Heterostracans

@article{doi1023071437499,
    author = "Myers, George S. and Berg, L. S.",
    title = "Classification of Fishes, Both Recent and Fossil",
    year = "1941",
    journal = "Copeia",
    url = "https://doi.org/10.2307/1437499",
    doi = "10.2307/1437499",
    openalex = "W2017085139"
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Experiments are described in which the dorsal-aspect target strengths of a number of individual teleostean fishes of eight species were measured at various frequencies. The results of these experiments indicate that the variations of target strength with frequency are different for fishes in two major teleostean groups, the malacopterygians and the acanthopterygians. These results are combined with results from eight other sources and an empirical equation approximating the dorsal-aspect target strength of an individual fish determined for 0.7⩽L/λ⩽90, where L is the fish length and λ is the incident acoustic wavelength. The combined results are compared to similar results for the maximum side-aspect target strength of an individual fish, and curves showing the trend of dorsal-aspect and maximum side-aspect acoustic cross sections of an individual swimbladder-bearing fish are presented for all L/λ⩽90.

@article{doi10112111912422,
    author = "Love, Richard H.",
    title = "Dorsal-Aspect Target Strength of an Individual Fish",
    year = "1971",
    journal = "The Journal of the Acoustical Society of America",
    abstract = "Experiments are described in which the dorsal-aspect target strengths of a number of individual teleostean fishes of eight species were measured at various frequencies. The results of these experiments indicate that the variations of target strength with frequency are different for fishes in two major teleostean groups, the malacopterygians and the acanthopterygians. These results are combined with results from eight other sources and an empirical equation approximating the dorsal-aspect target strength of an individual fish determined for 0.7⩽L/λ⩽90, where L is the fish length and λ is the incident acoustic wavelength. The combined results are compared to similar results for the maximum side-aspect target strength of an individual fish, and curves showing the trend of dorsal-aspect and maximum side-aspect acoustic cross sections of an individual swimbladder-bearing fish are presented for all L/λ⩽90.",
    url = "https://doi.org/10.1121/1.1912422",
    doi = "10.1121/1.1912422",
    openalex = "W2008914868",
    references = "doi1023071437499"
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Summary Resemblances between cephalopods and fish 1. Modern cephalopods (coleoids < 1000 species) resemble modern fish (30,000 species) more closely than any of their ancestors did. They have not been replaced by the more diversified group in geological time. 2. The main body of the article (pp. 245–283) reviews these resemblances. They are to be found at all levels of analysis. 3. Basic physiological mechanisms of molluscs (pp. 262–5) have been incorporated into systems with performances comparable to those of vertebrate systems. For instance the cephalopod locomotory system (pp. 249–56) and hydrostatic control system (pp. 256–60), structurally very different from their fish counterparts, have similar adaptive radiation. 4. Behaviour (p. 278) and growth of the brain (p. 265) are characteristically vertebrate‐like. 5. Cephalopods and fish are considered as occupying the same broad adaptive zone though modal differences (pp. 283–5)‐in reproductive habits, growth rate and light‐dependent behaviour where extraocular photoreceptors appear to be important ‐ mean that they occupy different areas within that zone. (ii) Evolution of convergence 6. Evidence is presented (pp. 287–293) for considering the convergence as due not merely to similar physical demands of the marine environment, but to dynamic interactions between cephalopods and vertebrates from the late Palaeozoic onwards. 7. The convergence was set on its way when the two groups, independently of each other, acquired locomotory methods that allowed them to increase in size. 8. It is argued that reduction and eventually complete loss of the chambered shell (in all but sepiids) was an evolutionary response to the needs of increased mobility and to the need to go deeper as vertebrate predators pushed out into oceanic waters. 9. The ammonites (pp. 291–2) present a partial model of the course that coleoid ancestors may have taken. 10. Coleoids subsequently reinvaded surface and coastal waters, competing successfully in a teleost habitat. Their most striking adaptations are ones that they share with teleosts. 11. Behavioural interactions in a vertebrate‐dominated environment have probably been responsible for the vertebrate‐type eye of cephalopods (p. 293). 12. The conclusion that the common adaptive zone shared by cephalopods and fish has been achieved by mutual interactions between the two groups evokes no special evolutionary principles. It assumes that all cephalopod species have (at some period of their evolutionary history) been in competition for food with some vertebrate species and that vertebrates are a source of selection pressures ‐ largely operating through visual behaviour ‐ that maintain and promote convergence upon the ‘fish’ modal type. 13. Selection pressures also operate within behaviour space to maintain and promote the special differences that separate any competitively successful species from all others. Coleoids as a group appear to have retained adaptations associated with such molluscan features as high growth rate and rapid turnover of the population. They are still characteristically crepuscular in habits and have extensive vertical mobility.

@article{doi101111j1469185x1972tb00975x,
    author = "Packard, Andrew",
    title = "CEPHALOPODS AND FISH: THE LIMITS OF CONVERGENCE",
    year = "1972",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary Resemblances between cephalopods and fish 1. Modern cephalopods (coleoids < 1000 species) resemble modern fish (30,000 species) more closely than any of their ancestors did. They have not been replaced by the more diversified group in geological time. 2. The main body of the article (pp. 245–283) reviews these resemblances. They are to be found at all levels of analysis. 3. Basic physiological mechanisms of molluscs (pp. 262–5) have been incorporated into systems with performances comparable to those of vertebrate systems. For instance the cephalopod locomotory system (pp. 249–56) and hydrostatic control system (pp. 256–60), structurally very different from their fish counterparts, have similar adaptive radiation. 4. Behaviour (p. 278) and growth of the brain (p. 265) are characteristically vertebrate‐like. 5. Cephalopods and fish are considered as occupying the same broad adaptive zone though modal differences (pp. 283–5)‐in reproductive habits, growth rate and light‐dependent behaviour where extraocular photoreceptors appear to be important ‐ mean that they occupy different areas within that zone. (ii) Evolution of convergence 6. Evidence is presented (pp. 287–293) for considering the convergence as due not merely to similar physical demands of the marine environment, but to dynamic interactions between cephalopods and vertebrates from the late Palaeozoic onwards. 7. The convergence was set on its way when the two groups, independently of each other, acquired locomotory methods that allowed them to increase in size. 8. It is argued that reduction and eventually complete loss of the chambered shell (in all but sepiids) was an evolutionary response to the needs of increased mobility and to the need to go deeper as vertebrate predators pushed out into oceanic waters. 9. The ammonites (pp. 291–2) present a partial model of the course that coleoid ancestors may have taken. 10. Coleoids subsequently reinvaded surface and coastal waters, competing successfully in a teleost habitat. Their most striking adaptations are ones that they share with teleosts. 11. Behavioural interactions in a vertebrate‐dominated environment have probably been responsible for the vertebrate‐type eye of cephalopods (p. 293). 12. The conclusion that the common adaptive zone shared by cephalopods and fish has been achieved by mutual interactions between the two groups evokes no special evolutionary principles. It assumes that all cephalopod species have (at some period of their evolutionary history) been in competition for food with some vertebrate species and that vertebrates are a source of selection pressures ‐ largely operating through visual behaviour ‐ that maintain and promote convergence upon the ‘fish’ modal type. 13. Selection pressures also operate within behaviour space to maintain and promote the special differences that separate any competitively successful species from all others. Coleoids as a group appear to have retained adaptations associated with such molluscan features as high growth rate and rapid turnover of the population. They are still characteristically crepuscular in habits and have extensive vertical mobility.",
    url = "https://doi.org/10.1111/j.1469-185x.1972.tb00975.x",
    doi = "10.1111/j.1469-185x.1972.tb00975.x",
    openalex = "W2068922815",
    references = "denton1972the, doi1010079783662131473, doi101016s006528810860468x, doi101111j00221112200400433x, doi101111j13652656200701307x, doi101111j1469185x1966tb01624x, doi101111j155856461949tb00010x, doi101146annurevfl01010169002213, doi1015159781400875689, doi1023071375442, doi1023071420674, doi105962bhltitle52081, doi105962bhltitle7369, doi107312simp93764"
}

Summary 1. The heterostracan fishes were jawless, microphagous, devoid of paired fins and encased in a bony armour. The classification is based on the arrangement of the plates of the carapace — the primitive forms possessed a tessellated armour made up of numerous small polygonal plates. Several genera had a tessellated carapace ventrally but large discrete plates dorsally. All further groups are characterized by distinct patterns of plates which remain constant within each order. The proportions in some species suggest sexual dimorphism. 2. A study of the superficial ornamentation reveals patterns of growth. From the primitive tessellated condition different evolutionary lines can be followed leading to the fusion of these small elements into large discrete plates. Among the latest group of heterostracans there was a secondary redevelopment of tesserae. 3. Impressions on the inner surface of the plates of the carapace enable certain aspects of the internal anatomy to be reconstructed. The nasal sacs were double, the acousticolateralis system was primitive. The brain was little more than the nerve cord swollen in three places, there was no cranial flexure. Impressions of two pre‐otic somites were present, indicating that they had not migrated to form the extrinsic eye muscles. The branchial arches appear to have been of gnathostome type and in some genera spiracles were formed as an adaptation to a benthonic mode of life. 4. Microscopic sections of the armour demonstrate the existence of four tissues: aspidin, dentine, enameloid and calcified cartilage. Aspidin was originally acellular but later became cellular; the organic matrix was first organized like dentine, but subsequently like bone. Furthermore aspidin was capable of remodelling. Dentine appears to have acted as a skin‐like tissue and was capable of regeneration. The significance of enameloid and calcified cartilage in the dermal armour is not well understood. 5. Until the end of the Silurian the heterostracans inhabited marine waters but from the beginning of the Devonian they colonized the fresh‐water lakes and rivers of the Old Red Continent. One major group flourished in a large embayment on the edge of the Tungussian land mass. When the stratigraphical range and geographical distribution of the heterostracans is listed, evolutionary centres can be recognized and also migration routes: during the Upper Silurian the cyathaspids in the Canadian Arctic, the Lower Devonian pteraspids in Eastern Europe, the later Lower Devonian amphiaspids in north‐west Siberia (Tungussian Realm), and the Middle and Upper Devonian psammosteids in the Baltic province. Periods of migration from the Baltic to Scotland, the Timan, Ellesmereland, the Urals and Donbas have been documented. For the illustrations the author is indebted to Miss Jennifer Middleton and Mr John Smith.

