1
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Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024; 383:eabn3263. [PMID: 38422184 PMCID: PMC11313673 DOI: 10.1126/science.abn3263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
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Affiliation(s)
- Morgan E. Wirthlin
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Tobias A. Schmid
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Julie E. Elie
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Amanda Kowalczyk
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Ruby Redlich
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Varvara A. Shvareva
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Ashley Rakuljic
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Maria B. Ji
- Department of Psychology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Ninad S. Bhat
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Irene M. Kaplow
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Daniel E. Schäffer
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Alyssa J. Lawler
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
- Department of Biological Sciences, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Andrew Z. Wang
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - BaDoi N. Phan
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Siddharth Annaldasula
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Ashley R. Brown
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Present address: Department of Biomedical Engineering, Duke University; Durham, NC 27705
| | - Tianyu Lu
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Byung Kook Lim
- Neurobiology section, Division of Biological Science, University of California, San Diego; La Jolla, CA 92093, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies; La Jolla, CA 92037, USA
| | - Nathan L. Clark
- Department of Biological Sciences, University of Pittsburgh; Pittsburgh, PA 15213, USA
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University; Bethlehem, PA 18015, USA
| | | | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh; Pittsburgh, PA 15213, USA
| | - Michael M. Yartsev
- Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94708, USA
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA 94708, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, Carnegie Mellon University; Pittsburgh, PA 15213, USA
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2
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Nevue AA, Zemel BM, Friedrich SR, von Gersdorff H, Mello CV. Cell type specializations of the vocal-motor cortex in songbirds. Cell Rep 2023; 42:113344. [PMID: 37910500 PMCID: PMC10752865 DOI: 10.1016/j.celrep.2023.113344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Identifying molecular specializations in cortical circuitry supporting complex behaviors, like learned vocalizations, requires understanding of the neuroanatomical context from which these circuits arise. In songbirds, the robust arcopallial nucleus (RA) provides descending cortical projections for fine vocal-motor control. Using single-nuclei transcriptomics and spatial gene expression mapping in zebra finches, we have defined cell types and molecular specializations that distinguish RA from adjacent regions involved in non-vocal motor and sensory processing. We describe an RA-specific projection neuron, differential inhibitory subtypes, and glia specializations and have probed predicted GABAergic interneuron subtypes electrophysiologically within RA. Several cell-specific markers arise developmentally in a sex-dependent manner. Our interactive apps integrate cellular data with developmental and spatial distribution data from the gene expression brain atlas ZEBrA. Users can explore molecular specializations of vocal-motor neurons and support cells that likely reflect adaptations key to the physiology and evolution of vocal control circuits and refined motor skills.
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Affiliation(s)
- Alexander A Nevue
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA; Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin M Zemel
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA.
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3
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Asogwa NC, Toji N, He Z, Shao C, Shibata Y, Tatsumoto S, Ishikawa H, Go Y, Wada K. Nicotinic acetylcholine receptors in a songbird brain. J Comp Neurol 2022; 530:1966-1991. [PMID: 35344610 DOI: 10.1002/cne.25314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/07/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that mediate fast synaptic transmission and cell signaling, which contribute to learning, memory, and the execution of motor skills. Birdsong is a complex learned motor skill in songbirds. Although the existence of 15 nAChR subunits has been predicted in the avian genome, their expression patterns and potential contributions to song learning and production have not been comprehensively investigated. Here, we cloned all the 15 nAChR subunits (ChrnA1-10, B2-4, D, and G) from the zebra finch brain and investigated the mRNA expression patterns in the neural pathways responsible for the learning and production of birdsong during a critical period of song learning. Although there were no detectable hybridization signals for ChrnA1, A6, A9, and A10, the other 11 nAChR subunits were uniquely expressed in one or more major subdivisions in the song nuclei of the songbird brain. Of these 11 subunits, ChrnA3-5, A7, and B2 were differentially regulated in the song nuclei compared with the surrounding anatomically related regions. ChrnA5 was upregulated during the critical period of song learning in the lateral magnocellular nucleus of the anterior nidopallium. Furthermore, single-cell RNA sequencing revealed ChrnA7 and B2 to be the major subunits expressed in neurons of the vocal motor nuclei HVC and robust nucleus of the arcopallium, indicating the potential existence of ChrnA7-homomeric and ChrnB2-heteromeric nAChRs in limited cell populations. These results suggest that relatively limited types of nAChR subunits provide functional contributions to song learning and production in songbirds.
