Vertebrate evolution

@book{colbert1955evolution1,
    author = "Colbert, E. H",
    title = "Evolution of the Vertebrates [1st ed.]",
    year = "1955",
    publisher = "New York, Wiley and Sons, Inc",
    note = "talkorigins\_source = {true}; raw\_reference = {Colbert, E. H., 1955, Evolution of the Vertebrates [1st ed.]: New York, Wiley and Sons, Inc.}"
}

@article{bennett1968vertebrates,
    author = "Bennett, Jack",
    title = "Vertebrates Structure and Habit in Vertebrate Evolution G. S. Carter",
    year = "1968",
    journal = "BioScience",
    url = "https://doi.org/10.2307/1294206",
    doi = "10.2307/1294206",
    number = "7",
    pages = "741-741",
    volume = "18"
}

@misc{ebbesson1972a2,
    author = "Ebbesson, S. O. E",
    title = "A proposal for a common nomenclature for some optic nuclei in vertebrates and the evidence for a common origin of two such cell groups",
    year = "1972",
    howpublished = "Brain, Behavior and Evolution, v. 6, p. 75-91",
    note = "talkorigins\_source = {true}; raw\_reference = {Ebbesson, S. O. E., 1972, A proposal for a common nomenclature for some optic nuclei in vertebrates and the evidence for a common origin of two such cell groups: Brain, Behavior and Evolution, v. 6, p. 75-91.}"
}

@article{crossref1975structure,
    title = "Structure and Evolution of Vertebrates: A Laboratory Text for Comparative Vertebrate Anatomy Alan Feduccia",
    year = "1975",
    journal = "The American Biology Teacher",
    url = "https://doi.org/10.2307/4445299",
    doi = "10.2307/4445299",
    number = "6",
    pages = "379-379",
    volume = "37"
}

@misc{ebbesson1976neurology3,
    author = "Ebbesson, S. O. E. and Northcutt, R. G",
    title = "Neurology of Anamniotic Vertebrates, in Masterson, R. B., Campbell, C. B. G., Bitterman, M. E., and Hotton, N., eds., Evolution of the Brain and Behavior in Vertebrates",
    year = "1976",
    howpublished = "Hillsdale, New Jersey, Erlbaum",
    note = "talkorigins\_source = {true}; raw\_reference = {Ebbesson, S. O. E., and Northcutt, R. G., 1976, Neurology of Anamniotic Vertebrates, in Masterson, R. B., Campbell, C. B. G., Bitterman, M. E., and Hotton, N., eds., Evolution of the Brain and Behavior in Vertebrates: Hillsdale, New Jersey, Erlbaum.}"
}

@inproceedings{whiting1977cranial5,
    author = "Whiting, H. P",
    title = "Cranial Anatomy of the Ostracoderms in Relation to the Organisation of Larval Lampreys, in Andrews, S. M., Miles, R. S., and Walker, A. D., eds., Problems in Vertebrate Evolution",
    year = "1977",
    booktitle = "Essays Presented to Professor T.S. Westoll, F.R.S., F.L.S, 4 of Linnean Society Symposium Series: London, Academic Press, p. 1-23",
    note = "talkorigins\_source = {true}; raw\_reference = {Whiting, H. P., 1977, Cranial Anatomy of the Ostracoderms in Relation to the Organisation of Larval Lampreys, in Andrews, S. M., Miles, R. S., and Walker, A. D., eds., Problems in Vertebrate Evolution: Essays Presented to Professor T.S. Westoll, F.R.S., F.L.S, 4 of Linnean Society Symposium Series: London, Academic Press, p. 1-23.}"
}

@book{jarvik198019814,
    author = "Jarvik, E",
    title = "1981, Basic Structure and Evolution of Vertebrates",
    year = "1980",
    publisher = "London, Academic Press; 2 Volumes",
    note = "talkorigins\_source = {true}; raw\_reference = {Jarvik, E., 1980, 1981, Basic Structure and Evolution of Vertebrates: London, Academic Press; 2 Volumes.}"
}

