Extant organisms

A system of broad classification which recognized a plant kingdom of four divisions and an animal kingdom of ten to fifteen phyla was for many years stable and standardized. Significant changes have occurred, or are now proposed. Among these, three major lines of development are discussed: a. Classification of the algae has been fundamentally revised; seven or more algal series are distinguished primarily by characteristics of cells. The phylum concept, long established in zoological classification, has been brought into botanical classification in the systems of Pascher (1931) and Tippo (1942), in which the major algal series, the Bryophyta, and the Tracheophyta are regarded as phyla. b. Many authors have advocated recognition of kingdom of lower organisms, to meet the difficulty of dividing these between the plant and animal kingdoms. Two major possibilities for such a third kingdom are the Protista of Haeckel (1866, 1894), essentially identified with the unicellular organisms, and the Proctoctista of Hogg (1860) and Copeland (1947, 1956), comprising the nucleate, "acellular" organisms including protozoa, algae, and fungi. c. Study of the fungi has led to the view that these are probably derived from colorless flagellates as a line of evolution independent of true plants. The bacteria are better regarded as an ancient complex of many nutritive types, than as a group derived from the blue-green algae. In natural communities bacteria and fungi together form a major functional group (reducers) distinct from the green plants (producers) and animals (consumers). It is consequently appropriate to conceive the broad relations of the living world in terms of three modes of nutrition and directions of evolution rather than two-the photosynthetic of the green plants, the ingestive of the animals, and the absorptive of the bacteria and fungi. These three directions of evolution appear on three major levels of organization-the Monera, or bacteria and blue-green algae, which lack nuclear membranes; the Eunucleata, or unicellular organisms with nuclear membranes; and the multicellular and multinucleate higher plants, animals, and fungi. On this basis four kingdoms are here proposed: The Protista, or unicellular organisms; the Plantae, or multicellular plants; the Fungi; and the Animalia or multicellular animals. Among the Protista the subkingdoms Monera and Eunucleata and distinguished. Among the higher organisms the less widely successful lines of evolution into the multicellular and multinucleate conditions are recognized as the subkingdoms Rhodophyta and Phaeophyta among the plants, Myxomycota among the fungi, and Parazoa and Mesozoa among the animals. Other alternatives to the traditional two-kingdom system are discussed. Despite the general acceptance of the two-kingdom system, these alternatives have value in expressing current understanding of the broad relations among organisms. They should be judged in comparison with the two-kingdom system and with one another for their relative success in embodying these relations in a "natural" classification.

@article{doi101086402733,
    author = "Whittaker, R. H.",
    title = "On the Broad Classification of Organisms",
    year = "1959",
    journal = "The Quarterly Review of Biology",
    abstract = {A system of broad classification which recognized a plant kingdom of four divisions and an animal kingdom of ten to fifteen phyla was for many years stable and standardized. Significant changes have occurred, or are now proposed. Among these, three major lines of development are discussed: a. Classification of the algae has been fundamentally revised; seven or more algal series are distinguished primarily by characteristics of cells. The phylum concept, long established in zoological classification, has been brought into botanical classification in the systems of Pascher (1931) and Tippo (1942), in which the major algal series, the Bryophyta, and the Tracheophyta are regarded as phyla. b. Many authors have advocated recognition of kingdom of lower organisms, to meet the difficulty of dividing these between the plant and animal kingdoms. Two major possibilities for such a third kingdom are the Protista of Haeckel (1866, 1894), essentially identified with the unicellular organisms, and the Proctoctista of Hogg (1860) and Copeland (1947, 1956), comprising the nucleate, "acellular" organisms including protozoa, algae, and fungi. c. Study of the fungi has led to the view that these are probably derived from colorless flagellates as a line of evolution independent of true plants. The bacteria are better regarded as an ancient complex of many nutritive types, than as a group derived from the blue-green algae. In natural communities bacteria and fungi together form a major functional group (reducers) distinct from the green plants (producers) and animals (consumers). It is consequently appropriate to conceive the broad relations of the living world in terms of three modes of nutrition and directions of evolution rather than two-the photosynthetic of the green plants, the ingestive of the animals, and the absorptive of the bacteria and fungi. These three directions of evolution appear on three major levels of organization-the Monera, or bacteria and blue-green algae, which lack nuclear membranes; the Eunucleata, or unicellular organisms with nuclear membranes; and the multicellular and multinucleate higher plants, animals, and fungi. On this basis four kingdoms are here proposed: The Protista, or unicellular organisms; the Plantae, or multicellular plants; the Fungi; and the Animalia or multicellular animals. Among the Protista the subkingdoms Monera and Eunucleata and distinguished. Among the higher organisms the less widely successful lines of evolution into the multicellular and multinucleate conditions are recognized as the subkingdoms Rhodophyta and Phaeophyta among the plants, Myxomycota among the fungi, and Parazoa and Mesozoa among the animals. Other alternatives to the traditional two-kingdom system are discussed. Despite the general acceptance of the two-kingdom system, these alternatives have value in expressing current understanding of the broad relations among organisms. They should be judged in comparison with the two-kingdom system and with one another for their relative success in embodying these relations in a "natural" classification.},
    url = "https://doi.org/10.1086/402733",
    doi = "10.1086/402733",
    openalex = "W2060112742"
}