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Affiliation(s)
| | - Noriyuki Toji
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Ziwei He
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Chengru Shao
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yukino Shibata
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hiroe Ishikawa
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- Department of Physiological Sciences, National Institute for Physiological Sciences, Okazaki, Japan
| | - Kazuhiro Wada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
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4
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Kumari R, Fazekas EA, Morvai B, Udvari EB, Dóra F, Zachar G, Székely T, Pogány Á, Dobolyi Á. Transcriptomics of Parental Care in the Hypothalamic-Septal Region of Female Zebra Finch Brain. Int J Mol Sci 2022; 23:ijms23052518. [PMID: 35269661 PMCID: PMC8910180 DOI: 10.3390/ijms23052518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
(1) Background: The objective of this study was to uncover genomic causes of parental care. Since birds do not lactate and, therefore, do not show the gene expressional changes required for lactation, we investigate gene expression associated with parenting in caring and non-caring females in an avian species, the small passerine bird zebra finch (Taeniopygia guttata). Here, we compare expression patterns in the hypothalamic–septal region since, previously, we showed that this area is activated in parenting females. (2) Methods: Transcriptome sequencing was first applied in a dissected part of the zebra finch brain related to taking care of the nestlings as compared to a control group of social pairs without nestlings. (3) Results: We found genes differentially expressed between caring and non-caring females. When introducing a log2fold change threshold of 1.5, 13 annotated genes were significantly upregulated in breeding pairs, while 39 annotated genes were downregulated. Significant enrichments of dopamine and acetylcholine biosynthetic processes were identified among upregulated pathways, while pro-opiomelanocortin and thyroid hormone pathways were downregulated, suggesting the importance of these systems in parental care. Network analysis further suggested neuro-immunological changes in mothers. (4) Conclusions: The results confirm the roles of several hypothesized major pathways in parental care, whereas novel pathways are also proposed.
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Affiliation(s)
- Rashmi Kumari
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Eötvös Loránd Network of Research Excellence and Eötvös Loránd University, 1117 Budapest, Hungary; (R.K.); (E.A.F.); (E.B.U.)
- Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Emese A. Fazekas
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Eötvös Loránd Network of Research Excellence and Eötvös Loránd University, 1117 Budapest, Hungary; (R.K.); (E.A.F.); (E.B.U.)
- Department of Ethology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.M.); (Á.P.)
| | - Boglárka Morvai
- Department of Ethology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.M.); (Á.P.)
| | - Edina B. Udvari
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Eötvös Loránd Network of Research Excellence and Eötvös Loránd University, 1117 Budapest, Hungary; (R.K.); (E.A.F.); (E.B.U.)
| | - Fanni Dóra
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1093 Budapest, Hungary; (F.D.); (G.Z.)
| | - Gergely Zachar
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1093 Budapest, Hungary; (F.D.); (G.Z.)
| | - Tamás Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK;
| | - Ákos Pogány
- Department of Ethology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.M.); (Á.P.)
| | - Árpád Dobolyi
- MTA-ELTE Laboratory of Molecular and Systems Neurobiology, Eötvös Loránd Network of Research Excellence and Eötvös Loránd University, 1117 Budapest, Hungary; (R.K.); (E.A.F.); (E.B.U.)
- Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-372-2500 (ext. 8775)
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5
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Resurgent Na + currents promote ultrafast spiking in projection neurons that drive fine motor control. Nat Commun 2021; 12:6762. [PMID: 34799550 PMCID: PMC8604930 DOI: 10.1038/s41467-021-26521-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
The underlying mechanisms that promote precise spiking in upper motor neurons controlling fine motor skills are not well understood. Here we report that projection neurons in the adult zebra finch song nucleus RA display robust high-frequency firing, ultra-narrow spike waveforms, superfast Na+ current inactivation kinetics, and large resurgent Na+ currents (INaR). These properties of songbird pallial motor neurons closely resemble those of specialized large pyramidal neurons in mammalian primary motor cortex. They emerge during the early phases of song development in males, but not females, coinciding with a complete switch of Na+ channel subunit expression from Navβ3 to Navβ4. Dynamic clamping and dialysis of Navβ4's C-terminal peptide into juvenile RA neurons provide evidence that Navβ4, and its associated INaR, promote neuronal excitability. We thus propose that INaR modulates the excitability of upper motor neurons that are required for the execution of fine motor skills.
