Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date; after six months, it is available under a Creative Commons License.-- et al.The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought—involving ∼12% of the ancestral bilaterian genome—and that cis-regulatory constraints are crucial in determining metazoan genome architecture.M.I., M.S.A., S.W.R., and H.B.F. were funded by NIH grant 1R21HG005240-01A1. H.B.F. is an Alfred P. Sloan Fellow and Pew Scholar in the Biomedical Sciences. J.J.T., A.F-M., O.B., E.C-M., and J.L.G-S. were funded by grants BFU2010-14839, CSD2007-00008, and Proyecto de Excelencia CVI-3488.Peer reviewe

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No ERC-StG-LS2-637591 to M.I.), the Spanish Ministry of Economy and Competitiveness (grant BFU2014-58908P to J.G.-F, BFU2014-55076-P to M.I., and the 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208), and ICREA - Generalitat de Catalunya (Academia Prize to J.G.-F). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya. D.B. held an APIF fellowship from University of Barcelona, Y.M. an EMBO Long Term postdoctoral fellowship (ALTF 1505-2015), C.R. an EMBO long-term fellowship (ALTF 1608-2014), ATM an FPI-SO fellowship

A half century of Romance linguistics: Selected proceedings of the 50th Linguistic Symposium on Romance Languages

The present volume presents a selection of the revised and peer-reviewed proceedings articles of the 50th Linguistic Symposium on Romance Languages (LSRL 50) which was hosted virtually by the faculty and students from the University of Texas at Austin. With contributions from rising and senior scholars from Europe and the Americas, the volume demonstrates the breadth of research in contemporary Romance linguistics with articles that apply corpus-based and laboratory methods, as well as theory, to explore the structure, use, and development of the Romance languages. The articles cover a wide range of fields including morphosyntax, semantics, language variation and change, sociophonetics, historical linguistics, language acquisition, and computational linguistics. In an introductory article, the editors document the sudden transition of LSRL 50 to a virtual format and acknowledge those who helped them to ensure the continuity of this annual scholarly meeting

A half century of Romance linguistics: Selected proceedings of the 50th Linguistic Symposium on Romance Languages

The present volume presents a selection of the revised and peer-reviewed proceedings articles of the 50th Linguistic Symposium on Romance Languages (LSRL 50) which was hosted virtually by the faculty and students from the University of Texas at Austin. With contributions from rising and senior scholars from Europe and the Americas, the volume demonstrates the breadth of research in contemporary Romance linguistics with articles that apply corpus-based and laboratory methods, as well as theory, to explore the structure, use, and development of the Romance languages. The articles cover a wide range of fields including morphosyntax, semantics, language variation and change, sociophonetics, historical linguistics, language acquisition, and computational linguistics. In an introductory article, the editors document the sudden transition of LSRL 50 to a virtual format and acknowledge those who helped them to ensure the continuity of this annual scholarly meeting

A half century of Romance linguistics: Selected proceedings of the 50th Linguistic Symposium on Romance Languages

The present volume presents a selection of the revised and peer-reviewed proceedings articles of the 50th Linguistic Symposium on Romance Languages (LSRL 50) which was hosted virtually by the faculty and students from the University of Texas at Austin. With contributions from rising and senior scholars from Europe and the Americas, the volume demonstrates the breadth of research in contemporary Romance linguistics with articles that apply corpus-based and laboratory methods, as well as theory, to explore the structure, use, and development of the Romance languages. The articles cover a wide range of fields including morphosyntax, semantics, language variation and change, sociophonetics, historical linguistics, language acquisition, and computational linguistics. In an introductory article, the editors document the sudden transition of LSRL 50 to a virtual format and acknowledge those who helped them to ensure the continuity of this annual scholarly meeting

A half century of Romance linguistics: Selected proceedings of the 50th Linguistic Symposium on Romance Languages

