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Roggenbuck EC, Hall EA, Hanson IB, Roby AA, Zhang KK, Alkatib KA, Carter JA, Clewner JE, Gelfius AL, Gong S, Gordon FR, Iseler JN, Kotapati S, Li M, Maysun A, McCormick EO, Rastogi G, Sengupta S, Uzoma CU, Wolkov MA, Clowney EJ. Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria. WIREs Mech Dis 2024; 16:e1636. [PMID: 38185860 DOI: 10.1002/wsbm.1636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.
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Affiliation(s)
- Emma C Roggenbuck
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elijah A Hall
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabel B Hanson
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa A Roby
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine K Zhang
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle A Alkatib
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Carter
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarred E Clewner
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna L Gelfius
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Shiyuan Gong
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Finley R Gordon
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolene N Iseler
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Samhita Kotapati
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Marilyn Li
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Areeba Maysun
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elise O McCormick
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Geetanjali Rastogi
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Srijani Sengupta
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Chantal U Uzoma
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Madison A Wolkov
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, Michigan, USA
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2
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Robinson CD, Hale MD, Wittman TN, Cox CL, John-Alder HB, Cox RM. Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration in Sceloporus lizards. J Hered 2023; 114:637-653. [PMID: 37498153 DOI: 10.1093/jhered/esad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Phenotypic sexual dimorphism often involves the hormonal regulation of sex-biased expression for underlying genes. However, it is generally unknown whether the evolution of hormonally mediated sexual dimorphism occurs through upstream changes in tissue sensitivity to hormone signals, downstream changes in responsiveness of target genes, or both. Here, we use comparative transcriptomics to explore these possibilities in 2 species of Sceloporus lizards exhibiting different patterns of sexual dichromatism. Sexually dimorphic S. undulatus develops blue and black ventral coloration in response to testosterone, while sexually monomorphic S. virgatus does not, despite exhibiting similar sex differences in circulating testosterone levels. We administered testosterone implants to juveniles of each species and used RNAseq to quantify gene expression in ventral skin. Transcriptome-wide responses to testosterone were stronger in S. undulatus than in S. virgatus, suggesting species differences in tissue sensitivity to this hormone signal. Species differences in the expression of genes for androgen metabolism and sex hormone-binding globulin were consistent with this idea, but expression of the androgen receptor gene was higher in S. virgatus, complicating this interpretation. Downstream of androgen signaling, we found clear species differences in hormonal responsiveness of genes related to melanin synthesis, which were upregulated by testosterone in S. undulatus, but not in S. virgatus. Collectively, our results indicate that hormonal regulation of melanin synthesis pathways contributes to the development of sexual dimorphism in S. undulatus, and that changes in the hormonal responsiveness of these genes in S. virgatus contribute to the evolutionary loss of ventral coloration.
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Affiliation(s)
| | - Matthew D Hale
- University of Virginia, Department of Biology, Charlottesville, VA, United States
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, United States
| | - Tyler N Wittman
- University of Virginia, Department of Biology, Charlottesville, VA, United States
| | - Christian L Cox
- Florida International University, Department of Biological Sciences and Institute of Environment, Miami, FL, United States
| | - Henry B John-Alder
- Rutgers University, Department of Ecology, Evolution, and Natural Resources, New Brunswick, NJ, United States
| | - Robert M Cox
- University of Virginia, Department of Biology, Charlottesville, VA, United States
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3
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Anderson AP, Renn SCP. The Ancestral Modulation Hypothesis: Predicting Mechanistic Control of Sexually Heteromorphic Traits Using Evolutionary History. Am Nat 2023; 202:241-259. [PMID: 37606950 DOI: 10.1086/725438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
AbstractAcross the animal kingdom there are myriad forms within a sex across, and even within, species, rendering concepts of universal sex traits moot. The mechanisms that regulate the development of these trait differences are varied, although in vertebrates, common pathways involve gonadal steroid hormones. Gonadal steroids are often associated with heteromorphic trait development, where the steroid found at higher circulating levels is the one involved in trait development for that sex. Occasionally, there are situations in which a gonadal steroid associated with heteromorphic trait development in one sex is involved in heteromorphic or monomorphic trait development in another sex. We propose a verbal hypothesis, the ancestral modulation hypothesis (AMH), that uses the evolutionary history of the trait-particularly which sex ancestrally possessed higher trait values-to predict the regulatory pathway that governs trait expression. The AMH predicts that the genomic architecture appears first to resolve sexual conflict in an initially monomorphic trait. This architecture takes advantage of existing sex-biased signals, the gonadal steroid pathway, to generate trait heteromorphism. In cases where the other sex experiences evolutionary pressure for the new phenotype, that sex will co-opt the existing architecture by altering its signal to match that of the original high-trait-value sex. We describe the integrated levels needed to produce this pattern and what the expected outcomes will be given the evolutionary history of the trait. We present this framework as a testable hypothesis for the scientific community to investigate and to create further engagement and analysis of both ultimate and proximate approaches to sexual heteromorphism.
