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

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.

Methods
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 Xiphophorus 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.