The present volume presents a selection of the revised and peer-reviewed proceedings articles of the 50th Linguistic Symposium on Romance Languages (LSRL 50) which was hosted virtually by the faculty and students from the University of Texas at Austin. With contributions from rising and senior scholars from Europe and the Americas, the volume demonstrates the breadth of research in contemporary Romance linguistics with articles that apply corpus-based and laboratory methods, as well as theory, to explore the structure, use, and development of the Romance languages. The articles cover a wide range of fields including morphosyntax, semantics, language variation and change, sociophonetics, historical linguistics, language acquisition, and computational linguistics. In an introductory article, the editors document the sudden transition of LSRL 50 to a virtual format and acknowledge those who helped them to ensure the continuity of this annual scholarly meeting

A half century of Romance linguistics: Selected proceedings of the 50th Linguistic Symposium on Romance Languages

The present volume presents a selection of the revised and peer-reviewed proceedings articles of the 50th Linguistic Symposium on Romance Languages (LSRL 50) which was hosted virtually by the faculty and students from the University of Texas at Austin. With contributions from rising and senior scholars from Europe and the Americas, the volume demonstrates the breadth of research in contemporary Romance linguistics with articles that apply corpus-based and laboratory methods, as well as theory, to explore the structure, use, and development of the Romance languages. The articles cover a wide range of fields including morphosyntax, semantics, language variation and change, sociophonetics, historical linguistics, language acquisition, and computational linguistics. In an introductory article, the editors document the sudden transition of LSRL 50 to a virtual format and acknowledge those who helped them to ensure the continuity of this annual scholarly meeting. The proceedings can be found at the publisher website: http://langsci-press.org/catalog/book/369Table of Contents: Acknowledgements (p. iii) -- The digital transformation of the LSRL: The first 50 years of Romance linguistics in the Americas ends virtually / by Barbara E. Bullock, Cinzia Russi & Almeida Jacqueline Toribio (p. v) -- For an integrative approach to variation and change in French nasal vowel systems / by Zsuzsanna Fagyal (p. 1) -- Assessing change in a Gallo-Romance regional minority language: 1PL verbal morphology and referential restriction in Picard / by Julie Auger & Anne-José Villeneuve (p. 21) -- The partial loss of free inversion and of referential null subjects in Brazilian Portuguese / by Mary A. Kato & Maria Eugenia Lammoglia Duarte (p. 41) -- The antipassive as a Romance phenomenon: A case study of Italian / by Karina High (p. 63) -- The role of SE in Spanish agreement variation / by Irene Fernández-Serrano (p. 85) -- Object control into temporal adjuncts: The case of Spanish clitics / by Katie VanDyne (p. 107) -- Overt vs. null subjects in infinitival constructions in Colombian Spanish / by Kryzzya Gómez, Maia Duguine & Hamida Demirdache (p. 131) -- Oblique DOM and co-occurrence restrictions: How many types? / by Monica Alexandrina Irimia (p. 157) -- A superlative challenge for a syntactic account of connectivity sentences / by Nicoletta Loccioni (p. 181) -- Revisiting sociophonetic competence: Variable spectral moments in phrase-final fricative epithesis for L1 & L2 speakers of French / by Amanda Dalola & Keiko Bridwell (p. 195) -- Does social identity play a role in the L2 acquisition of French intonation? Preliminary data from Canadian French-as-a-second-language classroom learners / by Hilary Walton (p. 221) -- Sociophonetic analysis of mid front vowel production in Barcelona / by Annie Helms (p. 249) -- Prosodic correlates of mirative and new information focus in Spanish wh-in-situ questions / by Carolina González & Lara Reglero (p. 269) -- Mechanical vs. functional processes in subject pronoun expression in Spanish second language learners / by Ana de Prada Pérez & Nick Feroce (p. 299) -- Frequency and efficiency in Spanish proverbs / by Ernesto R. Gutiérrez Topete (p. 323) -- Index (p. 347)Linguistic