Lower vertebrates

@article{greenwood1973interrelationships2,
    author = "Greenwood, P. H. and Miles, R. S. and Patterson, C",
    title = "Interrelationships of Fishes",
    year = "1973",
    journal = "London, Academic Press; [Supplement No.1 to the Zoological Journal of the Linnean Society, 53]",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., Miles, R. S., and Patterson, C., 1973, Interrelationships of Fishes: London, Academic Press; [Supplement No.1 to the Zoological Journal of the Linnean Society, 53].}"
}

@article{bonde1974interrelationships,
    author = "Bonde, Niels and Greenwood, P. H. and Patterson, C.",
    title = "Interrelationships of Fishes.",
    year = "1974",
    journal = "Systematic Zoology",
    url = "https://doi.org/10.2307/2412482",
    doi = "10.2307/2412482",
    number = "4",
    openalex = "W2321151333",
    pages = "562",
    volume = "23"
}

@book{florkin1974chemical1,
    author = "Florkin, M. and Scheer, B. T",
    title = "Chemical Zoology",
    year = "1974",
    publisher = "London, Academic Press, v. VIII. Deuterostomians, cyclostomes and fishes",
    note = "talkorigins\_source = {true}; raw\_reference = {Florkin, M., and Scheer, B. T., 1974, Chemical Zoology: London, Academic Press, v. VIII. Deuterostomians, cyclostomes and fishes.}"
}

The Structurally similar diterpenoid alcohols pachydictyol-A and dictyol-E are produced by the brown seaweed Dictyota dichotoma. This seaweed and several related species that also produce these compounds are known to be relatively low preference foods for tropical fishes and urchins. We evaluated the effect of various concentrations of these compounds on feeding by the three common types of herbivores that co-occur with Dictyota in coastal North Carolina. Fish (Diplodus holbrooki), sea urchins (Arbacia punctulata), and a mixed species group of gammarid amphipods were offered pieces of the palatable seaweed Gracilaria tikvahiae coated with either (1) dictyol-E or pachydictyol-A dissolved in diethyl ether or (2) diethyl ether alone. Dictyol-E significantly reduced consumption by fish and urchins at concentrations of 0.5 and 1.0% of algal dry mass, but had no effect on amphipod grazing. Pachydictyol-A significantly reduced fish grazing at the relatively high concentrations of 1.0 and 1.3% of plant dry mass; at 0.5% it tended to decrease grazing, but the effect was not significant (P =.07). Pachydictyol-A had no effect on urchin grazing and significantly increased amphipod grazing. When Pachydictyol-A was fed to fish as 1.0% of food dry mass, their growth rate was reduced by a significant 48%. In feeding preference experiments with several seaweeds, Dictyota ranks low for fish and urchins but high for amphipods. This is consistent with the hypothesis that the secondary metabolites produced by Dictyota play a major role in determining its susceptibility to herbivores. The ability of amphipods to circumvent the chemical defenses (Dictyota, and the fact that the two species of algae most readily consumed by amphipods (Codium and Dictyota) were the two species least readily consumed by fish, suggest that predation and herbivory by fishes may be major factors selecting for amphipods that can live on, and eat, seaweeds that are unpalatable to fishes. Amphipods that fed on Dictyota did not appear to sequester the Dictyota metabolites; when exposed to fish predation, Dictyota-fed amphipods were eaten as readily as amphipods that had fed on an alga with no defensive chemistry. Tubicolous amphipods and other small marine herbivores that may spend significant portions of their lives on only a few plants my be under very different evolutionary constraints than the larger, more mobile herbivores that commonly moved between many plants. Several characteristics of these smaller, less mobile, and much less studied, marine herbivores suggest that they may be ecologically similar to terrestrial insects and may play a large, but presently unappreciated, role in structuring marine plant communities.

