Lobe-fins

@article{crossref1903origin,
    title = "Origin of the Fins of Fishes",
    year = "1903",
    journal = "Scientific American",
    url = "https://doi.org/10.1038/scientificamerican02141903-22671asupp",
    doi = "10.1038/scientificamerican02141903-22671asupp",
    number = "1415supp",
    openalex = "W4210639665",
    pages = "22671-22671",
    volume = "55"
}

@article{crossref1969vertebrate,
    title = "Vertebrate Palaeontology: Lobe Finned Fishes",
    year = "1969",
    journal = "Nature",
    url = "https://doi.org/10.1038/221803b0",
    doi = "10.1038/221803b0",
    number = "5183",
    openalex = "W4255762652",
    pages = "803-804",
    volume = "221"
}

Summary 1. Interpretation of structural evolution in a group such as the Sarcopterygii requires consideration of a combination of all possible functions, rather than single functions. 2. The Dipnoi are probably more closely related to the Crossopterygii than to other groups of fishes. The Sarcopterygii are a ‘natural’ group. Certain characters in common between the elasmobranchs and the Dipnoi or Coelacanthini seem to be the result of convergent evolution. 3. Evolution of the skull, in connexion with both respiratory and feeding mechanisms, has resulted in extreme specialization in all Sarcopterygii. The crossopterygian intracranial kinesis has evolved from an earlier mobility between the skull and neck and is adapted for increasing the power of the bite and for enclosing the prey from both above and below, in addition to other factors. Adaptive radiation is seen in the feeding mechanisms of all forms. The evolution of the Amphibia proceeded through elongation of the anterior division of the skull (which is not correlated with any changes in brain morphology) and loss of the kinetic mechanism in this sequence is at least partially associated with improved buccal pumping mechanisms for lung ventilation. 4. Adaptive radiation of the respiratory system in Dipnoi shows a progressive increase in the use of aerial respiration. The aquatic condition seen in Neoceratodus is probably secondary. Comparison of the three living genera shows a striking correlation between respiratory physiology and habit. There is little indication of reduction of the branchial respiratory system in known Rhipidistia, in which respiration was probably primarily aquatic. In Dipnoi and Rhipidistia, evolution of the lung allowed a partial control of the hydrostatic properties of the body. In coelacanths, aerial respiration was abandoned, except in certain secondarily freshwater forms, and the single lung is modified as an organ of hydrostatic balance. These changes are reflected in the over‐all body proportions. 5. Locomotion in Sarcopterygii (except the coelacanths Laugia and Piveteauia) is adapted for contact with the substrate in relatively shallow water in most cases. Adaptive radiation of the locomotor apparatus is seen with respect to the relative roles and functions of the paired and unpaired fins, over‐all body shape, caudal fin shape, and absolute size. An important function of the pectoral fins in advanced Rhipidistia was in supporting the body in shallow water and thus aiding lung ventilation. 6. Aestivation is an early feature of dipnoan biology, but was not evolved in Rhipidistia. The common faculty of urea production via the ornithine cycle and urea retention in coelacanths and dipnoans are adaptations to conditions in which the body tissues may become dehydrated (salt water and desiccation, respectively). The common pattern of nitrogen metabolism seems to have evolved during a marine phase in sarcopterygian evolution. 7. There is evidence that the earliest members of all sarcopterygian lines included marine forms. However, the subsequent major radiations of Dipnoi and Rhipidistia occurred in fresh waters. The distribution of Sarcopterygii was entirely tropical. The late Palaeozoic distribution of the freshwater forms seems to offer evidence for the occurrence of Continental Drift. Coelacanths were primarily coastal fishes. 8. The evolution of a major group of organisms requires a different pattern of evolutionary change than that by which adaptive radiations are produced. It evolves the structural and temporal correlation of modification in a number of different functional systems rather than the separate modification of each system without reference to other systems. 9. The first tetrapods evolved in a highly seasonal swampy environment on the shores of inland lakes or rivers, in permanently moist conditions.