@article{ballard1982major,
    author = "Ballard, W. W.",
    title = "Major Review of Vertebrate Evolution Basic Structure and Evolution of Vertebrates Erik Jarvik",
    year = "1982",
    journal = "BioScience",
    url = "https://doi.org/10.2307/1308861",
    doi = "10.2307/1308861",
    number = "5",
    pages = "347-347",
    volume = "32"
}

Living jawed vertebrates can be readily assigned to two major well-supported clades: the cartilaginous Chondrichthyes (sharks and their kin) and the ‘bony fishes’, the Osteichthyes (which include tetrapods, and to which humans belong). Together, these make up the crown group Gnathostomata. Chondrichthyes and Osteichthyes shared a most recent common ancestor no less than 423 million years ago, allowing ample time for the living members of these groups to diverge and acquire new characters and character states, and resulting in a lack of clarity regarding the ancestral conditions of Gnathostomata as a whole. The assignment of fossil taxa to the osteichthyan, chondrichthyan, and gnathostome stem groups is necessary to understand the ancestral conditions and evolutionary origins of these vertebrates, but determining the phylogenetic relationships of Paleozoic gnathostomes presents a challenge, exacerbated by a relative dearth of well-preserved fossil material from the Silurian and Early Devonian. The Man On The Hill (MOTH) locality in the Northwest Territories of Canada has yielded beautifully preserved fossils of Early Devonian gnathostomes, providing a unique opportunity to investigate their diversity and adding new data to formulate and test hypotheses of evolutionary relationships. In particular, MOTH is one of the only fossil sites in the world to preserve articulated skeletons of an enigmatic group of fishes known as acanthodians. Recently, acanthodians have received increased attention, as they represent a likely sister group to the Chondrichthyes. In this phylogenetic context, acanthodian features may provide insight into the primitive characters of Chondrichthyes, and possibly the primitive conditions for Gnathostomata. This thesis provides a comprehensive study of acanthodian fossils, particularly those belonging to the order of acanthodians called Ischnacanthiformes. This group is particularly poorly known, being represented primarily by isolated jaw bones. As a part of this study, four new genera comprising six new species of ischnacanthiform acanthodians are described, greatly increasing our comprehension of the diversity of the group. The presence of several closely related species coexisting in a relatively restricted geographic area has been hypothesized to indicate trophic niche partitioning; this hypothesis is indirectly tested here through the use of three-dimensional reconstructions of articulated pairs of jaws, revealing different styles of occlusion and feeding mechanics in different species of ischnacanthiforms from MOTH. The differences in jaw occlusion as well as in patterns of tooth wear support the hypothesized trophic niche differentiation among ischnacanthiform species from MOTH, and suggests that rather than being indiscriminate generalist predators, at least some of these early jawed vertebrates may have specialized in capture and processing of preferred prey items. Previously unidentified morphological and histological structures are also described from MOTH acanthodians, with comments on the potential phylogenetic implications of these discoveries. A new hypothesis is proposed for the mechanism of jaw bone growth and tooth attachment in ischnacanthiform acanthodians. In providing some insight into the diversity, ecology, and evolutionary history of the Ischnacanthiformes, I hope to have provided a better picture not only of their phylogenetic affinities, but also of the ancient world in which these animals lived, and how they may have interacted with their environment and with each other.

