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Data and code for: Parthenogenesis is self-destructive for scaled reptiles

Citation

Moreira, Matthew; Rojas, Danny; Fonseca, Carlos (2021), Data and code for: Parthenogenesis is self-destructive for scaled reptiles, Dryad, Dataset, https://doi.org/10.5061/dryad.sqv9s4n3c

Abstract

Parthenogenesis is rare in nature. With 39 described true parthenogens, scaled reptiles (Squamata) are the only vertebrates that evolved this reproductive strategy. Parthenogenesis is ecologically advantageous in the short-term, but the young age and rarity of parthenogenetic species indicate it is less advantageous in the long-term. This suggests parthenogenesis is self-destructive: it arises often but is lost due to increased extinction rates, high rates of reversal or both. However, this role of parthenogenesis as a self-destructive trait remains unknown. We used a phylogeny of Squamata (5,388 species), tree metrics, null simulations and macroevolutionary scenarios of trait diversification to address the factors that best explain the rarity of parthenogenetic species. We show that parthenogenesis can be considered as self-destructive, with high extinction rates mainly responsible for its rarity in nature. Since these parthenogenetic species occur, this trait should be ecologically relevant in the short-term.

Methods

We obtained two phylogenies for this study. The first phylogeny, used in the main text, was obtained from Tonini et al. [1]. Specifically, we used the posterior distribution of 10,000 phylogenies of Squamata with 9,754 species each (9,755 if we included the Tuatara) [1]. We pruned all trees using ape v5.3 in R [2] to the species with molecular data in [1]. The final set of phylogenies included 5,388 species each. Finally, we calculated the 50% majority-rule consensus tree in MrBayes v3.2 [3]. The final consensus tree (ESM 2.tre) includes 5,388 species and was used in the primary analyses. The second phylogeny was obtained from Zheng & Wiens [4]. The original phylogeny includes 4,169 species. We removed duplicates and the outgroup (n=46). The final alternative phylogeny (ESM 3.tre) includes 4,123 species and was used in the alternative analyses.

References

1. Tonini JFR, Beard KH, Ferreira RB, Jetz W, Pyron RA. 2016 Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conserv. 204, 23–31. (doi:10.1016/j.biocon.2016.03.039)

2. Paradis E, Schliep K. 2019 ape 5.3: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528. (doi:10.1093/bioinformatics/bty633)

3. Ronquist F et al. 2012 MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542. (doi:10.1093/sysbio/sys029)

4. Zheng Y, Wiens JJ. 2016 Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. 94, 537–547. (doi:10.1016/j.ympev.2015.10.009)

Usage Notes

The ESM 4.R script includes the code to run the analyses in this study. Specifically, it includes: 1) calculation of TARS, NoTO, SSCD and FPD; 2) 100 trees simulation for each macroevolutionary scenario; 3) calculation of TARS, NoTO, SSCD and FPD for each simulated tree; 4) power analyses and false discovery rates for the primary phylogeny. 

Funding

Fundação para a Ciência e a Tecnologia, Award: PD/BD/135554/2018

Fundação para a Ciência e a Tecnologia, Award: UIDP/50017/2020+UIDB/50017/2020

Pontificia Universidad Javeriana Cali, Award: Project 230 & 1053