Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)

Abstract

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.

Preface: How far has Neotropical Ichthyology progressed in twenty years?

“…We have also advanced greatly in our knowledge of the phylogeny and evolution of Neotropical fishes, with recent molecular, morphological and combined studies frequently resolving stable reconstructions among families and genera within each order (Oliveira et al, 2011;Birindelli, 2014;Lujan et al, 2015;Lopez-Fernandez et al, 2010;Dillman et al, 2016;Tagliacollo et al, 2016;Ilves et al, 2018;Mirande, 2018;Carvalho et al, 2018). Yet, not all studies agree, and new data have challenged existing classifications (Covain et al, 2016), refined longstanding phylogenetic hypotheses (Melo et al, 2018) or identified recalcitrant nodes that challenge even the most current analyses (Ilves et al, 2018).…”

“…We have also advanced greatly in our knowledge of the phylogeny and evolution of Neotropical fishes, with recent molecular, morphological and combined studies frequently resolving stable reconstructions among families and genera within each order (Oliveira et al, 2011;Birindelli, 2014;Lujan et al, 2015;Lopez-Fernandez et al, 2010;Dillman et al, 2016;Tagliacollo et al, 2016;Ilves et al, 2018;Mirande, 2018;Carvalho et al, 2018). Yet, not all studies agree, and new data have challenged existing classifications (Covain et al, 2016), refined longstanding phylogenetic hypotheses (Melo et al, 2018) or identified recalcitrant nodes that challenge even the most current analyses (Ilves et al, 2018). Some of the most substantial uncertainty surrounds the resolution of the major lineages within Ostariophysi, with some molecular studies returning paraphyly of the two major characiform suborders or not recovering a sister relationship between Siluriformes and Gymnotiformes (Nakatani et al, 2011;Chakrabarty et al, 2016), as long supported by morphological data (Fink, Fink, 1981), and as also recovered by a prominent phylogenomic study (Arcila et al, 2017).…”

An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species

“…This approach has been used for the successful resolution of species phylogenies (e.g. Ilves & López-Fernández, 2014;Bossert & Danforth, 2018;Ilves et al, 2018). It is also an effective method for capturing and enriching degraded and contaminated ancient DNA from extinct groups in paleontology (e.g.…”

Morphological and molecular identification of Geophagus sveni Lucinda, Lucena & Assis, 2010 (Cichlidae, Cichliformes) from the Paraná river basin, Argentina

“…The family Cichlidae is a very diverse fish group with 1711 species (Fricke et al 2018) distributed in fresh-and brackish waters of North, Central, and South America, Africa, the Jordan Valley in the Middle East, Madagascar, Iran, southern India, and Sri Lanka (Kullander 2003). Historically classified as part of the taxonomically conflictive Perciformes, recent phylogenetic works suggested that together with monotypic Pholidichthyidae, they belong to the order Cichliformes (Betancur-R. et al 2013, Mirande 2017, Betancur-R. et al 2017, Ilves et al 2018.…”

“…Those characters define the Geophagus sensu stricto species group and are absent in the species from the "Geophagus" brasiliensis and "Geophagus" steindachneri species groups. Molecular phylogenetic studies (López-Fernández et al 2010, Ilves et al 2018) also split species of Geophagus in these 3 different clades. Geopha-gus sensu stricto and "Geophagus" steindachneri groups are related to Gymnogeophagus (Geophagines), whereas "Geophagus" brasiliensis group is more closely related to Mikrogeophagus (Mikrogeophagines) and Biotodoma (Ilves et al 2018).…”