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6
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Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. Genome Res 2021; 31:2035-2049. [PMID: 34667117 PMCID: PMC8559704 DOI: 10.1101/gr.275989.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022]
Abstract
Vocal learning, the ability to imitate sounds from conspecifics and the environment, is a key component of human spoken language and learned song in three independently evolved avian groups—oscine songbirds, parrots, and hummingbirds. Humans and each of these three bird clades exhibit specialized behavioral, neuroanatomical, and brain gene expression convergence related to vocal learning, speech, and song. To understand the evolutionary basis of vocal learning gene specializations and convergence, we searched for and identified accelerated genomic regions (ARs), a marker of positive selection, specific to vocal learning birds. We found avian vocal learner-specific ARs, and they were enriched in noncoding regions near genes with known speech functions or brain gene expression specializations in humans and vocal learning birds, including FOXP2, NEUROD6, ZEB2, and MEF2C, and near genes with major neurodevelopmental functions, including NR2F1, NRP2, and BCL11B. We also found enrichment near the SFARI class S genes associated with syndromic vocal communication forms of autism spectrum disorders. These findings reveal strong candidate noncoding regions near genes for the evolutionary adaptations that distinguish vocal learning species from their close vocal nonlearning relatives and provide further evidence of molecular convergence between birdsong and human spoken language.
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7
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Gordon RL, Ravignani A, Hyland Bruno J, Robinson CM, Scartozzi A, Embalabala R, Niarchou M, Cox NJ, Creanza N. Linking the genomic signatures of human beat synchronization and learned song in birds. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200329. [PMID: 34420388 DOI: 10.1098/rstb.2020.0329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The development of rhythmicity is foundational to communicative and social behaviours in humans and many other species, and mechanisms of synchrony could be conserved across species. The goal of the current paper is to explore evolutionary hypotheses linking vocal learning and beat synchronization through genomic approaches, testing the prediction that genetic underpinnings of birdsong also contribute to the aetiology of human interactions with musical beat structure. We combined state-of-the-art-genomic datasets that account for underlying polygenicity of these traits: birdsong genome-wide transcriptomics linked to singing in zebra finches, and a human genome-wide association study of beat synchronization. Results of competitive gene set analysis revealed that the genetic architecture of human beat synchronization is significantly enriched for birdsong genes expressed in songbird Area X (a key nucleus for vocal learning, and homologous to human basal ganglia). These findings complement ethological and neural evidence of the relationship between vocal learning and beat synchronization, supporting a framework of some degree of common genomic substrates underlying rhythm-related behaviours in two clades, humans and songbirds (the largest evolutionary radiation of vocal learners). Future cross-species approaches investigating the genetic underpinnings of beat synchronization in a broad evolutionary context are discussed. This article is part of the theme issue 'Synchrony and rhythm interaction: from the brain to behavioural ecology'.
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Affiliation(s)
- Reyna L Gordon
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Andrea Ravignani
- Comparative Bioacoustics Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | | | - Cristina M Robinson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Alyssa Scartozzi
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Rebecca Embalabala
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Maria Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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- 23andMe, Inc., Sunnyvale, CA, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Nicole Creanza
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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8
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Day LB, Helmhout W, Pano G, Olsson U, Hoeksema JD, Lindsay WR. Correlated evolution of acrobatic display and both neural and somatic phenotypic traits in manakins (Pipridae). Integr Comp Biol 2021; 61:1343-1362. [PMID: 34143205 DOI: 10.1093/icb/icab139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/22/2022] Open
Abstract
Brightly colored manakin (Aves: Pipridae) males are known for performing acrobatic displays punctuated by non-vocal sounds (sonations) in order to attract dull colored females. The complexity of the display sequence and assortment of display elements involved (e.g., sonations, acrobatic maneuvers, and cooperative performances) varies considerably across manakin species. Species-specific display elements coevolve with display-distinct specializations of the neuroanatomical, muscular, endocrine, cardiovascular, and skeletal systems in the handful of species studied. Conducting a broader comparative study, we previously found positive associations between display complexity and both brain mass and body mass across 8 manakin genera, indicating selection for neural and somatic expansion to accommodate display elaboration. Whether this gross morphological variation is due to overall brain and body mass expansion (concerted evolution) versus size increases in only functionally relevant brain regions and growth of particular body ("somatic") features (mosaic evolution) remains to be explored. Here we test the hypothesis that cross-species variation in male brain mass and body mass is driven by mosaic evolution. We predicted positive associations between display complexity and variation in the volume of the cerebellum and sensorimotor arcopallium, brain regions which have roles in sensorimotor processes, and learning and performance of precisely timed and sequenced thoughts and movements, respectively. In contrast, we predicted no associations between the volume of a limbic arcopallial nucleus or a visual thalamic nucleus and display complexity as these regions have no-specific functional relationship to display behavior. For somatic features, we predicted that the relationship between body mass and complexity would not include contributions of tarsus length based on a recent study suggesting selection on tarsus length is less labile than body mass. We tested our hypotheses in males from 12 manakin species and a closely related flycatcher. Our analyses support mosaic evolution of neural and somatic features functionally relevant to display and indicate sexual selection for acrobatic complexity may increase the capacity for procedural learning via cerebellar enlargement and maneuverability via a reduction in tarsus length in species with lower overall complexity scores.
