J. Andrés López

The Tree of Life and a New Classification of Bony Fishes

The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes.

This study examines phylogenetic placement of the enigmatic Western Australian Lepidogalaxias, and extends previous studies by including eight new taxa to enable re-examination phylogenetic relationships of lower euteleostean fishes at the ordinal level, based on mitochondrial genomes from 39 ingroup taxa and 17 outgroups. Our results suggest that Lepidogalaxias occupies a basal position among all euteleosts, in contrast with earlier hypotheses that variously suggested a closer relationship to esocid fishes, or to the galaxiid Lovettia. In addition our evidence shows that Osmeriformes should be restricted Retropinnidae, Osmeridae, Plecoglossidae and Salangidae. This reduced Osmeriformes is supported in our results as the sister group of Stomiiformes. Galaxiidae, which is often closely linked to Osmeriformes, emerges as sister group of a combined Osmeriformes, Stomiiformes, Salmoniformes, Esociformes and Argentiformes, and we give Galaxiiformes the rank of order to include all remaining galaxioid fishes (Galaxias and allied taxa, Aplochiton and Lovettia). Our results also support a sister group relationship between Salmoniformes and Esociformes, which are together the sister group of Argentiniformes.

Phylogenetic Relationships of Extant Esocid Species (Teleostei: Salmoniformes) Based on Morphological and Molecular Characters

Abstract The phylogenetic relationships of extant species of Esox were investigated using both morphological and molecular data. The complete mtDNA cytochrome b gene (cytb) and the second intron of the RAG1 gene were sequenced from multiple specimens of each species and analyzed using maximum parsimony and maximum likelihood. The resulting cladograms were compared with each other and to the morphological cladogram for congruence. Data from all three sources strongly support the monophyly of the genus, and the monophyly of the subgenera Esox (i.e., pikes) and Kenoza (i.e., pickerels). Our data support the sister-group relationship between Esox reicherti and Esox lucius (the Amur and Northern Pike, respectively). Incongruent results between the morphological and RAG1 data and the cytb data, with respect to pickerel interrelationships, suggest hybridization and introgression among pickerel species. Additional research is necessary to explore these results further. This study represents the first study to integrate both morphological and molecular data into a phylogenetic analysis of Esox. It aims to provide a better understanding of esocid evolution and lay the foundation for the interpretation of fossil material assigned to Esox. It also provides preliminary genetic evidence of hybridization among the pickerels.

Pike and salmon as sister taxa: Detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences

The increasing number of taxa and loci in molecular phylogenetic studies of basal euteleosts has brought stability in a controversial area. A key emerging aspect to these studies is a sister Esociformes (pike) and Salmoniformes (salmon) relationship. We evaluate mitochondrial genome support for a sister Esociformes and Salmoniformes hypothesis by surveying many potential outgroups for these taxa, employing multiple phylogenetic approaches, and utilizing a thorough sampling scheme. Secondly, we conduct a simultaneous divergence time estimation and phylogenetic inference in a Bayesian framework with fossil calibrations focusing on relationships within Esociformes+Salmoniformes. Our dataset supports a sister relationship between Esociformes and Salmoniformes; however the nearest relatives of Esociformes+Salmoniformes are inconsistent among analyses. Within the order Esociformes, we advocate for a single family, Esocidae. Subfamily relationships within Salmonidae are poorly supported as Salmoninae sister to Thymallinae+Coregoninae.

Phylogenetic Relationships of Esocoid Fishes (Teleostei) Based on Partial Cytochrome b and 16S Mitochondrial DNA Sequences

Abstract The phylogenetic systematics of esocoid fishes are examined using comparisons of partial DNA sequences of the mitochondrial genes coding for the transmembrane protein cytochrome b and the 16S RNA ribosomal subunit. Nucleotide sequences from all species of umbrids, three species of esocids, and salmonid, osmerid, cypriniform, and neoteleostean outgroups were compared to determine patterns of molecular evolution and uncover evidence of phylogenetic relationships. Multiple sequence alignments for each of the two DNA regions examined were used to characterize the amount and type of change shown by the data. The sequences were analyzed under different models of molecular evolution using maximum-parsimony and maximum-likelihood optimality criteria of phylogenetic reconstruction. The phylogenetic analyses revealed previously undiscovered affinities between species of umbrids and esocids that imply the paraphyly of the Umbridae as currently defined. The following set of esocoid interrelationships is proposed: (((Esox, Novumbra), Dallia), Umbra). Esocoid classification is revised based on present findings.