@article{doi1023071939849,
    author = "Hay, Mark E. and Duffy, J. Emmett and Pfister, Catherine A. and Fenical, William",
    title = "Chemical Defense Against Different Marine Herbivores: Are Amphipods Insect Equivalents?",
    year = "1987",
    journal = "Ecology",
    abstract = "The Structurally similar diterpenoid alcohols pachydictyol-A and dictyol-E are produced by the brown seaweed Dictyota dichotoma. This seaweed and several related species that also produce these compounds are known to be relatively low preference foods for tropical fishes and urchins. We evaluated the effect of various concentrations of these compounds on feeding by the three common types of herbivores that co-occur with Dictyota in coastal North Carolina. Fish (Diplodus holbrooki), sea urchins (Arbacia punctulata), and a mixed species group of gammarid amphipods were offered pieces of the palatable seaweed Gracilaria tikvahiae coated with either (1) dictyol-E or pachydictyol-A dissolved in diethyl ether or (2) diethyl ether alone. Dictyol-E significantly reduced consumption by fish and urchins at concentrations of 0.5 and 1.0\% of algal dry mass, but had no effect on amphipod grazing. Pachydictyol-A significantly reduced fish grazing at the relatively high concentrations of 1.0 and 1.3\% of plant dry mass; at 0.5\% it tended to decrease grazing, but the effect was not significant (P =.07). Pachydictyol-A had no effect on urchin grazing and significantly increased amphipod grazing. When Pachydictyol-A was fed to fish as 1.0\% of food dry mass, their growth rate was reduced by a significant 48\%. In feeding preference experiments with several seaweeds, Dictyota ranks low for fish and urchins but high for amphipods. This is consistent with the hypothesis that the secondary metabolites produced by Dictyota play a major role in determining its susceptibility to herbivores. The ability of amphipods to circumvent the chemical defenses (Dictyota, and the fact that the two species of algae most readily consumed by amphipods (Codium and Dictyota) were the two species least readily consumed by fish, suggest that predation and herbivory by fishes may be major factors selecting for amphipods that can live on, and eat, seaweeds that are unpalatable to fishes. Amphipods that fed on Dictyota did not appear to sequester the Dictyota metabolites; when exposed to fish predation, Dictyota-fed amphipods were eaten as readily as amphipods that had fed on an alga with no defensive chemistry. Tubicolous amphipods and other small marine herbivores that may spend significant portions of their lives on only a few plants my be under very different evolutionary constraints than the larger, more mobile herbivores that commonly moved between many plants. Several characteristics of these smaller, less mobile, and much less studied, marine herbivores suggest that they may be ecologically similar to terrestrial insects and may play a large, but presently unappreciated, role in structuring marine plant communities.",
    url = "https://doi.org/10.2307/1939849",
    doi = "10.2307/1939849",
    openalex = "W2018060669",
    references = "doi101086282907, doi101111j155856461964tb01674x, doi101126science2114485887, doi101126science2304728895, doi101146annureves12110181002201, doi1023071292926, doi1023072259845, doi1023072260079, ehrlich1964butterflies, openalexw2045291252"
}

@article{gardiner1989interrelationships,
    author = "GARDINER, B. G. and SCHAEFFER, BOBB",
    title = "Interrelationships of lower actinopterygian fishes",
    year = "1989",
    journal = "Zoological Journal of the Linnean Society",
    url = "https://doi.org/10.1111/j.1096-3642.1989.tb00550.x",
    doi = "10.1111/j.1096-3642.1989.tb00550.x",
    number = "2",
    openalex = "W1996571114",
    pages = "135-187",
    volume = "97",
    references = "bonde1974interrelationships, doi101016s0016699588800664, doi1023071441916, doi1023072412685, doi1023072413058, doi1023072413259, doi1023073514548, doi105962bhlpart28698, doi105962bhltitle61854, openalexw115975037"
}

