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[dinosaur] Fish-to-tetrapod transition + squamate genomes + reptile embryo development + more




Ben Creisler
bcreisler@gmail.com


Some recent non-dino papers that may be of interest:


Free pdf:

Thomas W. P. Wood and Tetsuya Nakamura (2018)
Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens.
Frontiers in Cell and Developmental Biology 6:70
doi: 10.3389/fcell.2018
https://www.frontiersin.org/articles/10.3389/fcell.2018.00070/full


The fish-to-tetrapod transition is one of the fundamental problems in evolutionary biology. A significant amount of paleontological data has revealed the morphological trajectories of skeletons, such as those of the skull, vertebrae, and appendages in vertebrate history. Shifts in bone differentiation, from dermal to endochondral bones, are key to explaining skeletal transformations during the transition from water to land. However, the genetic underpinnings underlying the evolution of dermal and endochondral bones are largely missing. Recent genetic approaches utilizing model organismsâzebrafish, frogs, chickens, and miceâreveal the molecular mechanisms underlying vertebrate skeletal development and provide new insights for how the skeletal system has evolved. Currently, our experimental horizons to test evolutionary hypotheses are being expanded to non-model organisms with state-of-the-art techniques in molecular biology and imaging. An integration of functional genomics, developmental genetics, and high-resolution CT scanning into evolutionary inquiries allows us to reevaluate our understanding of old specimens. Here, we summarize the current perspectives in genetic programs underlying the development and evolution of the dermal skull roof, shoulder girdle, and appendages. The ratio shifts of dermal and endochondral bones, and its underlying mechanisms, during the fish-to-tetrapod transition are particularly emphasized. Recent studies have suggested the novel cell origins of dermal bones, and the interchangeability between dermal and endochondral bones, obscuring the ontogenetic distinction of these two types of bones. Assimilation of ontogenetic knowledge of dermal and endochondral bones from different structures demands revisions of the prevalent consensus in the evolutionary mechanisms of vertebrate skeletal shifts.


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Free pdf:

Giulia I. M. Pasquesi, Richard H. Adams, Daren C. Card, Drew R. Schield, Andrew B. Corbin, Blair W. Perry, Jacobo Reyes-Velasco, Robert P. Ruggiero, Michael W. Vandewege, Jonathan A. Shortt & Todd A. Castoe (2018)
Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals.
Nature Communications 9, Article number: 2774Â
https://doi.org/10.1038/s41467-018-05279-1
https://www.nature.com/articles/s41467-018-05279-1
https://www.nature.com/articles/s41467-018-05279-1.pdf


Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25â73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny.

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Free pdf:

Daniel W. A. Noble, Vaughn Stenhouse, Julia L. Riley, Daniel A. Warner, Geoffrey M. While, Wei-Guo Du, Tobias Uller & Lisa E. Schwanz (2018)
A comprehensive database of thermal developmental plasticity in reptiles.
Scientific Data volume 5, Article number: 180138Â
https://www.nature.com/articles/sdata2018138
https://www.nature.com/articles/sdata2018138.pdf


How temperature influences development has direct relevance to ascertaining the impact of climate change on natural populations. Reptiles have served as empirical models for understanding how the environment experienced by embryos can influence phenotypic variation, including sex ratio, phenology and survival. Such an understanding has important implications for basic eco-evolutionary theory and conservation efforts worldwide. While there is a burgeoning empirical literature of experimental manipulations of embryonic thermal environments, addressing widespread patterns at a comparative level has been hampered by the lack of accessible data in a format that is amendable to updates as new studies emerge. Here, we describe a database with nearly 10, 000 phenotypic estimates from 155 species of reptile, collected from 300 studies manipulating incubation temperature (published between 1974â2016). The data encompass various morphological, physiological, behavioural and performance traits along with growth rates, developmental timing, sex ratio and survival (e.g., hatching success). This resource will serve as an important data repository for addressing overarching questions about thermal plasticity of reptile embryos.


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Free pdf:


JiÅàMoravec, JiÅà ÅmÃd, Jan Åtundl, & Edgar Lehr (2018)
Systematics of Neotropical microteiid lizards (Gymnophthalmidae, Cercosaurinae), with the description of a new genus and species from the Andean montane forests.Â
ZooKeys 774: 105-139
doi:Â https://doi.org/10.3897/zookeys.774.25332
https://ipc5.sciencesconf.org/data/pages/scientific_sessions_IPC5.pdf