Are flatfishes (Pleuronectiformes) monophyletic

All extant species of flatfish (order Pleuronectiformes) are thought to descend from a common ancestor, and therefore to represent a monophyletic group. This hypothesis is based largely on the dramatic bilateral asymmetry and associated ocular migration characteristics of all flatfish. Yet, molecular-based phylogenetic studies have been inconclusive on this premise. Support for flatfish monophyly has varied with differences in taxonomic and gene region sampling schemes. Notably, the genus Psettodes has been found to be more related to non-flatfishes than to other flatfishes in many recent studies. The polyphyletic nature of the Pleuronectiformes is often inferred to be the result of weak historical signal and/or artifact of phylogenetic inference due to a bias in the data. In this study, we address the question of pleuronectiform monophyly with a broad set of markers (from six phylogenetically informative nuclear loci) and inference methods designed to limit the influence of phylogenetic artifacts. Concomitant with a character-rich analytical strategy, an extensive taxonomic sampling of flatfish and potential close relatives is used to increase power and resolution. Results of our analyses are most consistent with a non-monophyletic Pleuronectiformes with Psettodes always being excluded. A fossil-calibrated Bayesian relaxed clock analysis estimates the age of Pleuronectoidei to be 73 Ma, and the time to most recent common ancestor of Pleuronectoidei, Psettodes, and other relative taxa to be 77 Ma. The ages are much older than the records of any fossil pleuronectiform currently recognized. We discuss our findings in the context of the available morphological evidence and discuss the compatibility of our molecular hypothesis with morphological data regarding extinct and extant flatfish forms.

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.

Molecular data do not provide unambiguous support for the monophyly of flatfishes (Pleuronectiformes): A reply to Betancur-R and Ortí

Betancur-R and Ortí (2014) offer a criticism of our recent examination of the monophyly of extant flatfishes (Pleuronectiformes; Campbell et al., 2013). We welcome this opportunity to examine and respond to the main issues presented in Betancur-R and Ortí (2014). Briefly, this debate centers on the question of whether or not analyses of the available evidence support a stable and confident conclusion regarding a sister group relationship between the two recognized pleuronectiform suborders: Psettodoidei (four species) and Pleuronectoidei (>700 species). In Campbell et al. (2013), we reported results based on sequences from six nuclear genes compatible with monophyly of Pleuronectoidei but not with that of Pleuronectiformes. In our analyses, the most closely related percomorph family to the Pleuronectoidei was resolved to be the Centropomidae. In Campbell et al. (2013), we also provided a critical review of the morphological evidence in favor flatfish monophyly showing that this evidence requires a careful re-examination where it concerns psettodoids. Here we present our perspective on the issues raised in Betancur-R and Ortí (2014).

The Phylogenetic Affinities of the Mysterious Anguilliform Genera Coloconger and Thalassenchelys as Supported by mTDNA Sequences

Abstract The family Colocongridae and the genus Thalassenchelys are two enigmatic anguilliform taxa whose phylogenetic affinities are poorly understood. Here we present results from parsimony and Bayesian phylogenetic analyses of mitochondrial ribosomal RNA sequences from a taxonomic sample designed to test alternative placements of colocongrids and Thalassenchelys among anguilliforms. The phylogenetic analysis invariably and robustly supports a clade composed of Coloconger and Thalassenchelys, which, in turn, is supported as most closely related to the derichthyids. The degree of DNA sequence divergence observed between Coloconger and Thalassenchelys is comparable to that observed between congeners in the genus Ophichthus and lower than that observed between two members of the subfamily Muraeninae. Because no evidence has been offered to support an alternative placement of Thalassenchelys, we propose that it be included in the Colocongridae. In addition, the results of the present study are congruent with recent molecular-based hypotheses that suggest a close relationship between Anguillidae, Serrivomeridae, and Nemichthyidae, and a monophyletic group comprised of the families Congridae, Ophichthidae, Colocongridae, Derichthyidae, Muraenesocidae, and Nettastomatidae. We found no support for the three major anguilliform lineages that have been proposed based on morphology.

Two New Species of Marine Saprotrophic Sphaeroformids in the Mesomycetozoea Isolated From the Sub-Arctic Bering Sea

The genus Sphaeroforma previously encompassed organisms isolated exclusively from animal symbionts in marine systems. The first saprotrophic sphaeroformids (Mesomycetozoea) isolated from non-animal hosts are described here. Sphaeroforma sirkka and S. napiecek are also the first species in the genus possessing endogenous DNA-containing motile propagules and central vacuoles, traits that have previously guided morphological differentiation of sphaeroformids from the genus Creolimax. Phylogenetic analysis of DNA sequences from the 18S rRNA and the ITS1-5.8S--ITS2 loci firmly place S. sirkka and S. napiecek within Sphaeroforma, extending the number of known species to six within this genus. The discovery of these species increases the geographical range, cellular variation and life history complexity of the sphaeroformids.