@article{doi101111j1469185x1973tb01005x,
    author = "Halstead, L. B.",
    title = "THE HETEROSTRACAN FISHES",
    year = "1973",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary 1. The heterostracan fishes were jawless, microphagous, devoid of paired fins and encased in a bony armour. The classification is based on the arrangement of the plates of the carapace — the primitive forms possessed a tessellated armour made up of numerous small polygonal plates. Several genera had a tessellated carapace ventrally but large discrete plates dorsally. All further groups are characterized by distinct patterns of plates which remain constant within each order. The proportions in some species suggest sexual dimorphism. 2. A study of the superficial ornamentation reveals patterns of growth. From the primitive tessellated condition different evolutionary lines can be followed leading to the fusion of these small elements into large discrete plates. Among the latest group of heterostracans there was a secondary redevelopment of tesserae. 3. Impressions on the inner surface of the plates of the carapace enable certain aspects of the internal anatomy to be reconstructed. The nasal sacs were double, the acousticolateralis system was primitive. The brain was little more than the nerve cord swollen in three places, there was no cranial flexure. Impressions of two pre‐otic somites were present, indicating that they had not migrated to form the extrinsic eye muscles. The branchial arches appear to have been of gnathostome type and in some genera spiracles were formed as an adaptation to a benthonic mode of life. 4. Microscopic sections of the armour demonstrate the existence of four tissues: aspidin, dentine, enameloid and calcified cartilage. Aspidin was originally acellular but later became cellular; the organic matrix was first organized like dentine, but subsequently like bone. Furthermore aspidin was capable of remodelling. Dentine appears to have acted as a skin‐like tissue and was capable of regeneration. The significance of enameloid and calcified cartilage in the dermal armour is not well understood. 5. Until the end of the Silurian the heterostracans inhabited marine waters but from the beginning of the Devonian they colonized the fresh‐water lakes and rivers of the Old Red Continent. One major group flourished in a large embayment on the edge of the Tungussian land mass. When the stratigraphical range and geographical distribution of the heterostracans is listed, evolutionary centres can be recognized and also migration routes: during the Upper Silurian the cyathaspids in the Canadian Arctic, the Lower Devonian pteraspids in Eastern Europe, the later Lower Devonian amphiaspids in north‐west Siberia (Tungussian Realm), and the Middle and Upper Devonian psammosteids in the Baltic province. Periods of migration from the Baltic to Scotland, the Timan, Ellesmereland, the Urals and Donbas have been documented. For the illustrations the author is indebted to Miss Jennifer Middleton and Mr John Smith.",
    url = "https://doi.org/10.1111/j.1469-185x.1973.tb01005.x",
    doi = "10.1111/j.1469-185x.1973.tb01005.x",
    openalex = "W1980068371",
    references = "doi101098rstb19520012, doi101111j136530911964tb00459x, doi101111j136530911965tb01561x, doi101130gsab3153, doi1023071375442, doi1023071441916, doi1023071796776, doi1023072407204, doi105962bhltitle118830, openalexw115975037"
}

@article{halstead1973the1,
    author = "Halstead, L. B",
    title = "The heterostracan fishes",
    year = "1973",
    journal = "Biological Reviews, v. 48, p. 279-332",
    note = "talkorigins\_source = {true}; raw\_reference = {Halstead, L. B., 1973, The heterostracan fishes: Biological Reviews, v. 48, p. 279-332.}"
}

Preface. Teaching as Applied Behavior Analysis: A Professional Difference. The Learn Unit: A Natural Fracture of Teaching. The Repertoires of Teachers Who Are Behavior Analysts. The Strategic Analysis of Instruction and Learning. Teacher Repertoires for Students from Prelistener to Early Reader Status. Teaching Practices for Students with Advanced Repertoires of Verbal Behavior (Reader to Editor of Own Written Work). Behavioral Selection and the Content of Curriculum. Writing and Designing Curricula. Teaching and Mentoring Teachers. The School Psychologist and Other Supportive Personnel: A Contemporary Behavioral Perspective. Glossary. Index.

@article{doi1023072412482,
    author = "Bonde, Niels and Greenwood, P. H. and Patterson, C.",
    title = "Interrelationships of Fishes.",
    year = "1974",
    journal = "Systematic Zoology",
    abstract = "Preface. Teaching as Applied Behavior Analysis: A Professional Difference. The Learn Unit: A Natural Fracture of Teaching. The Repertoires of Teachers Who Are Behavior Analysts. The Strategic Analysis of Instruction and Learning. Teacher Repertoires for Students from Prelistener to Early Reader Status. Teaching Practices for Students with Advanced Repertoires of Verbal Behavior (Reader to Editor of Own Written Work). Behavioral Selection and the Content of Curriculum. Writing and Designing Curricula. Teaching and Mentoring Teachers. The School Psychologist and Other Supportive Personnel: A Contemporary Behavioral Perspective. Glossary. Index.",
    url = "https://doi.org/10.2307/2412482",
    doi = "10.2307/2412482",
    openalex = "W2321151333"
}

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.

@article{doi105281zenodo15997053,
    author = "Hobson, Edmund S.",
    title = "Feeding relationships of teleostean fishes on coral reefs in Kona, Hawaii",
    year = "1974",
    journal = "Biodiversity Heritage Library (Smithsonian Institution)",
    abstract = "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.",
    url = "https://doi.org/10.5281/zenodo.15997053",
    doi = "10.5281/zenodo.15997053",
    openalex = "W2254852082",
    references = "doi1023071437499"
}

@article{doi101038255725a0,
    author = "Wardle, C. S.",
    title = "Limit of fish swimming speed",
    year = "1975",
    journal = "Nature",
    url = "https://doi.org/10.1038/255725a0",
    doi = "10.1038/255725a0",
    openalex = "W2006132307"
}

@article{openalexw1491336618,
    author = "Parenti, Lynne R.",
    title = "A phylogenetic and biogeographic analysis of cyprinodontiform fishes (Teleostei, Atherinomorpha)",
    year = "1981",
    journal = "Smithsonian Digital Repository (Smithsonian Institution)",
    openalex = "W1491336618",
    references = "doi101093sysbio232265, doi1023071437499, openalexw1575479768"
}

@article{doi1023071937507,
    author = "Werner, Earl E. and Mittelbach, Gary G. and Hall, Donald J. and Gilliam, James F.",
    title = "Experimental Tests of Optimal Habitat Use in Fish: The Role of Relative Habitat Profitability",
    year = "1983",
    journal = "Ecology",
    url = "https://doi.org/10.2307/1937507",
    doi = "10.2307/1937507",
    openalex = "W2163509599"
}

@article{doi101038347550a0,
    author = "Meyer, Axel and Kocher, Thomas D. and Basasibwaki, Pereti and Wilson, Allan C.",
    title = "Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences",
    year = "1990",
    journal = "Nature",
    url = "https://doi.org/10.1038/347550a0",
    doi = "10.1038/347550a0",
    openalex = "W2042521784",
    references = "doi101038290457a0, doi101073pnas86166196, doi101073pnas86239350, doi10108002541858198311447831, doi101111j155856461985tb00420x, doi101111j155856461987tb02473x, doi1023071442393, doi1023072408798, doi1023073421, openalexw2060759128"
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@article{doi101038379628a0,
    author = "Sansom, Ivan J. and Smith, Moya Meredith and Smith, M. Paul",
    title = "Scales of thelodont and shark-like fishes from the Ordovician of Colorado",
    year = "1996",
    journal = "Nature",
    url = "https://doi.org/10.1038/379628a0",
    doi = "10.1038/379628a0",
    openalex = "W2046064129",
    references = "doi101130gsab3153"
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▪ Abstract Resource polymorphism in vertebrates is generally underappreciated as a diversifying force and is probably more common than is currently recognized. Research across diverse taxa suggest they may play important roles in population divergence and speciation. They may involve various kinds of traits, including morphological and behavioral traits and those related to life history. Many of the evolutionary, ecological, and genetic mechanisms producing and maintaining resource polymorphisms are similar among phylogenetically distinct species. Although further studies are needed, the genetic basis may be simple, in some cases under the control of a single locus, with phenotypic plasticity playing a proximate role in some taxa. Divergent selection including either directional, disruptive, or frequency-dependent selection is important in their evolution. Generally, the invasion of “open” niches or underutilized resources requiring unique trophic characters and decreased interspecific competition have promoted the evolution of resource polymorphisms. Further investigations centered on their role in speciation, especially adaptive radiation, are likely to be fruitful.

@article{doi101146annurevecolsys271111,
    author = "Smith, Thomas B. and Skúlason, Skúli",
    title = "EVOLUTIONARY SIGNIFICANCE OF RESOURCE POLYMORPHISMS IN FISHES, AMPHIBIANS, AND BIRDS",
    year = "1996",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract Resource polymorphism in vertebrates is generally underappreciated as a diversifying force and is probably more common than is currently recognized. Research across diverse taxa suggest they may play important roles in population divergence and speciation. They may involve various kinds of traits, including morphological and behavioral traits and those related to life history. Many of the evolutionary, ecological, and genetic mechanisms producing and maintaining resource polymorphisms are similar among phylogenetically distinct species. Although further studies are needed, the genetic basis may be simple, in some cases under the control of a single locus, with phenotypic plasticity playing a proximate role in some taxa. Divergent selection including either directional, disruptive, or frequency-dependent selection is important in their evolution. Generally, the invasion of “open” niches or underutilized resources requiring unique trophic characters and decreased interspecific competition have promoted the evolution of resource polymorphisms. Further investigations centered on their role in speciation, especially adaptive radiation, are likely to be fruitful.",
    url = "https://doi.org/10.1146/annurev.ecolsys.27.1.111",
    doi = "10.1146/annurev.ecolsys.27.1.111",
    openalex = "W2111382033",
    references = "doi101017s0094837300006588, doi101086285404, doi101126science18241191305"
}

Abstract This chapter describes the species richness and phylogenetic relationships among the Neotropical freshwater fish, emphasizing the main diagnostic characteristics of each group. Both themes are effervescent, involving studies and discussions that require constant updates. They also face a high rate of descriptions of new species and new relationship hypotheses. In this chapter, we provide a picture of the knowledge available through early 2018, and we suggest that readers use it to search for updated information.