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Affiliation(s)
- Lainy B Day
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA.,Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Wilson Helmhout
- Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Glendin Pano
- Neuroscience Minor, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18, SE-413-90 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Jason D Hoeksema
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA
| | - Willow R Lindsay
- Department of Biology, University of Mississippi, 30 University Avenue, University, MS 38677, USA.,Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18, SE-413-90 Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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9
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Choe HN, Jarvis ED. The role of sex chromosomes and sex hormones in vocal learning systems. Horm Behav 2021; 132:104978. [PMID: 33895570 DOI: 10.1016/j.yhbeh.2021.104978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Vocal learning is the ability to imitate and modify sounds through auditory experience, a rare trait found in only a few lineages of mammals and birds. It is a critical component of human spoken language, allowing us to verbally transmit speech repertoires and knowledge across generations. In many vocal learning species, the vocal learning trait is sexually dimorphic, where it is either limited to males or present in both sexes to different degrees. In humans, recent findings have revealed subtle sexual dimorphism in vocal learning/spoken language brain regions and some associated disorders. For songbirds, where the neural mechanisms of vocal learning have been well studied, vocal learning appears to have been present in both sexes at the origin of the lineage and was then independently lost in females of some subsequent lineages. This loss is associated with an interplay between sex chromosomes and sex steroid hormones. Even in species with little dimorphism, like humans, sex chromosomes and hormones still have some influence on learned vocalizations. Here we present a brief synthesis of these studies, in the context of sex determination broadly, and identify areas of needed investigation to further understand how sex chromosomes and sex steroid hormones help establish sexually dimorphic neural structures for vocal learning.
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Affiliation(s)
- Ha Na Choe
- Duke University Medical Center, The Rockefeller University, Howard Hughes Medical Institute, United States of America.
| | - Erich D Jarvis
- Duke University Medical Center, The Rockefeller University, Howard Hughes Medical Institute, United States of America.
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10
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O'Rourke T, Martins PT, Asano R, Tachibana RO, Okanoya K, Boeckx C. Capturing the Effects of Domestication on Vocal Learning Complexity. Trends Cogn Sci 2021; 25:462-474. [PMID: 33810982 DOI: 10.1016/j.tics.2021.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022]
Abstract
Domesticated and vocal learning species can serve as informative model organisms for the reduction of reactive aggression and emergence of speech in our lineage. Amidst mounting evidence that domestication modifies vocal repertoires across different species, we focus on the domesticated Bengalese finch, which has a more complex song than the wild-type white-rumped munia. Our explanation for this effect revolves around the glutamate neurotransmitter system. Glutamate signaling (i) is implicated in birdsong learning, (ii) controls dopamine activity in neural circuits crucial for vocal learning, (iii) is disproportionately targeted in the evolution of domesticates, and (iv) regulates stress responses and aggressive behaviors attenuated under domestication. We propose that attenuated excitation of stress-related neural circuits potentiates vocal learning via altered dopaminergic signaling.