@article{crossref1966mcgrawhill,
    title = "McGraw-Hill encyclopedia",
    year = "1966",
    journal = "Physics Today",
    url = "https://doi.org/10.1063/1.3048233",
    doi = "10.1063/1.3048233",
    number = "5",
    openalex = "W4214489217",
    pages = "113-113",
    volume = "19"
}

@techreport{greenwood1966phyletic1,
    author = "Greenwood, P. H. and Miles, R. S. and Patterson, C. and Rosen, D. E. and Weitzman, S. H. and Myers, G. S",
    title = "Phyletic studies of teleostean fishes, with a provisional classification of living forms",
    year = "1966",
    howpublished = "Bulletin of the American Museum of Natural History, v. 131, no. Art. 4, p. 339-456",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., Miles, R. S., Patterson, C., Rosen, D. E., Weitzman, S. H., and Myers, G. S., 1966, Phyletic studies of teleostean fishes, with a provisional classification of living forms: Bulletin of the American Museum of Natural History, v. 131, no. Art. 4, p. 339-456.}"
}

p. 341-455, [3] p. of plates: ill.; 27 cm.

@article{openalexw1845290859,
    author = "Greenwood, Peter Humphry and Rosen, Donn Eric and Weitzman, Stanley H. and Myers, George S.",
    title = "Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bulletin of the AMNH; v. 131, article 4",
    year = "1966",
    journal = "Biodiversity Heritage Library (Smithsonian Institution)",
    abstract = "p. 341-455, [3] p. of plates: ill.; 27 cm.",
    openalex = "W1845290859"
}

@article{applegate1967phyletic,
    author = "Applegate, Shelton P. and Greenwood, P. Humphrey and Rosen, Donn E. and Weitzman, Stanley H. and Myers, George S.",
    title = "Phyletic Studies of Teleostean Fishes, with a Provisional Classification of Living Forms",
    year = "1967",
    journal = "Copeia",
    url = "https://doi.org/10.2307/1442263",
    doi = "10.2307/1442263",
    number = "3",
    pages = "693",
    volume = "1967"
}

This book is an important addition to a growing body of literature on functional morphology—the study of form and structure in animals as related to the functions of the various body parts. The author is particularly concerned with clarifying the interrelationships between evolutionary changes in morphology and the classification of this large group of fishes. He starts from the premise that the classification should summarize evolutionary relationships and that major steps in evolution are expressed in modifications of functional systems. In the author’s view, changes in the abilities of fish to maneuver in the water, to obtain food, and to force water over the gills—changes that are reflected in the morphology, particularly of skeletal elements—are among the most important advances that have been made within the teleostean group of fishes. With great skill and insight, Dr. Gosline develops these difficult concepts in the first section of the book. In working out his system of classification of teleosts, presented in the second section, the author’s major effort was placed on clarifying the underlying zoological problems: he views the system primarily as a vehicle for discussing zoological information that suggests relationships between teleostean groups. Any student of zoology—not only ichthyologists—will welcome this original and thoughtful approach to problems of animal classification.

@book{doi1015159780824885311,
    author = "Gosline, William A.",
    title = "Functional Morphology and Classification of Teleostean Fishes",
    year = "1971",
    booktitle = "University of Hawaii Press eBooks",
    abstract = "This book is an important addition to a growing body of literature on functional morphology—the study of form and structure in animals as related to the functions of the various body parts. The author is particularly concerned with clarifying the interrelationships between evolutionary changes in morphology and the classification of this large group of fishes. He starts from the premise that the classification should summarize evolutionary relationships and that major steps in evolution are expressed in modifications of functional systems. In the author’s view, changes in the abilities of fish to maneuver in the water, to obtain food, and to force water over the gills—changes that are reflected in the morphology, particularly of skeletal elements—are among the most important advances that have been made within the teleostean group of fishes. With great skill and insight, Dr. Gosline develops these difficult concepts in the first section of the book. In working out his system of classification of teleosts, presented in the second section, the author’s major effort was placed on clarifying the underlying zoological problems: he views the system primarily as a vehicle for discussing zoological information that suggests relationships between teleostean groups. Any student of zoology—not only ichthyologists—will welcome this original and thoughtful approach to problems of animal classification.",
    url = "https://doi.org/10.1515/9780824885311",
    doi = "10.1515/9780824885311",
    openalex = "W1517274358"
}

