No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)
... The order comprises 99 valid species classified into the following four families: Argentinidae (2 genera and 29 species), Opisthoproctidae (10 genera and 23 species), Microstomatidae (3 genera and 22 species), and Bathylagidae (8 genera and 25 species) (Van der Laan and Fricke, 2024). The hypotheses about the phylogenetic position of Argentiniformes have changed, since some early studies suggested a close relationship with Alepocephaliformes (see Nelson et al., 2016 for a complete discussion) but recent studies suggest that they are more closely related to Salmoniformes (see a revision in Near and Thacker, 2024). On the other hand, morphological and molecular evidence agree that the order is monophyletic (Near and Thacker, 2024). ...
... The hypotheses about the phylogenetic position of Argentiniformes have changed, since some early studies suggested a close relationship with Alepocephaliformes (see Nelson et al., 2016 for a complete discussion) but recent studies suggest that they are more closely related to Salmoniformes (see a revision in Near and Thacker, 2024). On the other hand, morphological and molecular evidence agree that the order is monophyletic (Near and Thacker, 2024). ...
... Both morphological and molecular evidence supports that the order Argentiniformes is monophyletic (review in Near and Thacker, 2024), however the relationship among families is still controversial. Using morphological characters, Rosen (1974) first found Argentinidae as sister group of Bathylagidae plus Opisthoproctidae and the same result was found in posterior morphological studies by Begle (1992) and Patterson and Johnson (1997). ...
The deep sea environment is the largest environment and host some of the most extreme ecosystems on Earth, therefore, possessing a large and unique fish diversity that encompasses about 15% of all known species. Our knowledge about these fishes is still very limited in many biological fields basically due to the complexity to obtain specimens for research. In the present study, we describe the complete mitochondrial genome of Argentina brasiliensis, aiming a species characterization and the study of the phylogenetic relationships in the order Argentiniformes. The mitogenome is composed by 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop), as found in other vertebrates. The phylogenetic results show that the order Argentiniformes is composed by two family groups the first formed by Argentinidae and Opisthoproctidae and the second formed by Bathylagidae and Microstomatidae. Additionally, we found that the genus Argentina is not monophyletic, and we suggest additional studies in the family Argentinidae to better investigate this question.
... In this study, we follow the conventions of the PhyloCode, which was recently formally applied to ray-finned fish systematics [43], for describing clades [44]. In practice, this means that we refer to total clades using the prefix 'pan-'. ...
... In practice, this means that we refer to total clades using the prefix 'pan-'. We also follow emerging conventions in italicizing all clade names [43][44][45]. ...
Among cartilaginous fishes, Holocephali represents the species-depauperate, morphologically conservative sister to sharks, rays and skates and the last survivor of a once far greater Palaeozoic and Mesozoic diversity. Currently, holocephalan diversity is concentrated in deep-sea species, suggesting that this lineage might contain relictual diversity that now persists in the ocean depths. However, the relationships of living holocephalans to their extinct relatives and the timescale of their diversification remain unclear. Here, we reconstruct the evolutionary history of holocephalans using comprehensive morphological and DNA sequence datasets. Our results suggest that crown holocephalans entered and diversified in deep (below 1000 m) ocean waters after the Cretaceous–Palaeogene mass extinction, contrasting with the hypothesis that this ecosystem has acted as a refugium of ancient cartilaginous fishes. These invasions were decoupled from the evolution of key features of the holocephalan body plan, including crushing dentition, a single frontal clasper, and holostylic jaw suspension, during the Palaeozoic Era. However, these invasions considerably postdated the appearance of extant holocephalan families 150 million years ago during a major period of biotic turnover in oceans termed the Mesozoic Marine Revolution. These results clarify the origins of living holocephalans as the recent diversification of a single surviving clade among numerous Palaeozoic lineages.
... Molecular phylogenetic studies consistently (and, I would add, quite counterintuitively) identify the anguilliform, blenny-like Indo-Pacific reef fish genus Pholidichthys, with two species, as the sister clade of the Cichlidae, and the leaffishes (Polycentridae) as sister of this pair (Near and Thacker 2024). Therefore, in the results below, some description is provided of the relevant character states observed in those sister groups, especially the more cichlidlike polycentrids, along with those of cichlids. ...
... Pholidichthys, polycentrids, and cichlids together comprise the basal clade of the Order Blenniiformes sensu Near and Thacker (2024). A cladogram (Fig. 3) including Pholidichthys, polycentrids and all cichlid subfamilies, tribes and subtribes is given for reference in evaluating the data in the following sections. ...
Background
The iconic freshwater cichlid fishes (Cichlidae) comprise about 1750 validly named species and hundreds more that are known, but not yet described and named. Cichlids are an important source of protein for millions of people on several continents, are model organisms in studies of evolution, speciation, ecology, development, behaviour and physiology and are popular as aquarium fishes. Yet, comparative studies of cichlid internal anatomy are rare. Even their osteology has not been taxonomically surveyed. The cichlid postcranial skeleton has been especially neglected.
New information
Here, I provide the first survey in cichlids of the considerable variation in numbers of vertebrae, supraneurals and dorsal- and anal-fin supports (pterygiophores), as well as the patterns with which the pterygiophores insert between the neural or haemal spines. The study includes some 1700 specimens of nearly 400 cichlid species. Focusing on the largest subfamily, the African cichlids or Pseudocrenilabrinae, the survey furnishes data from species in all but one of its 166 genera. Limited data from species in the other cichlid subfamilies (Etroplinae, Ptychochrominae and Cichlinae) and from the related leaffishes, Polycentridae, are also presented. Key examples of pterygiophore insertion patterns from throughout the range of variation are illustrated and discussed. Detailed analytical tables and all raw data are provided in supplementary files.
A bizarre specialisation in Cyprichromis is noted, evidently for the first time. Uniquely in this Lake Tanganyikan genus, five to seven anal pterygiophores are abdominal in position, located anterior to the anal fin and inserting toward or between successive pairs of pleural ribs.
Taxonomic changes: The most speciose tribe of African cichlids, currently known as Haplochromini, is correctly called Pseudocrenilabrini. Based chiefly on the molecular phylogenetic findings of other workers, I propose four pseudocrenilabrine subtribes, one occurring in rivers and three endemic to Lake Malawi. I also re-assign the Lake Tanganyikan tribe Tropheini as another subtribe of Pseudocrenilabrini, in line with numerous molecular studies placing tropheines firmly within this tribe. The remaining genera of Pseudocrenilabrini remain incertae sedis in this tribe pending clarification of their phylogenetic relationships.
The character complex here surveyed is a promising source of taxonomically and phylogenetically informative characteristics distinguishing or uniting cichlid taxa at multiple hierarchical levels, from species through subfamily. This reference set of novel character data can also provide information for palaeontological studies of African cichlids. These attributes are skeletal features potentially available for study in well preserved fossils and may help determine their correct taxonomic placement.
... These small, predominantly benthic fishes are significant components of shallow marine ecosystems, and are also abundant in brackish and freshwater habitats (Patzner et al. 2011;Brandl et al. 2018). Currently, gobioids are classified into one extinct family, the †Pirkseniidae, and eight or nine extant families, including Rhyacichthyidae, Odontobutidae, Milyeringidae, Eleotridae, Butidae, Thalasseleotrididae, Gobiidae, Oxudercidae, and, depending on the author, Xenisthmidae (Springer 1983(Springer , 1988Thacker 2003;Agorreta et al. 2013;Thacker et al. 2015;Nelson et al. 2016;McCraney et al. 2020;Reichenbacher et al. 2020;Near and Thacker 2024). The Gobiidae and Oxudercidae comprise the majority of their present-day diversity, with 1280 species (152 genera) in the Gobiidae and 704 species (107 genera) in the Oxudercidae (Fricke et al. 2024). ...
... The systematic classification and clade definitions follow Near and Thacker (2024). Series Percomorpha Hay, 1903Order Gobiiformes Bleeker, 1859Suborder Gobioidei Bleeker, 1849 Family incertae sedis, possible stem lineage of †Pirskeniidae Obrhelová, 1961 Genus †Laubeichthys gen. ...
... Taxonomic names of orders and families are given according to Tan and Ambruster (2018) and Near and Thacker (2024), while species names are given according to Eschmeyer's catalog of fishes (Van der Laan et al., 2024). ...
This investigation and critical revision of the ichthyofauna of Tajikistan is the result of two nationwide surveys completed by the authors in 2017 and 2019 combined with an analytical examination of previous studies. The ichthyofauna of Tajikistan includes 60 species, of which 44 are native and 15 are nonnative, while one species (Cyprinus carpio) is represented by populations of native and alien origin. Seven species recorded in neighboring countries could potentially be found in Tajikistan, 12 introduced species are nonnaturalized, two were erroneously identified as belonging to the ichthyofauna of Tajikistan, and two are extinct.
... Otoliths were archived at the Marine Paleontology Lab, Biodiversity Research Center, Academia Sinica, registered under the code CHLOL. We follow Nelson et al. (2016) for general classification and incorporate recent modifications from newly published research (Smith et al. 2022;Near and Thacker 2024). Scientific names and taxonomic attributions adhere to the latest edition of the Catalog of Fishes (Fricke et al. 2024). ...
Dongsha Island, situated in the northern part of the South China Sea, is surrounded by coral reefs and deep-sea habitats. The coastal areas of the atoll, a marine protected area, serve as important nursery habitats for many reef fish species. At the same time, the offshore deep-sea continental slopes are historically important fishing grounds. Although previous inventories primarily focused on coral reef fishes within the atoll listing 652 species from 73 families, comprehensive surveys of fishes from deeper waters have been incomplete. In this study, the species composition of the fish fauna around Dongsha was updated by analyzing large volumes of frozen bycatch from commercial deep-sea trawlers operating in the area for the past four years and reviewing the existing literature. The species list increased to 1087 species belonging to 167 families, including several documented as new records and potentially undescribed species. This updated checklist also includes images of each species and most of their sagittal otoliths. This will assist further taxonomic work and significantly enhance understanding of marine biodiversity in the South China Sea.