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4
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Beckman EJ, Vargas Campos W, Benham PM, Schmitt CJ, Cheviron ZA, Witt CC. Selection on embryonic haemoglobin in an elevational generalist songbird. Biol Lett 2022; 18:20220105. [PMCID: PMC9554719 DOI: 10.1098/rsbl.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animals developing at high elevation experience a suite of environmental challenges, most notably the low partial pressure of oxygen (PO2) in ambient air. In low PO2, bird species with high-elevation ancestry consistently demonstrate higher hatching success than lowland counterparts, suggesting highland birds are adapted to restricted O2 (hypoxia) in early development. Haemoglobin (Hb), the critical oxygen-transport protein, is a likely target of PO2-related selection across ontogeny since Hb isoforms expressed at distinct developmental stages demonstrate different O2 affinities. To test if Hb function is under PO2-related selection at different ontogenetic stages, we sampled a songbird, the hooded siskin (Spinus magellanicus), across two approximately 4000 m elevational transects. We sequenced all of the loci that encode avian Hb isoforms, and tested for signatures of spatially varying selection by comparing divergence patterns in Hb loci to other loci sampled across the genome. We found strong signatures of diversifying selection at non-synonymous sites in loci that contribute to embryonic (απ, βH) and definitive (βA) Hb isoforms. This is the first evidence for selection on embryonic haemoglobin in high-elevation Neoaves. We conclude that selection on Hb function at brief, but critical stages of ontogeny may be a vital component to high elevation adaptation in birds.
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Affiliation(s)
- Elizabeth J. Beckman
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Walter Vargas Campos
- Centro de Ornitología y Biodiversidad, Calle Sta. Rita 105, Oficina 202, Santiago de Surco, Lima, Perú
| | - Phred M. Benham
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - C. Jonathan Schmitt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | | | - Christopher C. Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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5
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Cox RM, Hale MD, Wittman TN, Robinson CD, Cox CL. Evolution of hormone-phenotype couplings and hormone-genome interactions. Horm Behav 2022; 144:105216. [PMID: 35777215 DOI: 10.1016/j.yhbeh.2022.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/05/2022] [Accepted: 06/20/2022] [Indexed: 12/22/2022]
Abstract
When selection favors a new relationship between a cue and a hormonally mediated response, adaptation can proceed by altering the hormonal signal that is produced or by altering the phenotypic response to the hormonal signal. The field of evolutionary endocrinology has made considerable progress toward understanding the evolution of hormonal signals, but we know much less about the evolution of hormone-phenotype couplings, particularly at the hormone-genome interface. We briefly review and classify the mechanisms through which these hormone-phenotype couplings likely evolve, using androgens and their receptors and genomic response elements to illustrate our view. We then present two empirical studies of hormone-phenotype couplings, one rooted in evolutionary quantitative genetics and another in comparative transcriptomics, each focused on the regulation of sexually dimorphic phenotypes by testosterone (T) in the brown anole lizard (Anolis sagrei). First, we illustrate the potential for hormone-phenotype couplings to evolve by showing that coloration of the dewlap (an ornament used in behavioral displays) exhibits significant heritability in its responsiveness to T, implying that anoles harbor genetic variance in the architecture of hormonal pleiotropy. Second, we combine T manipulations with analyses of the liver transcriptome to ask whether and how statistical methods for characterizing modules of co-expressed genes and in silico techniques for identifying androgen response elements (AREs) can improve our understanding of hormone-genome interactions. We conclude by emphasizing important avenues for future work at the hormone-genome interface, particularly those conducted in a comparative evolutionary framework.