@book{openalexw3001739384,
    author = "Malabarba, Luiz Roberto and Malabarba, Maria Claudia",
    title = "Phylogeny and classification of neotropical fishes",
    year = "1998",
    abstract = "Abstract This chapter describes the species richness and phylogenetic relationships among the Neotropical freshwater fish, emphasizing the main diagnostic characteristics of each group. Both themes are effervescent, involving studies and discussions that require constant updates. They also face a high rate of descriptions of new species and new relationship hypotheses. In this chapter, we provide a picture of the knowledge available through early 2018, and we suggest that readers use it to search for updated information.",
    openalex = "W3001739384",
    references = "doi101002aja1001590307, doi101007978940171356617, doi101007pl00006514, doi101093icb222241, doi101111j109636421981tb01575x, doi101111j109636421996tb02189x, doi101159000006600, doi1011632666064402801038, doi1023071441405, doi1023071446263"
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@article{doi101016s1055790302003317,
    author = "Inoue, Jun and Miya, Masaki and Tsukamoto, Katsumi and Nishida, Mutsumi",
    title = "Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the “ancient fish”",
    year = "2002",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/s1055-7903(02)00331-7",
    doi = "10.1016/s1055-7903(02)00331-7",
    openalex = "W2022122623",
    references = "doi101093oxfordjournalsmolbeva003741, doi1023071437499, doi105962p313860"
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How long-extinct jawless fishes fed is poorly understood, yet interpretations of feeding are an important component of many hypotheses concerning the origin and early evolution of vertebrates. Heterostracans were the most diverse clade of armoured jawless vertebrates (stem gnathostomes), and the structure of the mouth and its use in feeding are the subjects of long-standing and heated controversy. I present here evidence that heterostracan feeding structures exhibit recurrent patterns of in vivo wear, are covered internally by microscopic oral denticles, and that the mouth may have been less flexible than has been thought. These data, particularly the absence of wear at the tips of oral plates, and the evidence that the mouth was lined with delicate outwardly directed denticles, effectively falsify all but one hypothesis of feeding in heterostracans: heterostracans were microphagous suspension feeders. This has a direct bearing on hypotheses that address ecological aspects of early vertebrate diversity and evolution, contradicting the widespread view that the pattern of early vertebrate evolution reflects a long-term trend towards increasingly active and predatory habits.

@article{doi101098rspb20011826,
    author = "Purnell, Mark A.",
    title = "Feeding in extinct jawless heterostracan fishes and testing scenarios of early vertebrate evolution",
    year = "2002",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "How long-extinct jawless fishes fed is poorly understood, yet interpretations of feeding are an important component of many hypotheses concerning the origin and early evolution of vertebrates. Heterostracans were the most diverse clade of armoured jawless vertebrates (stem gnathostomes), and the structure of the mouth and its use in feeding are the subjects of long-standing and heated controversy. I present here evidence that heterostracan feeding structures exhibit recurrent patterns of in vivo wear, are covered internally by microscopic oral denticles, and that the mouth may have been less flexible than has been thought. These data, particularly the absence of wear at the tips of oral plates, and the evidence that the mouth was lined with delicate outwardly directed denticles, effectively falsify all but one hypothesis of feeding in heterostracans: heterostracans were microphagous suspension feeders. This has a direct bearing on hypotheses that address ecological aspects of early vertebrate diversity and evolution, contradicting the widespread view that the pattern of early vertebrate evolution reflects a long-term trend towards increasingly active and predatory habits.",
    url = "https://doi.org/10.1098/rspb.2001.1826",
    doi = "10.1098/rspb.2001.1826",
    openalex = "W2148862468",
    references = "doi101017s0006323199005472, doi101038374798a0, doi101038ng0498345, doi101071mf9920123, doi101086285404, doi101086413055, doi101111j109636421996tb01658x, doi101111j160007221998tb02212x, doi101126science2204594268, openalexw3126673768"
}

Osteichthyan and chondrichthyan fish present an astonishing diversity of skeletal and dental tissues that are often difficult to classify into the standard textbook categories of bone, cartilage, dentine and enamel. To address the question of how the tissues of the dermal skeleton evolved from the ancestral situation and gave rise to the diversity actually encountered, we review previous data on the development of a number of dermal skeletal elements (odontodes, teeth and dermal denticles, cranial dermal bones, postcranial dermal plates and scutes, elasmoid and ganoid scales, and fin rays). A comparison of developmental stages at the tissue level usually allows us to identify skeletogenic cell populations as either odontogenic or osteogenic on the basis of the place of formation of their dermal papillae and of the way of deposition of their tissues. Our studies support the evolutionary affinities (1) between odontodes, teeth and denticles, (2) between the ganoid scales of polypterids and the elasmoid scales of teleosts, and (3) to a lesser degree between the different bony elements. There is now ample evidence to ascertain that the tissues of the elasmoid scale are derived from dental and not from bony tissues. This review demonstrates the advantage that can be taken from developmental studies, at the tissue level, to infer evolutionary relationships within the dermal skeleton in chondrichthyans and osteichthyans.

@article{doi101017s1464793102006073,
    author = "Sire, Jean‐Yves and Huysseune, Ann",
    title = "Formation of dermal skeletal and dental tissues in fish: a comparative and evolutionary approach",
    year = "2003",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Osteichthyan and chondrichthyan fish present an astonishing diversity of skeletal and dental tissues that are often difficult to classify into the standard textbook categories of bone, cartilage, dentine and enamel. To address the question of how the tissues of the dermal skeleton evolved from the ancestral situation and gave rise to the diversity actually encountered, we review previous data on the development of a number of dermal skeletal elements (odontodes, teeth and dermal denticles, cranial dermal bones, postcranial dermal plates and scutes, elasmoid and ganoid scales, and fin rays). A comparison of developmental stages at the tissue level usually allows us to identify skeletogenic cell populations as either odontogenic or osteogenic on the basis of the place of formation of their dermal papillae and of the way of deposition of their tissues. Our studies support the evolutionary affinities (1) between odontodes, teeth and denticles, (2) between the ganoid scales of polypterids and the elasmoid scales of teleosts, and (3) to a lesser degree between the different bony elements. There is now ample evidence to ascertain that the tissues of the elasmoid scale are derived from dental and not from bony tissues. This review demonstrates the advantage that can be taken from developmental studies, at the tissue level, to infer evolutionary relationships within the dermal skeleton in chondrichthyans and osteichthyans.",
    url = "https://doi.org/10.1017/s1464793102006073",
    doi = "10.1017/s1464793102006073",
    openalex = "W2036850921",
    references = "doi101002jmor1051660303, doi10100797814615696887, doi101111j1469185x1999tb00045x, doi101111j160007221998tb02212x"
}

The fish gill is a multipurpose organ that, in addition to providing for aquatic gas exchange, plays dominant roles in osmotic and ionic regulation, acid-base regulation, and excretion of nitrogenous wastes. Thus, despite the fact that all fish groups have functional kidneys, the gill epithelium is the site of many processes that are mediated by renal epithelia in terrestrial vertebrates. Indeed, many of the pathways that mediate these processes in mammalian renal epithelial are expressed in the gill, and many of the extrinsic and intrinsic modulators of these processes are also found in fish endocrine tissues and the gill itself. The basic patterns of gill physiology were outlined over a half century ago, but modern immunological and molecular techniques are bringing new insights into this complicated system. Nevertheless, substantial questions about the evolution of these mechanisms and control remain.

@article{doi101152physrev000502003,
    author = "Evans, David H. and Piermarini, Peter M. and Choe, Keith",
    title = "The Multifunctional Fish Gill: Dominant Site of Gas Exchange, Osmoregulation, Acid-Base Regulation, and Excretion of Nitrogenous Waste",
    year = "2004",
    journal = "Physiological Reviews",
    abstract = "The fish gill is a multipurpose organ that, in addition to providing for aquatic gas exchange, plays dominant roles in osmotic and ionic regulation, acid-base regulation, and excretion of nitrogenous wastes. Thus, despite the fact that all fish groups have functional kidneys, the gill epithelium is the site of many processes that are mediated by renal epithelia in terrestrial vertebrates. Indeed, many of the pathways that mediate these processes in mammalian renal epithelial are expressed in the gill, and many of the extrinsic and intrinsic modulators of these processes are also found in fish endocrine tissues and the gill itself. The basic patterns of gill physiology were outlined over a half century ago, but modern immunological and molecular techniques are bringing new insights into this complicated system. Nevertheless, substantial questions about the evolution of these mechanisms and control remain.",
    url = "https://doi.org/10.1152/physrev.00050.2003",
    doi = "10.1152/physrev.00050.2003",
    openalex = "W2039031569",
    references = "doi101001jama195102920260071031, doi101002jmor1051390403, doi101086413055, doi101111j1768322x1989tb00830x, doi101242jeb1982273, doi1023073514548, openalexw566484607, s23a98e59a754307ee654adec93e64df58927f80fc"
}

In the first part of this paper we review current knowledge regarding fish scales, focusing on elasmoid scales, the only type found in two model species, the zebrafish and the medaka. After reviewing the structure of scales and their evolutionary origin, we describe the formation of the squamation pattern. The regularity of this process suggests a pre-patterning of the skin before scale initiation. We then summarise the dynamics of scale development on the basis of morphological observations. In the absence of molecular data, these observations support the existence of genetic cascades involved in the control of scale development. In the second part of this paper, we illustrate the potential that scale development offers as a model to study organogenesis mediated by epithelial-mesenchymal interactions. Using the zebrafish (Danio rerio), we have combined alizarin red staining, light and transmission electron microscopy and in situ hybridisation using an anti-sense RNA probe for the sonic hedgehog (shh) gene. Scales develop late in ontogeny (30 days post-fertilisation) and close to the epidermal cover. Only cells of the basal epidermal layer express shh. Transcripts are first detected after the scale papillae have formed. Thus, shh is not involved in the mechanisms controlling squamation patterning and scale initiation. As the scales enlarge, shh expression is progressively restricted to a subset of basal epidermal cells located in the region that overlies their posterior field. This pattern of expression suggests that shh may be involved in the control of scale morphogenesis and differentiation in relationship with the formation of the epidermal fold in the posterior region.