@phdthesis{blais2015ischnacanthiform,
    author = "Blais, Stephanie A.",
    title = "Ischnacanthiform dentitions and the origin and evolution of vertebrate teeth",
    year = "2015",
    publisher = "University of Alberta Library",
    abstract = "Living jawed vertebrates can be readily assigned to two major well-supported clades: the cartilaginous Chondrichthyes (sharks and their kin) and the ‘bony fishes’, the Osteichthyes (which include tetrapods, and to which humans belong). Together, these make up the crown group Gnathostomata. Chondrichthyes and Osteichthyes shared a most recent common ancestor no less than 423 million years ago, allowing ample time for the living members of these groups to diverge and acquire new characters and character states, and resulting in a lack of clarity regarding the ancestral conditions of Gnathostomata as a whole. The assignment of fossil taxa to the osteichthyan, chondrichthyan, and gnathostome stem groups is necessary to understand the ancestral conditions and evolutionary origins of these vertebrates, but determining the phylogenetic relationships of Paleozoic gnathostomes presents a challenge, exacerbated by a relative dearth of well-preserved fossil material from the Silurian and Early Devonian. The Man On The Hill (MOTH) locality in the Northwest Territories of Canada has yielded beautifully preserved fossils of Early Devonian gnathostomes, providing a unique opportunity to investigate their diversity and adding new data to formulate and test hypotheses of evolutionary relationships. In particular, MOTH is one of the only fossil sites in the world to preserve articulated skeletons of an enigmatic group of fishes known as acanthodians. Recently, acanthodians have received increased attention, as they represent a likely sister group to the Chondrichthyes. In this phylogenetic context, acanthodian features may provide insight into the primitive characters of Chondrichthyes, and possibly the primitive conditions for Gnathostomata. This thesis provides a comprehensive study of acanthodian fossils, particularly those belonging to the order of acanthodians called Ischnacanthiformes. This group is particularly poorly known, being represented primarily by isolated jaw bones. As a part of this study, four new genera comprising six new species of ischnacanthiform acanthodians are described, greatly increasing our comprehension of the diversity of the group. The presence of several closely related species coexisting in a relatively restricted geographic area has been hypothesized to indicate trophic niche partitioning; this hypothesis is indirectly tested here through the use of three-dimensional reconstructions of articulated pairs of jaws, revealing different styles of occlusion and feeding mechanics in different species of ischnacanthiforms from MOTH. The differences in jaw occlusion as well as in patterns of tooth wear support the hypothesized trophic niche differentiation among ischnacanthiform species from MOTH, and suggests that rather than being indiscriminate generalist predators, at least some of these early jawed vertebrates may have specialized in capture and processing of preferred prey items. Previously unidentified morphological and histological structures are also described from MOTH acanthodians, with comments on the potential phylogenetic implications of these discoveries. A new hypothesis is proposed for the mechanism of jaw bone growth and tooth attachment in ischnacanthiform acanthodians. In providing some insight into the diversity, ecology, and evolutionary history of the Ischnacanthiformes, I hope to have provided a better picture not only of their phylogenetic affinities, but also of the ancient world in which these animals lived, and how they may have interacted with their environment and with each other.",
    url = "https://ualberta.scholaris.ca/handle/123456789/100929",
    doi = "10.7939/r3c24r27v"
}

@incollection{bels2019feeding,
    author = "Bels, Vincent and Herrel, Anthony",
    title = "Feeding, a Tool to Understand Vertebrate Evolution Introduction to “Feeding in Vertebrates”",
    year = "2019",
    booktitle = "Fascinating Life Sciences",
    url = "https://doi.org/10.1007/978-3-030-13739-7\_1",
    doi = "10.1007/978-3-030-13739-7\_1",
    pages = "1-18"
}

A disparate range in eye complexity exists between vertebrates and their sister group, tunicates. In tunicates, “eyes” take the shape of simple shadow-detecting photoreceptive patches, while vertebrates possess one of the most intricate and complex eyes seen in the animal kingdom. We do not yet know how the complex vertebrate eye could have arisen from a highly simplified eye structure in the shared ancestor with tunicates. With no extant transitionary forms between tunicates and vertebrates, we must use the earliest diverging vertebrates to better understand the evolutionary history of vertebrate eyes. Hagfish are one of two surviving jawless fish lineages, and so represent one of the earliest examples of vertebrate eyes. Despite being vertebrates, hagfish lack many of the conserved vertebrate eye features that are conserved from lamprey to humans. Their eye is unpigmented, obscured by a transparent epidermis, and lacks a three-layered retina, lens, and ocular musculature. This makes hagfish a unique case in vertebrate evolution. The cause of this simplicity has been explained by several different potential histories. One school of thought is that the rudimentary features can be thought of as ancestral, meaning that the hagfish eye represents an early stage in vertebrate eye evolution that existed prior to the evolution of the typical vertebrate camera-style eye. However, this hypothesis indirectly suggests that lamprey evolved their eye in parallel with jawed vertebrates, which is in opposition to a number of molecular phylogenetic studies. Our competing hypothesis conversely suggests that these rudimentary features are a result of regression from an ancestrally complex eye. Very little molecular data exist to characterize the eyes of hagfish, and so we set out to test our hypothesis by defining the molecular characters of the retina of the Pacific hagfish (Epatatretus stouii). In order to do this, we produced a hagfish eye transcriptome from which we pulled a iii number of novel transcripts including homologs of retinoid cycling genes (RPE65, LRAT, and others) and interneuron markers (PKC-a, calbindin, Pax6 and others). By in situ hybridization, we were able to localize the expression of several of these novel transcripts to regions of the hagfish retina homologous with those in other vertebrates. Identification of these novel transcripts revealed the presence of a greater diversity of cell types within the retina than previously characterized, including the first evidence of interneurons and a supporting functional retinal epithelium. The presence of these features in conjunction with the presence of these features in lamprey and jawed vertebrates, suggests that hagfish eyes share a highly conserved eye with other vertebrates. Our work to identify novel features of the hagfish retina has opened the door to a number of future studies and provided substantial evidence to support the degenerative eye hypothesis.

