Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Abstract

Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

“…To estimate the spatiotemporal loss/persistence pattern of TGD-derived gene (hereafter gene lineage; Fig. 1B) pairs, we accurately identified orthologous and paralogous relationships between tetrapod and teleost genes (involving TGD-derived gene lineage pairs in teleosts) by conducting rigorous phylogenetic and reconciliation analyses with the species tree for all protein-coding gene sequences retrieved (11,41) with the timing of genome duplication events at the base of vertebrates (VGD1/2) and teleosts (TGD), and the number of extant species (26). Species used in this study are connected by solid branches.…”

“…Using these numbers of TGD-derived paired gene lineages, we parsimoniously estimated the ancestral number of gene lineage pairs at each node (a-h in Fig. 1A) of the teleost time-calibrated phylogenetic tree (11). Plotting the number of gene lineage pairs at every node against its divergence time, we estimated the temporal pattern of gene loss/persistence (Fig.…”

Myxobolus marajoensis sp. n. (Myxosporea: Myxobolidae), parasite of the freshwater catfish Rhamdia quelen from the Brazilian Amazon region

“…The phylogenetic relatedness of the Myxobolus and Henneguya species reflects a tendency for the formation of parasite clades related closely to their host species (CARRIERO et al, 2013), indicating coevolutionary relationships between the ancestral parasites and their hosts (BROUGHTON et al, 2013). In fact, the cladogram (Figure 2) reflects a grouping associated more closely with the hosts than the morphological or biogeographic characteristics of the parasites themselves.…”

Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology

“…However, quantifying both interindividual and interspecies variability in drug uptake and metabolism, and extrapolating between individual physiological responses and adverse population-level effects, represent major sources of uncertainty in pharmaceutical environmental risk assessment (ERA) [16]. Fish make up half of all vertebrate species, inhabiting virtually all aquatic environments [20] and exhibiting enormous diversity in morphology, physiology, behaviour, reproductive biology and population ecology [21]. ERAs concerning the susceptibility of fish to pharmaceuticals, however, are based on studies on only a few model fish species and rarely extend to the quantification of population-level effects.…”

“…proteins that share a common evolutionary origin to human and veterinary drug targets, may be more responsive than species lacking orthologues. Fish underwent evolutionary divergence from other vertebrates 450 Ma [21], but they nevertheless exhibit high evolutionary conservation of human and veterinary drug targets compared with other taxonomic groups used in aquatic ERA. For example, in zebrafish and threespined stickleback, orthologues are predicted for 86% of human drug targets [3].…”