@article{doi101387ijdb15272389,
    author = "Sire, Jean‐Yves and Akimenko, Marie‐Andrée",
    title = "Scale development in fish: a review, with description of sonic hedgehog (shh) expression in the zebrafish (Danio rerio).",
    year = "2004",
    journal = "The International Journal of Developmental Biology",
    abstract = "In the first part of this paper we review current knowledge regarding fish scales, focusing on elasmoid scales, the only type found in two model species, the zebrafish and the medaka. After reviewing the structure of scales and their evolutionary origin, we describe the formation of the squamation pattern. The regularity of this process suggests a pre-patterning of the skin before scale initiation. We then summarise the dynamics of scale development on the basis of morphological observations. In the absence of molecular data, these observations support the existence of genetic cascades involved in the control of scale development. In the second part of this paper, we illustrate the potential that scale development offers as a model to study organogenesis mediated by epithelial-mesenchymal interactions. Using the zebrafish (Danio rerio), we have combined alizarin red staining, light and transmission electron microscopy and in situ hybridisation using an anti-sense RNA probe for the sonic hedgehog (shh) gene. Scales develop late in ontogeny (30 days post-fertilisation) and close to the epidermal cover. Only cells of the basal epidermal layer express shh. Transcripts are first detected after the scale papillae have formed. Thus, shh is not involved in the mechanisms controlling squamation patterning and scale initiation. As the scales enlarge, shh expression is progressively restricted to a subset of basal epidermal cells located in the region that overlies their posterior field. This pattern of expression suggests that shh may be involved in the control of scale morphogenesis and differentiation in relationship with the formation of the epidermal fold in the posterior region.",
    url = "https://doi.org/10.1387/ijdb.15272389",
    doi = "10.1387/ijdb.15272389",
    openalex = "W2094026255",
    references = "doi101002jmor1051660303, doi10100797814615696887, doi105962bhltitle4275"
}

@article{doi101038nature04639,
    author = "Daeschler, Edward B. and Shubin, Neil H. and Jenkins, Farish A.",
    title = "A Devonian tetrapod-like fish and the evolution of the tetrapod body plan",
    year = "2006",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature04639",
    doi = "10.1038/nature04639",
    openalex = "W2094370487",
    references = "doi101016b9780126709506500187, doi101017s0263593300002340, doi101017s0263593300006787, doi101038nature03893, doi101038nature04119, doi101038nature04637, doi101093oso97801985404720010001, doi101111j109636421991tb00905x, doi101111j150239311996tb01839x, doi101130dnaggnae, doi10182618200376605199601, doi1023071378479, doi1023071447582, doi105860choice402180"
}

The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.

@article{doi101098rspb20063749,
    author = "Hurley, Imogen and Mueller, Rachel Lockridge and Dunn, Katherine A. and Schmidt, E. and Friedman, Matt and Ho, Robert K. and Prince, Victoria and Yang, Ziheng and Thomas, Mark and Coates, Michael I.",
    title = "A new time-scale for ray-finned fish evolution",
    year = "2006",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.",
    url = "https://doi.org/10.1098/rspb.2006.3749",
    doi = "10.1098/rspb.2006.3749",
    openalex = "W1980001465",
    references = "bonde1974interrelationships, doi101016jgene200501008, doi101016jtree200504008, doi10108002724634199810011114, doi101093oso97801985404720010001, gardiner1989interrelationships"
}

@article{doi101016jaquaculture200702053,
    author = "Lall, Santosh P. and Lewis‐McCrea, Leah M.",
    title = "Role of nutrients in skeletal metabolism and pathology in fish — An overview",
    year = "2007",
    journal = "Aquaculture",
    url = "https://doi.org/10.1016/j.aquaculture.2007.02.053",
    doi = "10.1016/j.aquaculture.2007.02.053",
    openalex = "W2146714688"
}

@article{doi101016jcbpb200801011,
    author = "Subramanian, Sangeetha and Ross, Neil W. and MacKinnon, Shawna L.",
    title = "Comparison of antimicrobial activity in the epidermal mucus extracts of fish",
    year = "2008",
    journal = "Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology",
    url = "https://doi.org/10.1016/j.cbpb.2008.01.011",
    doi = "10.1016/j.cbpb.2008.01.011",
    openalex = "W2066252622",
    references = "doi101016jdci200608009"
}

@article{doi101038nmat2231,
    author = "Bruet, Benjamin J. F. and Song, Juha and Boyce, Mary C. and Ortiz, Christine",
    title = "Materials design principles of ancient fish armour",
    year = "2008",
    journal = "Nature Materials",
    url = "https://doi.org/10.1038/nmat2231",
    doi = "10.1038/nmat2231",
    openalex = "W2009937382",
    references = "doi101071mf9920123, openalexw115975037"
}

Resorption and remodelling of skeletal tissues is required for development and growth, mechanical adaptation, repair, and mineral homeostasis of the vertebrate skeleton. Here we review for the first time the current knowledge about resorption and remodelling of the skeleton in teleost fish, the largest and most diverse group of extant vertebrates. Teleost species are increasingly used in aquaculture and as models in biomedical skeletal research. Thus, detailed knowledge is required to establish the differences and similarities between mammalian and teleost skeletal remodelling, and between distantly related species such as zebrafish (Danio rerio) and medaka (Oryzias latipes). The cellular mechanisms of differentiation and activation of osteoclasts and the functions of teleost skeletal remodelling are described. Several characteristics, related to skeletal remodelling, distinguish teleosts from mammals. These characteristics include (a) the absence of osteocytes in most species; (b) the absence of haematopoietic bone marrow tissue; (c) the abundance of small mononucleated osteoclasts performing non-lacunar (smooth) bone resorption, in addition to or instead of multinucleated osteoclasts; and (d) a phosphorus- rather than calcium-driven mineral homeostasis (mainly affecting the postcranial dermal skeleton). Furthermore, (e) skeletal resorption is often absent from particular sites, due to sparse or lacking endochondral ossification. Based on the mode of skeletal remodelling in early ontogeny of all teleosts and in later stages of development of teleosts with acellular bone we suggest a link between acellular bone and the predominance of mononucleated osteoclasts, on the one hand, and cellular bone and multinucleated osteoclasts on the other. The evolutionary origin of skeletal remodelling is discussed and whether mononucleated osteoclasts represent an ancestral type of resorbing cells. Revealing the differentiation and activation of teleost skeletal resorbing cells, in the absence of several factors that trigger mammalian osteoclast differentiation, is a current challenge. Understanding which characters of teleost bone remodelling are derived and which characters are conserved should enhance our understanding of the process in fish and may provide insights into alternative pathways of bone remodelling in mammals.

@article{doi101111j1469185x200900077x,
    author = "Witten, P. Eckhard and Huysseune, Ann",
    title = "A comparative view on mechanisms and functions of skeletal remodelling in teleost fish, with special emphasis on osteoclasts and their function",
    year = "2009",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Resorption and remodelling of skeletal tissues is required for development and growth, mechanical adaptation, repair, and mineral homeostasis of the vertebrate skeleton. Here we review for the first time the current knowledge about resorption and remodelling of the skeleton in teleost fish, the largest and most diverse group of extant vertebrates. Teleost species are increasingly used in aquaculture and as models in biomedical skeletal research. Thus, detailed knowledge is required to establish the differences and similarities between mammalian and teleost skeletal remodelling, and between distantly related species such as zebrafish (Danio rerio) and medaka (Oryzias latipes). The cellular mechanisms of differentiation and activation of osteoclasts and the functions of teleost skeletal remodelling are described. Several characteristics, related to skeletal remodelling, distinguish teleosts from mammals. These characteristics include (a) the absence of osteocytes in most species; (b) the absence of haematopoietic bone marrow tissue; (c) the abundance of small mononucleated osteoclasts performing non-lacunar (smooth) bone resorption, in addition to or instead of multinucleated osteoclasts; and (d) a phosphorus- rather than calcium-driven mineral homeostasis (mainly affecting the postcranial dermal skeleton). Furthermore, (e) skeletal resorption is often absent from particular sites, due to sparse or lacking endochondral ossification. Based on the mode of skeletal remodelling in early ontogeny of all teleosts and in later stages of development of teleosts with acellular bone we suggest a link between acellular bone and the predominance of mononucleated osteoclasts, on the one hand, and cellular bone and multinucleated osteoclasts on the other. The evolutionary origin of skeletal remodelling is discussed and whether mononucleated osteoclasts represent an ancestral type of resorbing cells. Revealing the differentiation and activation of teleost skeletal resorbing cells, in the absence of several factors that trigger mammalian osteoclast differentiation, is a current challenge. Understanding which characters of teleost bone remodelling are derived and which characters are conserved should enhance our understanding of the process in fish and may provide insights into alternative pathways of bone remodelling in mammals.",
    url = "https://doi.org/10.1111/j.1469-185x.2009.00077.x",
    doi = "10.1111/j.1469-185x.2009.00077.x",
    openalex = "W2161222213",
    references = "doi101002jemt10217, doi10100797814615696887, doi101016jcoi200708003, doi101046j1365294x199800358x"
}

@article{doi101007s101260109279x,
    author = "Magnadóttir, Bergljót",
    title = "Immunological Control of Fish Diseases",
    year = "2010",
    journal = "Marine Biotechnology",
    url = "https://doi.org/10.1007/s10126-010-9279-x",
    doi = "10.1007/s10126-010-9279-x",
    openalex = "W2094637827",
    references = "doi101016jdci200608009, doi101016jfsi200504004"
}

@article{doi101038nature10276,
    author = "Gai, Zhikun and Donoghue, Philip C. J. and Zhu, Min and Janvier, Philippe and Stampanoni, Marco",
    title = "Fossil jawless fish from China foreshadows early jawed vertebrate anatomy",
    year = "2011",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature10276",
    doi = "10.1038/nature10276",
    openalex = "W1970226440",
    references = "doi1010079783642182624, doi101007978364218262412, doi101007s0033900635072, doi101007s1151500700226, doi101016jtree200504008, doi101038282831a0, doi101038282833a0, doi101038361129a0, doi101038nature04890, doi101046j1525142x200000062x, doi101073pnas1010350107, doi101093oso97801985404720010001, doi101111j146364091979tb00640x, doi101126science2204594268, doi105860choice454992, halstead1979agnathans"
}

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"
}

Abstract: Fishes include more than half of all living animals with backbones, but large‐scale palaeobiological patterns in this assemblage have not received the same attention as those for terrestrial vertebrates. Previous surveys of the fish record have generally been anecdotal, or limited either in their stratigraphic or in their taxonomic scope. Here, we provide a broad overview of the Phanerozoic history of fish diversity, placing a special emphasis on intervals of turnover, evolutionary radiation, and extinction. In particular, we provide in‐depth reviews of changes during, and ecological and evolutionary recovery after, the end‐Devonian (Hangenberg) and Cretaceous–Palaeogene (K–Pg) extinctions.