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Affiliation(s)
- Thomas O'Rourke
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain
| | - Pedro Tiago Martins
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain
| | - Rie Asano
- Department of Systematic Musicology, University of Cologne, 50923 Cologne, Germany
| | - Ryosuke O Tachibana
- Center for Evolutionary Cognitive Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 153-8902 Tokyo, Japan
| | - Kazuo Okanoya
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 153-8902 Tokyo, Japan
| | - Cedric Boeckx
- Section of General Linguistics, University of Barcelona, 08007 Barcelona, Spain; University of Barcelona Institute for Complex Systems (UBICS), 08028 Barcelona, Spain; Catalan Institute for Advanced Studies and Research (ICREA), 08010 Barcelona, Spain.
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11
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Diddens J, Coussement L, Frankl-Vilches C, Majumdar G, Steyaert S, Ter Haar SM, Galle J, De Meester E, De Keulenaer S, Van Criekinge W, Cornil CA, Balthazart J, Van Der Linden A, De Meyer T, Vanden Berghe W. DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon. Front Cell Dev Biol 2021; 9:583555. [PMID: 33816458 PMCID: PMC8017237 DOI: 10.3389/fcell.2021.583555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Song learning in zebra finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
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Affiliation(s)
- Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis Coussement
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gaurav Majumdar
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sandra Steyaert
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Sita M Ter Haar
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jeroen Galle
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sarah De Keulenaer
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Charlotte A Cornil
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jacques Balthazart
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Annemie Van Der Linden
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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12
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Choe HN, Tewari J, Zhu KW, Davenport M, Matsunami H, Jarvis ED. Estrogen and sex-dependent loss of the vocal learning system in female zebra finches. Horm Behav 2021; 129:104911. [PMID: 33422557 PMCID: PMC7996629 DOI: 10.1016/j.yhbeh.2020.104911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
Sex hormones alter the organization of the brain during early development and coordinate various behaviors throughout life. In zebra finches, song learning is limited to males, with the associated song learning brain pathways only maturing in males and atrophying in females. While this atrophy can be prevented by treating females with exogenous estrogen during early post-hatch development, the requirement of estrogen during normal male song system development is uncertain. For the first time in songbirds, we administered exemestane, a potent third generation estrogen synthesis inhibitor, from the day of hatching until adulthood in order to reassess the role of estrogen in song circuit development. We examined the behavior, brain anatomy, and transcriptomes of individual song nuclei in these pharmacologically manipulated animals. We found that males with long-term exemestane treatment had diminished male-specific plumage and impaired song learning, but minimal effect on song nuclei sizes and their specialized transcriptome. Consistent with prior findings, females with long-term estrogen treatment retained a functional song system with song nuclei that had specialized gene expression similar, but not identical to males. We also observed that different song nuclei responded to estrogen manipulation differently, with Area X in the striatum being the most altered by estrogen modulation. These findings support the hypothesis that song learning is an ancestral trait in both sexes that was subsequently suppressed in females of some species and that estrogen has come to play a critical role in modulating this suppression as well as refinement of song learning.
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Affiliation(s)
- Ha Na Choe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Jeevan Tewari
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kevin W Zhu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Matthew Davenport
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA; The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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13
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Shi Z, Zhang Z, Schaffer L, Huang Z, Fu L, Head S, Gaasterland T, Wang X, Li X. Dynamic transcriptome landscape in the song nucleus HVC between juvenile and adult zebra finches. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10035. [PMID: 36618441 PMCID: PMC9744550 DOI: 10.1002/ggn2.10035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 09/25/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023]
Abstract
Male juvenile zebra finches learn to sing by imitating songs of adult males early in life. The development of the song control circuit and song learning and maturation are highly intertwined processes, involving gene expression, neurogenesis, circuit formation, synaptic modification, and sensory-motor learning. To better understand the genetic and genomic mechanisms underlying these events, we used RNA-Seq to examine genome-wide transcriptomes in the song control nucleus HVC of male juvenile (45 d) and adult (100 d) zebra finches. We report that gene groups related to axon guidance, RNA processing, lipid metabolism, and mitochondrial functions show enriched expression in juvenile HVC compared to the rest of the brain. As juveniles mature into adulthood, massive gene expression changes occur. Expression of genes related to amino acid metabolism, cell cycle, and mitochondrial function is reduced, accompanied by increased and enriched expression of genes with synaptic functions, including genes related to G-protein signaling, neurotransmitter receptors, transport of small molecules, and potassium channels. Unexpectedly, a group of genes with immune system functions is also developmentally regulated, suggesting potential roles in the development and functions of HVC. These data will serve as a rich resource for investigations into the development and function of a neural circuit that controls vocal behavior.
