DOI: 10.5061/dryad.80gb5mm12
title: Data and R Script from: The ancestor of sharks and rays laid eggs, but ancestral state reconstructions need empirically supported traits and transparent reporting

description: We recently published a study in Biological Reviews that examined the
 evolution of reproductive modes in chondrichthyan fishes using ancestral
 state reconstruction (Blackburn and Hughes 2024). While our paper was in
 the review process, the study by Katona et al. (2023) appeared in the
 Journal of Evolutionary Biology with comparable goals and methods as our
 own. Although these two published analyses agreed that the common ancestor
 of sharks and rays was oviparous, they reached dramatically different
 conclusions about the evolution of reproductive patterns. For example,
 although our study found that transformations from oviparity to viviparity
 were unidirectional, Katona et al. (2023) claimed multiple reversals from
 viviparity back to oviparity. Likewise, while our analysis concluded that
 lecithotrophic (“yolk-only”) viviparity probably evolved irreversibly into
 matrotrophy (maternal provision of nutrients), their study inferred
 multiple reversions from matrotrophy back to the ancestral mode. Further,
 we concluded that placentotrophy originated in a basal viviparous
 carcharhiniform shark, but their analysis supported numerous independent
 origins and losses of placentotrophy in the group. Overall, our analysis
 concluded that reproductive evolution in chondrichthyan fish involved as
 few as 19 reproductive mode transformations, while theirs supported ~57
 such transformations. Because our two studies drew upon similar
 phylogenetic sources to reconstruct traits in the same taxonomic group,
 such major discrepancies between our results could lead readers to infer
 that little that is definitive can be concluded about
 chondrichthyan reproductive evolution. We believe that such an inference
 would be unjustified. Given long-standing (e.g., Compagno 1990; Musick and
 Ellis 2005) and recent (Marion et al. 2024; Mull et al. 2024) interest in
 this topic, we undertook a detailed comparison between the two studies to
 bring clarity to reproductive mode evolution in sharks and rays. We have
 identified two factors that cast doubt on the findings of Katona et al.
 (2023): 1) problematic assignments of reproductive patterns to species in
 their analysis; and 2) ambiguous methodological procedures. We find that
 these aspects explain discrepancies between our analyses and that their
 resolution yields an evolutionary reconstruction that is more empirically
 justified and methodologically sound.
description: Our paper is a critique of another study, in which we used
 quantitative metrics to draw inferences between studies. We took this
 approach to point out possible reasons for discrepancies between the paper
 we were critiquing (Katona et al. 2023) and our original study on the same
 subject (Blackburn and Hughes, 2024). The primary dataset we used in our
 critique was provided by Katona et al. (2023) and originally collected
 through a literature review. We processed this primary dataset to be used
 in four separate analyses based on specific criteria as a means to compare
 results among those choices and to those of Blackburn & Hughes
 (2024), our original paper on the subject. Briefly, the first dataset is
 the original data provided by Katona et al. (2023) with their coding of
 species traits (for results, see D in Table 2 of Hughes &
 Blackburn [2025]). The second dataset is a corrected version of the
 original data provided by Katona et al. (2023), where we fixed definite
 errors in their assignments of reproductive modes (for results, see E in
 Table 2 of Hughes & Blackburn [2025]). The third and fourth
 datasets include the corrected version of the original data provided by
 Katona et al. (2023), but we also recoded the species traits into fewer
 categories for analysis, which is why there are two datasets here (for
 results, see F in Table 2 of Hughes & Blackburn [2025]). All
 datasets were analyzed via the Stein et al. (2018) consensus phylogeny. See our critique paper (Hughes & Blackburn [2025]) for more details. The datasets from our original study and that which we critiqued are both available as supplemental material in their respective publications: Original dataset 1: Katona et al. (2023) Evolution of reproductive modes in sharks and rays. <em>Journal of Evolutionary Biology</em>, 36(11): 1630–1640. https://doi.org/10.1111/jeb.14231 Original dataset 2: Blackburn & Hughes (2024) Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes. <em>Biological Reviews</em>, 99(4): 1314–1356. https://doi.org/10.1111/brv.13070
description: # Data and R Script from: The ancestor of sharks and rays laid eggs, but