ABSTRACT The comparative osteology and phylogenetic relationships of fossil and living paddlefishes (Polyodontidae) are investigated in detail for the first time. This peculiar, poorly known group is of great significance to phylogenetic studies of primitive actinopterygians, because it is one of only two chondrostean families that have survived to the present. Consequently the group is frequently used as an outgroup for studies of the many fossil chondrostean groups and for higher-level studies of actinopterygian (and even osteichthyan) interrelationships. The family has a long but spotty fossil record dating back to the Upper Cretaceous, including species represented by relatively complete skeletons or at least skulls. These relatively complete fossils are extremely rare and belong to the species †Paleopsephurus wilsoni MacAlpin, 1947 from the Upper Cretaceous Hell Creek Formation of Montana (redescribed here); †Polyodon sp. nov. from the lower Paleocene Tullock Formation of Montana (described here); and †Crossopholis magnicaudatus Cope, 1883 from lower Eocene deposits of the Green River Formation in Wyoming (described in detail here for the first time based on much new material). Among the fossils, †Crossopholis is of particular interest, because it is now known by several nearly complete skeletons (reported and described here for the first time). †Paleopsephurus and †Polyodon sp. nov. are known from a single partial skull each, and some fragmentary postcranial material, but are well enough represented to include in our phylogenetic analysis. Other, more fragmentary, Upper Cretaceous and Paleocene material (some newly reported here) is placed in Polyodontidae incertae sedis. There are two extant species in the family, frequently referred to in the literature as “living fossils.” These two species are Polyodon spathula from the Mississippi River drainage of North America, and Psephurus gladius primarily from the upper Yangtze River drainage in China. The osteology of Psephurus gladius is described here in detail for the first time. Previous studies of Polyodontidae have been almost exclusively based on Polyodon spathula, because specimens of the other species are extremely rare and very poorly known. After accumulating and preparing material for several years, we were able to describe more fully all polyodontid species and examine the family phylogenetically. Our study reveals that Polyodon spathula is a highly derived member of the family, and generally not a good representative of the family when the family is used as an outgroup for higher-level phylogenetic studies of actinopterygians. The use of Polyodon spathula as the primitive polyodontid has previously led to several serious errors in the literature. We therefore also summarize certain primitive characters of Polyodontidae in this paper. Contrary to previous studies, we show that †Paleopsephurus has the stellate rostral bones unique to polyodontids (in addition to the long median rostral bones and extremely elongate snout also unique to the group). Also contrary to previous studies, Polyodontidae (at least primitively) does have ossifications of the quadratojugal, interclavicle and postcleithrum. We also report several other osteological features previously unknown from the family. Our study results in a phylogenetic hypothesis for paddlefishes that is radically different from the only other published cladogram (Gardiner, 1984b). We demonstrate that †Paleopsephurus clearly belongs in Polyodontidae, rather than Acipenseridae as proposed by Gardiner (1984b). †Paleopsephurus is the sistergroup to Polyodontinae, new subfamily (a group containing Psephurus, †Crossopholis, and two species of Polyodon). Psephurus is the sistergroup to Polyodontini, new tribe (a group containing †Crossopholis and Polyodon). Polyodon contains the extant Polyodon spathula as well as a new fossil species from early Paleocene freshwater deposits of Montana. A better understanding of polyodontid osteology also enables us to provide a phylogenetic hypothesis for Acipenseriformes (assuming monophyly of Acipenseridae) that differs from that of previous authors. In particular we find that †Chondrosteidae is the sistergroup to a group containing Acipenseridae plus Polyodontidae. Polyodontidae also provide evidence that the supraneurals in actinopterygians are the serial homologues of epurals, and not of fin radials. As has previously been apparent, Polyodontidae is one of several groups that indicate a transpacific biogeographic relationship for western North America (west of the continental divide) during the Early Tertiary. We also describe ontogenetic and intraspecific variation in paddlefish osteology. Based on the large amount of variation, we conclude that, in at least some fishes, it is important to examine large numbers of specimens, including extremely old individuals (i.e., “upper end ontogeny”) in the developmental series to more completely document the morphology. Normal-sized, reproductively active adult paddlefishes lack particular ossifications of the scapulocoracoid, vertebral column and neurocranium present in other osteichthyans; but as we show here, these elements eventually ossify in very large, older individuals. In this sense, paddlefishes appear to be the axolotls of the fish world, offering one of the best documented cases of paedomorphosis (or neoteny) known to date.