... Discrete morphological characters have been used to reconstruct the evolutionary history of organisms since the dawn of phylogenetic systematics (Hennig, 1965;Kluge and Farris, 1969). Despite the molecular phylogenetic revolution providing an unprecedented amount of data and shaking up major portions of the Tree of Life (Savolainen and Chase, 2003;Delsuc et al., 2005;Near and Thacker, 2024), morphology remains the exclusive source of data to infer the phylogenetic relationships of extinct species-barred exceptional preservation of molecules in deep time (Hagelberg et al., 2015;Paterson et al., 2024). Moreover, interest in morphological phylogenetics is currently on the rise, thanks to methodological advances allowing for the joint estimation of phylogeny and divergence times of both extant and extinct taxa combined (Zhang et al., 2016;Wright et al., 2022), to improved morphological data collection and availability (Davies et al., 2017;Blackburn et al., 2024;Goswami and Clavel, 2024), and to the recognition that ignoring data from extinct species can bias inferences on macroevolutionary processes (Slater et al., 2012;Betancur-R et al., 2015; Lloyd and Slater, 2021;Faurby et al., 2024;Goswami and Clavel, 2024). ...
Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model---which introduces an acquisition bias correction for sampling only characters that are observed to be variable---and for models of among-character rate variation (ACRV), routinely applied by researchers to relax the equal-rates assumption of Mkv. However, the interaction between variable character acquisition bias and ACRV has never been explored before.
We demonstrate that there are two distinct approaches to condition the likelihood on variable characters when there is ACRV, and we call them joint and marginal acquisition bias. Far from being just a trivial mathematical detail, we show that the way in which the variable character conditional likelihood is calculated results in different assumptions about how rate variation is distributed in morphological datasets. Simulations demonstrate that tree length and amount of ACRV in the data are systematically biased when conditioning on variable characters differently from how the data was simulated. Moreover, an empirical case study with extant and extinct taxa reveals a potential impact not only on the estimation of branch lengths, but also of phylogenetic relationships. We recommend the use of the marginal acquisition bias approach for morphological datasets modeled with ACRV. Finally, we urge developers of phylogenetic software to clarify which acquisition bias correction is implemented for both estimation and simulation, and we discuss the implications of our findings on modeling variable characters for the future of morphological phylogenetics.
... This sampling added our 51 Holostean sequences to 123 sequences from Acanthuriformes (n=8); Anguilliformes (n=11); Atheriniformes (n=17); Beryciformes (n=1); Blenniiformes (n=20); Carangiformes (n=7); Characiformes (n=3); Clupeiformes (n=3); Cypriniformes (n=16); Gobiiformes (n=3); Gymnotiformes (n=1); Labriformes (n=2); Osmeriformes (n=2); Osteoglossiformes (n=4); Perciformes (n=4); Polypteridae (n=4); Salmoniformes (n=12); Salmoniformes (n=12); Siluriformes (n=2); and Synbranchiformes (n=4). The above clade names follow the phylogenetic classification of ray-finned fishes (Dornburg and Near 2021;Near and Thacker 2024). Peptide sequences corresponding to intronic regions were removed from protein sequences for subsequent analyses. ...
Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes. However, the immune repertoire of holosteans remains relatively unexplored. Here, we investigate the evolution of PSMB8, a core component of the immunoproteasome responsible for cleaving intracellular proteins into peptides for presentation by MHC class I molecules. We identify two holostean PSMB8 types—S type and K type—that are unique among vertebrates. These types likely cause significant biochemical changes to the S1 binding pocket involved in antigen cleavage which could result in the presentation of novel peptides by MHC class I. Integrating comparative analyses across major ray-finned fish lineages demonstrates that bowfins and gars independently evolved the PSMB8 S type within separate PSMB8 paralog lineages, while the PSMB8-K type is an evolutionary novelty found only in gars. Our results provide new perspectives into PSMB8 haplotypes and their role in peptide antigen processing, offering unique insights into the molecular evolution of the vertebrate immunity and antigen presentation.
... Snooks belong to the series Carangaria, order Carangiformes, alongside the families Latidae and Sphyraenidae all of which share some morphological similarities (Betancur-R et al. 2017;Girard, Davis, and Smith 2020;Near and Thacker 2023). The phylogenetic relationships between these families are still a subject of debate. ...
Aim
Amphiamerican New World fishes provide a unique opportunity to explore the impact of geological processes and the formation of geographic barriers on biological diversification across both spatial and temporal dimensions. We employed phylogenetic and biogeographic methods to assess the impact of the emergence of the Isthmus of Panama on the evolutionary history of snooks.
Location
Eastern tropical Pacific and western Atlantic Oceans.
Methods
Bayesian methods were used for phylogenetic inference and divergence time estimation, incorporating the fossil record of Carangidae, Centropomidae, Istiophoriformes, Latidae and Sphyraenidae to establish a timeline using the methods of stratigraphic intervals for node calibration density specification. Biogeographic models were fitted to test the hypothesis that transisthmian vicariant events are coeval with the Isthmus closure. To estimate ancestral range probability and perform stochastic mapping, we utilised BioGeoBears and the parameters from the best‐fitting model. This allowed us to estimate the quantity and kind of biogeographical events.
Results
Our results suggest a sister relationship between Centropomidae and Sphyraenidae with a common ancestor that originated in the Upper Cretaceous (~78.51 Ma). The biogeographic model BAYAreaLIKE + j indicated speciation in sympatry and dispersal (founder effect) as the primary modes of speciation in the genus Centropomus . The dispersion in the family Centropomidae was estimated from the Tropical Eastern Pacific to the tropical western Atlantic since the Oligocene.
Main Conclusions
The alignment of divergence times with ancestral species distributions suggests a possible synchrony between the current distribution in Centropomus species and the processes of the formation of the Isthmus of Panama during the Miocene. However, the evidence of only two transisthmic pair suggests that this event was not determinant in allopatric interbasin speciation. Furthermore, recent diversification events within each basin imply an influence of post‐closure environmental conditions on the evolution of this group of fishes.
... Blennies are a diverse family of fishes that have experienced exceptional lineage diversification (e.g. just shy of the diversification rate documented for the extensive adaptive radiation of cichlids- Hundt et al., 2014;Near et al., 2013;Near & Thacker, 2024). There have been up to seven independent origins of amphibious behaviour in intertidal blennies (Ord & Cooke, 2016). ...
Colonisation of novel habitats are important events in evolution, but the factors that initially prompt such ecological transitions are often unknown. The invasion of land by fish is an extreme habitat transition that offers an opportunity to empirically investigate the causes of major ecological transitions.
The intertidal ecotone—and rock pools in particular—have been an important staging ground for transitions onto land. Classic hypotheses focus on the adverse abiotic conditions of rock pools at low tide as the instigator of fish voluntarily stranding themselves out of water, which can then lead to the evolution of an amphibious lifestyle. To test these hypotheses, we studied the abiotic conditions of 54 rock pools on the island of Guam where there are various species of aquatic, amphibious and terrestrial blenny fishes.
We found little support for the expected deterioration of abiotic conditions in standing pools at low tide (salinity, pH and oxygen), and fish were not seen to be excluded from those pools that were found to exhibit poor abiotic conditions (temperature, salinity and pH). Hypoxia was the only factor that might account for the absence of blennies from certain rock pools.
Next, we experimentally measured oxygen depletion by an aquatic, mildly amphibious and highly amphibious species of blenny found on Guam in a simulated rockpool to infer the proportion of rock pools at low tide outside the tolerable range of blennies. Rock pools were found to have oxygen levels within the requirements of most blennies and those of other marine fishes reported in the literature.
We conclude that the abiotic environment of rock pools alone was unlikely to have instigated the evolution of amphibious behaviour in blennies, at least on Guam. Instead, the broad range of abiotic conditions experienced in rock pools suggests these conditions could have primed amphibious blennies to better endure the novel conditions on land. Any ecotone typified by fluctuations or gradients in abiotic conditions is likely a key transitional environment for the invasion of novel habitats and, as such, are an important location for adaptive evolution and species diversification.
Read the free Plain Language Summary for this article on the Journal blog.
... The oldest supposed acipenseriform, †Eochondrosteus sinensis Lu et al. 2005 from the Lower Triassic of China (originally interpreted as Permian in age by Lu et al. [2005]) is proposed as the earliest-diverging acipenseriform (Lu et al., 2020), although other authors are skeptical about including this taxon within Acipenseriformes (Hilton et al., 2021). A recent alternative rank-free phylogeny for Actinopterygii proposes Acipenseroidei as a synonym of Acipenseriformes but with the exclusion of Chondrosteidae and Peipiaosteidae as "pan-acipenseriforms" (Near & Thacker, 2024). Both fossil and living acipenseriforms are endemic to the northern hemisphere (but see Martill [2023] for a possible acipenseroid from the Upper Cretaceous of Gondwana) and have anatomically specialized skeletons with highly reduced bone ossification (Bemis et al., 1997;. ...