@article{thomson1969the,
    author = "THOMSON, KEITH STEWART",
    title = "THE BIOLOGY OF THE LOBE‐FINNED FISHES",
    year = "1969",
    journal = "Biological Reviews",
    abstract = "Summary 1. Interpretation of structural evolution in a group such as the Sarcopterygii requires consideration of a combination of all possible functions, rather than single functions. 2. The Dipnoi are probably more closely related to the Crossopterygii than to other groups of fishes. The Sarcopterygii are a ‘natural’ group. Certain characters in common between the elasmobranchs and the Dipnoi or Coelacanthini seem to be the result of convergent evolution. 3. Evolution of the skull, in connexion with both respiratory and feeding mechanisms, has resulted in extreme specialization in all Sarcopterygii. The crossopterygian intracranial kinesis has evolved from an earlier mobility between the skull and neck and is adapted for increasing the power of the bite and for enclosing the prey from both above and below, in addition to other factors. Adaptive radiation is seen in the feeding mechanisms of all forms. The evolution of the Amphibia proceeded through elongation of the anterior division of the skull (which is not correlated with any changes in brain morphology) and loss of the kinetic mechanism in this sequence is at least partially associated with improved buccal pumping mechanisms for lung ventilation. 4. Adaptive radiation of the respiratory system in Dipnoi shows a progressive increase in the use of aerial respiration. The aquatic condition seen in Neoceratodus is probably secondary. Comparison of the three living genera shows a striking correlation between respiratory physiology and habit. There is little indication of reduction of the branchial respiratory system in known Rhipidistia, in which respiration was probably primarily aquatic. In Dipnoi and Rhipidistia, evolution of the lung allowed a partial control of the hydrostatic properties of the body. In coelacanths, aerial respiration was abandoned, except in certain secondarily freshwater forms, and the single lung is modified as an organ of hydrostatic balance. These changes are reflected in the over‐all body proportions. 5. Locomotion in Sarcopterygii (except the coelacanths Laugia and Piveteauia) is adapted for contact with the substrate in relatively shallow water in most cases. Adaptive radiation of the locomotor apparatus is seen with respect to the relative roles and functions of the paired and unpaired fins, over‐all body shape, caudal fin shape, and absolute size. An important function of the pectoral fins in advanced Rhipidistia was in supporting the body in shallow water and thus aiding lung ventilation. 6. Aestivation is an early feature of dipnoan biology, but was not evolved in Rhipidistia. The common faculty of urea production via the ornithine cycle and urea retention in coelacanths and dipnoans are adaptations to conditions in which the body tissues may become dehydrated (salt water and desiccation, respectively). The common pattern of nitrogen metabolism seems to have evolved during a marine phase in sarcopterygian evolution. 7. There is evidence that the earliest members of all sarcopterygian lines included marine forms. However, the subsequent major radiations of Dipnoi and Rhipidistia occurred in fresh waters. The distribution of Sarcopterygii was entirely tropical. The late Palaeozoic distribution of the freshwater forms seems to offer evidence for the occurrence of Continental Drift. Coelacanths were primarily coastal fishes. 8. The evolution of a major group of organisms requires a different pattern of evolutionary change than that by which adaptive radiations are produced. It evolves the structural and temporal correlation of modification in a number of different functional systems rather than the separate modification of each system without reference to other systems. 9. The first tetrapods evolved in a highly seasonal swampy environment on the shores of inland lakes or rivers, in permanently moist conditions.",
    url = "https://doi.org/10.1111/j.1469-185x.1969.tb00823.x",
    doi = "10.1111/j.1469-185x.1969.tb00823.x",
    number = "1",
    openalex = "W1968014620",
    pages = "91-154",
    volume = "44",
    references = "doi101002jmor1051110306, doi1010160031018265900131, doi101016s0021925818767999, doi101111j146979981961tb06080x, doi101111j155856461959tb03005x, doi10113000167606196778353forbim20co2, doi105962bhltitle82144, howells1950genetics, openalexw1575479768"
}

@book{thompson1980the1,
    author = "Thompson, K. S",
    title = "The Ecology of the Lobe-Finned Fishes, in Panchen, A. L., ed., The Terrestrial Environment and the Origin of Land Vertebrates",
    year = "1980",
    publisher = "London, Academic Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Thompson, K. S., 1980, The Ecology of the Lobe-Finned Fishes, in Panchen, A. L., ed., The Terrestrial Environment and the Origin of Land Vertebrates: London, Academic Press.}"
}

Some 405 million years ago multicellular plants and animals began a slow colonization of the continents.First traces are in the shallow waters of the Late Silurian, followed by rapidly increasing records of plants during the Devonian and invertebrates and vertebrates from the late Devonian and Carboniferous.Much of the earliest history of both the animals and plants remains obscure, but in the 19th and 20th centuries, during which speculation and accumulation of data has gone on apace, substantive data have been accumulated and ways of looking at the problems have changed immensely.An older way of looking at evolution during the later Paleozoic through a group-by-group analysis has partially given way to coordinated studies of associations of organisms in community systems and considerations of the ecology and taphonomy of their occurrences.A. L. Panchen, the moving force behind the symposium presented in this volume, expanded the original plan to treat the origin of tetrapods from their fish ancestors, to include plants, invertebrates and vertebrates and the field of ecological aspects of the origin of tetrapods.The result has been a happy synthesis of morphology, systematics, ecology and taphonomy within an evolutionary framework.Altogether 20 students have contributed to the volume.Topics range through biogeography, plants, invertebrates and vertebrates viewed in a variety of contexts.The volume is a gold mine of information on the origin of tetrapods and related subjects.To one who has been interested in this area for many years and watched attitudes and philosophies change, one of the striking aspects of the volume is its clear portrayal of the continuing controversy between so called "orthodox" and "cladistic" systematics and phylogenetics.The broad impact of the development of cladistic methods, as presented by Hennig and greatly modified to date, is evident throughout the book, even in the papers of some who reject the approach.Awareness of the need to erect testable hypotheses is found in the majority of papers.Although the method has had a strongly affirmative effect on systematics and phylogeny, it remains clear that in the initial steps of analysis, and,

