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 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.