Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy.

The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae. [Characiformes; exon capture; ichthyochory; molecular time-calibration; piscivory.].

Temporal changes in hamlet communities (Hypoplectrus spp., Serranidae) over 17 years.

Transect surveys of hamlet communities (Hypoplectrus spp., Serranidae) covering 14 000 m2 across 16 reefs off La Parguera, Puerto Rico, are presented and compared with a previous survey conducted in the year 2000. The hamlet community has noticeably changed over 17 years, with a > 30% increase in relative abundance of the yellowtail hamlet Hypoplectrus chlorurus on the inner reefs at the expense of the other hamlet species. The data also suggest that the density of H. chlorurus has declined and that its distribution has shifted towards shallower depths. Considering that H. chlorurus has been previously identified as one of the few fish showing a positive association with seawater turbidity on the inner reefs of La Parguera and that sedimentation of terrestrial origin has increased over recent decades on these reefs, it is proposed that turbidity may constitute an important but so far overlooked ecological driver of hamlet communities.

No longer a circumtropical species: revision of the lizardfishes in the Trachinocephalus myops species complex, with description of a new species from the Marquesas Islands.

Trachinocephalus, a formerly monotypic and nearly circumtropical genus of lizardfishes, is split into three valid species. Trachinocephalus gauguini n. sp. is described from the Marquesas Islands and is distinguished from the two other species in the genus by having a shorter snout, a narrower interorbital space, larger eye and modally fewer anal-fin and pectoral-fin rays. The distribution of Trachinocephalus myops (type species) is restricted to the Atlantic Ocean and the name Trachinocephalus trachinus is resurrected for populations from the Indo-West Pacific Ocean. Principal component analyses and bivariate plots based on the morphometric data differentiated T. gauguini from the other two species, but a substantial overlap between T. myops and T. trachinus exists. Phylogenetic evidence based on mtDNA COI sequences unambiguously supports the recognition of at least three species in Trachinocephalus, revealing deep divergences between the Atlantic Ocean, Indo-West Pacific Ocean and Marquesas entities. Additional analyses of species delimitations using the generalized mixed Yule coalescent model and the Poisson tree processes model provide a more liberal assessment of species in Trachinocephalus, indicating that many more cryptic species may exist. Finally, a taxonomic key to identify the three species recognized here is provided.

Chromosomal diversity in tropical reef fishes is related to body size and depth range.

Tropical reef fishes show contrasting patterns of karyotypic diversity. Some families have a high chromosomal conservatism while others show wide variation in karyotypic macrostructure. However, the influence of life-history traits on karyotypic diversity is largely unknown. Using phylogenetic comparative methods, we assessed the effects of larval and adult species traits on chromosomal diversity rates of 280 reef species in 24 families. We employed a novel approach to account for trait variation within families as well as phylogenetic uncertainties. We found a strong negative relationship between karyotypic diversity rates and body size and depth range. These results suggest that lineages with higher dispersal potential and gene flow possess lower karyotypic diversity. Taken together, these results provide evidence that biological traits might modulate the rate of karyotypic diversity in tropical reef fishes.

Molecular phylogenetics supports multiple evolutionary transitions from marine to freshwater habitats in ariid catfishes.

Transitions between the marine and freshwater environments represent an extraordinary ecological shift that has promoted diversification in many groups of aquatic organisms. Here, molecular phylogenetics is utilized to investigate habitat transitions in a group of catfishes (Ariidae) that includes species inhabiting marine and brackish waters (>110 species) as well as freshwater environments (approximately 40 species). The Ariidae is nested within the Otophysi, the largest clade of primary freshwater fishes with four orders and 67 families. Optimizations of habitat transitions (freshwater vs. marine) onto a previously inferred phylogeny suggest a single invasion of marine waters at the root of the ariid tree followed by 10-15 events of freshwater colonization, implying reversion to the primitive otophysan condition. Thus, ariids provide an extraordinary example of bidirectional habitat transitions in fishes. Freshwater recolonization has occurred in all major provinces where ariids are present, such as the New World (Mesoamerica and South America), Madagascar, Africa, Southeast Asia, and the Sahul continent (Australia and New Guinea). The remarkable diversity of freshwater ariids in Australia-New Guinea and Mesoamerica is presumed to have been facilitated by the originally depauperate freshwater ichthyofaunas in both regions, particularly the low diversity of primary otophysan families in Mesoamerica and their absence in Australia and New Guinea. The lack of phylogenetic resolution among basal Sahul lineages coupled with their extraordinary level of morphological divergence and trophic diversity suggests an ancient rapid radiation promoted by freshwater colonization. For this reason, Sahul ariids represent an excellent system for studying diversification associated with habitat transitions.