These are the publications of the Neurogenetics of Vocal Communication Group

Displaying 1 - 15 of 15
  • Anijs, M., Devanna, P., & Vernes, S. C. (2022). ARHGEF39, a gene implicated in developmental language disorder, activates RHOA and is involved in cell de-adhesion and neural progenitor cell proliferation. Frontiers in Molecular Neuroscience, 15: 941494. doi:10.3389/fnmol.2022.941494.

    Abstract

    ARHGEF39 was previously implicated in developmental language disorder (DLD) via a functional polymorphism that can disrupt post-transcriptional regulation by microRNAs. ARHGEF39 is part of the family of Rho guanine nucleotide exchange factors (RhoGEFs) that activate small Rho GTPases to regulate a wide variety of cellular processes. However, little is known about the function of ARHGEF39, or how its function might contribute to neurodevelopment or related disorders. Here, we explore the molecular function of ARHGEF39 and show that it activates the Rho GTPase RHOA and that high ARHGEF39 expression in cell cultures leads to an increase of detached cells. To explore its role in neurodevelopment, we analyse published single cell RNA-sequencing data and demonstrate that ARHGEF39 is a marker gene for proliferating neural progenitor cells and that it is co-expressed with genes involved in cell division. This suggests a role for ARHGEF39 in neurogenesis in the developing brain. The co-expression of ARHGEF39 with other RHOA-regulating genes supports RHOA as substrate of ARHGEF39 in neural cells, and the involvement of RHOA in neuropsychiatric disorders highlights a potential link between ARHGEF39 and neurodevelopment and disorder. Understanding the GTPase substrate, co-expression network, and processes downstream of ARHGEF39 provide new avenues for exploring the mechanisms by which altered expression levels of ARHGEF39 may contribute to neurodevelopment and associated disorders.

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  • Doronina, L., Hughes, G. M., Moreno-Santillan, D., Lawless, C., Lonergan, T., Ryan, L., Jebb, D., Kirilenko, B. M., Korstian, J. M., Dávalos, L. M., Vernes, S. C., Myers, E. W., Teeling, E. C., Hiller, M., Jermiin, L. S., Schmitz, J., Springer, M. S., & Ray, D. A. (2022). Contradictory phylogenetic signals in the laurasiatheria anomaly zone. Genes, 13(5): 766. doi:10.3390/genes13050766.

    Abstract

    Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.
  • Formenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Ciofi, C., Crottini, A., Godoy, J. A., Höglund, J., Malukiewicz, J., Mouton, A., Oomen, R. A., Sadye, P., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Svardal, H., Theofanopoulou, C., De Vries, J. and 6 moreFormenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Ciofi, C., Crottini, A., Godoy, J. A., Höglund, J., Malukiewicz, J., Mouton, A., Oomen, R. A., Sadye, P., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Svardal, H., Theofanopoulou, C., De Vries, J., Waldvogel, A.-M., Zhang, G., Mazzoni, C. J., Jarvis, E. D., Bálint, M., & European Reference Genome Atlas (ERGA) Consortium (2022). The era of reference genomes in conservation genomics. Trends in Ecology and Evolution, 37(3), 197-202. doi:10.1016/j.tree.2021.11.008.

    Abstract

    Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
  • Hoeksema, N., Hagoort, P., & Vernes, S. C. (2022). Piecing together the building blocks of the vocal learning bat brain. In A. Ravignani, R. Asano, D. Valente, F. Ferretti, S. Hartmann, M. Hayashi, Y. Jadoul, M. Martins, Y. Oseki, E. D. Rodrigues, O. Vasileva, & S. Wacewicz (Eds.), The evolution of language: Proceedings of the Joint Conference on Language Evolution (JCoLE) (pp. 294-296). Nijmegen: Joint Conference on Language Evolution (JCoLE).
  • Vernes, S. C., Devanna, P., Hörpel, S. G., Alvarez van Tussenbroek, I., Firzlaff, U., Hagoort, P., Hiller, M., Hoeksema, N., Hughes, G. M., Lavrichenko, K., Mengede, J., Morales, A. E., & Wiesmann, M. (2022). The pale spear‐nosed bat: A neuromolecular and transgenic model for vocal learning. Annals of the New York Academy of Sciences, 1517, 125-142. doi:10.1111/nyas.14884.