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Affiliation(s)
- Zhimin Shi
- Neuroscience Center of ExcellenceLouisiana State University School of MedicineNew OrleansLouisianaUSA
| | - Zeyu Zhang
- Key Laboratory of Genetic Network BiologyInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | | | - Zhi Huang
- Neuroscience Center of ExcellenceLouisiana State University School of MedicineNew OrleansLouisianaUSA
| | - Lijuan Fu
- Neuroscience Center of ExcellenceLouisiana State University School of MedicineNew OrleansLouisianaUSA,Present address:
California Medical Innovations InstituteSan DiegoCaliforniaUSA
| | - Steven Head
- Scripps Research InstituteLa JollaCaliforniaUSA
| | - Terry Gaasterland
- Scripps Research InstituteLa JollaCaliforniaUSA,University of California at San DiegoLa JollaCaliforniaUSA
| | - Xiu‐Jie Wang
- Key Laboratory of Genetic Network BiologyInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - XiaoChing Li
- Neuroscience Center of ExcellenceLouisiana State University School of MedicineNew OrleansLouisianaUSA
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14
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Molecular specializations of deep cortical layer analogs in songbirds. Sci Rep 2020; 10:18767. [PMID: 33127988 PMCID: PMC7599217 DOI: 10.1038/s41598-020-75773-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
How the evolution of complex behavioral traits is associated with the emergence of novel brain pathways is largely unknown. Songbirds, like humans, learn vocalizations via tutor imitation and possess a specialized brain circuitry to support this behavior. In a comprehensive in situ hybridization effort, we show that the zebra finch vocal robust nucleus of the arcopallium (RA) shares numerous markers (e.g. SNCA, PVALB) with the adjacent dorsal intermediate arcopallium (AId), an avian analog of mammalian deep cortical layers with involvement in motor function. We also identify markers truly unique to RA and thus likely linked to modulation of vocal motor function (e.g. KCNC1, GABRE), including a subset of the known shared markers between RA and human laryngeal motor cortex (e.g. SLIT1, RTN4R, LINGO1, PLXNC1). The data provide novel insights into molecular features unique to vocal learning circuits, and lend support for the motor theory for vocal learning origin.
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15
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Castiglione GM, Xu Z, Zhou L, Duh EJ. Adaptation of the master antioxidant response connects metabolism, lifespan and feather development pathways in birds. Nat Commun 2020; 11:2476. [PMID: 32424161 PMCID: PMC7234996 DOI: 10.1038/s41467-020-16129-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Birds (Aves) display high metabolic rates and oxygen consumption relative to mammals, increasing reactive oxygen species (ROS) formation. Although excess ROS reduces lifespan by causing extensive cellular dysfunction and damage, birds are remarkably long-lived. We address this paradox by identifying the constitutive activation of the NRF2 master antioxidant response in Neoaves (~95% of bird species), providing an adaptive mechanism capable of counterbalancing high ROS levels. We demonstrate that a KEAP1 mutation in the Neoavian ancestor disrupted the repression of NRF2 by KEAP1, leading to constitutive NRF2 activity and decreased oxidative stress in wild Neoaves tissues and cells. Our evidence suggests this ancient mutation induced a compensatory program in NRF2-target genes with functions beyond redox regulation-including feather development-while enabling significant metabolic rate increases that avoid trade-offs with lifespan. The strategy of NRF2 activation sought by intense clinical investigation therefore appears to have also unlocked a massively successful evolutionary trajectory.
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Affiliation(s)
- Gianni M Castiglione
- Department of Ophthalmology, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD, 21287, USA
| | - Zhenhua Xu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD, 21287, USA
| | - Lingli Zhou
- Department of Ophthalmology, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD, 21287, USA
| | - Elia J Duh
- Department of Ophthalmology, Johns Hopkins University School of Medicine, 400 N Broadway, Baltimore, MD, 21287, USA.