@article{doi10108002724634199110011424,
    author = "Grande, Lance and Bemis, William E.",
    title = "Osteology and Phylogenetic Relationships of Fossil and Recent Paddlefishes (Polyodontidae) with Comments on the Interrelationships of Acipenseriformes",
    year = "1991",
    journal = "Journal of Vertebrate Paleontology",
    abstract = "ABSTRACT The comparative osteology and phylogenetic relationships of fossil and living paddlefishes (Polyodontidae) are investigated in detail for the first time. This peculiar, poorly known group is of great significance to phylogenetic studies of primitive actinopterygians, because it is one of only two chondrostean families that have survived to the present. Consequently the group is frequently used as an outgroup for studies of the many fossil chondrostean groups and for higher-level studies of actinopterygian (and even osteichthyan) interrelationships. The family has a long but spotty fossil record dating back to the Upper Cretaceous, including species represented by relatively complete skeletons or at least skulls. These relatively complete fossils are extremely rare and belong to the species †Paleopsephurus wilsoni MacAlpin, 1947 from the Upper Cretaceous Hell Creek Formation of Montana (redescribed here); †Polyodon sp. nov. from the lower Paleocene Tullock Formation of Montana (described here); and †Crossopholis magnicaudatus Cope, 1883 from lower Eocene deposits of the Green River Formation in Wyoming (described in detail here for the first time based on much new material). Among the fossils, †Crossopholis is of particular interest, because it is now known by several nearly complete skeletons (reported and described here for the first time). †Paleopsephurus and †Polyodon sp. nov. are known from a single partial skull each, and some fragmentary postcranial material, but are well enough represented to include in our phylogenetic analysis. Other, more fragmentary, Upper Cretaceous and Paleocene material (some newly reported here) is placed in Polyodontidae incertae sedis. There are two extant species in the family, frequently referred to in the literature as “living fossils.” These two species are Polyodon spathula from the Mississippi River drainage of North America, and Psephurus gladius primarily from the upper Yangtze River drainage in China. The osteology of Psephurus gladius is described here in detail for the first time. Previous studies of Polyodontidae have been almost exclusively based on Polyodon spathula, because specimens of the other species are extremely rare and very poorly known. After accumulating and preparing material for several years, we were able to describe more fully all polyodontid species and examine the family phylogenetically. Our study reveals that Polyodon spathula is a highly derived member of the family, and generally not a good representative of the family when the family is used as an outgroup for higher-level phylogenetic studies of actinopterygians. The use of Polyodon spathula as the primitive polyodontid has previously led to several serious errors in the literature. We therefore also summarize certain primitive characters of Polyodontidae in this paper. Contrary to previous studies, we show that †Paleopsephurus has the stellate rostral bones unique to polyodontids (in addition to the long median rostral bones and extremely elongate snout also unique to the group). Also contrary to previous studies, Polyodontidae (at least primitively) does have ossifications of the quadratojugal, interclavicle and postcleithrum. We also report several other osteological features previously unknown from the family. Our study results in a phylogenetic hypothesis for paddlefishes that is radically different from the only other published cladogram (Gardiner, 1984b). We demonstrate that †Paleopsephurus clearly belongs in Polyodontidae, rather than Acipenseridae as proposed by Gardiner (1984b). †Paleopsephurus is the sistergroup to Polyodontinae, new subfamily (a group containing Psephurus, †Crossopholis, and two species of Polyodon). Psephurus is the sistergroup to Polyodontini, new tribe (a group containing †Crossopholis and Polyodon). Polyodon contains the extant Polyodon spathula as well as a new fossil species from early Paleocene freshwater deposits of Montana. A better understanding of polyodontid osteology also enables us to provide a phylogenetic hypothesis for Acipenseriformes (assuming monophyly of Acipenseridae) that differs from that of previous authors. In particular we find that †Chondrosteidae is the sistergroup to a group containing Acipenseridae plus Polyodontidae. Polyodontidae also provide evidence that the supraneurals in actinopterygians are the serial homologues of epurals, and not of fin radials. As has previously been apparent, Polyodontidae is one of several groups that indicate a transpacific biogeographic relationship for western North America (west of the continental divide) during the Early Tertiary. We also describe ontogenetic and intraspecific variation in paddlefish osteology. Based on the large amount of variation, we conclude that, in at least some fishes, it is important to examine large numbers of specimens, including extremely old individuals (i.e., “upper end ontogeny”) in the developmental series to more completely document the morphology. Normal-sized, reproductively active adult paddlefishes lack particular ossifications of the scapulocoracoid, vertebral column and neurocranium present in other osteichthyans; but as we show here, these elements eventually ossify in very large, older individuals. In this sense, paddlefishes appear to be the axolotls of the fish world, offering one of the best documented cases of paedomorphosis (or neoteny) known to date.",
    url = "https://doi.org/10.1080/02724634.1991.10011424",
    doi = "10.1080/02724634.1991.10011424",
    openalex = "W1980955783",
    references = "doi101038170405e0, doi101111j109636421932tb01553x, doi105281zenodo16298542, doi105962bhltitle159141, doi105962bhltitle6408, gardiner1989interrelationships, openalexw2246336267, openalexw610180004"
}

@incollection{forey1996interrelationships,
    author = "Forey, P.L. and Littlewood, D.T.J. and Ritchie, P. and Meyer, A.",
    title = "Interrelationships of Elopomorph Fishes",
    year = "1996",
    booktitle = "Interrelationships of Fishes",
    url = "https://doi.org/10.1016/b978-012670950-6/50010-2",
    doi = "10.1016/b978-012670950-6/50010-2",
    openalex = "W2909967840",
    pages = "175-191",
    references = "applegate1967phyletic, bonde1974interrelationships, doi1010160031942280850047, doi1010160378111988900662, doi1010160378111988903307, doi101073pnas74125463, doi101073pnas86166196, doi101093bioscience1610752a, doi101126science2448875, doi1023071444873"
}

