A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle

A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

An enigmatic pelagic fish with internalized red muscle: A future regional endotherm or forever an ectotherm?

Ectothermy and endothermy in extant fishes are defined by distinct integrated suites of characters. Although only ⁓0.1% of fishes are known to have endothermic capacity, recent discoveries suggest that there may still be uncommon pelagic fish species with yet to be discovered endothermic traits. Among the most rarely encountered marine fishes, the louvar Luvarus imperialis is a remarkable example of adaptive evolution as the only extant pelagic species in the order Acanthuriformes (including surgeonfishes, tangs, unicornfishes and Moorish idol). Magnetic resonance imaging and gross necropsy did not yield evidence of cranial or visceral endothermy but revealed a central-posterior distribution of myotomal red muscle that is a mixture of the character states typifying ectotherms (lateral-posterior) and red muscle endotherms (central-anterior). Dissection of a specimen confirmed, and an osteological proxy supported, that L. imperialis has not evolved the vascular rete that is vital to retaining heat in the red muscle. The combination of presumably relying on caudal propulsion while exhibiting internal red muscle without associated retia is unique to L. imperialis among all extant fishes, raising the macroevolutionary question of whether this species - in geologic timescales - will remain an ectotherm or evolve red muscle endothermy.

Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.

Mosaic adaptive peak shifts underlie body shape diversification in pelagiarian fishes (Acanthomorpha: Percomorpha)

Extreme body elongation in fishes is a major evolutionary transformation that extends the boundaries of morphological diversity and alters aspects of function, behaviour and ecology. Prior studies have identified features of the cranial and axial skeleton that characterize elongate fishes, but a lack of detailed reconstructions of anatomical evolution has limited inferences about factors that underlie major shifts in body shape. In this study, we fitted multi-peak adaptive (Ornstein–Uhlenbeck) evolutionary models to species body shape and anatomical dimensions in Pelagiaria, a radiation of open-ocean fishes whose species span a continuum from deep bodied to highly elongate. We inferred an ancestral fusiform adaptive peak that is retained by several major pelagiarian lineages (e.g. Scombridae) and found robust support for multiple transitions to deep-bodied optima (in the families Stromateidae, Bramidae and Caristiidae) and elongate-bodied optima (within Trichiuroidei), including two instances of sequential shifts towards increasingly elongate optima that followed distinct paths of anatomical evolution. Within Trichiuridae, initial increases in head length and the number of vertebrae were followed by changes in head and vertebral shape. Within an elongate-bodied subclade of taxa traditionally identified as ‘gempylids’, changes in head and vertebral shape and in the number of precaudal vertebrae preceded an increase in the number of caudal vertebrae. Altogether, this mosaic of anatomical peak shifts suggests that body shape transformations were associated with differing selective demands and developmental changes.

Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae)

Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous-Palaeogene mass extinction. Here we infer a time-calibrated phylogeny using ultraconserved elements that samples 91.4% of all acanthomorph families and investigate patterns of body shape disparity. Our results show that acanthomorph lineages steadily accumulated throughout the Cenozoic and underwent a significant expansion of among-clade morphological disparity several million years after the end-Cretaceous. These acanthomorph lineages radiated into and diversified within distinct regions of morphospace that characterize iconic lineages, including fast-swimming open-ocean predators, laterally compressed reef fishes, bottom-dwelling flatfishes, seahorses and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of multiple species-rich and phenotypically disparate lineages independently diversifying across the globe under a wide range of ecological conditions.