@phdthesis{dong2019novel,
    author = "Dong, Emily M",
    title = "Novel vertebrate features identified in the rudimentary eye of the Pacific hagfish (Eptatretus stoutii)",
    year = "2019",
    publisher = "University of Alberta Library",
    abstract = "A disparate range in eye complexity exists between vertebrates and their sister group, tunicates. In tunicates, “eyes” take the shape of simple shadow-detecting photoreceptive patches, while vertebrates possess one of the most intricate and complex eyes seen in the animal kingdom. We do not yet know how the complex vertebrate eye could have arisen from a highly simplified eye structure in the shared ancestor with tunicates. With no extant transitionary forms between tunicates and vertebrates, we must use the earliest diverging vertebrates to better understand the evolutionary history of vertebrate eyes. Hagfish are one of two surviving jawless fish lineages, and so represent one of the earliest examples of vertebrate eyes. Despite being vertebrates, hagfish lack many of the conserved vertebrate eye features that are conserved from lamprey to humans. Their eye is unpigmented, obscured by a transparent epidermis, and lacks a three-layered retina, lens, and ocular musculature. This makes hagfish a unique case in vertebrate evolution. The cause of this simplicity has been explained by several different potential histories. One school of thought is that the rudimentary features can be thought of as ancestral, meaning that the hagfish eye represents an early stage in vertebrate eye evolution that existed prior to the evolution of the typical vertebrate camera-style eye. However, this hypothesis indirectly suggests that lamprey evolved their eye in parallel with jawed vertebrates, which is in opposition to a number of molecular phylogenetic studies. Our competing hypothesis conversely suggests that these rudimentary features are a result of regression from an ancestrally complex eye. Very little molecular data exist to characterize the eyes of hagfish, and so we set out to test our hypothesis by defining the molecular characters of the retina of the Pacific hagfish (Epatatretus stouii). In order to do this, we produced a hagfish eye transcriptome from which we pulled a iii number of novel transcripts including homologs of retinoid cycling genes (RPE65, LRAT, and others) and interneuron markers (PKC-a, calbindin, Pax6 and others). By in situ hybridization, we were able to localize the expression of several of these novel transcripts to regions of the hagfish retina homologous with those in other vertebrates. Identification of these novel transcripts revealed the presence of a greater diversity of cell types within the retina than previously characterized, including the first evidence of interneurons and a supporting functional retinal epithelium. The presence of these features in conjunction with the presence of these features in lamprey and jawed vertebrates, suggests that hagfish eyes share a highly conserved eye with other vertebrates. Our work to identify novel features of the hagfish retina has opened the door to a number of future studies and provided substantial evidence to support the degenerative eye hypothesis.",
    url = "https://ualberta.scholaris.ca/handle/123456789/102391",
    doi = "10.7939/r3-399z-y395"
}