Several fragmentary remains of an enigmatic acipenseriform, the order of fishes that includes living sturgeons and paddlefishes, are described from the Upper Jurassic Kimmeridge Clay Formation of southern England. These remains are significant because they represent the first definitive evidence of an acipenseriform from the Upper Jurassic described outside of Asia. In total, five associated dorsal caudal fulcra from the caudal fin and a paired pelvic fin from at least two separate individuals are identified as acipenseriform, although it is uncertain to which family they belong. Three families of Mesozoic acipenseriform are considered: the †Chondrostei (Lower Jurassic, Europe), the †Peipiaosteidae (Upper Jurassic to Lower Cretaceous, Asia), and the extant Acipenseroidei (Lower Cretaceous-recent, Laurasia). The new Kimmeridgian Clay acipenseriform fossils would significantly extend the temporal and spatial distribution of whichever family they are ascribed, but their affinities remain unclear. Regardless, the stratigraphic and paleobiogeographic occurrence of the new specimens holds novel implications for the poorly known evolutionary history of this primitive clade of extant non-Neopterygian fishes.
... In the past 30 years, the classification of major fish groups has been revised to incorporate advancements in our understanding of these groups and the application of molecular data to construct robust phylogenies (Near and Thacker 2024). Among Siluriformes, Lundberg et al. (1988Lundberg et al. ( , 1991 identified three monophyletic groups within the former Pimelodidae, which they initially recognized as subfamilies. ...
Neotropical tetras of the family Characidae form the largest and most taxonomically complex clade within the order Characiformes. Previous phylogenetic relationships concur on the recognition of four major subclades, whereas knowledge on intergeneric and interspecific relationships remains largely incomplete or nonexistent. We sampled 575 specimens of 494 species and 123 genera classified in Characidae, generated new molecular data of ultraconserved elements (UCEs), and used likelihood and Bayesian analyses. The phylogeny (1348 UCE loci: 538 472 bp) yielded clades with unprecedented resolution at species- and genus-levels, allowing us to propose a new classification of former Characidae into four families: Spintherobolidae, Stevardiidae, Characidae, and Acestrorhamphidae. The family Stevardiidae includes nine subfamilies: Landoninae, Xenurobryconinae,
Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, and Diapominae. The family Characidae includes five subfamilies: Aphyocharacinae, Cheirodontinae, Exodontinae, Tetragonopterinae, and Characinae. The family Acestrorhamphidae congregates 15 subfamilies: Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, Stichonodontinae, unnamed subfamily, Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, Hyphessobryconinae, Thayeriinae, Rhoadsiinae, Grundulinae, and Acestrorhamphinae. The phylogeny resolves intergeneric relationships and supports revalidation of Myxiops, Megalamphodus, Ramirezella, Holopristis, and Astyanacinus, synonymy of Aphyodite, Genycharax, and Psellogrammus, and expansion of Cyanogaster, Makunaima, Deuterodon, Hasemania, Hemigrammus, Bario, Ctenobrycon, and Psalidodon. The phylogeny opens avenues for new systematic reviews and redefinitions of included genera.
... A total of 65 reference sequences, representing 23 species of the ingroup and one outgroup (Opistognathus aurifrons, Opistognathidae), in addition to 39 sequences from our larvae dataset that could not be confidently identified by nBLAST and BOLD IE (total of 104 sequences), were included in both ML and MP analyses. Taxonomic classification above the genus level follow Ghezelayagh et al. (2022) and Near & Thacker (2024). ...
Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species ( P. marmoreus and P. pilicornis ), while Labrisomus included three species ( L. cricota , L. conditus and L. nuchipinnis ). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species.
... However, recent molecular studies (Betancur-R. et al., 2013;Near et al., 2012;Near & Thacker, 2024;Nelson et al., 2016) have placed them within the order Acanthuriformes. ...
Pogonias blettleri sp. nov., a new species of black drum (Acanthuriformes, Sciaenidae) from the marine Upper Miocene Paraná Formation, which crops out in the Province of Entre Ríos, Argentina, is described. The holotype specimen comprises a large and nearly complete skull articulated with the anterior vertebral column and associated with fragmentary remains of the pectoral and pelvic girdles, as well as a complete pectoral fin. Morphological and phylogenetic analyses including several Western Atlantic sciaenid taxa confirm the assignment of the fossil specimen to the genus Pogonias Lacepede, 1802, as the sister taxon to the clade of Pogonias cromis + Pogonias courbina. The erection of a new species is based on the presence of a combination of primitive and derived characters, such as: the sub-triangular dorsal outline of the anterior neurocranium, with the lateral borders of frontals delimiting an isosceles triangle; the cavernous frontals with wide bridge-like bony struts; a conspicuous dorsal protuberance of frontals; a crescent-shaped preoperculum, with a smooth posterior margin and a strongly thickened anteroventral edge; and a robust and craniocaudally wide hyomandibula, with a strongly ossified anterior expansion. The palaeoenvironmental reconstruction of the upper levels of the Paraná Formation suggests that P. blettleri sp. nov. inhabited brackish and shallow waters in estuarine environments, particularly in areas near large river run-offs. The known palaeontological content from this unit includes potential prey of the black drum, suggesting that P. blettleri sp. nov. likely fed on annelids, crabs, molluscs, and small fish, similar to its extant counterparts.
... Despite unclear position of the root within the phylogenetic tree of these three lineages (see Phylogenetic position of Osteoglossomorpha in Hilton and Lavoué, 2018), Elopomorpha was accepted to be a sister group to Osteoglossocephala (Osteoglossomorpha+Clupeocephala) (e.g., Betancur et al., 2017). However, the latest analyses suggest monophyly of Oseanacephala (synonym Eloposteoglossocephala), a clade, that comprises Elopomorpha and Osteoglossomorpha (Near and Thacker, 2023;Parey et al., 2023). ...
Osteoglossiformes (bonytongue fishes) possess many morphological specializations associated with functions such as airbreathing, feeding, and electroreception. The olfactory organ also varies among species, notably in the family Osteoglossidae. Herein, we describe the olfactory organ of an osteoglossid, Heterotis niloticus, to compare it with the olfactory organs of other osteoglossiforms. We demonstrate the presence of an olfactory rosette within the olfactory chamber. This structure consists of a short median raphe surrounded by olfactory lamellae, which possess dorsal lamellar processes. On the surface of the olfactory lamellae, there are secondary lamellae formed by the olfactory epithelium. Within the olfactory epithelium, two zones can be distinguished: parallel brands of sensory cells located in the cavities between the secondary lamellae and a nonsensory area covering the remaining part of the olfactory lamellae. The olfactory epithelium is formed by ciliated and microvillus olfactory sensory neurons, supporting cells, goblet cells, basal cells and ciliated nonsensory cells. Additionally, rodlet cells were observed. The results confirm large variability in terms of the olfactory organ of Osteoglossiformes, particularly of Osteoglossidae, and support the secondary lamellae evolution hypothesis within this family.
The Weberian apparatus is a hearing specialization unique to the otophysan fishes, and an unexpected degree of morphological variation exists in species of the Noturus catfishes. Our aim in this study is to investigate relationships between morphological variations and ecology that may drive this variation. Sampling 48 specimens representing 25 species, we investigated morphological diversity and accounted for ecological variables using landmark‐based 3D geometric morphometrics and x‐ray‐based computed tomography (CT) images. We tested five ecological variables using three landmark sets in three focused regions: the tripus, scaphium, and overall shape of the peripheral structures including the complex vertebra. We performed phylogenetic signal tests, and phylogenetic influence is not significant within Noturus in any of the three regions. Among the tested ecological variables, stream velocity and coloration (a proxy for substrate) were found to be significantly associated with the morphology of the tripus and scaphium, the first and the last ossicles of the sound transmitting chain. This eco‐morphology connection may be mediated through stream velocity's dominant role in defining the soundscape of aquatic environments and substrate material properties contributing to which sounds are produced and propagated. We conclude that Noturus catfishes could be acoustically adapted to their microhabitats.
A new signalfish from the Grand Passage north of Grande Terre, New Caledonia, Acanthopsaron striatum n. gen. n. sp., is described, characterized by 7 spines in the first dorsal, anal-fin rays mostly branched, branched caudal-fin rays 10, scales small compared to other signalfishes, cycloid, lateral-line scales 60, peripheral ctenoid; pelvic fin short, not reaching to anus when adpressed; snout terminal, neither jaws projecting; maxillary tentacle absent; maxillary spine absent; maxillary notch present, weakly developed; opercle with a single, strong spine; subopercle with a weak spine; barbel on lower-jaw tip absent; anterior-nostril projections absent; iris flap absent. Pteropsaron flavissimum n. sp. is also described from a single specimen also trawled in the Grand Passage of New Caledonia, characterised by having 6 spines in the first dorsal fin, 18 rays in the second dorsal fin, ca. 22 rays in the anal fin, gill rakers 0 + 8, 46 lateral-line scales, first dorsal fin low, without filaments; anal fin normal, without extended rays; head length 3.6 in SL, preorbital length 1.7 in eye diameter; pelvic fin extending to fifth anal-fin membrane when adpressed; body colour rosy-pink, with wide yellow streak dorsally extending from tip of snout to upper caudal-fin base; first dorsal fin pale, without black markings. The new species are compared with allied species. A key to the genera and species of the family Hemerocoetidae is presented.