A fossil assemblage from the mid-late Maastrichtian of Gavdos Island, Greece, provides insights into the pre-extinction pelagic ichthyofaunas of the Tethys

The global body-fossil record of marine 'fishes' from the time interval immediately preceding the Cretaceous-Paleogene Extinction is markedly poor. This deficiency appears to be further exacerbated with regards to offshore and deep-water taxa, obscuring our understanding of the state and composition of corresponding vertebrate faunas at the onset of this major extinction event. Recent fieldwork in the mid-late Maastrichtian exposures of the Pindos Unit in Gavdos Island, Greece, yielded a small but informative sample of fossil 'fishes', which inhabited the Tethys approximately three to four million years before the extinction. In this work we describe this sample, which comprises between eight and nine discrete morphotypes of various size classes, belonging to †Ichthyodectoidei, Aulopiformes (†Dercetidae, †Enchodontidae, †Ichthyotringidae), cf. †Sardinioididae, as well as the hexanchid shark †Gladioserratus sp. The new material expands the faunal list for the Maastrichtian of Gavdos Island, and the Pindos Unit as a whole, and further allows for the description of a new genus and species of †Enchodontidae and a new species of †Ichthyotringidae. The two new taxa are found to be widespread in the Maastrichtian of the Pindos Unit. The overall character of the assemblage agrees with previous interpretations of an offshore and rather deep depositional environment for the fossiliferous horizons. Furthermore, it exhibits a higher diversity than, and little taxonomic overlap with penecontemporaneous teleost assemblages from the Tethys, and informs on the otherwise poorly known Maastrichtian offshore and deep-water marine ichthyofaunas of the region.

Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes

Background

Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific.

Methods

We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22-39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations.

Results

In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age.

Main conclusions

The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.

Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

More than half the ray-finned fishes and about one-quarter of all living vertebrates belong to Percomorphacea. Among its 30 orders, Stromateiformes encompass 77 species in 16 genera and six families. Stromateiform monophyly has never been tested using morphology, and it has been rejected by molecular analyses. This comprehensive revision of Stromateiformes includes all its valid genera of all percomorph families previously aligned with the order. We sampled 207 phenotypic characters in 66 terminal taxa representing 14 orders and 46 acanthopterygian families. This dataset significantly surpasses all previous phenotype-based phylogenies of Stromateiformes, which analysed only a fraction of these characters. Stromateiformes is recovered as monophyletic, supported by eight unequivocal synapomorphies. Amarsipidae is the sister group of all other Stromateiformes (= Stromateoidei). Centrolophidae is paraphyletic, with three of its genera allocated into an early-diverging clade and the other four appearing as successive sister groups to a lineage containing the remaining stromateiforms. All other stromateoid families are monophyletic, with the following cladistic arrangement: (Nomeidae (Stromateidae (Tetragonuridae, Ariommatidae))). Our analysis convincingly refutes recent molecular phylogenetic interpretations that fail to recover a monophyletic Stromateiformes. These findings call into question large-scale conclusions of percomorph relationships and trait evolution based solely on molecular data.

Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication

Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.

Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades

Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.

Extreme Morphology, Functional Trade-offs, and Evolutionary Dynamics in a Clade of Open-Ocean Fishes (Perciformes: Bramidae)

When novel or extreme morphologies arise, they are oft met with the burden of functional trade-offs in other aspects of anatomy, which may limit phenotypic diversification and make particular adaptive peaks inaccessible. Bramids (Perciformes: Bramidae) comprise a small family of 20 extant species of fishes, which are distributed throughout pelagic waters worldwide. Within the Bramidae, the fanfishes (Pteraclis and Pterycombus) differ morphologically from the generally stout, laterally compressed species that typify the family. Instead, Pteraclis and Pterycombus exhibit extreme anterior positioning of the dorsal fin onto the craniofacial skeleton. Consequently, they possess fin and skull anatomies that are radically different from other bramid species. Here, we investigate the anatomy, development, and evolution of the Bramidae to test the hypothesis that morphological innovations come at functional (proximate) and evolutionary (ultimate) costs. Addressing proximate effects, we find that the development of an exaggerated dorsal fin is associated with neurocrania modified to accommodate an anterior expansion of the dorsal fin. This occurs via reduced development of the supraoccipital crest (SOC), providing a broad surface area on the skull for insertion of the dorsal fin musculature. While these anatomical shifts are presumably associated with enhanced maneuverability in fanfishes, they are also predicted to result in compromised suction feeding, possibly limiting the mechanisms of feeding in this group. Phylogenetic analyses suggest craniofacial and fin morphologies of fanfishes evolved rapidly and are evolutionarily correlated across bramids. Furthermore, fanfishes exhibit a similar rate of lineage diversification as the rest of the Bramidae, lending little support for the prediction that exaggerated medial fins are associated with phylogenetic constraint. Our phylogeny places fanfishes at the base of the Bramidae and suggests that nonfanfish bramids have reduced medial fins and re-evolved SOCs. These observations suggest that the evolution of novel fin morphologies in basal species has led to the phylogenetic coupling of head and fin shape, possibly predisposing the entire family to a limited range of feeding. Thus, the evolution of extreme morphologies may have carryover effects, even after the morphology is lost, limiting ecological diversification of lineages.