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16
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Lovell PV, Wirthlin M, Kaser T, Buckner AA, Carleton JB, Snider BR, McHugh AK, Tolpygo A, Mitra PP, Mello CV. ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies. J Comp Neurol 2020; 528:2099-2131. [PMID: 32037563 DOI: 10.1002/cne.24879] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/14/2022]
Abstract
An in-depth understanding of the genetics and evolution of brain function and behavior requires a detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species and a first for any sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among many fundamental themes.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Taylor Kaser
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Alexa A Buckner
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Julia B Carleton
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Brian R Snider
- Center for Spoken Language Understanding, Institute on Development and Disability, Oregon Health and Science University, Portland, Oregon
| | - Anne K McHugh
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | | | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
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17
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New Insights into the Avian Song System and Neuronal Control of Learned Vocalizations. THE NEUROETHOLOGY OF BIRDSONG 2020. [DOI: 10.1007/978-3-030-34683-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Friedrich SR, Lovell PV, Kaser TM, Mello CV. Exploring the molecular basis of neuronal excitability in a vocal learner. BMC Genomics 2019; 20:629. [PMID: 31375088 PMCID: PMC6679542 DOI: 10.1186/s12864-019-5871-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/31/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Vocal learning, the ability to learn to produce vocalizations through imitation, relies on specialized brain circuitry known in songbirds as the song system. While the connectivity and various physiological properties of this system have been characterized, the molecular genetic basis of neuronal excitability in song nuclei remains understudied. We have focused our efforts on examining voltage-gated ion channels to gain insight into electrophysiological and functional features of vocal nuclei. A previous investigation of potassium channel genes in zebra finches (Taeniopygia guttata) revealed evolutionary modifications unique to songbirds, as well as transcriptional specializations in the song system [Lovell PV, Carleton JB, Mello CV. BMC Genomics 14:470 2013]. Here, we expand this approach to sodium, calcium, and chloride channels along with their modulatory subunits using comparative genomics and gene expression analysis encompassing microarrays and in situ hybridization. RESULTS We found 23 sodium, 38 calcium, and 33 chloride channel genes (HGNC-based classification) in the zebra finch genome, several of which were previously unannotated. We determined 15 genes are missing relative to mammals, including several genes (CLCAs, BEST2) linked to olfactory transduction. The majority of sodium and calcium but few chloride channels showed differential expression in the song system, among them SCN8A and CACNA1E in the direct motor pathway, and CACNG4 and RYR2 in the anterior forebrain pathway. In several cases, we noted a seemingly coordinated pattern across multiple nuclei (SCN1B, SCN3B, SCN4B, CACNB4) or sparse expression (SCN1A, CACNG5, CACNA1B). CONCLUSION The gene families examined are highly conserved between avian and mammalian lineages. Several cases of differential expression likely support high-frequency and burst firing in specific song nuclei, whereas cases of sparse patterns of expression may contribute to the unique electrophysiological signatures of distinct cell populations. These observations lay the groundwork for manipulations to determine how ion channels contribute to the neuronal excitability properties of vocal learning systems.
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Affiliation(s)
- Samantha R. Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Peter V. Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Taylor M. Kaser
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Claudio V. Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
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19
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Mello CV, Kaser T, Buckner AA, Wirthlin M, Lovell PV. Molecular architecture of the zebra finch arcopallium. J Comp Neurol 2019; 527:2512-2556. [PMID: 30919954 DOI: 10.1002/cne.24688] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/23/2022]
Abstract
The arcopallium, a key avian forebrain region, receives inputs from numerous brain areas and is a major source of descending sensory and motor projections. While there is evidence of arcopallial subdivisions, the internal organization or the arcopallium is not well understood. The arcopallium is also considered the avian homologue of mammalian deep cortical layers and/or amygdalar subdivisions, but one-to-one correspondences are controversial. Here we present a molecular characterization of the arcopallium in the zebra finch, a passerine songbird species and a major model organism for vocal learning studies. Based on in situ hybridization for arcopallial-expressed transcripts (AQP1, C1QL3, CBLN2, CNTN4, CYP19A1, ESR1/2, FEZF2, MGP, NECAB2, PCP4, PVALB, SCN3B, SCUBE1, ZBTB20, and others) in comparison with cytoarchitectonic features, we have defined 20 distinct regions that can be grouped into six major domains (anterior, posterior, dorsal, ventral, medial, and intermediate arcopallium, respectively; AA, AP, AD, AV, AM, and AI). The data also help to establish the arcopallium as primarily pallial, support a unique topography of the arcopallium in passerines, highlight similarities between the vocal robust nucleus of the arcopallium (RA) and AI, and provide insights into the similarities and differences of cortical and amygdalar regions between birds and mammals. We also propose the use of AMV (instead of nucleus taenia/TnA), AMD, AD, and AI as initial steps toward a universal arcopallial nomenclature. Besides clarifying the internal organization of the arcopallium, the data provide a coherent basis for further functional and comparative studies of this complex avian brain region.