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Affiliation(s)
- Robert M Cox
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | - Matthew D Hale
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Tyler N Wittman
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Christian L Cox
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Biological Sciences, Florida International University, Miami, FL, USA
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6
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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7
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Alcami P, Totagera S, Sohnius-Wilhelmi N, Leitner S, Grothe B, Frankl-Vilches C, Gahr M. Extensive GJD2 Expression in the Song Motor Pathway Reveals the Extent of Electrical Synapses in the Songbird Brain. BIOLOGY 2021; 10:biology10111099. [PMID: 34827092 PMCID: PMC8615078 DOI: 10.3390/biology10111099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/06/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Birdsong is a precisely timed animal behavior. The connectivity of song premotor neural networks has been proposed to underlie the temporal patterns of neuronal activity that control vocal muscle movements during singing. Although the connectivity of premotor nuclei via chemical synapses has been characterized, electrical synapses and their molecular identity remain unexplored. We show with in situ hybridizations that GJD2 mRNA, coding for the major channel-forming electrical synapse protein in mammals, connexin 36, is expressed in the two nuclei that control song production, HVC and RA from canaries and zebra finches. In canaries' HVC, GJD2 mRNA is extensively expressed in GABAergic and only a fraction of glutamatergic cells. By contrast, in RA, GJD2 mRNA expression is widespread in glutamatergic and GABAergic neurons. Remarkably, GJD2 expression is similar in song nuclei and their respective embedding brain regions, revealing the widespread expression of GJD2 in the avian brain. Inspection of a single-cell sequencing database from zebra and Bengalese finches generalizes the distributions of electrical synapses across cell types and song nuclei that we found in HVC and RA from canaries, reveals a differential GJD2 mRNA expression in HVC glutamatergic subtypes and its transient increase along the neurogenic lineage. We propose that songbirds are a suitable model to investigate the contribution of electrical synapses to motor skill learning and production.
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Affiliation(s)
- Pepe Alcami
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
- Division of Neurobiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, D-82152 Planegg-Martinsried, Germany;
| | - Santhosh Totagera
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
- Division of Neurobiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, D-82152 Planegg-Martinsried, Germany;
| | - Nina Sohnius-Wilhelmi
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
| | - Stefan Leitner
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
| | - Benedikt Grothe
- Division of Neurobiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, D-82152 Planegg-Martinsried, Germany;
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319 Starnberg, Germany; (S.T.); (N.S.-W.); (S.L.); (C.F.-V.); (M.G.)
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8
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Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
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Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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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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Ko MC, Frankl-Vilches C, Bakker A, Gahr M. The Gene Expression Profile of the Song Control Nucleus HVC Shows Sex Specificity, Hormone Responsiveness, and Species Specificity Among Songbirds. Front Neurosci 2021; 15:680530. [PMID: 34135731 PMCID: PMC8200640 DOI: 10.3389/fnins.2021.680530] [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: 03/14/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
Singing occurs in songbirds of both sexes, but some species show typical degrees of sex-specific performance. We studied the transcriptional sex differences in the HVC, a brain nucleus critical for song pattern generation, of the forest weaver (Ploceus bicolor), the blue-capped cordon-bleu (Uraeginthus cyanocephalus), and the canary (Serinus canaria), which are species that show low, medium, and high levels of sex-specific singing, respectively. We observed persistent sex differences in gene expression levels regardless of the species-specific sexual singing phenotypes. We further studied the HVC transcriptomes of defined phenotypes of canary, known for its testosterone-sensitive seasonal singing. By studying both sexes of canaries during both breeding and non-breeding seasons, non-breeding canaries treated with testosterone, and spontaneously singing females, we found that the circulating androgen levels and sex were the predominant variables associated with the variations in the HVC transcriptomes. The comparison of natural singing with testosterone-induced singing in canaries of the same sex revealed considerable differences in the HVC transcriptomes. Strong transcriptional changes in the HVC were detected during the transition from non-singing to singing in canaries of both sexes. Although the sex-specific genes of singing females shared little resemblance with those of males, our analysis showed potential functional convergences. Thus, male and female songbirds achieve comparable singing behaviours with sex-specific transcriptomes.
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Affiliation(s)
- Meng-Ching Ko
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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11
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Martini D, Dussex N, Robertson BC, Gemmell NJ, Knapp M. Evolution of the "world's only alpine parrot": Genomic adaptation or phenotypic plasticity, behaviour and ecology? Mol Ecol 2021; 30:6370-6386. [PMID: 33973288 DOI: 10.1111/mec.15978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023]
Abstract
Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (Nestor notabilis) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes? We use whole genome data of the kea and its close, forest adapted sister species, the kākā (Nestor meridionalis) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both Nestor species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.