@article{doi101111j155856461981tb04969x,
    author = "Olson, Everett C.",
    title = "THE TERRESTRIAL ENVIRONMENT AND THE ORIGIN OF LAND VERTEBRATES",
    year = "1981",
    journal = "Evolution",
    abstract = {Some 405 million years ago multicellular plants and animals began a slow colonization of the continents.First traces are in the shallow waters of the Late Silurian, followed by rapidly increasing records of plants during the Devonian and invertebrates and vertebrates from the late Devonian and Carboniferous.Much of the earliest history of both the animals and plants remains obscure, but in the 19th and 20th centuries, during which speculation and accumulation of data has gone on apace, substantive data have been accumulated and ways of looking at the problems have changed immensely.An older way of looking at evolution during the later Paleozoic through a group-by-group analysis has partially given way to coordinated studies of associations of organisms in community systems and considerations of the ecology and taphonomy of their occurrences.A. L. Panchen, the moving force behind the symposium presented in this volume, expanded the original plan to treat the origin of tetrapods from their fish ancestors, to include plants, invertebrates and vertebrates and the field of ecological aspects of the origin of tetrapods.The result has been a happy synthesis of morphology, systematics, ecology and taphonomy within an evolutionary framework.Altogether 20 students have contributed to the volume.Topics range through biogeography, plants, invertebrates and vertebrates viewed in a variety of contexts.The volume is a gold mine of information on the origin of tetrapods and related subjects.To one who has been interested in this area for many years and watched attitudes and philosophies change, one of the striking aspects of the volume is its clear portrayal of the continuing controversy between so called "orthodox" and "cladistic" systematics and phylogenetics.The broad impact of the development of cladistic methods, as presented by Hennig and greatly modified to date, is evident throughout the book, even in the papers of some who reject the approach.Awareness of the need to erect testable hypotheses is found in the majority of papers.Although the method has had a strongly affirmative effect on systematics and phylogeny, it remains clear that in the initial steps of analysis, and,},
    url = "https://doi.org/10.1111/j.1558-5646.1981.tb04969.x",
    doi = "10.1111/j.1558-5646.1981.tb04969.x",
    openalex = "W2053841024"
}

@article{doi1023072413059,
    author = "Kluge, Arnold G. and Panchen, Alec L.",
    title = "The Terrestrial Environment and the Origin of Land Vertebrates.",
    year = "1981",
    journal = "Systematic Zoology",
    url = "https://doi.org/10.2307/2413059",
    doi = "10.2307/2413059",
    openalex = "W2326141228"
}

@article{doi101038375678a0,
    author = "Sordino, Paolo and van der Hoeven, F. and Duboule, Denis",
    title = "Hox gene expression in teleost fins and the origin of vertebrate digits",
    year = "1995",
    journal = "Nature",
    url = "https://doi.org/10.1038/375678a0",
    doi = "10.1038/375678a0",
    openalex = "W2090533250"
}