@article{doi101111j14754983201201165x,
    author = "Friedman, Matt and Sallan, Lauren",
    title = "Five hundred million years of extinction and recovery: a phanerozoic survey of large‐scale diversity patterns in fishes",
    year = "2012",
    journal = "Palaeontology",
    abstract = "Abstract: Fishes include more than half of all living animals with backbones, but large‐scale palaeobiological patterns in this assemblage have not received the same attention as those for terrestrial vertebrates. Previous surveys of the fish record have generally been anecdotal, or limited either in their stratigraphic or in their taxonomic scope. Here, we provide a broad overview of the Phanerozoic history of fish diversity, placing a special emphasis on intervals of turnover, evolutionary radiation, and extinction. In particular, we provide in‐depth reviews of changes during, and ecological and evolutionary recovery after, the end‐Devonian (Hangenberg) and Cretaceous–Palaeogene (K–Pg) extinctions.",
    url = "https://doi.org/10.1111/j.1475-4983.2012.01165.x",
    doi = "10.1111/j.1475-4983.2012.01165.x",
    openalex = "W1522554964",
    references = "brinkman1990paleooecology, brinkman2002teleost, crossref1977patterns, doi101002gj1072, doi1010079781468464658, doi101016jpalaeo200907017, doi101016jpalaeo200910010, doi101016s0016699588800664, doi101017s0022336000024331, doi101017s0094837300005352, doi101017s0094837300008174, doi101017s1477201908002551, doi101038nature01264, doi101038nature07855, doi101038nature08745, doi101038nature09038, doi101073pnas0811087106, doi101073pnas1010350107, doi101073pnas1117332109, doi10108002724634199710010948, doi101098rspb20011826, doi101098rspb20080715, doi101111j1469185x1999tb00045x, doi101111j14754983201001019x, doi101111j150239311983tb01993x, doi101126science1177265, doi101126science1598573, doi101126science21545391501, doi101146annurevearth040809152556, doi101146annurevecolsys35021103105715, doi1016710272463420010210438anscft20co2, doi1023071441916, doi1023073514548, doi102475ajs2882101, doi104072rbp2005205, doi105252g2010n4a1, doi105860choice435902, doi105962bhltitle4275, openalexw1485830652, openalexw2106559152, openalexw2208603329, openalexw3001739384, openalexw595691412, openalexw606525048"
}

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"
}

Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.

@article{doi101371journalpone0073535,
    author = "Miya, Masaki and Friedman, Matt and Satoh, Takashi and Takeshima, Hirohiko and Sado, Tetsuya and Iwasaki, Wataru and Yamanoue, Yusuke and Nakatani, Masanori and Mabuchi, Kohji and Inoue, Jun and Poulsen, Jan Yde and Fukunaga, Tsukasa and Sato, Yukuto and Nishida, Mutsumi",
    title = "Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families",
    year = "2013",
    journal = "PLoS ONE",
    abstract = {Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.},
    url = "https://doi.org/10.1371/journal.pone.0073535",
    doi = "10.1371/journal.pone.0073535",
    openalex = "W2087061078",
    references = "doi101111j14754983201201165x"
}

Living vertebrates are divided into those that possess a fully formed and fully mineralised skeleton (gnathostomes) versus those that possess only unmineralised cartilaginous rudiments (cyclostomes). As such, extinct phylogenetic intermediates of these living lineages afford unique insights into the evolutionary assembly of the vertebrate mineralised skeleton and its canonical tissue types. Extinct jawless and jawed fishes assigned to the gnathostome stem evidence the piecemeal assembly of skeletal systems, revealing that the dermal skeleton is the earliest manifestation of a homologous mineralised skeleton. Yet the nature of the primitive dermal skeleton, itself, is poorly understood. This is principally because previous histological studies of early vertebrates lacked a phylogenetic framework required to derive evolutionary hypotheses. Nowhere is this more apparent than within Heterostraci, a diverse clade of primitive jawless vertebrates. To this end, we surveyed the dermal skeletal histology of heterostracans, inferred the plesiomorphic heterostracan skeleton and, through histological comparison to other skeletonising vertebrate clades, deduced the ancestral nature of the vertebrate dermal skeleton. Heterostracans primitively possess a four-layered skeleton, comprising a superficial layer of odontodes composed of dentine and enameloid; a compact layer of acellular parallel-fibred bone containing a network of vascular canals that supply the pulp canals (L1); a trabecular layer consisting of intersecting radial walls composed of acellular parallel-fibred bone, showing osteon-like development (L2); and a basal layer of isopedin (L3). A three layered skeleton, equivalent to the superficial layer L2 and L3 and composed of enameloid, dentine and acellular bone, is possessed by the ancestor of heterostracans + jawed vertebrates. We conclude that an osteogenic component is plesiomorphic with respect to the vertebrate dermal skeleton. Consequently, we interpret the dermal skeleton of denticles in chondrichthyans and jawless thelodonts as independently and secondarily simplified. J. Morphol. 276:657-680, 2015. © 2015 The Authors Journal of Morphology Published by Wiley Periodicals, Inc.

@article{doi101002jmor20370,
    author = "Keating, Joseph N. and Marquart, Chloe L. and Donoghue, Philip C. J.",
    title = "Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton",
    year = "2015",
    journal = "Journal of Morphology",
    abstract = "Living vertebrates are divided into those that possess a fully formed and fully mineralised skeleton (gnathostomes) versus those that possess only unmineralised cartilaginous rudiments (cyclostomes). As such, extinct phylogenetic intermediates of these living lineages afford unique insights into the evolutionary assembly of the vertebrate mineralised skeleton and its canonical tissue types. Extinct jawless and jawed fishes assigned to the gnathostome stem evidence the piecemeal assembly of skeletal systems, revealing that the dermal skeleton is the earliest manifestation of a homologous mineralised skeleton. Yet the nature of the primitive dermal skeleton, itself, is poorly understood. This is principally because previous histological studies of early vertebrates lacked a phylogenetic framework required to derive evolutionary hypotheses. Nowhere is this more apparent than within Heterostraci, a diverse clade of primitive jawless vertebrates. To this end, we surveyed the dermal skeletal histology of heterostracans, inferred the plesiomorphic heterostracan skeleton and, through histological comparison to other skeletonising vertebrate clades, deduced the ancestral nature of the vertebrate dermal skeleton. Heterostracans primitively possess a four-layered skeleton, comprising a superficial layer of odontodes composed of dentine and enameloid; a compact layer of acellular parallel-fibred bone containing a network of vascular canals that supply the pulp canals (L1); a trabecular layer consisting of intersecting radial walls composed of acellular parallel-fibred bone, showing osteon-like development (L2); and a basal layer of isopedin (L3). A three layered skeleton, equivalent to the superficial layer L2 and L3 and composed of enameloid, dentine and acellular bone, is possessed by the ancestor of heterostracans + jawed vertebrates. We conclude that an osteogenic component is plesiomorphic with respect to the vertebrate dermal skeleton. Consequently, we interpret the dermal skeleton of denticles in chondrichthyans and jawless thelodonts as independently and secondarily simplified. J. Morphol. 276:657-680, 2015. © 2015 The Authors Journal of Morphology Published by Wiley Periodicals, Inc.",
    url = "https://doi.org/10.1002/jmor.20370",
    doi = "10.1002/jmor.20370",
    openalex = "W2149505222",
    references = "doi1010079781489957405, doi101016s001600323892229x, doi101017cbo9780511897948, doi101029sc005p0175, doi101093oso97801985404720010001, doi101107s0909049512032864, doi101111j1469185x1990tb01427x, doi1023071437499, openalexw115975037, openalexw251296685"
}

@book{doi1010029781119174844,
    author = "Nelson, Joseph S. and Grande, Terry and Wilson, Mark V. H.",
    title = "Fishes of the World",
    year = "2016",
    url = "https://doi.org/10.1002/9781119174844",
    doi = "10.1002/9781119174844",
    openalex = "W2500817663"
}

@misc{doi101016bsmcb201609001,
    author = "Witten, P. Eckhard and Harris, M. P. and Huysseune, A. and Winkler, Christoph",
    title = "Small teleost fish provide new insights into human skeletal diseases",
    year = "2016",
    booktitle = "Methods in cell biology",
    url = "https://doi.org/10.1016/bs.mcb.2016.09.001",
    doi = "10.1016/bs.mcb.2016.09.001",
    openalex = "W2531817999",
    references = "doi101038nature14437"
}

). Using cell lineage tracing, we further demonstrate that trunk neural crest cells do, in fact, give rise to odontoblasts of trunk dermal denticles. These findings expand the repertoire of vertebrate trunk neural crest cell fates during normal development, highlight the likely primitive skeletogenic potential of this cell population, and point to a neural crest origin of dentine throughout the ancestral vertebrate dermal skeleton.

@article{doi101073pnas1713827114,
    author = "Gillis, J. Andrew and Alsema, Els C. and Criswell, Katharine E.",
    title = "Trunk neural crest origin of dermal denticles in a cartilaginous fish",
    year = "2017",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "). Using cell lineage tracing, we further demonstrate that trunk neural crest cells do, in fact, give rise to odontoblasts of trunk dermal denticles. These findings expand the repertoire of vertebrate trunk neural crest cell fates during normal development, highlight the likely primitive skeletogenic potential of this cell population, and point to a neural crest origin of dentine throughout the ancestral vertebrate dermal skeleton.",
    url = "https://doi.org/10.1073/pnas.1713827114",
    doi = "10.1073/pnas.1713827114",
    openalex = "W2769779238",
    references = "doi101002jez1402670309, doi101002jmor20370, doi101006dbio20010487, doi101016jcell200907049, doi101038nature13536, doi101111j1469185x1990tb01427x, doi101111j14697580200901046x, doi101242dev103supplement155, doi101242dev1172409, doi101242dev12781671, doi101387ijdb15272389"
}

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"
}

@article{doi101038s4155901804946,
    author = "Alfaro, Michael E. and Faircloth, Brant C. and Harrington, Richard and Sorenson, Laurie and Friedman, Matt and Thacker, Christine E. and Oliveros, Carl H. and Černý, David and Near, Thomas J.",
    title = "Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary",
    year = "2018",
    journal = "Nature Ecology \& Evolution",
    url = "https://doi.org/10.1038/s41559-018-0494-6",
    doi = "10.1038/s41559-018-0494-6",
    openalex = "W2790896447",
    references = "doi101073pnas1211526110, doi101073pnas1504985112, doi101111j14754983201201165x, doi101371journalpone0055161"
}

Vertebrate bone is composed of three main cell types: osteoblasts, osteoclasts and osteocytes, the latter being by far the most numerous. Osteocytes are thought to play a fundamental role in bone physiology and homeostasis, however they are entirely absent in most extant species of teleosts, a group that comprises the vast majority of bony 'fishes', and approximately half of vertebrates. Understanding how this acellular (anosteocytic) bone appeared and was maintained in such an important vertebrate group has important implications for our understanding of the function and evolution of osteocytes. Nevertheless, although it is clear that cellular bone is ancestral for teleosts, it has not been clear in which specific subgroup the osteocytes were lost. This review aims to clarify the phylogenetic distribution of cellular and acellular bone in teleosts, to identify its precise origin, reversals to cellularity, and their implications. We surveyed the bone type for more than 600 fossil and extant ray-finned fish species and optimised the results on recent large-scale molecular phylogenetic trees, estimating ancestral states. We find that acellular bone is a probable synapomorphy of Euteleostei, a group uniting approximately two-thirds of teleost species. We also confirm homoplasy in these traits: acellular bone occurs in some non-euteleosts (although rarely), and cellular bone was reacquired several times independently within euteleosts, in salmons and relatives, tunas and the opah (Lampris sp.). The occurrence of peculiar ecological (e.g. anadromous migration) and physiological (e.g. red-muscle endothermy) strategies in these lineages might explain the reacquisition of osteocytes. Our review supports that the main contribution of osteocytes in teleost bone is to mineral homeostasis (via osteocytic osteolysis) and not to strain detection or bone remodelling, helping to clarify their role in bone physiology.