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Affiliation(s)
- Denise Martini
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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12
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Recuerda M, Vizueta J, Cuevas-Caballé C, Blanco G, Rozas J, Milá B. Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology. Genome Biol Evol 2021; 13:evab034. [PMID: 33616654 PMCID: PMC8046334 DOI: 10.1093/gbe/evab034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Joel Vizueta
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cuevas-Caballé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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13
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Gazda MA, Toomey MB, Araújo PM, Lopes RJ, Afonso S, Myers CA, Serres K, Kiser PD, Hill GE, Corbo JC, Carneiro M. Genetic Basis of De Novo Appearance of Carotenoid Ornamentation in Bare Parts of Canaries. Mol Biol Evol 2021; 37:1317-1328. [PMID: 31930402 DOI: 10.1093/molbev/msaa006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Unlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel trait offers a unique opportunity to understand the mechanisms of bare-part coloration in birds. To identify the mutation producing the colorful phenotype, we resequenced the genome of urucum canaries and performed a range of analyses to search for genotype-to-phenotype associations across the genome. We identified a nonsynonymous mutation in the gene BCO2 (beta-carotene oxygenase 2, also known as BCDO2), an enzyme involved in the cleavage and breakdown of full-length carotenoids into short apocarotenoids. Protein structural models and in vitro functional assays indicate that the urucum mutation abrogates the carotenoid-cleavage activity of BCO2. Consistent with the predicted loss of carotenoid-cleavage activity, urucum canaries tended to have increased levels of full-length carotenoid pigments in bill tissue and reduced levels of carotenoid-cleavage products (apocarotenoids) in retinal tissue compared with other breeds of canaries. We hypothesize that carotenoid-based bare-part coloration might be readily gained, modified, or lost through simple switches in the enzymatic activity or regulation of BCO2 and this gene may be an important mediator in the evolution of bare-part coloration among bird species.
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Affiliation(s)
- Małgorzata Anna Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Matthew B Toomey
- Department of Biological Science, University of Tulsa, Tulsa, OK
| | - Pedro M Araújo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ricardo J Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Kyla Serres
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Philip D Kiser
- Department of Physiology & Biophysics, School of Medicine, Gillespie Neuroscience Research Facility, University of California, Irvine, Irvine, CA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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14
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Villavicencio CP, Windley H, D'Amelio PB, Gahr M, Goymann W, Quispe R. Neuroendocrine patterns underlying seasonal song and year-round territoriality in male black redstarts. Front Zool 2021; 18:8. [PMID: 33627161 PMCID: PMC7905601 DOI: 10.1186/s12983-021-00389-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The connection between testosterone and territoriality in free-living songbirds has been well studied in a reproductive context, but less so outside the breeding season. To assess the effects of seasonal androgenic action on territorial behavior, we analyzed vocal and non-vocal territorial behavior in response to simulated territorial intrusions (STIs) during three life-cycle stages in free-living male black redstarts: breeding, molt and nonbreeding. Concurrently, we measured changes in circulating testosterone levels, as well as the mRNA expression of androgen and estrogen receptors and aromatase in the preoptic, hypothalamic and song control brain areas that are associated with social and vocal behaviors. RESULTS Territorial behavior and estrogen receptor expression in hypothalamic areas did not differ between stages. But plasma testosterone was higher during breeding than during the other stages, similar to androgen receptor and aromatase expression in the preoptic area. The expression of androgen receptors in the song control nucleus HVC was lower during molt when birds do not sing or sing rarely, but similar between the breeding and the nonbreeding stage. Nevertheless, some song spectral features and the song repertoire differed between breeding and nonbreeding. Territorial behavior and song rate correlated with the expression of steroid receptors in hypothalamic areas, and in the song control nucleus lMAN. CONCLUSIONS Our results demonstrate seasonal modulation of song, circulating testosterone levels, and brain sensitivity to androgens, but a year-round persistency of territorial behavior and estrogen receptor expression in all life-cycle stages. This suggests that seasonal variations in circulating testosterone concentrations and brain sensitivity to androgens is widely uncoupled from territorial behavior and song activity but might still affect song pattern. Our study contributes to the understanding of the complex comparative neuroendocrinology of song birds in the wild.