Molecular phylogeny and taxonomic review of 1 genus and 3 species (Sphyraena japonica, Sphyraena obtusata and Sphyraena pinguis) in the family Sphyraenidae were conducted based on specimens collected from around the Korean waters. Molecular phylogeny using 685 bp mitochondrial DNA cytochrome b sequences showed that S. pinguis was the most closely clustered with S. obtusata (0.219~0.230), and was little far clustered with S. japonica (0.270~0.274), but S. obtusata was distantly clustered with S. japonica (0.350~0.358). In morphology, S. japonica was easily distinguished from S. obtusata and S. pinguis in meristic characters such as gill rakers (1 in S. japonica vs. 2 in S. obtusata and S. pinguis), the number of soft rays of anal fin (8 in S. japonica vs. 9 in S. obtusata and S. pinguis) and the number of pored lateral line scales (117~140 in S. japonica vs. 78~94 in S. obtusata and S. pinguis). In addition, S. obtusata and S. pinguis were distinguished in the number of scales above lateral line (5.5~6.5 in S. obtusata vs. 7.5~9.5 in S. pinguis), scales below lateral line (8.5~9.5 in S. obtusata vs. 10.5~12.5 in S. pinguis). In distribution, S. japonica and S. pinguis mainly occurred in the East Sea, Korea Strait and Jeju-do Island of Korea, but S. obtusata was very rarely found (only one specimen) in Korea.
Geological evidence supports the occurrence of an epicontinental Trans-Saharan Seaway bisecting the African continent during the Late Cretaceous to early Palaeogene. The seaway formed a wide saltwater channel connecting the Neotethys with the South Atlantic, yet no previous study has investigated its impact on freshwater fish diversification. Phylogenomic data and time-calibrated trees indicate a Late Cretaceous signature for the appearance of three modern lineages of characiform fishes. Phylogenetic analyses using ultraconserved elements of 83 characiforms reveal that Alestidae, Hepsetus, and Lepidarchidae fam. nov. originated during the Santonian–Campanian of the Late Cretaceous (84–77.5 Mya). Lepidarchidae consists of two monotypic taxa not previously recognized as sister species: the Niger tetra Arnoldichthys endemic to the lower Niger and Ogun rivers of Nigeria, and the dwarf jellybean tetra Lepidarchus from coastal rivers of Ghana, Côte d’Ivoire, Liberia, Sierra Leone, and Guinea. Microcomputed tomography scans of 117 characiforms provide three novel morphological characters supporting Hepsetus and Lepidarchidae, four characters for the monophyly of Lepidarchidae, and five for a restricted Alestidae. The Santonian–Campanian divergence indicates allopatric speciation processes influenced by the Trans-Saharan Seaway, partitioning the African ichthyofauna in a west–east orientation. The timing for African characiform cladogenesis aligns with the Cenomanian fossil record and is ~16–23 Myr younger than the earliest characiform-like fossils from Late Cretaceous outcrops of Morocco and Sudan. This study highlights the magnitude of Cretaceous transgression events shaping the freshwater biota and gaps in our understanding of the evolutionary history and palaeobiogeography of ray-finned fishes across the African continent.
Research interest in the diversity and evolutionary history of herring-like fossils (subcohort Clupei) has increased in recent decades. However, little is known about the relationships between fossils assigned to Clupei, particularly those that are demonstrably related to extant herring-like members of the order Clupeiformes. To help bridge this gap, we present a new morphological phylogeny that includes representatives of all major clupeiform lineages. The data matrix consists of 192 characters, drawn from 79 extant and 37 fossil taxa and selected to be readily identifiable in fossils. Most clupeiform families are recovered as monophyletic, and their interrelationships are generally compatible with previous morphological hypotheses. The phylogenetic positions of six fossil clupeiform taxa are resolved, as the results of all analyses (unconstrained/constrained parsimony and Bayesian inference) are consistent. Twenty-one fossil taxa are incertae sedis, including two species of Ellimmichtyiformes, which are recovered as Clupeoidei in the parsimony analyses. The relationships of the rest of the fossils are interpreted with varying degrees of certainty. The evolution of key morphological characters is discussed in light of the new results, and four fossil taxa are proposed as calibration points for future dating studies.
In preparation for the revised new edition of the 1997 book “The Fishes of the Galapagos Islands” by Jack Stein Grove and Robert J. Lavenberg, to be published next year by the EPCA, the East Pacific Corridor Alliance Foundation (www.epcafoundation.org), we have been reviewing literature and museum records and obtaining additional underwater photographs and specimens. A recent expedition sponsored by the EPCA in May 2024 conducted widespread surveys, and, in particular, intensive underwater photography and collecting for tissues for DNA sequencing (targeting cryptobenthic species, new records or species, and unresolved taxa). The fish species list published by us in Grove et al. (2022) is thus here updated, with a number of changes, mostly species added (usually deeper or mesopelagic species), but some species subtracted when we conclude evidence is lacking for inclusion, applying strict scientific criteria (see below). The total number of species listed is up to 683 from 644, the number of families is increased by 18 families to 178 (mostly added mesopelagic or deepwater families, a few taxonomic adjustments, and three removed).
The risk of predation is an important driver that tailors life histories in various ways. Using an evolutionary model based on hormonal control, we study how different predation regimes affect adaptive risk‐taking and growth in fish populations. Growth, metabolism and foraging in the modelled fish are regulated by three simplified hormone functions: growth hormone, orexin, and thyroid hormone. A dynamic state‐dependent optimization model finds optimal hormone profiles for adaptive growth strategies in juvenile fish. We consider a gradient from species where behaviour and metabolic activity have large consequences for risk (typically benthic and camouflaged species), to the opposite endpoint where behaviour may modify predation risk to a smaller degree (as in the pelagic). Along this gradient, the model predicts changes in the pace of life from slow to fast, enacted by up‐regulation of the three hormone functions which in turn increase foraging and metabolism and change the priorities of energy reserves versus growth. Under all types of predation risk investigated, growth is faster when food availability is higher. Energy reserves are maintained primarily during periods of poor food availability and are used to accelerate growth during periods when food availability is high. The thyroid hormone function is up‐regulated predominantly when food availability is high and has an important role in trade‐offs balancing energetic gain and survival. At the individual time scale, the hormone system improves organismic flexibility and robustness. Over the phylogenetic time scale, hormone system adaptations have also restricted the phenotypic plasticity of individuals.
Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical AFPI proteins originated from distinct genetic precursors in each lineage. Each lineage independently evolved a de novo coding region for the novel ice-binding protein while repurposing fragments from their respective ancestors into potential regulatory regions, representing partial de novo origination—a process that bridges de novo gene formation and the neofunctionalization of duplicated genes. The study supports existing models of new gene origination and introduces new ones: the Innovation-Amplification-Divergence (IAD) model, where novel changes precede gene duplication; the newly proposed Duplication-Degeneration-Divergence (DDD) model, which describes new functions arising from degenerated pseudogenes; and the DDD gene fission model, where each new sibling gene differentially degenerate and renovate distinct functional domains from their parental gene. These findings highlight the diverse evolutionary pathways through which a novel functional gene with convergent sequences at the protein level can evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
Vermillion Snapper ( Rhomboplites aurorubens , Lutjanidae) inhabits deep waters (20-300 m) from North America through Brazil, sustaining significant commercial and recreational fisheries. Despite its economic importance, knowledge of its biology is limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained 98% complete and single-copy BUSCO genes. This is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The Vermillion Snapper genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.
The bony-fishes of the clade Lepisosteidae, commonly called ‘gars’ or ‘gar-fish’, are a lineage of proficient piscivores with evolutionary history spanning about 150 million years, which are today represented by two genera inhabiting the freshwater and brackish areas of southeastern North America, Central America, and Cuba. This was not the case during the Late Cretaceous when lepisosteids were more diverse and had much wider geographical distribution. Gar fossils, albeit very fragmentary, are a common component of the Upper Cretaceous freshwater and brackish vertebrate assemblages in Europe, yet all of the pre-upper Campanian records come from the western and central parts of the Late Cretaceous European Archipelago. Here we describe new lepisosteid material from Bulgaria, comprising nine teeth and three scales found at the uppermost Santonian–lowermost Campanian Vrabchov Dol vertebrate locality. These fossils represent the easternmost record of gars within the European Archipelago to date. Despite being found in a lagoonal to foreshore deposits, the paleontological content of the locality, the incompleteness and preservational state of the material, as well as the predominantly non-marine ecology of modern and fossils gars suggest that these fossils belong to fishes which inhabited more inland, freshwater environments. The Vrabchov Dol lepisosteids remains are the first record of gars in Bulgaria and one of the rare documented occurrences of Mesozoic osteichthyans in the country. This material expands the paleobiogeographic distribution of the Lepisosteidae within the European Archipelago.
As the fossil record reveals, neopterygians had a major diversification after the great mass extinction at the Permian-Triassic boundary , including the appearance of the major clade Teleosteomorpha. Detailed studies of new taxa (Pseudopholidoctenus germanicus, Barschichthys ruedersdorfensis, and Ruedersdorfia berlinensis) from the lower Anisian (middle Muschelkalk) of Germany and their comparisons with other Triassic relatives are presented, including new information concerning size, shape, and diet. Two families, Pholidophoridae and Marcopoloichthyidae, made a modest appearance during the Anisian of Europe and Asia almost simultaneously , with Pseudopholidoctenus (and the teleosteomorphs Barschichthys and Ruedersdorfia) from the Germanic Basin, being the oldest stem teleosts (244 Ma), followed shortly by Marcopoloichthys ani from Italy. The early teleostean diversification was fast-already in the late Ladinian three lineages were present: Prohalecitiidae (Europe), Pholidophoridae (Asia, Europe), and Marcopoloichthyidae (Asia, Europe), with ca. 20 species inhabiting the Tethys Ocean during the Middle-Late Triassic. Most Triassic teleosteomorphs were small, ca. 50 mm standard length, and a few as possibly miniature, with torpedo or oblong shapes, and suction feeders-probably a plankton based-diet. These first Triassic radiations were replaced during the early Sinemurian of marine ecosystems of Europe with two major groups: (a) non-monophyletic 'pholidophoriforms' and (b) proleptolepids and leptolepids, having an average size (ca. 100 mm SL) longer than Triassic forms, with oblong and fusiform shapes. A fast dispersion from the Tethys to the Paleo-Pacific followed, as demonstrated by the presence of small (ca. 50 mm SL) suction feeder proleptolepids in the early Sinemurian of Chile.
