DOI: 10.5061/dryad.hqbzkh1n6
title: Astyanax cavefish body shape coordinates from: Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae)

description: The Astyanax mexicanus complex includes two different morphs, a surface
 and a cave-adapted ecotype, found at three mountain ranges in Northeastern
 Mexico: Sierra de El Abra, Sierra de Guatemala, and Sierra de la Colmena
 (Micos). Since their discovery, multiple studies have attempted to
 characterize the timing and the number of events that gave rise to the
 evolution of these cave-adapted ecotypes. Here, using RAD-seq and
 genome-wide sequencing, we assessed the phylogenetic relationships,
 genetic structure, and gene flow events between the cave and surface
 Astyanax mexicanus populations, to estimate the time and mode of evolution
 of the cave-adapted ecotypes. We also evaluated the body shape evolution
 across different cave lineages using geometric morphometrics to examine
 the role of phylogenetic signal vs. environmental pressures. We found
 strong evidence of parallel evolution of cave-adapted ecotypes derived
 from two separate lineages of surface fish and hypothesize that there may
 be up to four independent invasions of caves from surface fish. Moreover,
 a strong congruence between the genetic structure and geographic
 distribution was observed across the cave populations, with the Sierra de
 Guatemala the region exhibiting most genetic drift among the cave
 populations analyzed. Interestingly, we found no evidence of phylogenetic
 signal in body shape evolution, but we found support for parallel
 evolution in body shape across independent cave lineages, with cavefish
 from the Sierra de El Abra reflecting the most divergent morphology
 relative to surface and other cavefish populations.
description: To characterize the morphological divergence between surface and
 cavefish, we performed landmark<em>-</em>based Geometric
 Morphometrics (GM) analyses on lateral left-hand view of the body shape,
 for a total of 146 individuals from surface and cave populations. All
 photographs were transformed to a TPS file using the TPSUtil program. We
 digitized 12 homologous <em>landmarks</em> and a curve with 15
 <em>pseudo-landmarks </em>with the TPSDig2 v. 2.31 (Rohlf,
 2015). A Generalized Procrustes Analysis (GPA) was performed with the
 “<em>gpagen</em>” in Geomorph v. 4.02 (R Core Team, 2019), and
 with the ‘<em>curve</em>’ argument the sliders were defined
 with the Procrustes distance criterion to optimize the position of the
 sliding reference point during the GPA. To avoid a size effect by
 allometry, the residuals of the regression of the shape on the centroid
 size (CS) were calculated with the function
 "<em>procD.lm</em>". Once the residuals were
 obtained, an allometry-free shape was created, using these residuals of
 the morphological data. The analyses were made on this allometry-free
 shape. To assess the degree of variation in body shape between groups, we
 used principal component analysis using the
 “<em>gm.prcomp</em>” function.
description: The archive can be visualized with any text editor; the data was
 worked in TPS software and analyzed in R, with the
 <em>'geomoprh' </em>package.