nucleotide-based coalescent analyses (e.g., ROADIES, CASTER) yield strong support for FM, with Psettodes sister to all other flatfishes. Microsynteny analyses built from conserved gene-order blocks corroborate this result: topology tests, cluster-profile counts, and rearrangement-based trees favor FM over two competing FP topologies. Macrosynteny, based on chromosome-scale rearrangements, yields a more mixed signal, with support for FM depending on the metric and taxon-sampling scheme. We interpret this scale-dependent pattern in the context of the explosive post-Cretaceous radiation of Carangaria. The short intervals between speciation events that characterize rapid radiations appear to have left sufficient signal in fine-grained microsyntenic rearrangements, while chromosome-scale rearrangements were too rare to consistently resolve these closely spaced splits. When integrated with evidence from conserved developmental mechanisms active during metamorphosis, the stage at which flatfish asymmetry first emerges, and from the exceptionally complete fossil record, our multi-scale genomic evidence supports a single evolutionary origin of flatfish asymmetry.

evolutionary biology↗

bioRxiv2023

Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models

Phylogenetic inference can be influenced by both underlying biological processes and methodological factors. While biological processes can be modeled, these models frequently make the assumption that methodological factors do not significantly influence the outcome of phylogenomic analyses. Depending on their severity, methodological factors can introduce inconsistency and uncertainty into the inference process. Although search protocols have been proposed to mitigate these issues, many solutions tend to treat factors independently or assume a linear relationship among them. In this study, we capitalize on the increasing size of phylogenetic datasets, using them to train machine learning models. This approach transcends the linearity assumption, accommodating complex non-linear relationships among features. We examined two phylogenomic datasets for teleost fishes: a newly generated dataset for protacanthopterygians (salmonids, galaxiids, marine smelts, and allies), and a reanalysis of a dataset for carangarians (flatfishes and allies). Upon testing five supervised machine learning models, we found that all outperformed the linear model (p < 0.05), with the deep neural network showing the best fit for both empirical datasets tested. Feature importance analyses indicated that influential factors were specific to individual datasets. The insights obtained have the potential to significantly enhance decision-making in phylogenetic analyses, assisting, for example, in the choice of suitable DNA sequence models and data transformation methods. This study can serve as a baseline for future endeavors aiming to capture non-linear interactions of features in phylogenomic datasets using machine learning and complement existing tools for phylogenetic analyses.

evolutionary biology↗