    Abstract

    Vocal learning, the ability to produce modified vocalizations via learning from acoustic signals, is a key trait in the evolution of speech. While extensively studied in songbirds, mammalian models for vocal learning are rare. Bats present a promising study system given their gregarious natures, small size, and the ability of some species to be maintained in captive colonies. We utilize the pale spear-nosed bat (Phyllostomus discolor) and report advances in establishing this species as a tractable model for understanding vocal learning. We have taken an interdisciplinary approach, aiming to provide an integrated understanding across genomics (Part I), neurobiology (Part II), and transgenics (Part III). In Part I, we generated new, high-quality genome annotations of coding genes and noncoding microRNAs to facilitate functional and evolutionary studies. In Part II, we traced connections between auditory-related brain regions and reported neuroimaging to explore the structure of the brain and gene expression patterns to highlight brain regions. In Part III, we created the first successful transgenic bats by manipulating the expression of FoxP2, a speech-related gene. These interdisciplinary approaches are facilitating a mechanistic and evolutionary understanding of mammalian vocal learning and can also contribute to other areas of investigation that utilize P. discolor or bats as study species.

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    supplementary materials
  • Hoeksema, N., Villanueva, S., Mengede, J., Salazar-Casals, A., Rubio-García, A., Curcic-Blake, B., Vernes, S. C., & Ravignani, A. (2020). Neuroanatomy of the grey seal brain: Bringing pinnipeds into the neurobiological study of vocal learning. In A. Ravignani, C. Barbieri, M. Flaherty, Y. Jadoul, E. Lattenkamp, H. Little, M. Martins, K. Mudd, & T. Verhoef (Eds.), The Evolution of Language: Proceedings of the 13th International Conference (Evolang13) (pp. 162-164). Nijmegen: The Evolution of Language Conferences.
  • Hoeksema, N., Wiesmann, M., Kiliaan, A., Hagoort, P., & Vernes, S. C. (2020). Bats and the comparative neurobiology of vocal learning. In A. Ravignani, C. Barbieri, M. Flaherty, Y. Jadoul, E. Lattenkamp, H. Little, M. Martins, K. Mudd, & T. Verhoef (Eds.), The Evolution of Language: Proceedings of the 13th International Conference (Evolang13) (pp. 165-167). Nijmegen: The Evolution of Language Conferences.
  • Jebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L. S., Skirmuntt, E. C., Katzourakis, A., Burkitt-Gray, L., Ray, D. A., Sullivan, K. A. M., Roscito, J. G., Kirilenko, B. M., Dávalos, L. M., Corthals, A. P., Power, M. L., Jones, G., Ransome, R. D. and 9 moreJebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L. S., Skirmuntt, E. C., Katzourakis, A., Burkitt-Gray, L., Ray, D. A., Sullivan, K. A. M., Roscito, J. G., Kirilenko, B. M., Dávalos, L. M., Corthals, A. P., Power, M. L., Jones, G., Ransome, R. D., Dechmann, D., Locatelli, A. G., Puechmaille, S. J., Fedrigo, O., Jarvis, E. D., Hiller, M., Vernes, S. C., Myers, E. W., & Teeling, E. C. (2020). Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578-584. doi:10.1038/s41586-020-2486-3.