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Affiliation(s)
- Claudio V Mello
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Taylor Kaser
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Alexa A Buckner
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Peter V Lovell
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
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20
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Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Sci Rep 2019; 9:816. [PMID: 30692609 PMCID: PMC6349858 DOI: 10.1038/s41598-018-37057-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/25/2018] [Indexed: 12/31/2022] Open
Abstract
Songbirds communicate through learned vocalizations, using a forebrain circuit with convergent similarity to vocal-control circuitry in humans. This circuit is incomplete in female zebra finches, hence only males sing. We show that the UTS2B gene, encoding Urotensin-Related Peptide (URP), is uniquely expressed in a key pre-motor vocal nucleus (HVC), and specifically marks the neurons that form a male-specific projection that encodes timing features of learned song. UTS2B-expressing cells appear early in males, prior to projection formation, but are not observed in the female nucleus. We find no expression evidence for canonical receptors within the vocal circuit, suggesting either signalling to other brain regions via diffusion or transduction through other receptor systems. Urotensins have not previously been implicated in vocal control, but we find an annotation in Allen Human Brain Atlas of increased UTS2B expression within portions of human inferior frontal cortex implicated in human speech and singing. Thus UTS2B (URP) is a novel neural marker that may have conserved functions for vocal communication.
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21
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Asogwa NC, Mori C, Sánchez-Valpuesta M, Hayase S, Wada K. Inter- and intra-specific differences in muscarinic acetylcholine receptor expression in the neural pathways for vocal learning in songbirds. J Comp Neurol 2018; 526:2856-2869. [PMID: 30198559 DOI: 10.1002/cne.24532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 11/06/2022]
Abstract
Acetylcholine receptors (AChRs) abound in the central nervous system of vertebrates. Muscarinic AChRs (mAChRs), a functional subclass of AChRs, mediate neuronal responses via intracellular signal transduction. They also play roles in sensorimotor coordination and motor skill learning by enhancing cortical plasticity. Learned birdsong is a complex motor skill acquired through sensorimotor coordination during a critical period. However, the functions of AChRs in the neural circuits for vocal learning and production remain largely unexplored. Here, we report the unique expression of mAChRs subunits (chrm2-5) in the song nuclei of zebra finches. The expression of excitatory subunits (chrm3 and chrm5) was downregulated in the song nuclei compared with the surrounding brain regions. In contrast, the expression of inhibitory mAChRs (chrm2 and chrm4) was upregulated in the premotor song nucleus HVC relative to the surrounding nidopallium. Chrm4 showed developmentally different expression in HVC during the critical period. Compared with chrm4, individual differences in chrm2 expression emerged in HVC early in the critical period. These individual differences in chrm2 expression persisted despite testosterone administration or auditory deprivation, which altered the timing of song stabilization. Instead, the variability in chrm2 expression in HVC correlated with parental genetics. In addition, chrm2 expression in HVC exhibited species differences and individual variability among songbird species. These results suggest that mAChRs play an underappreciated role in the development of species and individual differences in song patterns by modulating the excitability of HVC neurons, providing a potential insight into the gating of auditory responses in HVC neurons.
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Affiliation(s)
- Norman C Asogwa
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Chihiro Mori
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | | | - Shin Hayase
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Wada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Biological Sciences, Hokkaido University, Sapporo, Japan.,Faculty of Science, Hokkaido University, Sapporo, Japan
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22
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Lovell PV, Huizinga NA, Getachew A, Mees B, Friedrich SR, Wirthlin M, Mello CV. Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. BMC Res Notes 2018; 11:309. [PMID: 29776372 PMCID: PMC5960091 DOI: 10.1186/s13104-018-3402-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/07/2018] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. DATA DESCRIPTION We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr_un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Nicole A Huizinga
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Abel Getachew
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Brianna Mees
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | | | - Morgan Wirthlin
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.,Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.
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