Organisms are capable of forming a diverse array of minerals, some of which cannot be formed inorganically in the biosphere. The initial precipitates may differ from the form in which they are finally stabilized, or during development of the organism one mineral may substitute for another. Biogenic minerals commonly have attributes which distinguish them from their inorganic counterparts. They fulfill important biological functions. They have been formed in ever-increasing amounts during the last 600 million years and have radically altered the character of the biosphere.

@article{doi101126science7008198,
    author = "Lowenstam, Heinz A.",
    title = "Minerals Formed by Organisms",
    year = "1981",
    journal = "Science",
    abstract = "Organisms are capable of forming a diverse array of minerals, some of which cannot be formed inorganically in the biosphere. The initial precipitates may differ from the form in which they are finally stabilized, or during development of the organism one mineral may substitute for another. Biogenic minerals commonly have attributes which distinguish them from their inorganic counterparts. They fulfill important biological functions. They have been formed in ever-increasing amounts during the last 600 million years and have radically altered the character of the biosphere.",
    url = "https://doi.org/10.1126/science.7008198",
    doi = "10.1126/science.7008198",
    openalex = "W2031846886",
    references = "doi1010160021979767902664, doi1010160025322770900010, doi101029jc077i003p00463, doi101038208365a0, doi101038273199a0, doi101126science170679, doi101126science20143601026, doi101126science20343871355, doi101128jb14027207291979, doi10113000167606196273435midcir20co2"
}

@misc{parker1982mcgrawhill2,
    author = "Parker, S. P",
    title = "McGraw-Hill Synopsis and Classification of Living Organisms",
    year = "1982",
    howpublished = "New York, McGraw-Hill; 2 Volumes",
    note = "talkorigins\_source = {true}; raw\_reference = {Parker, S. P., 1982, McGraw-Hill Synopsis and Classification of Living Organisms: New York, McGraw-Hill; 2 Volumes.}"
}

@article{saccone1995molecular,
    author = "Saccone, C. and Gissi, C. and Lanave, C. and Pesole, G.",
    title = "Molecular classification of living organisms",
    year = "1995",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf00163232",
    doi = "10.1007/bf00163232",
    number = "3",
    openalex = "W1993800856",
    pages = "273-279",
    volume = "40",
    references = "doi101007bf02101990, doi101073pnas86176661, doi101073pnas86239355, doi101073pnas87124576, doi101093nar20suppl2075, doi101093nar21133021, doi101126science2605108640, doi101128mmbr5122212711987, doi101128mr5122212711987, doi1023072412074"
}

@incollection{crossref20034432,
    title = "(4432) McGraw-Hill",
    year = "2003",
    booktitle = "Dictionary of Minor Planet Names",
    url = "https://doi.org/10.1007/978-3-540-29925-7\_4381",
    doi = "10.1007/978-3-540-29925-7\_4381",
    openalex = "W4235887303",
    pages = "381-381"
}

@incollection{crossref2012mcgrawhill,
    title = "Mcgraw-Hill",
    year = "2012",
    booktitle = "The Last American Diplomat",
    url = "https://doi.org/10.5040/9780755624034.ch-016",
    doi = "10.5040/9780755624034.ch-016",
    openalex = "W4243801099"
}

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

@article{doi101073pnas1206625109,
    author = "Near, Thomas J. and Eytan, Ron I. and Dornburg, Alex and Kuhn, Kristen L. and Moore, Jon A. and Davis, Matthew P. and Wainwright, Peter C. and Friedman, Matt and Smith, W. Leo",
    title = "Resolution of ray-finned fish phylogeny and timing of diversification",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."},
    url = "https://doi.org/10.1073/pnas.1206625109",
    doi = "10.1073/pnas.1206625109",
    openalex = "W2081778808",
    references = "doi101016b9780126709506500138, doi101016s1055790302003329, doi101073pnas0811087106, doi101093bioinformaticsbtl446, doi101093bioinformaticsbtq228, doi101093oso97801985404720010001, doi101111j14754983201201165x, doi101126science1157704, doi101126science1211028, doi101186147121487214, doi101371journalpbio0040088, doi1023072412685, openalexw653978695"
}