The vertebrate retina is a vital sensory structure that has a murky evolutionary origin. Living vertebrates possess a strikingly complex retina and eye with highly conserved development and physiology. In contrast, the photoreceptive organs of the closest non-vertebrate relatives are comparatively simple clusters of pigment cells and photoreceptors. No extant vertebrates possess characters that are suggestive of a ‘transitional state’ that could help guide interpretations of how the eye or retina may have initially formed. However, the early-branching jawless vertebrates (Cyclostomata - hagfishes and lamprey) are in an ideal phylogenetic position to shed light upon the origin of the vertebrate eye. The eyes of cyclostomes are vastly understudied compared to the eyes of jawed vertebrates (Gnathostomata). The available literature has revealed that both hagfish and lamprey eyes contain unique features not present in other vertebrates. Hagfish eyes are particularly notable as the eye (and retina) is small and rudimentary in form. The hagfish eye lacks pigment and a lens. The retinal layers are also more disorganized than in other vertebrates. These observations have led to the interpretation that the hagfish eye could represent the ancestral vertebrate eye condition. Recent morphological and molecular studies, including data in this thesis, now suggest that many of these features in the hagfish eye are due to secondary loss rather than retention of ancestral traits. However, further investigation of the cyclostome retina will be crucial for inferring the state of the ancestral vertebrate (proto-vertebrate) eye. Although several studies have investigated the morphology of cyclostome eyes, data on development of the eye and retina are extremely limited. This is particularly true for hagfish, whose embryos are notoriously difficult to acquire. Neurodevelopmental data could provide new insights on eye evolution where morphological data from extant organisms or fossil data are lacking. Here, I provide genomic and RNA sequencing data that suggest many genes critical for gnathostome retinal development are also expressed in the hagfish eye. In addition, recent work suggests adult Pacific hagfish (Eptatretus stoutii) have continued retinal growth past embryonic development. Therefore, in this thesis I have begun to characterize the mechanisms driving retinal development in the Pacific hagfish (E. stoutii) by taking advantage of a putative proliferative zone in the adult retina. To achieve this, I applied a brief pulse of EdU to several hagfish to label proliferating cells, if any, in the retina. I also utilized bioinformatics and in situ hybridization to assess if homologs of gnathostome retinal genes also drive retinogenesis in this jawless vertebrate. I observed EdU positive cells within the retinal periphery of the hagfish (a region reminiscent of the ciliary marginal zone of gnathostomes) and within the central retina. I also found evidence that hagfish possess homologs of several key genes required for retinal neurogenesis in other vertebrates and that these genes are expressed within the hagfish eye. Finally, through in situ hybridization I demonstrated that two of these genes, OtxA and Rx (retinal homeobox), are expressed in the hagfish retina (including at the proliferative retinal periphery). This work has revealed candidate genes and mechanisms that may be involved in hagfish retinogenesis. This establishes a starting point for future studies to dissect the pathways of retinal neurogenesis in jawless vertebrates. Further efforts comparing retinal development between cyclostomes and gnathostomes are warranted, as this work has also uncovered evidence for deeply conserved mechanisms for retinogenesis within the vertebrate lineage.