 ancestral state reconstructions need empirically supported traits and
 transparent reporting
 [https://doi.org/10.5061/dryad.80gb5mm12](https://doi.org/10.5061/dryad.80gb5mm12) ## Description of the data and file structure We used the data provided by Katona et al. (2023), which was originally collected from a literature review. We reanalyzed their dataset with ancestral state reconstruction and stochastic character mapping using the same analytical parameters described by Katona et al. (2023): 100 simulations using the default root prior. The only methodological difference is that we mapped characters onto the consensus tree topology provided by Stein et al. (2018).  ### Files and variables #### File: AllSharks1Tree.tre **Description:** Consensus tree topology provided by Stein et al. (2018) and is used in all analyses. #### File: keepspecies\_main\_D.csv **Description:** This is a file that includes only the species needed for the reanalysis of the original data from Katona et al. (2023), and results are presented in Table 2 of Hughes & Blackburn (2025), Column D. ##### Variables * Species names #### File: shark\_modepruned\_D.csv **Description:** This is a file that includes the species and their traits for the reanalysis of the original data from Katona et al. (2023), and results are presented in Table 2 of Hughes & Blackburn (2025), Column D. ##### Variables * species: Species names * mode: Assigned reproductive modes according to Katona et al. (2023): Egg-laying, Live-bearing_with_oophagy, Live-bearing_with_uterine_milk, Placental_viviparity, Yolk-only_viviparity. #### File: keepspecies\_main\_E.csv **Description:** This is a file that includes only the species needed for the reanalysis of the corrected data from Katona et al. (2023), and results are presented in Table 2 of Hughes & Blackburn (2025), Column E. ##### Variables * Species names #### File: shark\_modepruned\_E.csv **Description:** This is a file that includes the species and their traits for the reanalysis of the corrected data from Katona et al. (2023), and results are presented in Table 2 of Hughes & Blackburn (2025), Column E. ##### Variables * species: Species names * mode: Assigned reproductive modes according to Katona et al. (2023): Egg-laying, Live-bearing_with_oophagy, Live-bearing_with_uterine_milk, Placental_viviparity, Yolk-only_viviparity. #### File: keepspecies\_main\_F\_parity.csv **Description:** This is a file that includes only the species needed for the reanalysis of the corrected and recoded data from Katona et al. (2023) for parity mode only, and results are presented in Table 2 of Hughes & Blackburn (2025), Column F. ##### Variables * Species names #### File: shark\_modepruned\_F\_parity.csv **Description:** This is a file that includes the species and their traits for the reanalysis of the corrected and recoded data from Katona et al. (2023) for parity mode only, and results are presented in Table 2 of Hughes & Blackburn (2025), Column F. ##### Variables * species: Species names * mode: Corrected reproductive modes from Katona et al. (2023), which was limited to only those species with parity mode information: Live-bearing, Egg-laying. #### File: keepspecies\_main\_F\_nutrition.csv **Description:** This is a file that includes only the species needed for the reanalysis of the corrected and recoded data from Katona et al. (2023) for maternal nutrition mode only, and results are presented in Table 2 of Hughes & Blackburn (2025), Column F. ##### Variables * Species names #### File: shark\_modepruned\_F\_nutrition.csv **Description:** This is a file that includes the species and their traits for the reanalysis of the corrected and recoded data from Katona et al. (2023) for maternal nutrition mode only, and results are presented in Table 2 of Hughes & Blackburn (2025), Column F. ##### Variables * species: Species names * mode: Corrected reproductive modes from Katona et al. (2023), limited to only those species with maternal nutrition mode information, and renamed to conform to categories in Blackburn & Hughes (2024): Histotrophy, Lecithotrophy, Oophagy, Placentotrophy. ## Code/software Hughes&Blackburn_RScript_26Jan2025.R This file conducts all of the analyses used in the manuscript. ###### *Language and Environment* R Environment for Statistical Computing and R Studio ###### *Version* R version 4.4.2 (2024-10-31) -- "Pile of Leaves" ***Dependencies*** * ape * phytools * openxlsx * geiger * magrittr * plotrix ## Access information Data derived from the following sources: * Katona et al. (2023): [https://doi.org/10.1111/jeb.14231](https://doi.org/10.1111/jeb.14231) * Blackburn & Hughes (2024): [https://doi.org/10.1111/brv.13070](https://doi.org/10.1111/brv.13070)