@article{crossref1997interrelationships,
    title = "Interrelationships of fishes",
    year = "1997",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.34-4482",
    doi = "10.5860/choice.34-4482",
    number = "08",
    openalex = "W3126641984",
    pages = "34-4482-34-4482",
    volume = "34"
}

The stress response in teleost fish shows many similarities to that of the terrestrial vertebrates. These concern the principal messengers of the brain-sympathetic-chromaffin cell axis (equivalent of the brain-sympathetic-adrenal medulla axis) and the brain-pituitary-interrenal axis (equivalent of the brain-pituitary-adrenal axis), as well as their functions, involving stimulation of oxygen uptake and transfer, mobilization of energy substrates, reallocation of energy away from growth and reproduction, and mainly suppressive effects on immune functions. There is also growing evidence for intensive interaction between the neuroendocrine system and the immune system in fish. Conspicuous differences, however, are present, and these are primarily related to the aquatic environment of fishes. For example, stressors increase the permeability of the surface epithelia, including the gills, to water and ions, and thus induce systemic hydromineral disturbances. High circulating catecholamine levels as well as structural damage to the gills and perhaps the skin are prime causal factors. This is associated with increased cellular turnover in these organs. In fish, cortisol combines glucocorticoid and mineralocorticoid actions, with the latter being essential for the restoration of hydromineral homeostasis, in concert with hormones such as prolactin (in freshwater) and growth hormone (in seawater). Toxic stressors are part of the stress literature in fish more so than in mammals. This is mainly related to the fact that fish are exposed to aquatic pollutants via the extensive and delicate respiratory surface of the gills and, in seawater, also via drinking. The high bioavailability of many chemicals in water is an additional factor. Together with the variety of highly sensitive perceptive mechanisms in the integument, this may explain why so many pollutants evoke an integrated stress response in fish in addition to their toxic effects at the cell and tissue levels. Exposure to chemicals may also directly compromise the stress response by interfering with specific neuroendocrine control mechanisms. Because hydromineral disturbance is inherent to stress in fish, external factors such as water pH, mineral composition, and ionic calcium levels have a significant impact on stressor intensity. Although the species studied comprise a small and nonrepresentative sample of the almost 20,000 known teleost species, there are many indications that the stress response is variable and flexible in fish, in line with the great diversity of adaptations that enable these animals to live in a large variety of aquatic habitats.

@article{doi101152physrev1997773591,
    author = "Bonga, S.E. Wendelaar",
    title = "The stress response in fish",
    year = "1997",
    journal = "Physiological Reviews",
    abstract = "The stress response in teleost fish shows many similarities to that of the terrestrial vertebrates. These concern the principal messengers of the brain-sympathetic-chromaffin cell axis (equivalent of the brain-sympathetic-adrenal medulla axis) and the brain-pituitary-interrenal axis (equivalent of the brain-pituitary-adrenal axis), as well as their functions, involving stimulation of oxygen uptake and transfer, mobilization of energy substrates, reallocation of energy away from growth and reproduction, and mainly suppressive effects on immune functions. There is also growing evidence for intensive interaction between the neuroendocrine system and the immune system in fish. Conspicuous differences, however, are present, and these are primarily related to the aquatic environment of fishes. For example, stressors increase the permeability of the surface epithelia, including the gills, to water and ions, and thus induce systemic hydromineral disturbances. High circulating catecholamine levels as well as structural damage to the gills and perhaps the skin are prime causal factors. This is associated with increased cellular turnover in these organs. In fish, cortisol combines glucocorticoid and mineralocorticoid actions, with the latter being essential for the restoration of hydromineral homeostasis, in concert with hormones such as prolactin (in freshwater) and growth hormone (in seawater). Toxic stressors are part of the stress literature in fish more so than in mammals. This is mainly related to the fact that fish are exposed to aquatic pollutants via the extensive and delicate respiratory surface of the gills and, in seawater, also via drinking. The high bioavailability of many chemicals in water is an additional factor. Together with the variety of highly sensitive perceptive mechanisms in the integument, this may explain why so many pollutants evoke an integrated stress response in fish in addition to their toxic effects at the cell and tissue levels. Exposure to chemicals may also directly compromise the stress response by interfering with specific neuroendocrine control mechanisms. Because hydromineral disturbance is inherent to stress in fish, external factors such as water pH, mineral composition, and ionic calcium levels have a significant impact on stressor intensity. Although the species studied comprise a small and nonrepresentative sample of the almost 20,000 known teleost species, there are many indications that the stress response is variable and flexible in fish, in line with the great diversity of adaptations that enable these animals to live in a large variety of aquatic habitats.",
    url = "https://doi.org/10.1152/physrev.1997.77.3.591",
    doi = "10.1152/physrev.1997.77.3.591",
    openalex = "W2136061619"
}

