Data and R Script from: The ancestor of sharks and rays laid eggs, but ancestral state reconstructions need empirically supported traits and transparent reporting
Data files
Feb 24, 2025 version files 283.55 KB
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AllSharks1Tree.tre
54.97 KB
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keepspecies_main_D.csv
20.40 KB
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keepspecies_main_E.csv
20.36 KB
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keepspecies_main_F_nutrition.csv
20.36 KB
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keepspecies_main_F_parity.csv
20.38 KB
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README.md
4.88 KB
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shark_modepruned_D.csv
38.54 KB
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shark_modepruned_E.csv
38.42 KB
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shark_modepruned_F_nutrition.csv
33.28 KB
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shark_modepruned_F_parity.csv
31.96 KB
Abstract
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.
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.
R Environment for Statistical Computing and R Studio
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
- Blackburn & Hughes (2024): https://doi.org/10.1111/brv.13070
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. Journal of Evolutionary Biology, 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. Biological Reviews, 99(4): 1314–1356. https://doi.org/10.1111/brv.13070