DOI: 10.5061/dryad.sqv9s4n3c
title: Data and code for: Parthenogenesis is self-destructive for scaled reptiles

description: 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.
description: 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. <i>Biol. Conserv.</i> <b>204</b>, 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. <i>Bioinformatics</i> <b>35</b>, 526–528.
 (doi:10.1093/bioinformatics/bty633) 3. Ronquist
 F <i>et al.</i> 2012 MrBayes 3.2: efficient bayesian
 phylogenetic inference and model choice across a large model
 space. <i>Syst. Biol.</i> <b>61</b>, 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. <i>Mol. Phylogenet.
 Evol.</i> <b>94</b>, 537–547.
 (doi:10.1016/j.ympev.2015.10.009)
description: 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.