Fishes exhibit the greatest diversity of species among vertebrates, offering a number of relevant models for genetic and evolutionary studies. The investigation of sex chromosome differentiation is a very active and striking research area of fish cytogenetics, as fishes represent one of the most vital model groups. Neotropical fish species show an amazing variety of sex chromosome systems, where different stages of differentiation can be found, ranging from homomorphic to highly differentiated sex chromosomes. Here, we draw attention on the impact of recent developments in molecular cytogenetic analyses that helped to elucidate many unknown questions about fish sex chromosome evolution, using excellent characiform models occurring in the Neotropical region, namely the Erythrinidae family and the Triportheus genus. While in Erythrinidae distinct XY and/or multiple XY-derived sex chromosome systems have independently evolved at least four different times, representatives of Triportheus show an opposite scenario, i.e., highly conserved ZZ/ZW system with a monophyletic origin. In both cases, recent molecular approaches, such as mapping of repetitive DNA classes, comparative genomic hybridization (CGH), and whole chromosome painting (WCP), allowed us to unmask several new features linked to the molecular composition and differentiation processes of sex chromosomes in fishes.

@article{cioffi2017chromosomal,
    author = "Cioffi, Marcelo de Bello and Yano, Cassia Fernanda and Sember, Alexandr and Bertollo, Luiz Antônio Carlos",
    title = "Chromosomal Evolution in Lower Vertebrates: Sex Chromosomes in Neotropical Fishes",
    year = "2017",
    journal = "Genes",
    abstract = "Fishes exhibit the greatest diversity of species among vertebrates, offering a number of relevant models for genetic and evolutionary studies. The investigation of sex chromosome differentiation is a very active and striking research area of fish cytogenetics, as fishes represent one of the most vital model groups. Neotropical fish species show an amazing variety of sex chromosome systems, where different stages of differentiation can be found, ranging from homomorphic to highly differentiated sex chromosomes. Here, we draw attention on the impact of recent developments in molecular cytogenetic analyses that helped to elucidate many unknown questions about fish sex chromosome evolution, using excellent characiform models occurring in the Neotropical region, namely the Erythrinidae family and the Triportheus genus. While in Erythrinidae distinct XY and/or multiple XY-derived sex chromosome systems have independently evolved at least four different times, representatives of Triportheus show an opposite scenario, i.e., highly conserved ZZ/ZW system with a monophyletic origin. In both cases, recent molecular approaches, such as mapping of repetitive DNA classes, comparative genomic hybridization (CGH), and whole chromosome painting (WCP), allowed us to unmask several new features linked to the molecular composition and differentiation processes of sex chromosomes in fishes.",
    url = "https://doi.org/10.3390/genes8100258",
    doi = "10.3390/genes8100258",
    number = "10",
    openalex = "W2761677629",
    pages = "258",
    volume = "8",
    references = "doi101002dvdy23927, doi1010079783642881787, doi101016jgde200610007, doi101016s0044848602000571, doi101038nature06178, doi101038ncomms12087, doi101038sjhdy6800697, doi101146annurevgenet42110807091714, doi1011861471214811275, doi101371journalpbio1001899"
}

BACKGROUND: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny (www.deepfin.org). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS: The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

@article{doi101186s1286201709583,
    author = "Betancur‐R, Ricardo and Wiley, E. O. and Arratia, Gloria and P., Arturo Acero and Bailly, Nicolas and Miya, Masaki and Lecointre, Guillaume and Ortı́, Guillermo",
    title = "Phylogenetic classification of bony fishes",
    year = "2017",
    journal = "BMC Evolutionary Biology",
    abstract = "BACKGROUND: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny (www.deepfin.org). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS: The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or \textasciitilde 80\% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.",
    url = "https://doi.org/10.1186/s12862-017-0958-3",
    doi = "10.1186/s12862-017-0958-3",
    openalex = "W2727370449",
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}