A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species’ dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.
Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences, and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi, but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.
The Rhamphosidae is an extinct family of syngnathiform fishes from the lower Eocene deposits of Europe, primarily known from specimens derived from the Ypresian Konservat-Lagerstätte of Bolca (Verona province, Italy). A descriptive analysis of 28 specimens of Rhamphosus from Bolca revealed the existence of six species, showing
a greater taxonomic diversity compared to the previous scenario of only two species (the type species Rhamphosus rastrum and Rhamphosus biserratus). Four new species are established herein: Rhamphosus bloti n. sp., characterized by a peculiar and unique rostrum with a discoid shape; Rhamphosus brevirostris n. sp., which exhibits a moderately large size associated with a relatively short rostrum; Rhamphosus longispinatus n. sp., characterized by having the longest dorsal-fin spine and rostrum of all the Rhamphosus species; Rhamphosus tubulirostris n. sp., which shows a peculiar slim rostrum, long-based dorsal and anal fins, and a unique squamation characterized by the presence of numerous bucklers. The species from Bolca are also compared to the only other known Rhamphosus species, Rhamphosus rosenkrantzi, from the Fur Formation, Denmark. A number of morphological features support the assignment of the Rhamphosidae to the syngnathiform clade Dactylopteroidei, together with the extant families Dactylopteridae and Pegasidae, representing the sister group to the Pegasidae.
Reef stonefish (Synanceia verrucosa) is one of the most venomous fishes, but its biomedical study has been restricted to molecular cloning and purification of its toxins, instead of high-throughput genetic research on related toxin genes. In this study, we constructed a chromosome-level haplotypic genome assembly for the reef stonefish. The genome was assembled into 24 pseudo-chromosomes, and the length totaled 689.74 Mb, reaching a contig N50 of 11.97 Mb and containing 97.8% of complete BUSCOs. A total of 24,050 protein-coding genes were annotated, of which metalloproteinases, C-type lectins, and stonustoxins (sntx) were the most abundant putative toxin genes. Multi-tissue transcriptomic and venom proteomic data showed that sntx genes, especially those clustered within a 50-kb region on the chromosome 2, had higher transcription levels than other types of toxins as well as those sntx genes scatteringly distributed on other chromosomes. Further comparative genomic analysis predicted an expansion of sntx-like genes in the Percomorpha lineage including nonvenomous fishes, but Scorpaenoidei species experienced extra independent sntx duplication events, marking the clear-cut origin of authentic toxic stonustoxins. In summary, this high-quality genome assembly and related comparative analysis of toxin genes highlight valuable genetic differences for potential involvement in the evolution of venoms among Scorpaeniformes fishes.
Two new Kneria species, K. luansaensis sp. nov. and K. maxi sp. nov., are described from the
Luansa River, a left bank tributary of the lower Luapula in the Bangweulu–Mweru ecoregion, based
on an integrative approach using morphological and COI barcoding evidence. While K. luansaensis
sp. nov. occurs from the source of the Luansa further downstream to above the last of the three
Sanshifolo Falls, K. maxi sp. nov. only occurs downstream of all these three major falls. In Kneria,
males of about �33 mm LS have an opercular and a postopercular organ. The number of lamellae
on the latter seems to contain some alpha-taxonomic information, although this requires further
study as allometric changes occur at about �45 mm LS. Additional external morphological characters
differ between sexes, i.e., the (i) pectoral fin width (wider in males than females), (ii) dorsal fin height
(longer in males than females), and (iii) length of the longest ray of the lower caudal fin lobe (longer
in males than females). Agriculture, fishing with ichthyotoxines, and logging are the most pressing
threats on the Luansa and thus to both the new species. Their discovery in one of the rivers of
the Kundelungu Plateau and its surroundings located outside the present-day boundaries of the
Kundelungu National Park highlights the need for a refined and improved protection strategy for
this freshwater key biodiversity area.
Dictyosoma burgeri widely distributed in the coastal water of China, Korea and Japan, while its phylogenomic and microsatellite DNA features have been poorly understood. Herein, we provide a new genome, D. burgeri, using the next-generation sequencing. About 632 Mb was assembled with GC contents of 42.09%, leading to be prediction of 59,252 protein-coding gene models. Phylogenomic analyses show that D. burgeri is closely related with the Cebidichthys violaceus using 298 single copy genes of genomes, while D. burgeri is closely related with the genus Pholis based on 13 protein-coding genes of mitogenomes. A total of 689,658 simple sequences repeats (SSRs) were identified, and dinucleotide microsatellite motifs (accounting for 57.35%) was the most abundant, followed with mononucleotide microsatellite motifs (accounting for 31.30%). These results will help to obtain genetic information of D. burgeri and lay a theoretical basis as well as reference for genome-wide analyses.
Larval attachment organs (LAOs) are unicellular or multicellular organs that enable the larvae of many actinopterygian fishes to adhere to a substrate before yolk‐sac absorption and the free‐swimming stage. Bowfins (Amiiformes) exhibit a sizable LAO on the snout, which was first described in the late 19th and early 20th centuries. In this study, we document the LAO of Amia ocellicauda (Richardson, 1836) using a combination of scanning electron microscopy (SEM) and light microscopy, and histochemistry. We examined material representing three stages with SEM ranging in size from 5.8 to 11.2 mm in notochord length and one stage histochemically. We compare the LAO of A. ocellicauda to that of the lepisosteid Atractosteus tropicus Gill, 1863 and show that although the LAOs of A. ocellicauda and A. tropicus are both super‐organs, the two differ in the ultrastructure of the entire organ. A. ocellicauda possesses two distinct lobes, with the organs arranged on the periphery with none in the middle, whereas A. tropicus also possesses two lobes, but with the organs scattered evenly across the super‐organ. The individual organs of A. ocellicauda possess adhesive cells set deep to support cells with the adhesive substance released through a pore, whereas A. tropicus possesses both support cells and adhesive cells sitting at a similar level, with the adhesive substance released directly onto the surface of the organ. We additionally provide a table summarizing vertebrate genera in which attachment organs have been documented and discuss the implications of our study for hypotheses of the homology of attachment organs in the Holostei.
The previously alleged 'eugnathid amiiform' Sinoeugnathus kueichowensis is a small-sized halecomorph from the Middle Triassic (Ladinian) marine deposits of Guizhou and Yunnan, China. A morphological redescription and taxonomic revision of this taxon are provided based on a detailed examination of the holotype and 15 new specimens. Studies of these specimens revealed some morphological details previously undescribed or misidentified for this taxon, including a hatchet-shaped antorbital, two broad suborbitals, a sensory canal in the maxilla, and three pairs of extrascapulars. For the first time, Sinoeugnathus was incorporated into an analysis of halecomorph phylogeny, and the results recover it as the sister taxon of the Anisian Subortichthys from Luoping, Yunnan, and both are grouped with two Ladinian genera Allolepidotus and Eoeugnathus from the Monte San Giorgio area into a monophyletic group (namely Subortichthyidae fam. nov. herein) at the base of Ionoscopiformes. This taxonomic reassessment of Subortichthys provides new insights into the phylogeny and paleogeographic evolution of Ionoscopiformes.
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.
Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.
The origin of crown Actinopterygii has been dated to near the Devonian-Carboniferous boundary, but poor phylogenetic signal occludes the origin of modern actinopterygian biodiversity. Scarcity of comparative endoskeletal anatomy from this period likely contributes to the uncertainty. For example, only a handful of neurocrania have been described from the Carboniferous period despite an abundance of fossil taxa. Here we present a new actinopterygian, Phoebeannaia mossae gen. et sp. nov., from the Bashkirian Coal Measures of Saddleworth, Greater Manchester, UK, represented by an exceptionally preserved neurocranium and associated dermal bones. Morphological similarities to the Virgilian Kansasiella eatoni prompted comparative study and construction of a new neurocranial character matrix. Subsequent systematic analysis enabled identification of a cluster of similar Late Palaeozoic neurocrania, exploration of trends in braincase evolution across time, and investigation of potential causes of cladistic instability. Our neurocranial dataset reliably places this new specimen on the neopterygian stem near Kansasiella, but it struggles to incorporate extant taxa such as Polypteriformes, leading to uncertainty in branching pattern and inferred neurocranial transformation series. This work triples the number of complete Carboniferous neurocrania described with modern microcomputed tomography and provides a framework for future testing of large-scale hypotheses regarding the diversification and origin of ray-finned fishes.
Lampriform fishes (Lampriformes), which primarily inhabit deep-sea environments, are large marine fishes varying from the whole-body endothermic opah to the world’s longest bony fish-giant oarfish, with species morphologies varying from long and thin to deep and compressed, making them an ideal model for studying the adaptive radiation of teleost fishes. Moreover, this group is important from a phylogenetic perspective owing to their ancient origins among teleosts. However, knowledge about the group is limited, which is, at least partially, due to the dearth of recorded molecular data. This study is the first to analyze the mitochondrial genomes of three lampriform species (Lampris incognitus, Trachipterus ishikawae, and Regalecus russelii) and infer a time-calibrated phylogeny, including 68 species among 29 orders. Our phylomitogenomic analyses support the classification of Lampriformes as monophyletic and sister to Acanthopterygii; hence, addressing the longstanding controversy regarding the phylogenetic status of Lampriformes among teleosts. Comparative mitogenomic analyses indicate that tRNA losses existed in at least five Lampriformes species, which may reveal the mitogenomic structure variation associated with adaptive radiation. However, codon usage in Lampriformes did not change significantly, and it is hypothesized that the nucleus transported the corresponding tRNA, which led to function substitutions. The positive selection analysis revealed that atp8 and cox3 were positively selected in opah, which might have co-evolved with the endothermic trait. This study provides important insights into the systematic taxonomy and adaptive evolution studies of Lampriformes species.