One of the most prominent characteristics of early vertebrates is the elongate caudal fin bearing fin rays. The caudal fin represents a fundamental design feature of vertebrates that predates the origin of jaws and is found in both agnathans and gnathostomes. The caudal fin also represents the most posterior region of the vertebrate axis and is the location where fluid, accelerated by movement of the body anteriorly, is shed into the surrounding medium. Despite the extensive fossil record of the caudal fin, the use of caudal characters for systematic studies, and the importance of tail function for understanding locomotor dynamics in fishes, few experimental studies have been undertaken of caudal fin function. In this paper I review two experimental approaches which promise to provide new insights into the function and evolution of the caudal fin: three-dimensional kinematic analysis, and quantitative flow measurements in the wake of freely-swimming fishes using digital particle image velocimetry (DPIV). These methods are then applied to the function of the caudal fin during steady swimming in fishes with heterocercal and homocercal morphologies: chondrichthyians (leopard sharks) and ray-fined fishes (sturgeon and bluegill sunfish). The caudal fin of leopard sharks functions in a manner consistent with the classical model of heterocercal tail function in which the caudal surface moves at an acute angle to the horizontal plane, and hence is expected to generate lift forces and torques which must be counteracted anteriorly by the body and pectoral fins. An alternative model in which the shark tail produces a reactive force that acts through the center of mass is not supported. The sturgeon heterocercal tail is extremely flexible and the upper tail lobe trails the lower during the fin beat cycle. The sturgeon tail does not function according to the classical model of the heterocercal tail, and is hypothesized to generate reactive forces oriented near the center of mass of the body which is tilted at an angle to the flow during steady locomotion. Functional analysis of the homocercal tail of bluegill shows that the dorsal and ventral lobes do not function symmetrically as expected. Rather, the dorsal lobe undergoes greater lateral excursions and moves at higher velocities than the ventral lobe. The surface of the dorsal lobe also achieves a significantly acute angle to the horizontal plane suggesting that the homocercal tail of bluegill generates lift during steady swimming. These movements are actively generated by the hypochordal longitudinalis muscle within the tail. This result, combined with DPIV flow visualization data, suggest a new hypothesis for the function of the homocercal tail: the homocercal tail generates tilted and linked vortex rings with a central jet inclined posteroventrally, producing an anterodorsal reactive force on the body which generates lift and torque in the manner expected of a heterocercal tail. These results show that the application of new techniques to the study of caudal fin function in fishes reveals a previously unknown diversity of homocercal and heterocercal tail function, and that morphological characterizations of caudal fins do not accurately reflect in vivo function.

@article{doi1016680003156920000400101fotcfd20co2,
    author = "Lauder, George",
    title = "Function of the Caudal Fin During Locomotion in Fishes: Kinematics, Flow Visualization, and Evolutionary Patterns1",
    year = "2000",
    journal = "American Zoologist",
    abstract = "One of the most prominent characteristics of early vertebrates is the elongate caudal fin bearing fin rays. The caudal fin represents a fundamental design feature of vertebrates that predates the origin of jaws and is found in both agnathans and gnathostomes. The caudal fin also represents the most posterior region of the vertebrate axis and is the location where fluid, accelerated by movement of the body anteriorly, is shed into the surrounding medium. Despite the extensive fossil record of the caudal fin, the use of caudal characters for systematic studies, and the importance of tail function for understanding locomotor dynamics in fishes, few experimental studies have been undertaken of caudal fin function. In this paper I review two experimental approaches which promise to provide new insights into the function and evolution of the caudal fin: three-dimensional kinematic analysis, and quantitative flow measurements in the wake of freely-swimming fishes using digital particle image velocimetry (DPIV). These methods are then applied to the function of the caudal fin during steady swimming in fishes with heterocercal and homocercal morphologies: chondrichthyians (leopard sharks) and ray-fined fishes (sturgeon and bluegill sunfish). The caudal fin of leopard sharks functions in a manner consistent with the classical model of heterocercal tail function in which the caudal surface moves at an acute angle to the horizontal plane, and hence is expected to generate lift forces and torques which must be counteracted anteriorly by the body and pectoral fins. An alternative model in which the shark tail produces a reactive force that acts through the center of mass is not supported. The sturgeon heterocercal tail is extremely flexible and the upper tail lobe trails the lower during the fin beat cycle. The sturgeon tail does not function according to the classical model of the heterocercal tail, and is hypothesized to generate reactive forces oriented near the center of mass of the body which is tilted at an angle to the flow during steady locomotion. Functional analysis of the homocercal tail of bluegill shows that the dorsal and ventral lobes do not function symmetrically as expected. Rather, the dorsal lobe undergoes greater lateral excursions and moves at higher velocities than the ventral lobe. The surface of the dorsal lobe also achieves a significantly acute angle to the horizontal plane suggesting that the homocercal tail of bluegill generates lift during steady swimming. These movements are actively generated by the hypochordal longitudinalis muscle within the tail. This result, combined with DPIV flow visualization data, suggest a new hypothesis for the function of the homocercal tail: the homocercal tail generates tilted and linked vortex rings with a central jet inclined posteroventrally, producing an anterodorsal reactive force on the body which generates lift and torque in the manner expected of a heterocercal tail. These results show that the application of new techniques to the study of caudal fin function in fishes reveals a previously unknown diversity of homocercal and heterocercal tail function, and that morphological characterizations of caudal fins do not accurately reflect in vivo function.",
    url = "https://doi.org/10.1668/0003-1569(2000)040[0101:fotcfd]2.0.co;2",
    doi = "10.1668/0003-1569(2000)040[0101:fotcfd]2.0.co;2",
    openalex = "W1837141699",
    references = "doi101242jeb40123"
}

