Introduction
Upon colonizing cave environments, a variety of animals (various arthropods, crustaceans, several vertebrates) have converged in morphology, physiology, and behavior (Juan et al. 2010; Romero 2011; Protas and Jeffery 2012). While common selective pressures leading to adaptation presumably account for such evolutionary convergence, the loss of traits in cave organisms has also been attributed to genetic drift (Wilkens and Strecker 2017; Policarpo et al. 2021). The remarkable degree to which different traits have evolved convergently and in concert also suggests that various constraints may place limits on adaptation and drive the course of evolution in cave systems (Franz-Odendaal and Hall 2006). At the molecular and developmental level, phenotypic changes associated with living in caves could be accounted for either by mutations in coding regions of genes (Kim et al. 2011; Warren et al. 2021) or by changes in patterns of gene expression (van der Weele and Jeffery 2022; Arcila et al. 2023), possibly involving phenotypic plasticity (Bilandžija et al. 2020) and epigenetics (Gore et al. 2018).
In fish, species in multiple evolutionary lineages have evolved convergently in caves (Chakrabarty et al. 2012; Armbruster et al. 2016; Hashemzadeh Segherloo et al. 2018). Losses or reductions in eyes and pigmentation are especially well known (Niemiller et al. 2019), but whether similar phenotypes of different fish species living in caves have evolved using equivalent molecular mechanisms remains to be determined. Also, existing information is insufficient to establish the relative importance of changes in coding regions of genes versus changes in regulatory regions that change patterns of gene expression to account for phenotypic evolution.
Developing new genomic resources is fundamental to pursue research in such systems. We recently assessed whether fishes in the Neotropical genus Trichomycterus (Siluriformes) inhabiting cave environments in the Eastern Cordillera of the Andes of Colombia and which lack eyes and pigmentation evolved via a: (1) single event of colonization of subterranean environments and subsequent vicariance or dispersal leading to the origin of new species; or (2) multiple colonizations of caves from surface environments followed by evolutionary convergence (Flórez et al. 2021). Employing mitochondrial DNA sequences to infer phylogeographic relationships, we found that caves in this region have been colonized separately by at least two different clades of Trichomycterus. In addition, we documented shallow to non-existent mtDNA
divergence between surface and cave populations, even though they differ considerably in morphology; this suggests that their divergence is recent or has proceeded in the face of gene flow, with selection counteracting homogenizing effects of migration (Flórez et al. 2021). In either case, the system is an attractive model to assess the genetic basis of adaptation to life in caves using genomic tools.
We report a high-quality de novo reference genome generated for the cave specialist species endemic to Colombia Trichomycterus rosablanca using long-read sequencing and the Vertebrate Genomes Project (VGP) genome assembly pipeline. This reference genome will serve as a vital resource for studies aimed at understanding the genetic basis of phenotypic evolution in cave environments.
«Artículos de Mauricio Torres con afiliación a la Fundación IGUAQUE»
Carlos Daniel Cadena / Laura Pabón / Carlos DoNascimiento / Linelle Abueg / Tatiana Tiley / Brian O-Toole / Dominic Absolon / Ying Sims / Giulio Formenti / Olivier Fedrigo / Erich D. Jarvis / Mauricio Torres
PARA VER EL ARTICULO COMPLETO VISITA:
https://www.biorxiv.org/content/biorxiv/early/2023/11/13/2023.11.11.566715.full.pdf