Synopsis
Seahorses, pipefishes, trumpetfishes, shrimpfishes, and allies are a speciose, globally distributed clade of marine and freshwater fishes that have evolved a large number of unusual body plans. Their clade that includes all these forms, Syngnathoidei, has become a model for the study of life history evolution, population biology, and biogeography. Yet, the timeline of syngnathoid evolution has remained highly contentious. This debate is largely attributable to the nature of the syngnathoid fossil record, which is both poorly described and patchy for several major lineages. Although fossil syngnathoids have been used to calibrate molecular phylogenies, the interrelationships of extinct species and their affinities to major living syngnathoid clades have never been quantitatively tested. Here, I use an expanded morphological dataset to reconstruct the evolutionary relationships and clade ages of fossil and extant syngnathoids. Phylogenies generated using different analytical methodologies are largely congruent with molecular phylogenetic trees of Syngnathoidei, but consistently find novel placements for several key taxa used as fossil calibrators in phylogenomic studies. Tip-dating of the syngnathoid phylogeny finds a timeline for their evolution that differs slightly from the one inferred using molecular trees but is generally congruent with a post-Cretaceous diversification event. These results emphasize the importance of quantitatively testing the relationships of fossil species, particularly when they are critical to assessing divergence times.
Flying fishes, which use their wing-like pectoral fins and hypocercal caudal fin to glide through the air to avoid underwater predators, have independently evolved flight behavior, making them ideal for the study of adaptive evolution. To investigate the adaptation of flight behavior in flying fishes and the origin of Beloniformes fishes, this study obtained the complete mitochondrial genomes of Cheilopogon nigricans and Oxyporhamphus micropterus and constructed the DNA sequences extracted from these newly sequenced mitochondrial genomes with the DNA sequences of 32 previously published mitochondrial genomes into a dataset for reconstructing the phylogenetic relationships of Beloniformes fishes. The phylogeny that emerged strongly supported the possibility that flying fishes developed from halfbeaks and the progressive transition of flying fishes from two-wing to four-wing gliding. The divergence time analysis showed that the split between the suborder Belonidei and the family Adrianichthyidae occurred roughly 77.08 Mya, which fell within the period of evolution of the Indian plate in the late Cretaceous. Selection analyses revealed that flying fishes have a lower dN/dS ratio than the other members of Beloniformes, indicating that flying fishes experienced stronger purifying selection to eliminate deleterious mutations to maintain efficient energy metabolism to adapt to flight behavior. Moreover, this work found the positively selected signal in the ND4 gene, suggesting that different mitogenomic genes might have undergone different selective patterns during adaptive evolution.
Cave loaches within the family Nemacheilidae are among the most diverse group of cavefish in southwestern China. Although certain species have been included in previous phylogenetic studies, the intergeneric and interspecific relationships of Chinese cave loaches in Nemacheilidae remain poorly investigated due to insufficient sampling. In this study, a total of 45 samples from 37 recognized species and two unidentified species of cave loaches were collected, accounting for 87.5% of the eight recognized genera of cave loaches within the family Nemacheilidae in China. The complete mitochondrial genome (mitogenome) and seven nuclear genes were sequenced, and the phylogenetic tree of Chinese cave loaches was reconstructed. Both Bayesian inference and maximum-likelihood analyses resolved the phylogenetic relationships at the generic and species levels, suggesting the effectiveness of this multilocus marker system in determining phylogenetic relationships in Chinese cave loaches. Phylogenetic analysis not only confirmed previous taxonomic hypotheses based on morphological data but also provided new insights into the relationships of many cave loaches at the genus and species levels as well as suggestions for the current taxonomy of cave loaches within the family Nemacheilidae.
Documenting the origins of megadiverse (sub)tropical aquatic ecosystems is an important goal for studies of evolution and ecology. Nonetheless, the geological and ecological establishment of the modern Yangtze River remains poorly understood. Here, we reconstruct the geographic and ecological history of an endemic clade of East Asian fishes based on the mitochondrial phylogenomics analysis of Cyprinidae using fifteen fossil calibrations. We estimate an ancestral condition of benthic spawning with demersal or adhesive eggs in southern East Asia before ~23 Ma and a derived condition of riverine spawning with semibuoyant eggs in the Yangtze by ~18 Ma. These results imply the formation of Yangtze riverine ecosystems around the Oligocene-Miocene boundary in response to plateau uplift and monsoon strengthening. Some of these cyprinids reverted to benthic spawning with adhesive eggs by ~15 Ma, a time of rising to peak net diversification rates, indicating the formation of potamo-lacustrine ecosystems by the mid-Miocene during a strong East Asian summer monsoon. Our study provides increased spatiotemporal resolution for the co-evolutionary histories of the Yangtze River and its biodiversity and highlights biological evidence concerning the geomorphological dynamics of the Yangtze River.
Since 2006, an ophidiiform larva with an ovoid body, elongate anterior dorsal-fin ray, and long trailing fleshy filament has been identified as Pycnocraspedum squamipinne. Similarly, the larvae of the ophidiid genus Luciobrotula have been tentatively identified since 1988, with posteriorly displaced dorsal fins and bulging or exterilium guts. However, neither of these larval forms morphologically agree with their adult counterparts. Recently, blackwater divers captured and photographed specimens of larval Luciobrotula and Pycnocraspedum off the coast of Hawaiʻi and Florida, making them available for both morphological and molecular sampling. After examining these larvae and analyzing DNA barcode sequences, as well as a newly captured and sequenced adult of Pycnocraspedum phyllosoma, we revise the previously identified “Pycnocraspedum” larvae to species of Luciobrotula. We describe the larvae of Luciobrotula bartschi and Luciobrotula corethromycter for the first time, highlighting an extraordinary loss of multiple anterior dorsal-fin elements in their ontogeny. We also generate the first DNA sequences for L. corethromycter and P. phyllosoma, adding to the depauperate number of sequences available for ophidiiforms. For the previously identified “Luciobrotula” larvae, neither morphological nor molecular characters provide definitive identification other than recovering them among the Bythitidae. We provide new morphological observations, revised descriptions, and generate a phylogeny of ophidiiform fishes based on COI to place these larvae in a phylogenetic context, prompting further investigation into the relationships of the Ophidiiformes using additional genetic markers. Our study emphasizes the importance of blackwater diving to improving our understanding of marine larval fishes and the need for additional molecular sampling of the diverse order of brotulas, cusk-eels, pearlfishes, and their allies.
The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of Ariosoma meeki (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of A. meeki has undergone gene rearrangement. The ND6 and the conjoint tRNA-Glu genes were translocated to the location between the tRNA-Thr and tRNA-Pro genes, and a duplicated D-loop region was translocated to move upstream of the ND6 gene. Second, comparative genomic analysis was carried out between the mitogenomes of A. meeki and Ariosoma shiroanago. The gene arrangement between them was found to be highly consistent, against the published A. meeki mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in Ariosoma mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the A. meeki mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.
This is the first report on the complete mitochondrial genome (mitogenome) of South African Thyrsites atun (Euphrasén, 1791) and its phylogenetic placement within the Gempylidae family. The complete mitogenome of snoek is 16,494 bp in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs, and one control region. Gene order is similar to that found in gempylids and other marine fishes. Reconstruction of Gempylidae phylogeny implies that the mitogenomes of snoek, black snoek Thyrsitoides marleyi, and snake mackerel, Gempylus serpens are closely related in evolutionary terms.
Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates – fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.
Bony fishes are among the best represented macrofossils from the earliest Eocene Fur Formation, northern Denmark. The most abundant fish of the formation has never been formally described, in spite of its abundance throughout the formation, and only referred to as an ‘argentinoid’. This work provides a taxonomic study of this argentinoid taxon, which is described herein as Surlykus longigracilis gen. et sp. nov. The caudal skeleton shows separated first preural and first ural centra, a unique condition within the Argentiniformes. In addition, it is characterised by having a large mouth and a single supramaxilla, which suggest that Surlykus gen. nov. occupies a basal position within the Argentiniformes, representing the sister-group to all the other lineages of this clade ([Argentinidae + Opisthoproctidae] + [Bathylagidae + Microstomatidae]), and, consequently, a stem-group Argentiniformes. Mass-mortality assemblages may indicate that Surlykus longigracilis gen. et sp. nov. formed large schools in the ancient North Sea Basin, where it probably represented the trophic nucleus of the fish communities.
The teleost order Anguilliformes, true eels, comprises more than 1,000 described species in 20 families, commonly known as eels, congers, morays, and gulper eels. Comprehensive studies of Anguilliformes are limited, resulting in a lack of consensus for morphology-based phylogenetic hypotheses. A detailed morphological analysis of the cephalic and opercular myology offers a promising new source of characters to help elucidate the intrarelationships of Anguilliformes. Our study is the most extensive myological analysis for the group and includes 97 terminal taxa, with representatives from each of the 20 families of Anguilliformes plus outgroup clades. Results demonstrate that muscle characters inform phylogenetic relationships within Anguilliformes, and we propose two new synapomorphies for all extant members, including Protanguilla palau, the "living fossil" - adductor mandibulae originating on the parietal (vs. restricted to suspensorium), and segmentum mandibularis absent (vs. present). Exceptions for the first condition characterize highly modified saccopharyngoids, and for the second one, Notacanthidae. More importantly, we suggest three new synapomorphies for the remaining extant anguilliforms (except in highly modified saccopharyngoids) - adductor mandibulae originates on the frontals (vs. frontals naked), adductor mandibulae stegalis is separated from the rictalis (vs. ricto-stegalis fused into a single piece), the levator operculi inserts on the lateral surface of the opercle (vs. medial surface of the opercle). Our phylogenetic optimization strongly corroborates the hypothesis that Protanguilla is the sister group of all other extant eels. A further goal of this paper is to clearly document the substantive conflicts between the available molecular data and the extensive and diverse morphological evidence. This article is protected by copyright. All rights reserved.