@article{doi101111brv12505,
    author = "Davesne, Donald and Meunier, François and Schmitt, Armin D. and Friedman, Matt and Otero, Olga and Benson, Roger",
    title = "The phylogenetic origin and evolution of acellular bone in teleost fishes: insights into osteocyte function in bone metabolism",
    year = "2019",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Vertebrate bone is composed of three main cell types: osteoblasts, osteoclasts and osteocytes, the latter being by far the most numerous. Osteocytes are thought to play a fundamental role in bone physiology and homeostasis, however they are entirely absent in most extant species of teleosts, a group that comprises the vast majority of bony 'fishes', and approximately half of vertebrates. Understanding how this acellular (anosteocytic) bone appeared and was maintained in such an important vertebrate group has important implications for our understanding of the function and evolution of osteocytes. Nevertheless, although it is clear that cellular bone is ancestral for teleosts, it has not been clear in which specific subgroup the osteocytes were lost. This review aims to clarify the phylogenetic distribution of cellular and acellular bone in teleosts, to identify its precise origin, reversals to cellularity, and their implications. We surveyed the bone type for more than 600 fossil and extant ray-finned fish species and optimised the results on recent large-scale molecular phylogenetic trees, estimating ancestral states. We find that acellular bone is a probable synapomorphy of Euteleostei, a group uniting approximately two-thirds of teleost species. We also confirm homoplasy in these traits: acellular bone occurs in some non-euteleosts (although rarely), and cellular bone was reacquired several times independently within euteleosts, in salmons and relatives, tunas and the opah (Lampris sp.). The occurrence of peculiar ecological (e.g. anadromous migration) and physiological (e.g. red-muscle endothermy) strategies in these lineages might explain the reacquisition of osteocytes. Our review supports that the main contribution of osteocytes in teleost bone is to mineral homeostasis (via osteocytic osteolysis) and not to strain detection or bone remodelling, helping to clarify their role in bone physiology.",
    url = "https://doi.org/10.1111/brv.12505",
    doi = "10.1111/brv.12505",
    openalex = "W2909860944",
    references = "doi101038s4155901806241, doi101098rspb20152917, doi101111zoj12111"
}

Actinopterygians (ray-finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re-acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.

@article{doi101002evl3219,
    author = "Lemopoulos, Alexandre and Montoya‐Burgos, Juan I.",
    title = "From scales to armor: Scale losses and trunk bony plate gains in ray-finned fishes",
    year = "2021",
    journal = "Evolution Letters",
    abstract = "Actinopterygians (ray-finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re-acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.",
    url = "https://doi.org/10.1002/evl3.219",
    doi = "10.1002/evl3.219",
    openalex = "W3138669000",
    references = "doi101098rspb20152917, doi101643cg17669"
}

@article{doi101016jcub202105053,
    author = "Li, Qiang and Zhu, You-an and Lü, Jing and Chen, Yang and Wang, Jianhua and Peng, Lijian and Wei, Guangbiao and Zhu, Min",
    title = "A new Silurian fish close to the common ancestor of modern gnathostomes",
    year = "2021",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2021.05.053",
    doi = "10.1016/j.cub.2021.05.053",
    openalex = "W3166444757",
    references = "doi1010179781316832172004, doi101371journalpone0228589"
}

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.

@article{doi101038s4158802100914y,
    author = "Thompson, Andrew W. and Hawkins, M. Brent and Parey, Elise and Wcisel, Dustin J. and Ota, Tatsuya and Kawasaki, Kazuhiko and Funk, Emily and Losilla, Mauricio and Fitch, Olivia E. and Pan, Qiaowei and Feron, Romain and Louis, Alexandra and Montfort, Jérôme and Milhes, Marine and Racicot, Brett and Childs, Kevin L. and Fontenot, Quenton and Ferrara, Allyse and David, Solomon R. and McCune, Amy R. and Dornburg, Alex and Yoder, Jeffrey A. and Guiguen, Yann and Crollius, Hugues Roest and Berthelot, Camille and Harris, Matthew P. and Braasch, Ingo",
    title = "The bowfin genome illuminates the developmental evolution of ray-finned fishes",
    year = "2021",
    journal = "Nature Genetics",
    abstract = "The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.",
    url = "https://doi.org/10.1038/s41588-021-00914-y",
    doi = "10.1038/s41588-021-00914-y",
    openalex = "W3198242174",
    references = "doi101016jisci2020102023, doi101038s415590201166x"
}

Abstract Although vertebrate carcasses––particularly those assigned to fishes––are abundant in the fossil record, the literature rarely mentions fishes as trace producers. Herein we present evidence that was possibly overlooked in previous studies. Study of more than 100 large, shallow, teardrop-shaped, imprints that are aligned, with few overlapping each other, from early Paleozoic (probably Silurian based on trace fossils) outcrops in western Gondwana (southeastern Argentina), are identified as the oldest example of shoaling behavior. To understand the nature of the behavior, we considered analog (vertebrate and invertebrate) extant and extinct taxa. We compare and discuss the superficial similarities with certain traces, in particular Selenichnites isp. and erect a new ichnotaxon, Raederichnus dondasi isp. nov. for the Argentinian material. We report for the first time from the Balcarce Formation Psammichnites isp., in association with Herradurichnus scagliai, both forming minor components of the ichnoassemblage. Raederichnus dondasi and the accompanying traces are preserved in three-dimensional dunes, developed in a tide-dominated shallow marine environment. Given the morphological resemblance, and paleoecological context, we consider that Raederichnus dondasi might have been produced by fish while “resting”. Finally, this aggregation of trace fossils suggests shoaling related to feeding or breeding on the shallow marine bottom surface.

@article{doi102110palo2021023,
    author = "Halpern, Karen and Gouiric‐Cavalli, Soledad and Taglioretti, Matías L. and Farenga, Marcelo and Scaglia, Fernando and Marcilese, Lydia Calvo and del Río, Julio Luis",
    title = "RAEDERICHNUS DONDASI A NEW TRACE FOSSIL FROM THE EARLY PALEOZOIC OF ARGENTINA REVEALS SHOALING BEHAVIOR IN EARLY FISH",
    year = "2022",
    journal = "Palaios",
    abstract = "Abstract Although vertebrate carcasses––particularly those assigned to fishes––are abundant in the fossil record, the literature rarely mentions fishes as trace producers. Herein we present evidence that was possibly overlooked in previous studies. Study of more than 100 large, shallow, teardrop-shaped, imprints that are aligned, with few overlapping each other, from early Paleozoic (probably Silurian based on trace fossils) outcrops in western Gondwana (southeastern Argentina), are identified as the oldest example of shoaling behavior. To understand the nature of the behavior, we considered analog (vertebrate and invertebrate) extant and extinct taxa. We compare and discuss the superficial similarities with certain traces, in particular Selenichnites isp. and erect a new ichnotaxon, Raederichnus dondasi isp. nov. for the Argentinian material. We report for the first time from the Balcarce Formation Psammichnites isp., in association with Herradurichnus scagliai, both forming minor components of the ichnoassemblage. Raederichnus dondasi and the accompanying traces are preserved in three-dimensional dunes, developed in a tide-dominated shallow marine environment. Given the morphological resemblance, and paleoecological context, we consider that Raederichnus dondasi might have been produced by fish while “resting”. Finally, this aggregation of trace fossils suggests shoaling related to feeding or breeding on the shallow marine bottom surface.",
    url = "https://doi.org/10.2110/palo.2021.023",
    doi = "10.2110/palo.2021.023",
    openalex = "W4293056445",
    references = "doi1010179781316832172004"
}

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.

@misc{dearden2023the,
    author = "Dearden, Richard and Jones, Andy and Giles, Sam and Lanzetti, Agnese and Grohganz, Madleen and Johanson, Zerina and Lautenschlager, Stephan and Randle, Emma and Donoghue, Philip C. J. and Sansom, Ivan J.",
    title = "The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes",
    year = "2023",
    abstract = "Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.",
    url = "https://doi.org/10.1101/2023.08.22.554283",
    doi = "10.1101/2023.08.22.554283",
    openalex = "W4386090618",
    references = "doi101016b978012824360200022x, doi101038nature14437, doi10108002724634198110011886, doi101093oso97801985404720010001, doi101098rsif20210741, doi101098rsos160342, doi101098rsos220519, doi101111j109636421996tb01658x, doi101111j1469185x1989tb00471x, doi101126science2204594268"
}

Major groups of jawed vertebrates exhibit contrasting conditions of dermal plates and scales. But the transition between these conditions remains unclear due to rare information on taxa occupying key phylogenetic positions. The 425-million-year-old fish Entelognathus combines an unusual mosaic of characters typically associated with jawed stem gnathostomes or crown gnathostomes. However, only the anterior part of the exoskeleton was previously known for this very crownward member of the gnathostome stem. Here, we report a near-complete post-thoracic exoskeleton of Entelognathus. Strikingly, its scales are large and some are rhomboid, bearing distinctive peg-and-socket articulations; this combination was previously only known in osteichthyans and considered a synapomorphy of that group. The presence in Entelognathus of an anal fin spine, previously only found in some stem chondrichthyans, further illustrates that many characters previously thought to be restricted to specific lineages within the gnathostome crown likely arose before the common ancestor of living jawed vertebrates.

