Data from: Recurrent evolution of small body size and loss of the sword ornament in Northern swordtail fish

Preising, Gabriel 1 ; Gunn, Theresa1; Baczenas, John1; Powell, Daniel1; Dodge, Tristram1; Sewell, Sean1; Pollock, Alexa1; Machin Kairuz, Jose Angel1; Savage, Markita2; Lu, Yuan2; Fitschen-Brown, Meredith3; Meyer, Axel4; Schartl, Manfred5; Cummings, Molly6; Thakur, Sunishka6; Inmam, Callen6; Rios-Cardenas, Oscar7; Morris, Molly3; Tobler, Michael8; Schumer, Molly1

Published Oct 03, 2024 on Dryad. https://doi.org/10.5061/dryad.sf7m0cggb

Data files

Oct 03, 2024 version files 55.66 KB

phy_test_info_20240430_recode.csv

34.67 KB
RAxML_bipartitions.NS_complete_20231215_treefile_addmorphs.txt.tre
712 B
README.md
4.01 KB
sl_dists.csv

9.58 KB
xipho_phen_m_comp_PC1-2.csv

6.69 KB

Abstract

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.

README: 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/

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