Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. Integrating meta-analysis, field data, and population modeling, we show that the ocean’s smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs.

LETTERSUndercover. Many Alpheidae shrimps live deep in the reef and are impossible to collect nonlethally. Published by AAAS

Mesophotic coral ecosystems, which occur at depths of ~40 to 150 m, have received recent scientific attention as potential refugia for organisms inhabiting deteriorating shallow reefs. These ecosystems merit research in their own right, as they harbor both depth-generalist species and a distinctive reef-fish fauna. Reef ecosystems just below the mesophotic are globally underexplored, and the scant recent literature that mentions them often suggests that mesophotic ecosystems transition directly into those of the deep sea. Through submersible-based surveys in the Caribbean Sea, we amassed the most extensive database to date on reef-fish diversity between ~40 and 309 m at any single tropical location. Our data reveal a unique reef-fish assemblage living between ~130 and 309 m that, while taxonomically distinct from shallower faunas, shares strong evolutionary affinities with them. Lacking an existing name for this reef-faunal zone immediately below the mesophotic but above the deep aphotic, we propose “rariphotic.” Together with the “altiphotic,” proposed here for the shallowest reef-faunal zone, and the mesophotic, the rariphotic is part of a depth continuum of discrete faunal zones of tropical reef fishes, and perhaps of reef ecosystems in general, all of which warrant further study in light of global declines of shallow reefs.

No abstract

This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding “coverages” for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the “Genetypes” naming system, which some have been reluctant to adopt because of the use of the “type” suffix in the terminology. In the new nomenclature, genetic sequences are labeled “genseq,” followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types – “genseq-1,” secondary types – “genseq-2,” collection-vouchered topotypes – “genseq-3,” collection-vouchered non-types – “genseq-4,” and non-types that lack specimen vouchers but have photo vouchers – “genseq-5.” To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital “G” and “S” when referring to the nomenclatural program) to provide a searchable tag (e.g., “genseq”; note lowercase “g” and “s” when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made.

Aim To investigate how marine barriers shaped the demographic history of Atlantic seahorses (Syngnathidae: Hippocampus). Location Atlantic Ocean. Methods Range‐wide sampling (n = 390) at mitochondrial and up to five nuclear DNA loci was carried out across the Hippocampus erectus species complex (H. erectus from the Caribbean/North America, H. patagonicus from South America and H. hippocampus from Europe and West Africa). Multi‐species coalescent and approximate Bayesian computation (ABC) frameworks were used to estimate support of competing biogeographical hypotheses and demographic parameters, including lineage divergence times, effective population sizes and magnitudes of population size change. Results We identified four distinct lineages within the H. erectus complex. A posterior probability of 0.626 and corresponding Bayes factors ranging from 3.68 to 11.38 gave moderate to strong support for a basal divergence between South American populations of H. patagonicus and Caribbean/North American populations of H. erectus coincident with the inter‐regional freshwater outflow of the Amazon River Barrier (ARB). Estimates of historical effective population sizes and divergence times indicate that European and West African populations of H. hippocampus expanded after colonization from a more demographically stable Caribbean/North American H. erectus. Main conclusions Our findings of trans‐Atlantic colonization followed by isolation across a deep oceanic divide, and isolation across a freshwater barrier, may demonstrate a contrast in marine divide permeability for this group of rafters. Demographic inference supports the establishment of an ancestral population of the H. erectus complex in the Americas, followed by the ARB splitting it into Caribbean/North and South American lineages at a time of increased sedimentation and outflow. Our estimates suggest that following this split, colonization occurred across the Atlantic via the Gulf Stream currents with subsequent trans‐Atlantic isolation. These results illustrate that rafting can be a means of range expansion over large distances, but may be insufficient for sustaining genetic connectivity across major barriers, thereby resulting in lineage divergence.