@article{lauder2002experimental,
    author = "Lauder, G. V.",
    title = "Experimental Hydrodynamics and Evolution: Function of Median Fins in Ray-finned Fishes",
    year = "2002",
    journal = "Integrative and Comparative Biology",
    url = "https://doi.org/10.1093/icb/42.5.1009",
    doi = "10.1093/icb/42.5.1009",
    number = "5",
    openalex = "W2123142369",
    pages = "1009-1017",
    volume = "42",
    references = "doi1010079783540723080, doi101007bf00190388, doi101098rspb19710085, doi101146annurevfluid32133, doi101242jeb202182393, doi1023071292845, doi1023072422556, doi105962p203769, openalexw1593581772, openalexw2040817479"
}

A defining feature of tetrapod evolutionary origins is the transition from fish fins to tetrapod limbs. A major change during this transition is the appearance of the autopod (hands, feet), which comprises two distinct regions, the wrist/ankle and the digits. When the autopod first appeared in Late Devonian fossil tetrapods, it was incomplete: digits evolved before the full complement of wrist/ankle bones. Early tetrapod wrists/ankles, including those with a full complement of bones, also show a sharp pattern discontinuity between proximal elements and distal elements. This suggests the presence of a discontinuity in the proximal-distal sequence of development. Such a discontinuity occurs in living urodeles, where digits form before completion of the wrist/ankle, implying developmental independence of the digits from wrist/ankle elements. We have observed comparable independent development of pectoral fin radials in the lungfish Neoceratodus (Osteichthyes: Sarcopterygii), relative to homologues of the tetrapod limb and proximal wrist elements in the main fin axis. Moreover, in the Neoceratodus fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii.

@article{doi101002jezb21197,
    author = "Johanson, Zerina and Joss, Jean M.P. and Boisvert, Catherine and Ericsson, Rolf and Sutija, Margareta and Ahlberg, Per",
    title = "Fish fingers: digit homologues in sarcopterygian fish fins",
    year = "2007",
    journal = "Journal of Experimental Zoology Part B Molecular and Developmental Evolution",
    abstract = "A defining feature of tetrapod evolutionary origins is the transition from fish fins to tetrapod limbs. A major change during this transition is the appearance of the autopod (hands, feet), which comprises two distinct regions, the wrist/ankle and the digits. When the autopod first appeared in Late Devonian fossil tetrapods, it was incomplete: digits evolved before the full complement of wrist/ankle bones. Early tetrapod wrists/ankles, including those with a full complement of bones, also show a sharp pattern discontinuity between proximal elements and distal elements. This suggests the presence of a discontinuity in the proximal-distal sequence of development. Such a discontinuity occurs in living urodeles, where digits form before completion of the wrist/ankle, implying developmental independence of the digits from wrist/ankle elements. We have observed comparable independent development of pectoral fin radials in the lungfish Neoceratodus (Osteichthyes: Sarcopterygii), relative to homologues of the tetrapod limb and proximal wrist elements in the main fin axis. Moreover, in the Neoceratodus fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii.",
    url = "https://doi.org/10.1002/jez.b.21197",
    doi = "10.1002/jez.b.21197",
    openalex = "W2165420842",
    references = "doi10103827421, doi101098rstb19840103, doi101111j109636421995tb00119x"
}

Tetrapods evolved from sarcopterygian fishes in the Devonian and were the first vertebrates to colonize land. The locomotor component of this transition can be divided into four major events: terrestriality, the origins of digited limbs, solid substrate-based locomotion, and alternating gaits that use pelvic appendages as major propulsors. As the sister group to tetrapods, lungfish are a morphologically and phylogenetically relevant sarcopterygian taxon for understanding the order in which these events occurred. We found that a species of African lungfish (Protopterus annectens) uses a range of pelvic fin-driven, tetrapod-like gaits, including walking and bounding, in an aquatic environment, despite having a derived limb endoskeleton and primitively small, muscularly supported pelvis. Surprisingly, given these morphological traits, P. annectens also lifts its body clear of the substrate using its pelvic fins, an ability thought to be a tetrapod innovation. Our findings suggest that some fundamental features of tetrapod locomotion, including pelvic limb gait patterns and substrate association, probably arose in sarcopterygians before the origin of digited limbs or terrestriality. It follows that the attribution of some of the nondigited Devonian fossil trackways to limbed tetrapods may need to be revisited.