Batrachoidiformes are benthic fishes that utilize the undersides of rocks as spawning nests. Their larvae are attached to the nest and nourished by a large yolk sac. The evolutionary shift from feeding, free-swimming larvae to sedentary larvae that are reliant on their yolk sac for nutrition can lead to changes in skeletal development. Batrachoidiformes also have many morphological specializations, such as five pectoral-fin radials (versus four in other acanthomorphs) that are of uncertain homology, the determination of which may have phylogenetic implications. A larval series of Porichthys notatus was collected and its skeletal ontogeny is described. In P. notatus the ossification of the pharyngeal toothplates occurs relatively later than in percomorphs with free-swimming larvae. The posterior basibranchial copula cartilage (= fourth basibranchial) in Porichthys notatus has a unique development among fishes: it initially develops as a paired element at 6.8–7.1 mm NL before fusing posteriorly and forming single median cartilage at 7.4 mm SL. Cartilages of hypobranchial four are transitory, being observed in two specimens of 6.8 and 7.3 mm NL before fusing with ceratobranchial four. The previously identified dorsalmost pectoral radial is a bone formed by a hypertrophied propterygium that ossifies later in development. The earliest stages of P. notatus have three dorsal spines, but during late larval development, the growth of the third dorsal spine is interrupted. The development of P. notatus is compared and discussed in context to that of other acanthomorph.
Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia , with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.
Many accounts of the early history of actinopterygians (ray-finned fishes) posit that the end-Devonian mass extinction had a major influence on their evolution. Existing phylogenies suggest this episode could have acted as a bottleneck, paring the early diversity of the group to a handful of survivors. This picture, coupled with increases in taxonomic and morphological diversity in the Carboniferous, contributes to a model of explosive post-extinction radiation. However, most actinopterygians from within a roughly 20-million year (Myr) window surrounding the extinction are poorly known, contributing to uncertainty about the meaning of these patterns. Here, we report an exceptionally preserved fossil from 7 Myr before the extinction that reveals unexpected anatomical features. Palaeoneiros clackorum gen. et sp. nov. nests within a clade of post-Devonian species and, in an expanded phylogenetic analysis, draws multiple lineages of Carboniferous actinopterygians into the Devonian. This suggests cryptic but extensive lineage diversification in the latest Devonian, followed by more conspicuous feeding and locomotor structure diversification in the Carboniferous. Our revised model matches more complex patterns of divergence, survival and diversification around the Devonian/Carboniferous boundary in other vertebrate clades. It also fundamentally recalibrates the onset of diversification early in the history of this major radiation. An actinopterygian fossil with unexpected anatomical features from 7 million years before the end-Devonian mass extinction suggests complex patterns of divergence and diversification around the Devonian/Carboniferous boundary for ray-finned fishes.
Background
The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissa tanganicae and Limnothrissa miodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids.
Results
We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S. tanganicae and L. miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissa obtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P. obtusirostris around 10.92 MYA [95% CI: 6.37–15.48].
Conclusions
These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe , e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies.
The nominal families considered here are the Kyphosidae, Scorpididae, Girellidae, Labracoglossidae, Oplegnathidae, Scatophagidae, Pomacanthidae, Chaetodontidae, Monodactylidae, Ephippidae and Drepanidae.All of these except the Pomacanthidae were recognized as families by Regan (1913) though the taxonomic status of some of them has been downgraded since.On the basis of morphological features these nominal families are divided into three groups: (1) the Ephippidae and Drepanidae, (2) the Monodactylidae, and (3) a series containing the remaining nominal families.It is postulated that the Ephippidae, probably the Monodactylidae, and the kyphosidchaetodontid series developed their deep body-forms independently and that many of their similarities are the result of secondary developments functionally associated with such a body-form.
Aim
Biotic interchanges between Africa, India, and Eurasia are central to explaining the present‐day distribution and diversity of freshwater organisms across these landmasses. Synbranchiformes is a diverse and species‐rich clade of freshwater acanthomorph fishes found on all southern continents except Antarctica, and include eel‐ and perch‐like, air‐breathing and non‐air‐breathing fishes. Lacking a comprehensive and resolved phylogeny of the entire clade, contemporary interpretations of synbranchiform biogeography invoke scenarios as disparate as Gondwanan vicariance and pan‐global rafting to explain their modern‐day distribution. Here, we study their biogeographic history of continental dispersal events and test whether these are associated with increases in lineage diversification.
Location
Asia, India, Africa freshwater habitats.
Taxon
Synbranchiformes (gouramis, snakeheads, swamp eels, and relatives).
Methods
We used nearly 1000 ultra‐conserved elements (UCEs) and Sanger‐sequenced genes to infer a phylogeny with representatives of all major synbranchiform lineages and nearly two‐thirds of its known species diversity. Incorporating fossil calibrations, we inferred a time‐calibrated phylogeny to which we apply Bayesian methods of ancestral area reconstruction and test for diversification rate shifts.
Results
Analyses of UCE data provide a resolved phylogeny for major synbranchiform lineages. Divergence times support a most recent common ancestor of the entire clade approximately 79.2 million years ago. We infer significant increases in lineage diversification in both the spiny eels (Mastacembelidae) and the genus Betta (Osphronemidae).
Main Conclusions
Our results reject the hypothesis of Gondwanan vicariance explaining synbranchiform biogeography. Instead, our analyses reconstruct a southeast Asian origin of the entire clade and independent dispersal events to other continents by snakeheads, anabantids, and spiny eels, with no signal of elevated lineage diversification occurring after these invasions. Higher lineage diversification rates in spiny eels pre‐date their arrival to Africa, while the high diversification rates observed in Betta were initiated prior to the flooding of insular Sundaland in southeast Asia.
Pantanodontinae described by Myers (1955) with monotypic genus (Pantanodon) and species (podoxys) have recently been elevated to family level in Cyprinodontiformes following molecular evidence, and parallelly fossil European cyprinodonts, previously placed in †Paralebias Gaudant 2013, were recently reassigned to the extant East African genus Pantanodon Myers 1955, as the only genus in Pantanodontidae, with all extant and fossil species sharing the laterally placed pelvic girdle and the adaptation of the pelvic fins in males. In this study the status and biogeographical distribution of all species (and all known institutional records) within Pantanodontidae is reviewed. Pantanodon is shown to be a diversified group of related species, recent, extant or fossil. Based on new data, on reassessments of old data and on new diagnoses, a division of Pantanodontidae into four genera is proposed: Pantanodon (nominotypical Tanzanian genus), Malagodon nov.gen. (Malagasy genus), Aliteranodon nov.gen. (Kenyan genus), three genera including (recent) East African species, and †Paralebias which includes all fossil Pantanodontidae European species. Pantanodon podoxys Myers, 1955 is revalidated as a distinct species and a closely related species from Tanga (Tanzania) is described as P. propinquus n.sp. Within Aliteranodon nov.gen., a recently collected species from Koreni (Kenya) is herein described as A. ndoano n.sp. and designated as its type species. Several more species are assigned to this new genus: Haplochilichthys stuhlmanni Ahl, 1924 with which Pantanodon podoxys was previously synonymized is revalidated with a new combination and its type locality is proposed as Pangani, in northeastern Tanzania, after a detailed review of Stuhlmann's collecting trips between 1894 and 1901; a misidentified species from Ngomeni (Kenya) is formally described as A. rostratus n.sp. and two misidentified miniature species from Tanzania are formally described as A. bucinus n.sp., from Zanzibar Island, and A. filimbi n.sp., from Bagamoyo mainland. Oryzias madagascariensis Arnoult, 1963 is designated as type species of Malagodon nov.gen.; Haplochilichthys jeanneli Pellegrin, 1935 is reviewed and a lectotype is designated following suspicions it may be placed in Pantanodontidae. Based on five significant osteological differences between recent and fossil species reestablishment of the fossil genus †Paralebias is proposed with a subdivision into three species-groups. For the first time the unique larval stage of A. stuhlmanni and A. ndoano n.sp. is disclosed.
A taxonomic revision of the genus Centrogenys (family: Centrogenyidae), having previously been regarded as mono-typic (also monotypic family) represented by Centrogenys vaigiensis, resulted in the recognition of three species, including two new species from Australia, Centrogenys algrahami, new species, and Centrogenys pogonoskii, new species. The two other nominal species of the genus, Centropristes scorpenoides and Sebastes stoliczkae, were regarded as junior synonyms of C. vaigiensis. Centrogenys vaigiensis is readily distinguished from the two new species by lacking scale patches on the membranes between dorsal-fin spines (a small patch of scales present on each interspinous membrane of the third to last dorsal-fin spines in the two new species). Centrogenys algrahami, new species, is characterized by having fewer body scales, including 31-36 pored lateral-line scales (vs. 37-44 in C. vaigiensis and 39-46 in C. pogonoskii, new species) and 31-36 scale rows in longitudinal series (vs. 36-43 and 39-47), and a slightly greater number of pectoral-fin rays 14-16 (modally 15; vs. 12-15 [modally 14] in C. vaigiensis and C. pogonoskii, new species). Moreover, C. pogonos-kii, new species, is distinguished from the two congeners by the presence of squamation on the lateral side of the snout (in specimens .34 mm SL), whereas it is naked in the congeners. The status of the three species resulting from the morphological analysis was also strongly supported by molecular evidence of a partial sequence of the COI gene. Centrogenys vaigiensis is widely distributed in the Indo-West Pacific, ranging from Mauritius east to Indonesia and north to southern Japan. In contrast, Centrogenys algrahami, new species, and Centrogenys pogonoskii, new species, are restricted to Australia.