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Affiliation(s)
- Camila P Villavicencio
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany. .,Department of Ecological Science, Institute of Ecology and Biodiversity, Faculty of Science, University of Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
| | - Harriet Windley
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany
| | - Pietro B D'Amelio
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany.,FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, 7701, South Africa
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany
| | - Wolfgang Goymann
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany
| | - René Quispe
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 6a, D-82319, Seewiesen, Germany.,Department of Marine Biology, Faculty of Ocean Sciences, Universidad Catolica del Norte (UCN), Larrondo 1281, Coquimbo, Chile
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15
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Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution. Cells 2021; 10:cells10020362. [PMID: 33572408 PMCID: PMC7916199 DOI: 10.3390/cells10020362] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
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16
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Hacohen-Kleiman G, Moaraf S, Kapitansky O, Gozes I. Sex-and Region-Dependent Expression of the Autism-Linked ADNP Correlates with Social- and Speech-Related Genes in the Canary Brain. J Mol Neurosci 2020; 70:1671-1683. [PMID: 32926339 DOI: 10.1007/s12031-020-01700-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 02/07/2023]
Abstract
The activity-dependent neuroprotective protein (ADNP) syndrome is an autistic-like disorder, instigated by mutations in ADNP. This syndrome is characterized by developmental delays, impairments in speech, motor function, abnormal hearing, and intellectual disabilities. In the Adnp-haploinsufficient mouse model, many of these impediments are evident, appearing in a sex-dependent manner. In zebra finch songbird (ZF; Taeniopygia guttata), an animal model used for song/language studies, ADNP mRNA most robust expression is observed in the cerebrum of young males, potentially corroborating with male ZF exclusive singing behavior and developed cerebral song system. Herein, we report a similar sex-dependent ADNP expression profile, with the highest expression in the cerebrum (qRT-PCR) in the brain of another songbird, the domesticated canary (Serinus canaria domestica). Additional analyses for the mRNA transcripts of the ADNP regulator, vasoactive intestinal peptide (VIP), sister gene ADNP2, and speech-related Forkhead box protein P2 (FoxP2) revealed multiple sex and brain region-dependent positive correlations between the genes (including ADNP). Parallel transcript expression patterns for FoxP2 and VIP were observed alongside specific FoxP2 increase in males compared with females as well as VIP/ADNP2 correlations. In spatial view, a sexually independent extensive form of expression was found for ADNP in the canary cerebrum (RNA in situ hybridization). The songbird cerebral mesopallium area stood out as a potentially high-expressing ADNP tissue, further strengthening the association of ADNP with sense integration and auditory memory formation, previously implicated in mouse and human.
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Affiliation(s)
- Gal Hacohen-Kleiman
- The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel
- Department of Natural and Life Sciences, The Open University of Israel, 43107, Ra'anana, Israel
| | - Stan Moaraf
- Department of Natural and Life Sciences, The Open University of Israel, 43107, Ra'anana, Israel
- School of Zoology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Oxana Kapitansky
- The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Illana Gozes
- The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel.
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17
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Gazda MA, Araújo PM, Lopes RJ, Toomey MB, Andrade P, Afonso S, Marques C, Nunes L, Pereira P, Trigo S, Hill GE, Corbo JC, Carneiro M. A genetic mechanism for sexual dichromatism in birds. Science 2020; 368:1270-1274. [DOI: 10.1126/science.aba0803] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022]
Abstract
Sexual dichromatism, a difference in coloration between males and females, may be due to sexual selection for ornamentation and mate choice. Here, we show that carotenoid-based dichromatism in mosaic canaries, a hybrid phenotype that arises in offspring of the sexually dichromatic red siskin and monochromatic canaries, is controlled by the gene that encodes the carotenoid-cleaving enzyme β-carotene oxygenase 2 (BCO2). Dichromatism in mosaic canaries is explained by differential carotenoid degradation in the integument, rather than sex-specific variation in physiological functions such as pigment uptake or transport. Transcriptome analyses suggest that carotenoid degradation in the integument might be a common mechanism contributing to sexual dichromatism across finches. These results suggest that differences in ornamental coloration between sexes can evolve through simple molecular mechanisms controlled by genes of major effect.