    Abstract

    Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease

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    41586_2020_2486_MOESM1_ESM.pdf
  • Lattenkamp, E. Z., Linnenschmidt, M., Mardus, E., Vernes, S. C., Wiegrebe, L., & Schutte, M. (2020). Impact of auditory feedback on bat vocal development. In A. Ravignani, C. Barbieri, M. Flaherty, Y. Jadoul, E. Lattenkamp, H. Little, M. Martins, K. Mudd, & T. Verhoef (Eds.), The Evolution of Language: Proceedings of the 13th International Conference (Evolang13) (pp. 249-251). Nijmegen: The Evolution of Language Conferences.
  • Lattenkamp, E. Z. (2020). Vocal learning in the pale spear-nosed bat, Phyllostomus discolor. PhD Thesis, Radboud University Nijmegen, Nijmegen.
  • Lattenkamp, E. Z., Vernes, S. C., & Wiegrebe, L. (2020). Vocal production learning in the pale spear-nosed bat, Phyllostomus discolor. Biology Letters, 16: 20190928. doi:10.1098/rsbl.2019.0928.

    Abstract

    Vocal production learning (VPL), or the ability to modify vocalizations through the imitation of sounds, is a rare trait in the animal kingdom. While humans are exceptional vocal learners, few other mammalian species share this trait. Owing to their singular ecology and lifestyle, bats are highly specialized for the precise emission and reception of acoustic signals. This specialization makes them ideal candidates for the study of vocal learning, and several bat species have previously shown evidence supportive of vocal learning. Here we use a sophisticated automated set-up and a contingency training paradigm to explore the vocal learning capacity of pale spear-nosed bats. We show that these bats are capable of directional change of the fundamental frequency of their calls according to an auditory target. With this study, we further highlight the importance of bats for the study of vocal learning and provide evidence for the VPL capacity of the pale spear-nosed bat.

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    Supplemental material dataset
  • Mengede, J., Devanna, P., Hörpel, S. G., Firzla, U., & Vernes, S. C. (2020). Studying the genetic bases of vocal learning in bats. In A. Ravignani, C. Barbieri, M. Flaherty, Y. Jadoul, E. Lattenkamp, H. Little, M. Martins, K. Mudd, & T. Verhoef (Eds.), The Evolution of Language: Proceedings of the 13th International Conference (Evolang13) (pp. 280-282). Nijmegen: The Evolution of Language Conferences.
  • Ravignani, A., Barbieri, C., Flaherty, M., Jadoul, Y., Lattenkamp, E. Z., Little, H., Martins, M., Mudd, K., & Verhoef, T. (Eds.). (2020). The Evolution of Language: Proceedings of the 13th International Conference (Evolang13). Nijmegen: The Evolution of Language Conferences. doi:10.17617/2.3190925.
  • Vernes, S. C. (2020). Understanding bat vocal learning to gain insight into speech and language. In A. Ravignani, C. Barbieri, M. Flaherty, Y. Jadoul, E. Lattenkamp, H. Little, M. Martins, K. Mudd, & T. Verhoef (Eds.), The Evolution of Language: Proceedings of the 13th International Conference (Evolang13) (pp. 6). Nijmegen: The Evolution of Language Conferences.
  • Vernes, S. C., & Wilkinson, G. S. (2020). Behaviour, biology, and evolution of vocal learning in bats. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 375(1789): 20190061. doi:10.1098/rstb.2019.0061.

    Abstract

    The comparative approach can provide insight into the evolution of human speech, language and social communication by studying relevant traits in animal systems. Bats are emerging as a model system with great potential to shed light on these processes given their learned vocalizations, close social interactions, and mammalian brains and physiology. A recent framework outlined the multiple levels of investigation needed to understand vocal learning across a broad range of non-human species, including cetaceans, pinnipeds, elephants, birds and bats. Here, we apply this framework to the current state-of-the-art in bat research. This encompasses our understanding of the abilities bats have displayed for vocal learning, what is known about the timing and social structure needed for such learning, and current knowledge about the prevalence of the trait across the order. It also addresses the biology (vocal tract morphology, neurobiology and genetics) and evolution of this trait. We conclude by highlighting some key questions that should be answered to advance our understanding of the biological encoding and evolution of speech and spoken communication. This article is part of the theme issue 'What can animal communication teach us about human language?'

    Additional information

    earlier version of article on BioRxiv

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