@phdthesis{bradshaw2023a,
    author = "Bradshaw, Sarah",
    title = "A characterization of adult retinal neurogenesis in the Pacific hagfish (Eptatretus stoutii) to elucidate the evolutionary origins of the vertebrate retina",
    year = "2023",
    publisher = "University of Alberta Library",
    abstract = "The vertebrate retina is a vital sensory structure that has a murky evolutionary origin. Living vertebrates possess a strikingly complex retina and eye with highly conserved development and physiology. In contrast, the photoreceptive organs of the closest non-vertebrate relatives are comparatively simple clusters of pigment cells and photoreceptors. No extant vertebrates possess characters that are suggestive of a ‘transitional state’ that could help guide interpretations of how the eye or retina may have initially formed. However, the early-branching jawless vertebrates (Cyclostomata - hagfishes and lamprey) are in an ideal phylogenetic position to shed light upon the origin of the vertebrate eye. The eyes of cyclostomes are vastly understudied compared to the eyes of jawed vertebrates (Gnathostomata). The available literature has revealed that both hagfish and lamprey eyes contain unique features not present in other vertebrates. Hagfish eyes are particularly notable as the eye (and retina) is small and rudimentary in form. The hagfish eye lacks pigment and a lens. The retinal layers are also more disorganized than in other vertebrates. These observations have led to the interpretation that the hagfish eye could represent the ancestral vertebrate eye condition. Recent morphological and molecular studies, including data in this thesis, now suggest that many of these features in the hagfish eye are due to secondary loss rather than retention of ancestral traits. However, further investigation of the cyclostome retina will be crucial for inferring the state of the ancestral vertebrate (proto-vertebrate) eye. Although several studies have investigated the morphology of cyclostome eyes, data on development of the eye and retina are extremely limited. This is particularly true for hagfish, whose embryos are notoriously difficult to acquire. Neurodevelopmental data could provide new insights on eye evolution where morphological data from extant organisms or fossil data are lacking. Here, I provide genomic and RNA sequencing data that suggest many genes critical for gnathostome retinal development are also expressed in the hagfish eye. In addition, recent work suggests adult Pacific hagfish (Eptatretus stoutii) have continued retinal growth past embryonic development. Therefore, in this thesis I have begun to characterize the mechanisms driving retinal development in the Pacific hagfish (E. stoutii) by taking advantage of a putative proliferative zone in the adult retina. To achieve this, I applied a brief pulse of EdU to several hagfish to label proliferating cells, if any, in the retina. I also utilized bioinformatics and in situ hybridization to assess if homologs of gnathostome retinal genes also drive retinogenesis in this jawless vertebrate. I observed EdU positive cells within the retinal periphery of the hagfish (a region reminiscent of the ciliary marginal zone of gnathostomes) and within the central retina. I also found evidence that hagfish possess homologs of several key genes required for retinal neurogenesis in other vertebrates and that these genes are expressed within the hagfish eye. Finally, through in situ hybridization I demonstrated that two of these genes, OtxA and Rx (retinal homeobox), are expressed in the hagfish retina (including at the proliferative retinal periphery). This work has revealed candidate genes and mechanisms that may be involved in hagfish retinogenesis. This establishes a starting point for future studies to dissect the pathways of retinal neurogenesis in jawless vertebrates. Further efforts comparing retinal development between cyclostomes and gnathostomes are warranted, as this work has also uncovered evidence for deeply conserved mechanisms for retinogenesis within the vertebrate lineage.",
    url = "https://ualberta.scholaris.ca/handle/123456789/98660",
    doi = "10.7939/r3-p8k1-d090"
}

The emergence of vertebrates represents one of the most significant evolutionary transitions in animal history. The earliest definitive vertebrate fossils appear in the Lower Cambrian Period (approximately 525-520 million years ago), with Myllokunmingia fengjiaoa and Haikouichthys ercaicunensis from the Chengjiang biota of China being among the oldest known specimens. These early vertebrates evolved from chordate ancestors, likely similar to modern lancelets (amphioxus). The key transition occurred through the development of neural crest cells, a mineralized skeleton, and a more complex brain. The foundation for vertebrate origins was laid in the Pre-Cambrian with early chordates like Pikaia gracilens, which exhibited basic chordate characteristics. The early Cambrian period witnessed a rapid diversification of vertebrate forms, leading to the establishment of major vertebrate lineages, including both jawless (agnathan) and later jawed (gnathostome) groups.

@misc{montgomery2024early,
    author = "Montgomery, Richard Murdoch",
    title = "Early Origins and Evolution of Vertebrates: From Cambrian Chordates to the First Vertebrate Radiation",
    year = "2024",
    abstract = "The emergence of vertebrates represents one of the most significant evolutionary transitions in animal history. The earliest definitive vertebrate fossils appear in the Lower Cambrian Period (approximately 525-520 million years ago), with Myllokunmingia fengjiaoa and Haikouichthys ercaicunensis from the Chengjiang biota of China being among the oldest known specimens. These early vertebrates evolved from chordate ancestors, likely similar to modern lancelets (amphioxus). The key transition occurred through the development of neural crest cells, a mineralized skeleton, and a more complex brain. The foundation for vertebrate origins was laid in the Pre-Cambrian with early chordates like Pikaia gracilens, which exhibited basic chordate characteristics. The early Cambrian period witnessed a rapid diversification of vertebrate forms, leading to the establishment of major vertebrate lineages, including both jawless (agnathan) and later jawed (gnathostome) groups.",
    url = "https://doi.org/10.20944/preprints202410.2262.v1",
    doi = "10.20944/preprints202410.2262.v1"
}