@article{doi101073pnas1118669109,
    author = "King, Heather M. and Shubin, Neil H. and Coates, Michael I. and Hale, Melina E.",
    title = "Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes",
    year = "2011",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Tetrapods evolved from sarcopterygian fishes in the Devonian and were the first vertebrates to colonize land. The locomotor component of this transition can be divided into four major events: terrestriality, the origins of digited limbs, solid substrate-based locomotion, and alternating gaits that use pelvic appendages as major propulsors. As the sister group to tetrapods, lungfish are a morphologically and phylogenetically relevant sarcopterygian taxon for understanding the order in which these events occurred. We found that a species of African lungfish (Protopterus annectens) uses a range of pelvic fin-driven, tetrapod-like gaits, including walking and bounding, in an aquatic environment, despite having a derived limb endoskeleton and primitively small, muscularly supported pelvis. Surprisingly, given these morphological traits, P. annectens also lifts its body clear of the substrate using its pelvic fins, an ability thought to be a tetrapod innovation. Our findings suggest that some fundamental features of tetrapod locomotion, including pelvic limb gait patterns and substrate association, probably arose in sarcopterygians before the origin of digited limbs or terrestriality. It follows that the attribution of some of the nondigited Devonian fossil trackways to limbed tetrapods may need to be revisited.",
    url = "https://doi.org/10.1073/pnas.1118669109",
    doi = "10.1073/pnas.1118669109",
    openalex = "W2051103595",
    references = "doi101002jmor1051900412"
}

@article{dores2011observations,
    author = "Dores, Robert M. and Majeed, Qais and Komorowski, Leanne",
    title = "Observations on the radiation of lobe-finned fishes, ray-finned fishes, and cartilaginous fishes: Phylogeny of the opioid/orphanin gene family and the 2R hypothesis",
    year = "2011",
    journal = "General and Comparative Endocrinology",
    url = "https://doi.org/10.1016/j.ygcen.2010.09.023",
    doi = "10.1016/j.ygcen.2010.09.023",
    number = "2",
    openalex = "W2082700706",
    pages = "253-264",
    volume = "170",
    references = "doi101016s0016699588800664, doi101038258577a0, doi101038278423a0, doi101038377532a0, doi101093genetics15141531, doi101126science2705237792, doi101242dev1994supplement125, doi101371journalpone, doi1023073514548, doi105962bhltitle82448"
}

@incollection{crossref2015flexible,
    title = "Flexible fins and fin rays as key transformations in ray-finned fishes",
    year = "2015",
    booktitle = "Great Transformations in Vertebrate Evolution",
    url = "https://doi.org/10.7208/chicago/9780226268392.003.0002",
    doi = "10.7208/chicago/9780226268392.003.0002",
    openalex = "W2492100642",
    pages = "31-46",
    references = "doi101007s0016200700452, doi101016s154650980523011x, doi101242jeb00209, doi101242jeb030932, doi101242jeb062711, doi101242jeb202182393, doi101242jeb204172943, doi1016680003156920000400101fotcfd20co2, openalexw1549935978, openalexw1964182146"
}

@incollection{clack2016sarcopterygians,
    author = "Clack, Jennifer A. and Ahlberg, Per Erik",
    title = "Sarcopterygians: From Lobe-Finned Fishes to the Tetrapod Stem Group",
    year = "2016",
    booktitle = "Springer Handbook of Auditory Research",
    url = "https://doi.org/10.1007/978-3-319-46661-3\_3",
    doi = "10.1007/978-3-319-46661-3\_3",
    openalex = "W2563056895",
    pages = "51-70",
    references = "doi101016b9780126709506500187, doi10103827421, doi101038nature04639, doi10108003115519608619475, doi101111j109636421977tb01031x, doi101111j109636421991tb00905x, doi1023071539358, doi1023072413058, openalexw1587561751, openalexw628087051"
}

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

@article{doi101073pnas1719358115,
    author = "Hughes, Lily C. and Ortı́, Guillermo and Huang, Yu and Sun, Ying and Baldwin, Carole C. and Thompson, Andrew W. and Arcila, Dahiana and Betancur‐R, Ricardo and Li, Chenhong and Becker, L.A. and Bellora, Nicolás and Zhao, Xiaomeng and Li, Xiaofeng and Wang, Min and Fang, Chao and Xie, Bing and Zhou, Zhuocheng and Huang, Hai and Chen, Songlin and Venkatesh, Byrappa and Shi, Qiong",
    title = "Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data",
    year = "2018",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.",
    url = "https://doi.org/10.1073/pnas.1719358115",
    doi = "10.1073/pnas.1719358115",
    openalex = "W2803572653",
    references = "doi101073pnas1206625109, doi10108010635150290069913, doi101093bioinformatics17121246, doi101093bioinformaticsbtt403, doi101093bioinformaticsbtu033, doi101093bioinformaticsbtu462, doi101093molbevmsm088, doi101093sysbiosys004, doi101111j109636421981tb01575x, doi101186s1286201709583, doi101371currentstol53ba26640df0ccaee75bb165c8c26288, doi101371journalpbio0030314, doi1023072412448"
}

