DOI: 10.5061/dryad.sf7m0cggb
title: Data from: Recurrent evolution of small body size and loss of the sword ornament in Northern swordtail fish

description: Across the tree of life, species have repeatedly evolved similar
 phenotypes. While well-studied for ecological traits, there is also
 evidence for recurrent evolution of sexually selected traits. Swordtail
 fish (Xiphophorus) are a classic model system for studying sexual
 selection, and female Xiphophorus exhibit strong mate preferences for
 large male body size and a range of sexually dimorphic ornaments.
 Interestingly, sexually selected traits have also been lost multiple times
 in the genus. However, there has been uncertainty over the number of
 losses of ornamentation and large body size because phylogenetic
 relationships between species in this group have historically been
 controversial, partially due to prevalent gene flow. Here, we use
 whole-genome sequencing approaches to re-examine phylogenetic
 relationships within a Xiphophorus clade that varies in the presence and
 absence of sexually selected traits. Using wild-caught individuals, we
 determine the phylogenetic placement of a small, unornamented species, X.
 continens, confirming an additional loss of ornamentation and large body
 size in the clade. With these revised phylogenetic relationships, we
 analyze evidence for coevolution between body size and other sexually
 selected traits using phylogenetic comparative methods. These results
 provide insights into the evolutionary pressures driving the recurrent
 loss of suites of sexually selected traits.
description: This repository includes the morphological measurements and
 Newick tree file from Preising et al. 2024: Recurrent evolution of small
 body size and loss of the sword ornament in Northern swordtail fish.
 Morphological data were collected from standardized lateral images of
 <em>Xiphophorus</em> and outgroup species with a scale bar for
 reference. Please refer to the methods and supplemental information of
 Preising et al. 2024 for details on phylogeny construction.
 Code that uses these datasets can be found at https://github.com/gpreising/phylogeny_update.
description: # DRYAD repository for Preising et al. 2024 - Recurrent evolution of small
 body size and loss of the sword ornament in Northern swordtail fish Data
 and associated scripts can also be found at
 [https://github.com/gpreising/phylogeny_update/](https://github.com/gpreising/phylogeny_update/) ## Morphological Datasets **phy_test_info_20240430_recode.csv** - main file that contains morphological measurements used for PGLS and PCA. This is also Table S2 in the manuscript. Continuous variables were measured in mm. The following variables were recorded: * **species** - species of the individual being measured * **sex** - sex of the individual being measured * **fish_ID** - individual ID for photo * **std_length** - standard length (in mm), measured from tip of the snout to posterior end of hypural plate * **swd_length** - sword length (in mm), measured as distance from the distal end of the caudal fin extension to the proximal end of the caudal fin extension where it joins with the distal edge of the caudal fin itself * **vertical_bars** - number of vertical bars (integer) * **caudal_fin_pigmentation** - caudal fin pigmentataion; 0/1 presence/absence * **dorsal_fin_pigmentation** - dorsal fin pigmentation; 0/1 presence/absence * **sword_pigmentation** - integer value for number of discrete pigments within the upper and lower sword edges (0/1 presence/absence in most cases, but a handful of *X. mayae* individuals showed 2 discrete colors) * **upper_sword_edge_width** - width (in mm) of upper black sword stripe at thickest point * **upper_sword_edge_width** - length (in mm) of upper black sword stripe from distal end of caudal fin extension to posterior end of hypural plate * **lower_sword_edge_width** - width (in mm) of lower black sword stripe at thickest point * **lower_sword_edge_length** - length (in mm) of lower black sword stripe from distal end of caudal fin extension to the endpoint of pigmentation into the body * **dorsal_fin_length** - distance (in mm) from first insertion of dorsal fin to last insertion of dorsal fin * **dorsal_fin_height** - height (in mm) of the longest ray of the dorsal fin * **body_depth** - distance (in mm) from first insertion of dorsal fin to first insertion of anal fin * **peduncle_depth** - distance (in mm) from ventral edge of caudal peduncle to dorsal edge of caudal peduncle, right before it rounds off towards the posterior of the fish * **caudal_fin_length** - length (in mm) of the longest ray of the caudal fin * **caudal_fin_height** - distance (in mm) from distal end of first ray to distal end of last ray when caudal fin is spread out * **false_gravid_spot** - 0/1; presence/absence false gravid spot pigmentation phenotype * **peduncle_edge** - length (in mm) of black ventral pigmentation from posterior end of caudal peduncle towards anterior end of fish * **lower_edge_2_peduncle** - length (in mm) of the lower sword edge from distal end of caudal fin extension to posterior end of caudal peduncle * **sc** - 0/1; presence/absence spotted caudal pigmentation phenotype * **atro** - 0/1; presence/absence atromatculatus pigmentation phenotype * **carbo** - 0/1; presence/absence carbomaculatus pigmentation phenotype * **cb** - 0/1; presence/absence caudal blotch pigmentation phenotype * **tactic** - sneaker/ambiguous/courter; reproductive tactic * **clade** - NS/P/SS; Northern swordtail clade, platyfish, Southern swordtail clade * **tree_lab** - species ID corresponding to labels in the Newick tree file **xipho_phen_m_comp_PC1-2.csv** - final processed male average traits used for PGLS with the addition of PC1 and PC2 from the sexual dimorphism pPCA (Fig 2B) **sl_dist.csv** - standard length distributions (in mm) used to test for bimodality used in Fig 2D ## Newick tree file **RAxML_bipartitions.NS_complete_20231215_treefile_addmorphs.txt.tre** - phylogeny generated with RAxML; please refer to the methods and supplementary information from Preising et al. 2024 for details on how this file was generated