PREreview of "Phylogenomics, Biogeography, and a New Family-level Classification of Silversides, Rainbowfishes, and Allies (Teleostei: Atheriniformes)"

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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/20753016. Overall assessment This manuscript presents a substantial phylogenomic and biogeographic investigation of Atheriniformes, integrating a large exon-capture dataset with extensive taxonomic sampling from GenBank and providing one of the most comprehensive evolutionary frameworks currently available for the group. The study addresses long-standing questions regarding interfamilial relationships, diversification history, and historical biogeography. Particularly noteworthy are the broad taxonomic coverage, the explicit consideration of long-branch attraction, and the attempt to incorporate geographically explicit biogeographic models. The resulting phylogenetic hypotheses and proposed taxonomic revisions will undoubtedly stimulate further research on the evolution of Atheriniformes. We view this as a valuable and timely contribution that substantially advances our understanding of a challenging and historically contentious group. We are confident that the manuscript will attract considerable interest from the systematic and evolutionary biology communities and will find an appropriate publication venue after revision. Our comments are intended to strengthen the manuscript and improve the transparency of several analytical decisions that are central to the authors' conclusions. Minor comments Writing and presentation The manuscript is generally well written, logically organized, and easy to follow. However, we recommend a careful revision of verb tenses throughout the Results section, where shifts occasionally affect consistency. The title accurately reflects the content of the manuscript and clearly communicates its scope. Nevertheless, it is somewhat descriptive and does not fully capture some of the most compelling aspects of the study, particularly the biogeographic findings and the proposed taxonomic revision, which are highlighted more effectively in the abstract. Introduction The manuscript is not structured around a single explicit hypothesis or prediction, but rather around a series of systematic, biogeographic, and taxonomic objectives. This is entirely reasonable given the scope of the study, although stating these objectives more explicitly may help readers understand the rationale behind the analyses. The biogeographic component represents one of the major strengths of the manuscript. However, the Introduction would benefit from a more detailed explanation of the conceptual basis of the DEC model and why geographically explicit models are expected to outperform traditional binary marine/freshwater coding schemes in this system. Given the complex taxonomic history of Atheriniformes and the proposed changes to family-level classification, an additional figure summarizing previous classifications and major phylogenetic hypotheses could substantially improve accessibility for non-specialist readers (e.g., Crawford et al 2012). Methods The overall methodological framework is appropriate and well aligned with the objectives of the study. The section describing the BioGeoBEARS analyses would benefit from additional detail. In particular, it is unclear whether alternative biogeographic models were formally compared before selecting DEC as the preferred framework. The lineage-through-time plot in the Results is a valuable addition, but the corresponding methodology and its purpose are currently missing from the Methods section. Please consider updating the Methods. Some methodological details currently occupying substantial space could potentially be moved to supplementary materials (e.g., details on calibration points for divergence time estimation), allowing greater emphasis on the biogeographic analyses and model-selection procedures. Results and figures Several figures could be reorganized to improve readability. In particular, some phylogenetic trees currently presented in the main text may be better suited for supplementary materials. The rationale for selecting specific phylogenetic trees for downstream analyses should be made more explicit. The interpretation of the lineage-through-time analysis in Figure 3B would benefit from further explanation. The organization of Figures 3 and 4 is somewhat confusing, particularly because portions of one figure appear to overlap conceptually with the other. Figure legends should more clearly indicate which topology was selected for each analysis and why that particular topology was preferred. Whenever geological periods or eras are discussed, approximate numerical ages should also be provided to improve accessibility for readers outside historical biogeography and palaeontology. Discussion and taxonomic conclusions The Discussion generally places the findings in an appropriate evolutionary context and acknowledges several limitations of the phylogenetic analyses. However, the manuscript lacks a dedicated conclusion section summarizing the principal findings and broader implications of the study. Because the proposed family-level reclassification is one of the most significant outcomes of the manuscript, the rationale supporting the taxonomic revision could be synthesized more explicitly. Briefly describing the major changes and their reasons at the beginning of this section would help. The status of Bleheratherina as incertae sedis should be further explained and justified, as readers may not immediately understand why this taxon could not be confidently assigned within the proposed classification. Major comments BioGeoBEARS analyses and model justification The biogeographic component is one of the most innovative and potentially impactful aspects of the manuscript. The explicit incorporation of multiple marine and freshwater regions represents a substantial improvement over traditional binary habitat coding and provides an elegant framework for investigating the evolutionary history of habitat transitions. However, the methodological justification for the choice of DEC requires further development. The manuscript states that DEC was selected as the best-fitting model, but it remains unclear whether alternative BioGeoBEARS models were formally evaluated and compared. Because model choice can strongly influence ancestral-range reconstructions and inferred numbers of habitat transitions, readers would benefit from a clearer description of the model-selection procedure and the criteria used to justify DEC over competing alternatives. More broadly, given that the central biogeographic conclusions depend heavily on these reconstructions, greater methodological detail regarding area definitions, dispersal constraints, and model comparison would substantially strengthen the manuscript. We encourage the authors to expand this section and provide sufficient information to allow readers to evaluate the robustness of the biogeographic inferences. Divergence-time estimation: methodological choices require stronger justification We encourage the authors to provide a more detailed justification for the divergence-time analyses. First, it is unclear why only twelve loci were selected for dating and why loci with the lowest proportion of missing data were considered the most appropriate choice. Missing-data levels alone are not necessarily informative regarding a locus's suitability for molecular dating. Loci with fewer missing sites are not inherently more clock-like, more informative, or better fitting to relaxed-clock models. Likewise, a lower proportion of missing data does not imply a greater number of informative sites (e.g., variable sites, parsimony-informative sites, or other measures of phylogenetic information content). Consequently, the rationale for selecting these twelve loci remains unclear. A potentially more defensible strategy would be to select loci based on clock-likeness metrics, using approaches such as SortaDate or similar methods specifically designe