@incollection{clement2019sarcopterygian,
    author = "Clement, Alice M.",
    title = "Sarcopterygian Fishes, the “Lobe-Fins”",
    year = "2019",
    booktitle = "Fascinating Life Sciences",
    url = "https://doi.org/10.1007/978-3-319-93560-7\_6",
    doi = "10.1007/978-3-319-93560-7\_6",
    openalex = "W2914981641",
    pages = "119-142",
    references = "doi101038001534a0, doi101038nature04637, doi101038nature04639, doi101038nature12027, doi101371currentstol53ba26640df0ccaee75bb165c8c26288, doi101371journalpone0059520, doi105860choice503274, openalexw1484431148, openalexw2173200745, openalexw2581839632"
}

Abstract Between 450 and 500 million years ago, some vertebrates evolved paired fins and jaws, which made them more efficient swimmers and fiercer predators. These jawed vertebrates (i.e., gnathostomes) diversified in the Devonian period, but most died out during the end-Devonian mass extinction. The surviving gnathostomes had a more complex vestibular apparatus than their jawless ancestors, an expanded set of olfactory receptor genes, and vomeronasal receptors. A major innovation in the brains of gnathostomes was the emergence of a cerebellum that is distinct from the cerebellum-like areas found in all vertebrates. The telencephalon of early vertebrates processed primarily olfactory information, but this olfactory dominance was independently reduced in three later lineages, namely in cartilaginous fishes, ray-finned fishes, and tetrapods. In concert with the reduction in olfactory dominance, these lineages enlarged their telencephalon, relative to other brain regions, and evolved a telencephalic “dorsal pallium” that receives non-olfactory sensory information from the diencephalon.

@incollection{doi101093oso97801951256890030003,
    author = "Striedter, Georg F. and Northcutt, R. Glenn",
    title = "The Origin of Jaws and Paired Fins",
    year = "2019",
    abstract = "Abstract Between 450 and 500 million years ago, some vertebrates evolved paired fins and jaws, which made them more efficient swimmers and fiercer predators. These jawed vertebrates (i.e., gnathostomes) diversified in the Devonian period, but most died out during the end-Devonian mass extinction. The surviving gnathostomes had a more complex vestibular apparatus than their jawless ancestors, an expanded set of olfactory receptor genes, and vomeronasal receptors. A major innovation in the brains of gnathostomes was the emergence of a cerebellum that is distinct from the cerebellum-like areas found in all vertebrates. The telencephalon of early vertebrates processed primarily olfactory information, but this olfactory dominance was independently reduced in three later lineages, namely in cartilaginous fishes, ray-finned fishes, and tetrapods. In concert with the reduction in olfactory dominance, these lineages enlarged their telencephalon, relative to other brain regions, and evolved a telencephalic “dorsal pallium” that receives non-olfactory sensory information from the diencephalon.",
    url = "https://doi.org/10.1093/oso/9780195125689.003.0003",
    doi = "10.1093/oso/9780195125689.003.0003",
    openalex = "W3036848363",
    references = "crossref2015flexible, doi101006zjls19960043"
}

The inferior lobes are prominent bilateral brain areas in the hypothalamus of neopterygians among the ray-finned fishes. They are known as multisensory integration centers. As such, they should play a major role in fish evolution. In this study, a comparative morphometric analysis was performed. The morphology of the hypothalamus, where the inferior lobe is considered as fully developed first in Lepisosteus, was then re-examined. One hundred brains from different species of 60 families of ray-finned fishes were stained with cresyl violet and embedded in methacrylate. They were then cut on a microtome while conducting block-face imaging. The volumes were determined for the whole brain, brain areas, and nuclei. Since visual input represents a major sensory input for the inferior lobe, the nucleus glomerulosus, a visual-related nucleus in paracanthopterygian and acanthopterygian teleosts, and the tectum opticum were included in the investigations. The morphometric analysis revealed that the relative volume of the inferior lobes increases significantly from species of the Lepisosteiformes to the Tetraodontiformes. In addition, a positive correlation was detected between the relative volume of the inferior lobes and either the relative volume of the nucleus glomerulosus or the relative volume of the tectum opticum. These correlations, in combination with findings from previous hodological and behavioral studies, give rise to the speculation that the inferior lobes may be involved in higher cognitive processes and complex social interactions.

