On the Typology of Relations

Mavrodiev, Evgeny V.; Williams, David M.; Ebach, Malte C.

doi:10.1007/s11692-018-9468-5

Cited by 38 publications

(6 citation statements)

References 74 publications

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“…We employ these three birds for several reasons. First, for comparative studies, a three-taxon analysis in which two taxa are more closely related than either are to a third taxon is generally accepted as a robust strategy for making the most parsimonious inferences about evolution ( Nelson and Platnick, 1991 ; Mavrodiev et al, 2019 ; Rineau et al, 2020 ). As Galliformes, chick and quail are closely related to each other phylogenetically (separated by around 50 million years) and they diverged from a common ancestor with Anseriformes, which include duck, over 100 million years ago ( Pereira and Baker, 2006 ; Hackett et al, 2008 ; Kan et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Smith

Chu

et al. 2022

eLife

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Precise developmental control of jaw length is critical for survival, but underlying molecular mechanisms remain poorly understood. The jaw skeleton arises from neural crest mesenchyme (NCM), and we previously demonstrated that these progenitor cells express more bone-resorbing enzymes including Matrix metalloproteinase 13 (Mmp13) when they generate shorter jaws in quail embryos versus longer jaws in duck. Moreover, if we inhibit bone resorption or Mmp13, we can increase jaw length. In the current study, we uncover mechanisms establishing species-specific levels of Mmp13 and bone resorption. Quail show greater activation of, and sensitivity to Transforming Growth Factor-Beta (TGFβ) signaling than duck; where mediators like SMADs and targets like Runx2, which bind Mmp13, become elevated. Inhibiting TGFβ signaling decreases bone resorption and overexpressing Mmp13 in NCM shortens the duck lower jaw. To elucidate the basis for this differential regulation we examine the Mmp13 promoter. We discover a SMAD binding element and single nucleotide polymorphisms (SNPs) near a RUNX2 binding element that distinguish quail from duck. Altering the SMAD site and switching the SNPs abolishes TGFβ-sensitivity in the quail Mmp13 promoter but makes the duck promoter responsive. Thus, differential regulation of TGFβ signaling and Mmp13 promoter structure underlie avian jaw development and evolution.

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Section: Introductionmentioning

confidence: 99%

Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Smith

Chu

et al. 2022

eLife

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“…Our goal is to distinguish between domains that are variable or conserved. Then we perform a series of in vitro and in vivo functional analyses of Runx2 primarily using a three-taxon comparison in which two taxa are more closely related than either are to a third, since this is considered a robust strategy for making parsimonious inferences about evolution (Nelson and Platnick, 1991;Mavrodiev et al, 2019;Rineau et al, 2020). We exploit duck, chick, and quail in particular, because their jaw skeletons differ in size (from relatively large to small), their genomes are sequenced and annotated, and their embryos can be easily matched using the Hamburger and Hamilton (HH) staging system (Hamburger and Hamilton, 1951;Koecke, 1958;Padgett and Ivey, 1960;Zacchei, 1961;Hamilton, 1965;Yamashita and Sohal, 1987;Le Douarin et al, 1996;Ricklefs and Starck, 1998;Starck and Ricklefs, 1998;Nakane and Tsudzuki, 1999;Schneider and Helms, 2003;Stern, 2005;Lwigale and Schneider, 2008;Sauka-Spengler and Barembaum, 2008;Jheon and Schneider, 2009;Ainsworth et al, 2010;Mitgutsch et al, 2011;Fish and Schneider, 2014a;Gammill et al, 2019;Chu et al, 2020;Smith et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution

Smith

Chu

et al. 2021

Preprint

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Developmental regulation of bone formation in the jaw skeleton is essential to species-specific adaptation. The jaws are derived from neural crest mesenchyme (NCM), a progenitor population that directs skeletal patterning by exerting temporal and spatial control over molecular and cellular programs for osteogenesis. One important NCM-mediated gene is Runx2, which is a transcription factor required for osteoblast differentiation. RUNX2 protein binds many target genes involved in the deposition and resorption of bone. To determine the extent to which changes in Runx2 structure, function, and expression underlie the evolution of the jaw skeleton, we compare Runx2 across vertebrates and within birds. Runx2 contains two alternative promoters, tandem repeats of glutamine and alanine with variable lengths in different species, a conserved DNA-binding domain, an exon that is alternatively spliced, as well as two possible C-termini. Such alternative splicing produces eight potential isoforms that show distinct stage- and species-specific patterns in the jaw primordia of chick, quail and duck embryos. We also find that certain isoforms are strongly induced by TGFβ signaling whereas others are not. Overexpressing Runx2 isoforms in NCM reveals that some are transcriptionally activating, while others are repressive. But context appears to be relevant since species-specific polymorphisms in the promoter of target genes like Mmp13, can modulate the effects of different isoforms. Overall, our study indicates that the structure and species-specific deployment of Runx2 isoforms affect the transcriptional activity of target genes in ways that may have played a generative and regulatory role in the evolution of the avian jaw skeleton.

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“…One of these most fundamental debates approaches the question of characters. Many authors questioned the nature of phylogenetic data (Pimentel & Riggins, 1987), their formalism (Sereno, 2007), and their representation (Cao et al, 2007;Mavrodiev et al, 2019;Prin, 2012;Williams & Ebach, 2006).…”

Section: Introduc�onmentioning

confidence: 99%

“…Our hypothesis is that the issues raised by Pleijel are caused by the use of partitions as structures for the representation of phylogenetic characters. Indeed, some authors have already shown that the conventional data matrix is incapable of effectively containing hypotheses of phylogenetic traits (Cao et al, 2007;Mavrodiev et al, 2019;Williams & Ebach, 2006). Moreover, Cao et al (2007) identified the problem not as the data matrix itself, but as its partitional structure and proposed a model of matrix able to contain information in another kind of mathematical structure: hierarchies.…”

Section: Introduc�onmentioning

confidence: 99%

Rethinking Pleijel’s (1995) characters under a hierarchical point of view

Faure‐Brac¹,

Rineau²,

Bagils³

2020

Preprint

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In 1995, Pleijel raised an issue on the coding of complex (multistate) characters: to find a unique coding approach satisfying both informational and semantical criteria. Following Pleijel′s work, this study aims to propose a new answer to this problematic. We proposed here to use hierarchical characters instead of classical partitional ones as hierarchy allows to deal effectively with the different uncertainties met by phylogeneticists since the beginning of phylogenetic data matrices: missing data, inapplicable data and polymorphism. We translated all previous proposed approaches into hierarchical ones and add three new approaches, only coded using hierarchy. Using phylogenetic and show with different metric how one of these new approaches displaces the other ones. The results from this study then supports the idea than phylogenetic characters should be coded using only hierarchies, as they offer a better management of uncertainties and propose new approaches more informative.

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On the Typology of Relations

Cited by 38 publications

References 74 publications

Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution

Rethinking Pleijel’s (1995) characters under a hierarchical point of view

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