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Affiliation(s)
- Małgorzata A. Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro M. Araújo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- MARE – Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ricardo J. Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Matthew B. Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biological Science, University of Tulsa, Tulsa, OK 74104, USA
| | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Cristiana Marques
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Luís Nunes
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paulo Pereira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sandra Trigo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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18
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Cox RM. Sex steroids as mediators of phenotypic integration, genetic correlations, and evolutionary transitions. Mol Cell Endocrinol 2020; 502:110668. [PMID: 31821857 DOI: 10.1016/j.mce.2019.110668] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023]
Abstract
In recent decades, endocrinologists have increasingly adopted evolutionary methods and perspectives to characterize the evolution of the vertebrate endocrine system and leverage it as a model for developing and testing evolutionary theories. This review summarizes recent research on sex steroids (androgens and estrogens) to illustrate three ways in which a detailed understanding of the molecular and cellular architecture of hormonally mediated gene expression can enhance our understanding of general evolutionary principles. By virtue of their massively pleiotropic effects on the expression of genes and phenotypes, sex steroids and their receptors can (1) structure the patterns of phenotypic variance and covariance that are available to natural selection, (2) alter the underlying genetic correlations that determine a population's evolutionary response to selection, and (3) facilitate evolutionary transitions in fitness-related phenotypes via subtle regulatory shifts in underlying tissues and genes. These principles are illustrated by the author's research on testosterone and sexual dimorphism in lizards, and by recent examples drawn from other vertebrate systems. Mechanistically, these examples call attention to the importance of evolutionary changes in (1) androgen- and estrogen-mediated gene expression, (2) androgen and estrogen receptor expression, and (3) the distribution of androgen and estrogen response elements in target genes throughout the genome. A central theme to emerge from this review is that the rapidly increasing availability of genomic and transcriptomic data from non-model organisms places evolutionary endocrinologist in an excellent position to address the hormonal regulation of the key evolutionary interface between genes and phenotypes.
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Affiliation(s)
- Robert M Cox
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA.
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19
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Ko MC, Van Meir V, Vellema M, Gahr M. Characteristics of song, brain-anatomy and blood androgen levels in spontaneously singing female canaries. Horm Behav 2020; 117:104614. [PMID: 31647922 DOI: 10.1016/j.yhbeh.2019.104614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022]
Abstract
Females of many northern temperate songbird species sing sporadically. However, detailed descriptions of female song are rare. Here we report a detailed analysis of song in a small number of spontaneously-singing female domesticated canaries (Serinus canaria) under non-breeding, laboratory conditions in a large population of domesticated birds. In-depth analysis showed that these females sang rarely, and the spontaneous songs varied between and within birds over time. Furthermore, spontaneous female songs were distinct from songs of testosterone-induced singing female canaries and from songs of male canaries in both temporal and spectral features. Singing females had significantly elevated plasma androgen levels and a larger size of the major song controlling brain nuclei HVC (used as a proper name) and the robust nucleus of the arcopallium (RA) than non-singing females housed under similar conditions. The sporadically observed production of song and accompanying differences in brain anatomy in female canaries may thus depend on minute intraspecific differences in androgen levels.
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Affiliation(s)
- Meng-Ching Ko
- Max Planck Institute for Ornithology, Dept. of Behavioural Neurobiology, Eberhard-Gwinner str. 6a, 82319 Seewiesen, Germany.
| | - Vincent Van Meir
- Max Planck Institute for Ornithology, Dept. of Behavioural Neurobiology, Eberhard-Gwinner str. 6a, 82319 Seewiesen, Germany
| | - Michiel Vellema
- Utrecht University, Dept. of Experimental Psychology, Yalelaan 2, 3584, CM, Utrecht, the Netherlands
| | - Manfred Gahr
- Max Planck Institute for Ornithology, Dept. of Behavioural Neurobiology, Eberhard-Gwinner str. 6a, 82319 Seewiesen, Germany
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20
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Feather Evolution from Precocial to Altricial Birds. Zool Stud 2019; 58:e24. [PMID: 31966325 DOI: 10.6620/zs.2019.58-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022]
Abstract
Birds are the most abundant terrestrial vertebrates and their diversity is greatly shaped by the feathers. How avian evolution is linked to feather evolution has long been a fascinating question. Numerous excellent studies have shed light on this complex relationship by investigating feather diversity and its underlying molecular mechanisms. However, most have focused on adult domestic birds, and the contribution of feather diversity to environmental adaptation has not been well-studied. In this review, we described bird diversity using the traditional concept of the altricial-precocial spectrum in bird hatchlings. We combined the spectrum with a recently published avian phylogeny to profile the spectrum evolution. We then focused on the discrete diagnostic character of the spectrum, the natal down, and propose a hypothesis for the precocial-to-altricial evolution. For the underlying molecular mechanisms in feather diversity and bird evolution, we reviewed the literature and constructed the known mechanisms for feather tract definition and natal down development. Finally, we suggested some future directions for research on altricial-precocial divergence, which may expand our understanding of the relationship between natal down diversity and bird evolution.