@article{schmidt2020evolution,
    author = "Schmidt, Matthias",
    title = "Evolution of the Hypothalamus and Inferior Lobe in Ray-Finned Fishes",
    year = "2020",
    journal = "Brain, Behavior and Evolution",
    abstract = "The inferior lobes are prominent bilateral brain areas in the hypothalamus of neopterygians among the ray-finned fishes. They are known as multisensory integration centers. As such, they should play a major role in fish evolution. In this study, a comparative morphometric analysis was performed. The morphology of the hypothalamus, where the inferior lobe is considered as fully developed first in Lepisosteus, was then re-examined. One hundred brains from different species of 60 families of ray-finned fishes were stained with cresyl violet and embedded in methacrylate. They were then cut on a microtome while conducting block-face imaging. The volumes were determined for the whole brain, brain areas, and nuclei. Since visual input represents a major sensory input for the inferior lobe, the nucleus glomerulosus, a visual-related nucleus in paracanthopterygian and acanthopterygian teleosts, and the tectum opticum were included in the investigations. The morphometric analysis revealed that the relative volume of the inferior lobes increases significantly from species of the Lepisosteiformes to the Tetraodontiformes. In addition, a positive correlation was detected between the relative volume of the inferior lobes and either the relative volume of the nucleus glomerulosus or the relative volume of the tectum opticum. These correlations, in combination with findings from previous hodological and behavioral studies, give rise to the speculation that the inferior lobes may be involved in higher cognitive processes and complex social interactions.",
    url = "https://doi.org/10.1159/000505898",
    doi = "10.1159/000505898",
    number = "6",
    openalex = "W3012704817",
    pages = "302-316",
    volume = "95",
    references = "doi1010029781119174844, doi101002ara20253, doi101002cne20183, doi101002cne20853, doi101016016622369593932n, doi101016s0361923001006992, doi101093icb424743, doi101098rspb19980569, doi101098rspb20063748, doi101159000101067"
}

SUMMARY Brain anatomy provides key evidence for ray-finned fish relationships 1, but two key limitations obscure our understanding of neuroanatomical evolution in this major vertebrate group. First, the deepest branching living lineages are separated from the group’s common ancestor by hundreds of millions of years, with indications that aspects of their brain morphology–like other aspects of their anatomy 2,3 –are specialised relative to primitive conditions. Second, there are no direct constraints on brain morphology in the earliest ray-finned fishes beyond the coarse picture provided by cranial endocasts: natural or virtual infillings of void spaces within the skull 4–8. Here we report brain and cranial nerve soft-tissue preservation in † Coccocephalichthys wildi, a ∼319-million-year-old (Myr) ray-finned fish. This oldest example of a well-preserved vertebrate brain provides a unique window into neural anatomy deep within ray-finned fish phylogeny. † Coccocephalichthys indicates a more complicated pattern of brain evolution than suggested by living species alone, highlighting cladistian apomorphies 9 and providing temporal constraints on the origin of traits uniting all extant ray-finned fishes 9–11. Our findings, along with a growing set of studies in other animal groups 12–16, point to the significance of ancient soft tissue preservation in understanding the deep evolutionary assembly of major anatomical systems outside of the narrow subset of skeletal tissues 17–20.

@misc{doi10110120220604492470,
    author = "Figueroa, Rodrigo Tinoco and Goodvin, Danielle and Kolmann, Matthew A. and Coates, Michael I. and Caron, Abigail M. and Friedman, Matt and Giles, Sam",
    title = "Exceptional fossil preservation and evolution of the ray-finned fish brain",
    year = "2022",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "SUMMARY Brain anatomy provides key evidence for ray-finned fish relationships 1, but two key limitations obscure our understanding of neuroanatomical evolution in this major vertebrate group. First, the deepest branching living lineages are separated from the group’s common ancestor by hundreds of millions of years, with indications that aspects of their brain morphology–like other aspects of their anatomy 2,3 –are specialised relative to primitive conditions. Second, there are no direct constraints on brain morphology in the earliest ray-finned fishes beyond the coarse picture provided by cranial endocasts: natural or virtual infillings of void spaces within the skull 4–8. Here we report brain and cranial nerve soft-tissue preservation in † Coccocephalichthys wildi, a ∼319-million-year-old (Myr) ray-finned fish. This oldest example of a well-preserved vertebrate brain provides a unique window into neural anatomy deep within ray-finned fish phylogeny. † Coccocephalichthys indicates a more complicated pattern of brain evolution than suggested by living species alone, highlighting cladistian apomorphies 9 and providing temporal constraints on the origin of traits uniting all extant ray-finned fishes 9–11. Our findings, along with a growing set of studies in other animal groups 12–16, point to the significance of ancient soft tissue preservation in understanding the deep evolutionary assembly of major anatomical systems outside of the narrow subset of skeletal tissues 17–20.",
    url = "https://doi.org/10.1101/2022.06.04.492470",
    doi = "10.1101/2022.06.04.492470",
    openalex = "W4281693793",
    references = "schmidt2020evolution"
}