This book is a comprehensive guide to the International Phonetic Alphabet, whose aim is to provide a universally agreed system of notation for the sounds of languages, and which has been widely used for over a century. The Handbook presents the basics of phonetic analysis so that the principles underlying the Alphabet can be readily understood, and gives examples of the use of each of the phonetic symbols. The application of the Alphabet is then demonstrated in nearly 30 'Illustrations' - concise analyses of the sound systems of a range of languages, each of them accompanied by a phonetic transcription of a passage of speech. The Handbook also includes the 'Extensions' to the Alphabet, covering speech sounds beyond the sound-systems of languages, and a listing of the internationally agreed computer codings for phonetic symbols. It is an essential reference work for all those involved in the analysis of speech.
This edited volume is provides an authoritative synthesis of knowledge about the history of life. All the major groups of organisms are treated, by the leading workers in their fields. With sections on: The Importance of Knowing the Tree of Life; The Origin and Radiation of Life on Earth; The Relationships of Green Plants; The Relationships of Fungi; and The Relationships of Animals. This book should prove indispensable for evolutionary biologists, taxonomists, ecologists interested in biodiversity, and as a baseline sourcebook for organismic biologists, botanists, and microbiologists. An essential reference in this fundamental area.
Ray-finned fishes, which compose nearly half of living vertebrate diversity, provide an excellent system for studying the evolution of novel body forms. Lampriformes is a species-poor lineage of acanthomorph ray-finned fishes that has evolved two very different and highly specialized body plans suited to life in pelagic oceanic habitats: the deep, round-bodied bathysomes and the ribbon-like taeniosomes. Here, we present a new phylogenetic hypothesis and divergence time estimates for lampriform fishes based on an updated morphological dataset and DNA sequences from nuclear genes for all but one of the living lampriform families and 55% of recognized extant genera. Our analyses resolve two major clades in Lampriformes: the Bathysomi and the Taeniosomi. A time calibrated phylogeny shows that the origin of living lampriforms coincides with the aftermath of the Cretaceous–Palaeogene extinction and that anatomically modern pelagic morphotypes evolved 10 Myr after the start of the Palaeogene.
Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.
Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.
Although Pangasiidae (four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais) is known to be a monophyletic family, the generic and phylogenetic relationships, as well as inter- and intrafamilial relationships of the catfish families in Siluroidei, are poorly resolved. In this study, we obtained complete mitogenomes from three catfish species of the Mekong River in Vietnam: Pangasius mekongensis (16,462 bp), Pangasius krempfi (16,475 bp), and Pangasianodon hypophthalmus (16,523 bp) and reconstructed a comprehensive phylogeny with 117 mitogenomes of 32 recognized siluriform families. The genomic features of the three mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. The phylogeny established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister group to the “Big Africa” major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly resolved the Pangasiidae’s intrafamilial and intergeneric relationships. Pangasianodon was monophyletic and conclusively as a sister to the (Pangasius + Helicophagus + Pseudolais) group. Pangasius. mekongensis was placed as a sister taxon to P. pangasius within the genus Pangasius, while Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon. However, in the single-gene phylogenies, this species was assigned to the [Pangasius + Helicophagus + Pseudolais] group. The datasets in this study are useful for reappraising pangasiid taxonomy, as well as for siluriform catfish identification, DNA barcoding, systematics, phylogenetics, population genetics, and timeline and mode of diversification studies.
The record of articulated marine fish fossils during the latest Cretaceous and earliest Cenozoic is sparse. The oldest-known definitive squirrelfishes and soldierfishes, like the first examples of many extant reef-dwelling clades, are known from early Eocene deposits of Europe. Here, we describe a new genus and species of holocentroid (Teleostei: Beryciformes: Holocentroidea) based on material from three individuals from early Paleocene (Danian) deposits of New Jersey, USA using micro-computed tomography. The specimens comprise a three-dimensionally preserved skull and partial postcranium, plus two isolated neurocrania. The new taxon, †Iridopristis parrisi, possesses a unique combination of characters, including a heterosulcoid otolith morphology and an edentulous premaxillary tooth-gap, while lacking a newly proposed character for the remainder of Cenozoic holocentroids: a lamina on the lateral surface of the anguloarticular, anterior to the jaw joint. Bayesian phylogenetic analysis of morphological, stratigraphical and molecular data under the fossilized birth-death process finds that the new taxon branches from the holocentrid stem, where it is joined by two of the three squirrelfish genera from the early Eocene (Ypresian) of Bolca, Italy. We estimate a Danian divergence between Myripristinae and Holocentrinae, the two reciprocally monophyletic subfamilies of Holocentridae. Our analysis suggests that several holocentroid lineages crossed the Cretaceous–Palaeogene boundary.
http://zoobank.org/urn:lsid:zoobank.org:pub:0B458336-EFCF-46D0-98D0-CE5AD371D7AF
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.
Reconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes, which includes nearly half of all living vertebrates, are no exception. Although most lineages of ray-finned fishes radiated around the Cretaceous-Paleogene boundary, a handful of ancient, species-poor clades still persist. These lineages can illuminate very old biogeographic trends, but their low species richness can also limit the reconstruction of these patterns. The seven extant species of gars distributed in freshwater habitats in North America and Cuba are an old clade with a fossil record spanning over 150 million years of Earth history. Using a genomic dataset of DNA sequences of 1,105 exons for the seven living species and an updated morphological matrix of extant and extinct taxa, we infer the phylogenetic relationships of gars and test how divergence times and biogeographic reconstructions are influenced by sequential and joint estimation and the effect on these inferences when using different taxon sets based on fossil completeness. Our analyses consistently show that the two extant gar genera Atractosteus and Lepisosteus diverged approximately 105 million years ago and many of the inferred divergences in the gar time-calibrated phylogeny closely track major Mesozoic tectonic events, including the separation of the Americas, the expansion of the early Atlantic, and the Cretaceous reorganization of North American river systems. The crown clades Atractosteus and Lepisosteus originated in the Cenozoic of eastern North America, implying that this region has served as both the origin of extant gar diversity and the refugium of this iconic ancient lineage. These results exemplify how combining phylogenomics with the fossil record provides congruence around the evolutionary history of ancient clades like gars and can reveal long-lost biogeographic patterns.
Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multilocus studies and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence 1,088 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades were largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in large, economically important groups of coral reef fishes. More broadly, we demonstrate how accounting for sources of biological variability from incomplete lineage sorting and exploring systematic error at conflicting nodes can aid in evaluating alternative phylogenetic hypotheses.
The resolution of phylogenetic relationships within rapid radiations poses a significant challenge in systematic biology. However, the integration of genome-scale DNA data with multispecies coalescent-based tree inference methods offers a strategy to resolve historically recalcitrant nodes within radiations of closely related species. Here, we analyze a dataset of over 60,000 loci captured via double digest restriction site-associated DNA sequencing (ddRADseq) using both concatenation- and coalescent-based approaches to infer the phylogenetic relationships of the Antarctic notothenioid lineage Artedidraconinae. Previous studies identify artedidraconines as the most rapidly diversifying subclade of notothenioids, but evolutionary studies of the clade are stymied by pervasive phylogenetic and taxonomic uncertainty. The results of our phylogenomic analyses provide clarity to several long-standing challenges in the systematics of artedidraconines, including the deep paraphyly of Artedidraco. Our findings enable the construction of a classification that reflects phylogenetic relationships, including the description of a new genus and the resurrection of a classification of Notothenioidei that places Artedidraconinae as a subfamily of Harpagiferidae. This work provides a phylogenetic perspective for investigations of the tempo and mode of diversification in artedidraconines, which is likely to provide new insights on the dynamics of the notothenioid adaptive radiation as a whole.
French zoologist and naturalist Georges Cuvier (1769–1832), one of the most eminent scientific figures of the early nineteenth century, is best known for laying the foundations of comparative anatomy and palaeontology. He spent his lifetime studying the anatomy of animals, and broke new ground by comparing living and fossil specimens - many he uncovered himself. However, Cuvier always opposed evolutionary theories and was during his day the foremost proponent of catastrophism, a doctrine contending that geological changes were caused by sudden cataclysms. He received universal acclaim when he published his monumental Le règne animal, which made significant advances over the Linnaean taxonomic system of classification and arranged animals into four large groups. The sixteen-volume English translation and expansion, The Animal Kingdom (1827–35), is also reissued in the Cambridge Library Collection. First published in 1817, Volume 1 of the original version covers mammals and birds.
French zoologist and naturalist Georges Cuvier (1769–1832), one of the most eminent scientific figures of the early nineteenth century, is best known for laying the foundations of comparative anatomy and palaeontology. He spent his lifetime studying the anatomy of animals, and broke new ground by comparing living and fossil specimens - many he uncovered himself. However, Cuvier always opposed evolutionary theories and was during his day the foremost proponent of catastrophism, a doctrine contending that geological changes were caused by sudden cataclysms. He received universal acclaim when he published his monumental Le règne animal, which made significant advances over the Linnaean taxonomic system of classification and arranged animals into four large groups. The sixteen-volume English translation and expansion, The Animal Kingdom (1827–35), is also reissued in the Cambridge Library Collection. First published in 1817, Volume 3 of the original version covers molluscs, arachnids and insects.
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.