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21
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Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
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Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
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22
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Anderson AP, Jones AG. erefinder: Genome-wide detection of oestrogen response elements. Mol Ecol Resour 2019; 19:1366-1373. [PMID: 31177626 DOI: 10.1111/1755-0998.13046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 11/28/2022]
Abstract
Oestrogen response elements (EREs) are specific DNA sequences to which ligand-bound oestrogen receptors (ERs) physically bind, allowing them to act as transcription factors for target genes. Locating EREs and ER responsive regions is therefore a potentially important component of the study of oestrogen-regulated pathways. Here, we report the development of a novel software tool, erefinder, which conducts a genome-wide, sliding-window analysis of oestrogen receptor binding affinity. We demonstrate the effects of adjusting window size and highlight the program's general agreement with ChIP studies. We further provide two examples of how erefinder can be used for comparative approaches. erefinder can handle large input files, has settings to allow for broad and narrow searches, and provides the full output to allow for greater data manipulation. These features facilitate a wide range of hypothesis testing for researchers and make erefinder an excellent tool to aid in oestrogen-related research.
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Affiliation(s)
- Andrew P Anderson
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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23
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Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019; 29:1712-1720.e7. [PMID: 31080084 PMCID: PMC6538971 DOI: 10.1016/j.cub.2019.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/16/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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Affiliation(s)
- Toni I Gossmann
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Bielefeld University, Department of Animal Behaviour, 33501 Bielefeld, Germany
| | - Achchuthan Shanmugasundram
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ludovic Duvaux
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France; BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Lemaire
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany; Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Lee D Roberts
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Sophia Schade
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna M Gostner
- Division of Medical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Falk Hildebrand
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Enrica Calvani
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Dominique Allaine
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Aurélie Cohas
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany.
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24
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Vellema M, Diales Rocha M, Bascones S, Zsebők S, Dreier J, Leitner S, Van der Linden A, Brewer J, Gahr M. Accelerated redevelopment of vocal skills is preceded by lasting reorganization of the song motor circuitry. eLife 2019; 8:43194. [PMID: 31099755 PMCID: PMC6570526 DOI: 10.7554/elife.43194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/16/2019] [Indexed: 01/16/2023] Open
Abstract
Complex motor skills take considerable time and practice to learn. Without continued practice the level of skill performance quickly degrades, posing a problem for the timely utilization of skilled motor behaviors. Here we quantified the recurring development of vocal motor skills and the accompanying changes in synaptic connectivity in the brain of a songbird, while manipulating skill performance by consecutively administrating and withdrawing testosterone. We demonstrate that a songbird with prior singing experience can significantly accelerate the re-acquisition of vocal performance. We further demonstrate that an increase in vocal performance is accompanied by a pronounced synaptic pruning in the forebrain vocal motor area HVC, a reduction that is not reversed when birds stop singing. These results provide evidence that lasting synaptic changes in the motor circuitry are associated with the savings of motor skills, enabling a rapid recovery of motor performance under environmental time constraints.
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Affiliation(s)
- Michiel Vellema
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Bio Imaging Lab, University of Antwerp, Antwerp, Belgium
| | - Mariana Diales Rocha
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Sabrina Bascones
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Sándor Zsebők
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Jes Dreier
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Stefan Leitner
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | | | - Jonathan Brewer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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25
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Kolchanova S, Kliver S, Komissarov A, Dobrinin P, Tamazian G, Grigorev K, Wolfsberger WW, Majeske AJ, Velez-Valentin J, Valentin de la Rosa R, Paul-Murphy JR, Guzman DSM, Court MH, Rodriguez-Flores JL, Martínez-Cruzado JC, Oleksyk TK. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes (Basel) 2019; 10:E54. [PMID: 30654561 PMCID: PMC6356210 DOI: 10.3390/genes10010054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/13/2018] [Accepted: 01/08/2019] [Indexed: 11/17/2022] Open
Abstract
Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.
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Affiliation(s)
- Sofiia Kolchanova
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Aleksei Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Pavel Dobrinin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Kirill Grigorev
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
| | - Walter W Wolfsberger
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
| | - Audrey J Majeske
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Beaumont BioBank, William Beaumont Hospital, Royal Oak, MI 48073, USA.
| | - Jafet Velez-Valentin
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande, PR 00745, USA.
| | - Ricardo Valentin de la Rosa
- The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo, PR 00613, USA.
| | - Joanne R Paul-Murphy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - David Sanchez-Migallon Guzman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Michael H Court
- Program in Individualized Medicine (PrIMe), Pharmacogenomics Laboratory, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, 100 Grimes Way, Pullman, WA 99164, USA.
| | | | | | - Taras K Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, PR 00680, USA.
- Department of Biological Sciences, Oakland University, 118 Library Drive, Rochester, MI 48309, USA.
- Department of Biological Sciences, Uzhhorod National University, 88000 Uzhhorod, Ukraine.