The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

@article{doi101371currentstol53ba26640df0ccaee75bb165c8c26288,
    author = "Betancur‐R, Ricardo and Broughton, Richard E. and Wiley, E. O. and Carpenter, Kent E. and López, J. Andrés and Li, Chenhong and Holcroft, Nancy I. and Arcila, Dahiana and Sanciangco, Millicent D. Alexandrov and Cureton, James C. and Zhang, Feifei and Buser, Thaddaeus John and Campbell, Matthew A. and Ballesteros, Jesús A. and Roa‐Varón, Adela and Willis, Stuart C. and Borden, W. Calvin and Rowley, Thaine and Reneau, Paulette C. and Hough, Daniel J. and Lu, Guoqing and Grande, Terry and Arratia, Gloria and Ortı́, Guillermo",
    title = "The Tree of Life and a New Classification of Bony Fishes",
    year = "2013",
    journal = "PLoS Currents",
    abstract = "The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.",
    url = "https://doi.org/10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288",
    doi = "10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288",
    openalex = "W1998591654",
    references = "applegate1967phyletic, doi101016b9780126709506500138, doi101016s1055790302003329, doi101038s4155901806241, doi101073pnas1206625109, doi10108010635150802429642, doi101086417338, doi101093bioinformatics192301, doi101093bioinformaticsbtl446, doi101093molbevmss020, doi101093molbevmst010, doi101093nargkq291, doi101093oxfordjournalsmolbeva003741, doi101093sysbio463523, doi101093sysbiosyr107, doi101098rspb20152917, doi101111j10960031201000329x, doi101111j109636421981tb01575x, doi101111j1469185x1990tb01427x, doi101111j14754983201201165x, doi1011646zootaxa388211, doi101186147121487214, gardiner1989interrelationships, openalexw3206657856"
}

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",
    references = "applegate1967phyletic, bonde1974interrelationships, doi1010029781119174844, doi101073pnas1206625109, doi101093bioinformaticsbtg412, doi101093sysbiosys004, doi101111j109600311988tb00514x, doi101111j2041210x201100169x, doi1011861471214811275, doi101186s1286201709583, doi1023071444873, doi105962bhltitle59991, forey1996interrelationships, openalexw3001739384"
}

The order Cypriniformes is the most diverse order of freshwater fishes. Recent phylogenetic studies have approached a consensus on the phylogenetic relationships of Cypriniformes and proposed a new phylogenetic classification of family-level groupings in Cypriniformes. The lack of a reference for the placement of genera amongst families has hampered the adoption of this phylogenetic classification more widely. We herein provide an updated compilation of the membership of genera to suprageneric taxa based on the latest phylogenetic classifications. We propose a new taxon: subfamily Esominae within Danionidae, for the genus Esomus.

@article{doi1011646zootaxa447614,
    author = "Tan, Milton and Armbruster, Jonathan W.",
    title = "Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi)",
    year = "2018",
    journal = "Zootaxa",
    abstract = "The order Cypriniformes is the most diverse order of freshwater fishes. Recent phylogenetic studies have approached a consensus on the phylogenetic relationships of Cypriniformes and proposed a new phylogenetic classification of family-level groupings in Cypriniformes. The lack of a reference for the placement of genera amongst families has hampered the adoption of this phylogenetic classification more widely. We herein provide an updated compilation of the membership of genera to suprageneric taxa based on the latest phylogenetic classifications. We propose a new taxon: subfamily Esominae within Danionidae, for the genus Esomus.",
    url = "https://doi.org/10.11646/zootaxa.4476.1.4",
    doi = "10.11646/zootaxa.4476.1.4",
    openalex = "W2889922768",
    references = "doi101016jympev201501014, doi101038nature12111, doi101111j14672979200600227x, doi1011646zootaxa388211, doi10118614712148738, doi101186s1286201709583, doi105860choice436531, openalexw2751068043, openalexw2965787927, openalexw597149003"
}

@misc{crossref2019a,
    title = "A Classification of Living Organisms",
    year = "2019",
    booktitle = "The Biology of Reproduction",
    url = "https://doi.org/10.1017/9781108758970.011",
    doi = "10.1017/9781108758970.011",
    openalex = "W3159954657",
    pages = "407-414",
    references = "doi1010079781489930439, doi101016b9780123705266x50016, doi101016s0044848602000571, doi101093acprofoso97801992679720010001, doi101371journalpbio1002533, doi1023075403, doi105840philstudies1954421, doi105962bhltitle82303, openalexw1523843460, openalexw1635425035"
}

Abstract 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.