Offshore marine actinopterygian assemblages from the Maastrichtian-Paleogene of the Pindos Unit in Eurytania, Greece

The fossil record of marine ray-finned fishes (Actinopterygii) from the time interval surrounding the Cretaceous–Paleogene (K–Pg) extinction is scarce at a global scale, hampering our understanding of the impact, patterns and processes of extinction and recovery in the marine realm, and its role in the evolution of modern marine ichthyofaunas. Recent fieldwork in the K–Pg interval of the Pindos Unit in Eurytania, continental Greece, shed new light on forgotten fossil assemblages and allowed for the collection of a diverse, but fragmentary sample of actinopterygians from both late Maastrichtian and Paleocene rocks. Late Maastrichtian assemblages are dominated by Aulopiformes (†Ichthyotringidae, †Enchodontidae), while †Dercetidae (also Aulopiformes), elopomorphs and additional, unidentified teleosts form minor components. Paleocene fossils include a clupeid, a stomiiform and some unidentified teleost remains. This study expands the poor record of body fossils from this critical time interval, especially for smaller sized taxa, while providing a rare, paleogeographically constrained, qualitative glimpse of open-water Tethyan ecosystems from both before and after the extinction event. Faunal similarities between the Maastrichtian of Eurytania and older Late Cretaceous faunas reveal a higher taxonomic continuum in offshore actinopterygian faunas and ecosystems spanning the entire Late Cretaceous of the Tethys. At the same time, the scarcity of Paleocene findings offers tentative clues for a depauperate state of Tethyan ichthyofaunas in the aftermath of the K–Pg Extinction.

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships

Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo.

Large-bodied sabre-toothed anchovies reveal unanticipated ecological diversity in early Palaeogene teleosts

Many modern groups of marine fishes first appear in the fossil record during the early Palaeogene (66-40 Ma), including iconic predatory lineages of spiny-rayed fishes that appear to have originated in response to ecological roles left empty after the Cretaceous/Palaeogene extinction. The hypothesis of extinction-mediated ecological release likewise predicts that other fish groups have adopted novel predatory ecologies. Here, we report remarkable trophic innovation in early Palaeogene clupeiforms (herrings and allies), a group whose modern representatives are generally small-bodied planktivores. Two forms, the early Eocene (Ypresian) †Clupeopsis from Belgium and a new genus from the middle Eocene (Lutetian) of Pakistan, bear conspicuous features indicative of predatory ecology, including large size, long gapes and caniniform dentition. Most remarkable is the presence of a single, massive vomerine fang offset from the midline in both. Numerous features of the neurocranium, suspensorium and branchial skeleton place these taxa on the engraulid (anchovy) stem as the earliest known representatives of the clade. The identification of large-bodied, piscivorous anchovies contributes to an emerging picture of a phylogenetically diverse guild of predatory ray-finned fishes in early Palaeogene marine settings, which include completely extinct lineages alongside members of modern marine groups and taxa that are today restricted to freshwater or deep-sea environments.