Cercosaurine lizards (subfamily Cercosaurinae of the family Gymnophthalmidae) represent a substantial component of the reptile fauna in the Neotropics. Several attempts have been made to reconstruct the phylogenetic relationships within this group, but most studies focused on particular genera or regions and did not cover the subfamily as a whole. In this study, material from the montane forests of Peru was newly sequenced. In combination with all cercosaurine sequences available on GenBank, an updated phylogeny of Cercosaurinae is provided. Monophyly was not supported for three of the currently recognised genera (Echinosaura, Oreosaurus, and Proctoporus). The genus Proctoporus is formed by five monophyletic groups, which should be used in future taxonomic revisions as feasible entities. Recognition of two previously identified undescribed clades (Unnamed clades 2 and 3) was supported and yet another undescribed clade (termed here Unnamed clade 4), which deserves recognition as an independent genus, was identified herein. Selvasaura brava, a new genus and new species of arboreal gymnophthalmid lizard is described from the montane forests of the Pui Pui Protected Forest, Provincia de Chanchamayo, RegiÃn JunÃn, Peru. The new species is characterised by its small size (SVL 42.1â45.9 mm), slender body, smooth head shields, presence of paired prefrontal shields, fused anteriormost supraocular and anteriormost superciliary shields, transparent not divided lower palpebral disc, slightly rugose subimbricate rectangular dorsal scales in adults (slightly keeled in juveniles), distinctly smaller but non-granular lateral scales, smooth squared to rectangular ventral scales, and hemipenial lobes large, distinct from the hemipenial body. Phylogenetic affinities of the new genus to the other cercosaurine genera, as well as basal phylogenetic relationships between the other cercosaurine genera remain unresolved.


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Rachel A. Settle, Jeffrey T. Briggler & Alicia Mathis (2018)
A quantitative field study of paternal care in Ozark hellbenders, North Americaâs giant salamanders.
Journal of Ethology (advance online publication)
DOI: https://doi.org/10.1007/s10164-018-0553-0
https://link.springer.com/article/10.1007/s10164-018-0553-0


Paternal care is relatively uncommon in tetrapods but appears to be the rule in the large aquatic salamanders of the primitive family Cryptobranchidae (North America: hellbenders, genus Cryptobranchus; Asia: giant salamanders, genus Andrias). For the Ozark hellbender, C. alleganiensis bishopi, a federally endangered subspecies, anecdotal observations of paternal care have been reported, but no quantitative assessments have been made. We quantified behavior of a guarding male hellbender from video footage collected over 6 weeks in 2008 from a naturally occurring nest. We quantified behavior of the guarding male to help develop hypotheses about costs and benefits of paternal care. Overall, there were high frequencies of tail fanning of the eggs and rocking behaviors (rhythmic, lateral back-and-forth movements of the body), which increase aeration of the nest. The male rarely left the nest unguarded and spent over half of the recorded time at the nest exposed at the nest entrance. Potential egg predators observed included centrarchid, cyprinid, ictalurid, and percid fishes, with centrarchids being the most common and exhibiting the most interest in the nest. The frequency of foraging by the male was low (nâ=â8 strikes at identifiable prey), with a 37% success rate. The male was observed to consume seven of his eggs. Our data represent the first systematic analysis of paternal care of Ozark hellbenders and elucidate some of the costs (low foraging success, potential energetic costs of tail fanning and rocking) and benefits (aeration of eggs, protection from egg predators) of paternal care.


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Marion Chevrinais, Zerina Johanson, Kate Trinajstic, John Long, Catherine Morel, Claude B. Renaud & Richard Cloutier (2018)
Evolution of vertebrate postcranial complexity: axial skeleton regionalization and paired appendages in a Devonian jawless fish.
Palaeontology (advance online publication)
doi: https://doi.org/10.1111/pala.12379
https://onlinelibrary.wiley.com/doi/10.1111/pala.12379


One of the major events in vertebrate evolution involves the transition from jawless (agnathan) to jawed (gnathostome) vertebrates, including a variety of cranial and postcranial innovations. It has long been assumed that characters such as the pelvic girdles and fins, male intromittent organs independent from the pelvic girdles, as well as a regionalized axial skeleton first appeared in various basal gnathostome groups if not at the origin of gnathostomes. Here we describe the first occurrence of pelvic girdles and intromittent organs in the Late Devonian jawless anaspidâlike fish Euphanerops longaevus Woodward (Miguasha LagerstÃtte, eastern Canada), associated with a morphologically differentiated region of the axial skeleton. Morphological differentiation of the axial skeleton is also described for the first time in an extant jawless fish, the sea lamprey Petromyzon marinus Linnaeus. Our data indicate that regionalization of the axial skeleton occurred earlier in vertebrate evolutionary history than previously appreciated. This regionalization is coupled with modifications of the appendicular skeleton in Euphanerops. These new observations combined with a new phylogenetic analysis of early vertebrates provide a more precise understanding of how the appendicular and axial skeletons developed and evolved within vertebrate evolutionary history.