@article{doi101038s41467023435579,
    author = "Cui, Xindong and Friedman, Matt and Yu, Yilun and Zhu, You-an and Zhu, Min",
    title = "Bony-fish-like scales in a Silurian maxillate placoderm",
    year = "2023",
    journal = "Nature Communications",
    abstract = "Major groups of jawed vertebrates exhibit contrasting conditions of dermal plates and scales. But the transition between these conditions remains unclear due to rare information on taxa occupying key phylogenetic positions. The 425-million-year-old fish Entelognathus combines an unusual mosaic of characters typically associated with jawed stem gnathostomes or crown gnathostomes. However, only the anterior part of the exoskeleton was previously known for this very crownward member of the gnathostome stem. Here, we report a near-complete post-thoracic exoskeleton of Entelognathus. Strikingly, its scales are large and some are rhomboid, bearing distinctive peg-and-socket articulations; this combination was previously only known in osteichthyans and considered a synapomorphy of that group. The presence in Entelognathus of an anal fin spine, previously only found in some stem chondrichthyans, further illustrates that many characters previously thought to be restricted to specific lineages within the gnathostome crown likely arose before the common ancestor of living jawed vertebrates.",
    url = "https://doi.org/10.1038/s41467-023-43557-9",
    doi = "10.1038/s41467-023-43557-9",
    openalex = "W4388909871",
    references = "doi101038nature20806, doi101098rspb20152917, doi101371journalpone0228589"
}

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.

@misc{doi10110120230822554283,
    author = "Dearden, Richard P. and Jones, Andy S. and Giles, Sam and Lanzetti, Agnese and Grohganz, Madleen and Johanson, Zerina and Lautenschlager, Stephan and Randle, Emma and Donoghue, Philip C. J. and Sansom, Ivan J.",
    title = "The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes",
    year = "2023",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.",
    url = "https://doi.org/10.1101/2023.08.22.554283",
    doi = "10.1101/2023.08.22.554283",
    openalex = "W4386090618",
    references = "doi101016b978012824360200022x, doi101038nature14437, doi10108002724634198110011886, doi101093oso97801985404720010001, doi101098rsif20210741, doi101098rsos160342, doi101098rsos220519, doi101111j109636421996tb01658x, doi101111j1469185x1989tb00471x, doi101126science2204594268"
}

Dunkleosteus terrelli, an arthrodire placoderm, is one of the most widely recognized fossil vertebrates due to its large size and status as one of the earliest vertebrate apex predators. However, the exact size of this taxon is unclear due to its head and thoracic armor being the only elements of its body regularly preserved in the fossil record. Lengths of 5–10 m are commonly cited, but these estimates are not based on rigorous statistical analysis. Here, I estimate the body size of D. terrelli using a new metric, orbit-opercular length, and a large dataset of arthrodires and extant fishes (3169 observations, 972 species). Orbit-opercular length strongly correlates with total length in fishes (r2 = 0.947, PEcf = 17.55%), and accurately predicts body size in arthrodires known from complete remains. Applying this method to Dunkleosteus terrelli results in much smaller sizes than previous studies: 3.4 m for typical adults (CMNH 5768) with the largest known individuals (CMNH 5936) reaching ~4.1 m. Arthrodires have a short, deep, and cylindrical body plan, distinctly different from either actinopterygians or elasmobranchs. Large arthrodires (Dunkleosteus, Titanichthys) were much smaller than previously thought and vertebrates likely did not reach sizes of 5 m or greater until the Carboniferous.

@article{doi103390d15030318,
    author = "Engelman, Russell K.",
    title = "A Devonian Fish Tale: A New Method of Body Length Estimation Suggests Much Smaller Sizes for Dunkleosteus terrelli (Placodermi: Arthrodira)",
    year = "2023",
    journal = "Diversity",
    abstract = "Dunkleosteus terrelli, an arthrodire placoderm, is one of the most widely recognized fossil vertebrates due to its large size and status as one of the earliest vertebrate apex predators. However, the exact size of this taxon is unclear due to its head and thoracic armor being the only elements of its body regularly preserved in the fossil record. Lengths of 5–10 m are commonly cited, but these estimates are not based on rigorous statistical analysis. Here, I estimate the body size of D. terrelli using a new metric, orbit-opercular length, and a large dataset of arthrodires and extant fishes (3169 observations, 972 species). Orbit-opercular length strongly correlates with total length in fishes (r2 = 0.947, PEcf = 17.55\%), and accurately predicts body size in arthrodires known from complete remains. Applying this method to Dunkleosteus terrelli results in much smaller sizes than previous studies: 3.4 m for typical adults (CMNH 5768) with the largest known individuals (CMNH 5936) reaching \textasciitilde 4.1 m. Arthrodires have a short, deep, and cylindrical body plan, distinctly different from either actinopterygians or elasmobranchs. Large arthrodires (Dunkleosteus, Titanichthys) were much smaller than previously thought and vertebrates likely did not reach sizes of 5 m or greater until the Carboniferous.",
    url = "https://doi.org/10.3390/d15030318",
    doi = "10.3390/d15030318",
    openalex = "W4321499769",
    references = "doi101038s41586022051662"
}

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition.

@article{dearden2024the,
    author = "Dearden, Richard P. and Jones, Andy S. and Giles, Sam and Lanzetti, Agnese and Grohganz, Madleen and Johanson, Zerina and Lautenschlager, Stephan and Randle, Emma and Donoghue, Philip C. J. and Sansom, Ivan J.",
    title = "The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes",
    year = "2024",
    journal = "Proceedings of the Royal Society B: Biological Sciences",
    abstract = "Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition.",
    url = "https://doi.org/10.1098/rspb.2023.2258",
    doi = "10.1098/rspb.2023.2258",
    number = "2019",
    openalex = "W4394759988",
    volume = "291",
    references = "dearden2024the, doi101002jezb21063, doi101017s0006323199005472, doi101038nature10207, doi101086413055, doi101093oso97801985404720010001, doi101098rsos160342, doi101098rsos220519, doi10110120230822554283, doi101111j109636421996tb01658x, doi101126science2204594268, doi1016710272463420050250478r20co2, doi1023072413058"
}

Fish air breathing is crucial for the transition of vertebrates from water to land. So far, the genes involved in fish air breathing have not been well identified. Here, we performed gene enrichment analysis of positively selected genes (PSGs) in loach (Misgurnus anguillicaudatus, an air-breathing fish) in comparison to Triplophysa tibetana (a non-air-breathing fish), haplotype-resolved genome assembly of the loach, and gene evolutionary analysis of air-breathing and non-air-breathing fishes and found that the PSG mex3a originated from ancient air-breathing fish species. Deletion of Mex3a impaired loach air-breathing capacity by inhibiting angiogenesis through its interaction with T-box transcription factor 20. Mex3a overexpression significantly promoted angiogenesis. Structural analysis and point mutation revealed the critical role of the 201st amino acid in loach Mex3a for angiogenesis. Our findings innovatively indicate that the ancient mex3a is a fish air-breathing gene, which holds significance for understanding fish air breathing and provides a valuable resource for cultivating hypoxia-tolerant fish varieties.

@article{doi101016jxgen2024100670,
    author = "Sun, Bing and Li, Qingshan and Xiao, Xinxin and Zhang, Jianwei and Zhou, Ying and Huang, Yuwei and Gao, Jian and Cao, Xiaojuan",
    title = "The loach haplotype-resolved genome and the identification of Mex3a involved in fish air breathing",
    year = "2024",
    journal = "Cell Genomics",
    abstract = "Fish air breathing is crucial for the transition of vertebrates from water to land. So far, the genes involved in fish air breathing have not been well identified. Here, we performed gene enrichment analysis of positively selected genes (PSGs) in loach (Misgurnus anguillicaudatus, an air-breathing fish) in comparison to Triplophysa tibetana (a non-air-breathing fish), haplotype-resolved genome assembly of the loach, and gene evolutionary analysis of air-breathing and non-air-breathing fishes and found that the PSG mex3a originated from ancient air-breathing fish species. Deletion of Mex3a impaired loach air-breathing capacity by inhibiting angiogenesis through its interaction with T-box transcription factor 20. Mex3a overexpression significantly promoted angiogenesis. Structural analysis and point mutation revealed the critical role of the 201st amino acid in loach Mex3a for angiogenesis. Our findings innovatively indicate that the ancient mex3a is a fish air-breathing gene, which holds significance for understanding fish air breathing and provides a valuable resource for cultivating hypoxia-tolerant fish varieties.",
    url = "https://doi.org/10.1016/j.xgen.2024.100670",
    doi = "10.1016/j.xgen.2024.100670",
    openalex = "W4403245132",
    references = "doi101038s41586022051662"
}

Teeth are a key vertebrate innovation; their evolution is generally associated with the origin of jawed vertebrates. However, tooth-like structures already occur in jawless stem-gnathostomes; heterostracans bear denticles and morphologically distinct tubercles on their oral plates. We analysed the histology of the heterostracan denticles and plates to elucidate their morphogenesis and test their homology to the gnathostome oral skeleton. We identified a general model of growth for heterostracan oral plates that exhibit proximal episodic addition of tubercle rows. The distal hook exhibits truncated lamellae compatible with resorption, but we observe growth layers to be continuous between denticles. The denticles show no evidence of patterns of apposition or replacement indicating tooth homology. The oral plates and dermal skeleton share the same histological layers. The denticles grew in a manner comparable to the oral plate tubercles and the rest of the dermal skeleton. Our test of phylogenetic congruence reveals that the distribution of internal odontodes is discontinuous, indicating that the capacity to form internal odontodes evolved independently several times among stem-gnathostomes. Our results support the 'outside-in' hypothesis and the origin of teeth through the spread of odontogenic competence from extra-oral to oral epithelia and the subsequent co-option to a tooth function in gnathostomes.

@article{doi101098rsos240836,
    author = "Grohganz, Madleen and Johanson, Zerina and Donoghue, Philip C. J. and Donoghue, Philip C. J.",
    title = "Morphogenesis of pteraspid heterostracan oral plates and the evolutionary origin of teeth",
    year = "2024",
    journal = "Royal Society Open Science",
    abstract = "Teeth are a key vertebrate innovation; their evolution is generally associated with the origin of jawed vertebrates. However, tooth-like structures already occur in jawless stem-gnathostomes; heterostracans bear denticles and morphologically distinct tubercles on their oral plates. We analysed the histology of the heterostracan denticles and plates to elucidate their morphogenesis and test their homology to the gnathostome oral skeleton. We identified a general model of growth for heterostracan oral plates that exhibit proximal episodic addition of tubercle rows. The distal hook exhibits truncated lamellae compatible with resorption, but we observe growth layers to be continuous between denticles. The denticles show no evidence of patterns of apposition or replacement indicating tooth homology. The oral plates and dermal skeleton share the same histological layers. The denticles grew in a manner comparable to the oral plate tubercles and the rest of the dermal skeleton. Our test of phylogenetic congruence reveals that the distribution of internal odontodes is discontinuous, indicating that the capacity to form internal odontodes evolved independently several times among stem-gnathostomes. Our results support the 'outside-in' hypothesis and the origin of teeth through the spread of odontogenic competence from extra-oral to oral epithelia and the subsequent co-option to a tooth function in gnathostomes.",
    url = "https://doi.org/10.1098/rsos.240836",
    doi = "10.1098/rsos.240836",
    openalex = "W4405484991",
    references = "dearden2024the, doi101098rspb20232258"
}

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition.