@article{doi101093zoolinneanzlae101,
    author = "de Melo, Bruno Francelino and Ota, Rafaela Priscila and Benine, Ricardo C. and Carvalho, Fernando Rogério and de Lima, Flávio César Thadeo and Mattox, George Mendes Taliaferro and Souza, Camila S. and Faria, Tiago C. and Reia, Lais and Roxo, Fábio Fernandes and Valdéz-Moreno, Martha and Near, Thomas J. and Oliveira, Cláudio",
    title = "Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)",
    year = "2024",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "Abstract 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.",
    url = "https://doi.org/10.1093/zoolinnean/zlae101",
    doi = "10.1093/zoolinnean/zlae101",
    openalex = "W4402170922",
    references = "doi10108000222931108692993, doi1011646zootaxa447614"
}

Classification of the tremendous diversity of ray-finned fishes (Actinopterygii) began with the designation of taxonomic groups on the basis of morphological similarity. Starting in the late 1960s morphological phylogenetics became the basis for the classification of Actinopterygii but failed to resolve many relationships, particularly among lineages within the hyperdiverse Percomorpha. The introduction of molecular phylogenetics led to a dramatic reconfiguration of actinopterygian phylogeny. Refined phylogenetic resolution afforded by molecular studies revealed an uneven diversity among actinopterygian lineages, resulting in a proliferation of redundant group names in Linnean-ranked classifications. Here we provide an unranked phylogenetic classification for actinopterygian fishes based on a summary phylogeny of 830 lineages of ray-finned fishes that includes all currently recognized actinopterygian taxonomic families and 287 fossil taxa. We provide phylogenetic definitions for 90 clade names and review seven previously defined names. For each of the 97 clade names, we review the etymology of the clade name, clade species diversity and constituent lineages, clade diagnostic morphological apomorphies, review synonyms, and provide a discussion of the clade's nomenclatural and systematic history. The new classification is free of redundant group names and includes only one new name among the 97 clade names we review and describe, yielding a comprehensive classification that is based explicitly on the phylogeny of ray-finned fishes that has emerged in the 21st century and rests on the foundation of the previous 200 years of research on the systematics of ray-finned fishes.

@article{doi1033740140650101,
    author = "Near, Thomas J. and Thacker, Christine E.",
    title = "Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)",
    year = "2024",
    journal = "Bulletin of the Peabody Museum of Natural History",
    abstract = "Classification of the tremendous diversity of ray-finned fishes (Actinopterygii) began with the designation of taxonomic groups on the basis of morphological similarity. Starting in the late 1960s morphological phylogenetics became the basis for the classification of Actinopterygii but failed to resolve many relationships, particularly among lineages within the hyperdiverse Percomorpha. The introduction of molecular phylogenetics led to a dramatic reconfiguration of actinopterygian phylogeny. Refined phylogenetic resolution afforded by molecular studies revealed an uneven diversity among actinopterygian lineages, resulting in a proliferation of redundant group names in Linnean-ranked classifications. Here we provide an unranked phylogenetic classification for actinopterygian fishes based on a summary phylogeny of 830 lineages of ray-finned fishes that includes all currently recognized actinopterygian taxonomic families and 287 fossil taxa. We provide phylogenetic definitions for 90 clade names and review seven previously defined names. For each of the 97 clade names, we review the etymology of the clade name, clade species diversity and constituent lineages, clade diagnostic morphological apomorphies, review synonyms, and provide a discussion of the clade's nomenclatural and systematic history. The new classification is free of redundant group names and includes only one new name among the 97 clade names we review and describe, yielding a comprehensive classification that is based explicitly on the phylogeny of ray-finned fishes that has emerged in the 21st century and rests on the foundation of the previous 200 years of research on the systematics of ray-finned fishes.",
    url = "https://doi.org/10.3374/014.065.0101",
    doi = "10.3374/014.065.0101",
    openalex = "W4394948439",
    references = "branson1962the, doi101007s1022801404445, doi10108000222931108692993, doi101093sysbiosyy085, doi101093zoolinneanzlx040, doi101111brv12473, doi101126scienceaav4632, doi1011646zootaxa447614, doi101643004585112002002053220co2, doi101643cg17669, doi105962bhltitle53990, forey1996interrelationships, openalexw2898156694, openalexw568207017, openalexw63312880"
}

@misc{crossrefNonectbmcgraw,
    title = "CTB/McGraw Hill",
    year = "None",
    booktitle = "Lexikon des gesamten Buchwesens Online",
    url = "https://doi.org/10.1163/9789004337862\_lgbo\_com\_030916",
    doi = "10.1163/9789004337862\_lgbo\_com\_030916",
    openalex = "W4245187714"
}