Data and R Script from: The ancestor of sharks and rays laid eggs, but ancestral state reconstructions need empirically supported traits and transparent reporting

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 m..., 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..., , # 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 ...