@article{doi101098rspb20232258,
    author = "Dearden, Richard P and Jones, Andy S and Giles, Sam and Lanzetti, Agnese and Grohganz, Madleen and Johanson, Zerina and Lautenschlager, Stephan and Randle, Emma and Donoghue, Philip C J and Sansom, Ivan J",
    title = "The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes.",
    year = "2024",
    journal = "Proceedings. Biological sciences",
    abstract = "Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC10965320/",
    doi = "10.1098/rspb.2023.2258",
    openalex = "W4394759988",
    pmcid = "PMC10965320",
    pmid = "38531402",
    references = "dearden2023the, doi101002jezb21063, doi101017s0006323199005472, doi101038nature10207, doi101086413055, doi101093oso97801985404720010001, doi101098rsos160342, doi101098rspb20232258, doi101111j109636421996tb01658x, doi101126science2204594268, doi1016710272463420050250478r20co2, doi1023072413058"
}

Early vertebrate evolution has been characterized as a gradual shift from passive to more active feeding modes. However, this evolutionary scenario is contingent on poorly constrained inferences of the feeding ecology of extinct stem-gnathostomes. Heterostracans are among the earliest members of the gnathostome stem-lineage. Pteraspidiform heterostracans possessed an oral apparatus composed of rod-like plates that have been alternately interpreted to have been used for passive suspension feeding or mechanical food processing. Direct tests of the suspension feeding interpretation are challenging and so we tested hypotheses of a mechanical function using a combination of microstructural and finite element analysis (FEA). Our results demonstrate a negative relationship between simulated negative minimum principal stress (compressive stress) and bone volume fraction (a proxy for internal microstructure); the higher the stress, the higher the bone volume fraction. This relationship is clearest in the oral plate shaft. The hook, where the load is applied, shows the highest bone volume fraction values. Our results are compatible with adaption of skeletal microstructure to a mechanical function in which bone adaptively remodels under applied load to become denser to withstand increased stress. On this basis we reject the suspension feeding hypothesis in favour of a mechanical function for oral plates, such as deposit feeding or scavenging, in support for which we observe wear patterns on the aboral surface and the distal tip of the hook compatible with repeated abrasive polishing.

@article{doi101111pala12733,
    author = "Grohganz, Madleen and Ballell, Antonio and Rayfield, Emily J. and Ferrón, Humberto G. and Johanson, Zerina and Donoghue, Philip C. J.",
    title = "Finite element and microstructural analyses indicate that pteraspid heterostracan oral plate microstructure was adapted to a mechanical function",
    year = "2024",
    journal = "Palaeontology",
    abstract = "Early vertebrate evolution has been characterized as a gradual shift from passive to more active feeding modes. However, this evolutionary scenario is contingent on poorly constrained inferences of the feeding ecology of extinct stem-gnathostomes. Heterostracans are among the earliest members of the gnathostome stem-lineage. Pteraspidiform heterostracans possessed an oral apparatus composed of rod-like plates that have been alternately interpreted to have been used for passive suspension feeding or mechanical food processing. Direct tests of the suspension feeding interpretation are challenging and so we tested hypotheses of a mechanical function using a combination of microstructural and finite element analysis (FEA). Our results demonstrate a negative relationship between simulated negative minimum principal stress (compressive stress) and bone volume fraction (a proxy for internal microstructure); the higher the stress, the higher the bone volume fraction. This relationship is clearest in the oral plate shaft. The hook, where the load is applied, shows the highest bone volume fraction values. Our results are compatible with adaption of skeletal microstructure to a mechanical function in which bone adaptively remodels under applied load to become denser to withstand increased stress. On this basis we reject the suspension feeding hypothesis in favour of a mechanical function for oral plates, such as deposit feeding or scavenging, in support for which we observe wear patterns on the aboral surface and the distal tip of the hook compatible with repeated abrasive polishing.",
    url = "https://doi.org/10.1111/pala.12733",
    doi = "10.1111/pala.12733",
    openalex = "W4404543270",
    references = "dearden2024the, doi101098rspb20232258"
}

Key unresolved questions about particle separation mechanisms in suspension-feeding fishes are identified and discussed, focusing on areas with the potential for substantial future discovery. The published hypotheses that are explored have broad applicability to biological filtration and bioinspired improvements in commercial and industrial crossflow microfiltration processes and microfluidics. As the first synthesis of the primary literature on the particle separation mechanisms of marine, estuarine, and freshwater suspension-feeding fishes, the goals are to enable comparisons with invertebrate suspension-feeding processes, stimulate future theoretical and empirical studies, and further the development of biomimetic physical and computational fluid dynamics models. Of the eight particle separation mechanisms in suspension-feeding fishes, six have been proposed within the past twenty years (inertial lift and shear-induced migration, reduction of effective gap size by vortices, cross-step filtration, vortical flow along outer faces of gill raker plates, ricochet filtration, and lateral displacement). The pace of discovery is anticipated to continue accelerating. Multidisciplinary collaboration and integration among biologists and engineers (including chemical, mechanical, biomedical, and filtration engineering) will result in new perspectives to identify patterns and potential unifying mechanisms across the breadth of suspension-feeding fish taxa, morphology, and function.

@article{doi103389fmars20241331164,
    author = "Sanderson, S. Laurie",
    title = "Particle separation mechanisms in suspension-feeding fishes: key questions and future directions",
    year = "2024",
    journal = "Frontiers in Marine Science",
    abstract = "Key unresolved questions about particle separation mechanisms in suspension-feeding fishes are identified and discussed, focusing on areas with the potential for substantial future discovery. The published hypotheses that are explored have broad applicability to biological filtration and bioinspired improvements in commercial and industrial crossflow microfiltration processes and microfluidics. As the first synthesis of the primary literature on the particle separation mechanisms of marine, estuarine, and freshwater suspension-feeding fishes, the goals are to enable comparisons with invertebrate suspension-feeding processes, stimulate future theoretical and empirical studies, and further the development of biomimetic physical and computational fluid dynamics models. Of the eight particle separation mechanisms in suspension-feeding fishes, six have been proposed within the past twenty years (inertial lift and shear-induced migration, reduction of effective gap size by vortices, cross-step filtration, vortical flow along outer faces of gill raker plates, ricochet filtration, and lateral displacement). The pace of discovery is anticipated to continue accelerating. Multidisciplinary collaboration and integration among biologists and engineers (including chemical, mechanical, biomedical, and filtration engineering) will result in new perspectives to identify patterns and potential unifying mechanisms across the breadth of suspension-feeding fish taxa, morphology, and function.",
    url = "https://doi.org/10.3389/fmars.2024.1331164",
    doi = "10.3389/fmars.2024.1331164",
    openalex = "W4393441926",
    references = "doi101098rsif20210741"
}

The evolution of jaws is hypothesized to have fueled radiations among vertebrates, contributing to their overwhelming success in the present day. Past work shows rapid early expansion of diversity in jaw structure in many lineages; however, the evolutionary dynamics underlying this pattern are unclear and hindered by the lack of a robust comparative framework. Here, using a macroevolutionary approach, we explore the diversification of lower jaws in early bony fishes, a major contributor to this initial radiation. Using newly generated three-dimensional mandibular shape data from 86 species, we find evidence of adaptive radiation in jaws during the earliest interval of bony fish evolutionary history (423-359 Ma). These patterns are principally driven by early lungfishes and coelacanths, which display high rates of jaw diversification, rapid shifts into novel functional regions of trait space, and substantial innovation in jaw morphology and feeding ecology, standing in contrast to their "living fossil" descendants of today. Conversely, ray-finned fishes and tetrapodomorphs, morphologically diverse groups in the present day, show little indication of their future success, possessing slow rates of jaw evolution and low functional diversity. This profound inversion of patterns in modern taxa highlights the significance of paleontological data in understanding drivers of evolutionary diversification and the limitations of approaches using only living species. Overall, our findings provide insight into the evolutionary dynamics associated with the evolution of jaws and provide context for the role of jaws in vertebrate success.

@article{doi101016jcub202508008,
    author = "Troyer, Emily M and Rivero-Vega, Rafael A and Cui, Xindong and Zhu, Min and Qiao, Tuo and Saad, Hadeel H and Figueroa, Rodrigo T and Andrews, James V and Clement, Alice M and Lebedev, Oleg A and Higgins, Robert and Igielman, Benjamin and Pierce, Stephanie E and Giles, Sam and Friedman, Matt",
    title = "Macroevolutionary role reversals in the earliest radiation of bony fishes.",
    year = "2025",
    journal = "Current biology: CB",
    abstract = {The evolution of jaws is hypothesized to have fueled radiations among vertebrates, contributing to their overwhelming success in the present day. Past work shows rapid early expansion of diversity in jaw structure in many lineages; however, the evolutionary dynamics underlying this pattern are unclear and hindered by the lack of a robust comparative framework. Here, using a macroevolutionary approach, we explore the diversification of lower jaws in early bony fishes, a major contributor to this initial radiation. Using newly generated three-dimensional mandibular shape data from 86 species, we find evidence of adaptive radiation in jaws during the earliest interval of bony fish evolutionary history (423-359 Ma). These patterns are principally driven by early lungfishes and coelacanths, which display high rates of jaw diversification, rapid shifts into novel functional regions of trait space, and substantial innovation in jaw morphology and feeding ecology, standing in contrast to their "living fossil" descendants of today. Conversely, ray-finned fishes and tetrapodomorphs, morphologically diverse groups in the present day, show little indication of their future success, possessing slow rates of jaw evolution and low functional diversity. This profound inversion of patterns in modern taxa highlights the significance of paleontological data in understanding drivers of evolutionary diversification and the limitations of approaches using only living species. Overall, our findings provide insight into the evolutionary dynamics associated with the evolution of jaws and provide context for the role of jaws in vertebrate success.},
    url = "https://pubmed.ncbi.nlm.nih.gov/40897172/",
    doi = "10.1016/j.cub.2025.08.008",
    pmid = "40897172"
}