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26
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Damas J, Kim J, Farré M, Griffin DK, Larkin DM. Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. Genome Biol 2018; 19:155. [PMID: 30290830 PMCID: PMC6173868 DOI: 10.1186/s13059-018-1544-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/18/2018] [Indexed: 11/29/2022] Open
Abstract
Background Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history. However, this is impeded by both the fragmented nature of the majority of genome assemblies and the limitations of the available software to work with them. These limitations are particularly apparent in birds, with only 10 chromosome-level assemblies reported thus far. Algorithmic approaches applied to fragmented genome assemblies can nonetheless help define patterns of chromosomal change in defined taxonomic groups. Results Here, we make use of the DESCHRAMBLER algorithm to perform the first large-scale study of ancestral chromosome structure and evolution in birds. This algorithm allows us to reconstruct the overall genome structure of 14 key nodes of avian evolution from the Avian ancestor to the ancestor of the Estrildidae, Thraupidae and Fringillidae families. Conclusions Analysis of these reconstructions provides important insights into the variability of rearrangement rates during avian evolution and allows the detection of patterns related to the chromosome distribution of evolutionary breakpoint regions. Moreover, the inclusion of microchromosomes in our reconstructions allows us to provide novel insights into the evolution of these avian chromosomes, specifically. Electronic supplementary material The online version of this article (10.1186/s13059-018-1544-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, UK.
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27
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Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting. Genes (Basel) 2018; 9:genes9040181. [PMID: 29584697 PMCID: PMC5924523 DOI: 10.3390/genes9040181] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/08/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.
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28
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Kretschmer R, de Lima VLC, de Souza MS, Costa AL, O’Brien PCM, Ferguson-Smith MA, de Oliveira EHC, Gunski RJ, Garnero ADV. Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions. COMPARATIVE CYTOGENETICS 2018; 12:97-110. [PMID: 29675139 PMCID: PMC5904361 DOI: 10.3897/compcytogen.v12i1.22344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Vanusa Lilian Camargo de Lima
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Marcelo Santos de Souza
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Alice Lemos Costa
- Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Patricia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
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29
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Colquitt BM, Mets DG, Brainard MS. Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning. Gigascience 2018; 7:1-6. [PMID: 29618046 PMCID: PMC5861438 DOI: 10.1093/gigascience/giy008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Accepted: 02/06/2018] [Indexed: 12/18/2022] Open
Abstract
Background Vocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood. Findings To establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes. Conclusions We provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.
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Affiliation(s)
- Bradley M Colquitt
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
| | - David G Mets
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
| | - Michael S Brainard
- Department of Physiology, University of California-San Francisco, San Francisco, 94158 California
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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30
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Frankl-Vilches C, Gahr M. Androgen and estrogen sensitivity of bird song: a comparative view on gene regulatory levels. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2018; 204:113-126. [PMID: 29209770 PMCID: PMC5790841 DOI: 10.1007/s00359-017-1236-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/02/2017] [Accepted: 11/09/2017] [Indexed: 12/16/2022]
Abstract
Singing of songbirds is sensitive to testosterone and its androgenic and estrogenic metabolites in a species-specific way. The hormonal effects on song pattern are likely mediated by androgen receptors (AR) and estrogen receptor alpha (ERα), ligand activated transcription factors that are expressed in neurons of various areas of the songbirds' vocal control circuit. The distribution of AR in this circuit is rather similar between species while that of ERα is species variant and concerns a key vocal control area, the HVC (proper name). We discuss the regulation of the expression of the cognate AR and ERα and putative splice variants. In particular, we suggest that transcription factor binding sites in the promoter of these receptors differ between bird species. Further, we suggest that AR- and ERα-dependent gene regulation in vocal areas differs between species due to species-specific DNA binding sites of putative target genes that are required for the transcriptional activity of the receptors. We suggest that species differences in the distribution of AR and ERα in vocal areas and in the genomic sensitivity to these receptors contribute to species-specific hormonal regulation of the song.
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Affiliation(s)
- Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
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31
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High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds. Proc Natl Acad Sci U S A 2017; 114:5219-5224. [PMID: 28465440 DOI: 10.1073/pnas.1700751114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Yellow, orange, and red coloration is a fundamental aspect of avian diversity and serves as an important signal in mate choice and aggressive interactions. This coloration is often produced through the deposition of diet-derived carotenoid pigments, yet the mechanisms of carotenoid uptake and transport are not well-understood. The white recessive breed of the common canary (Serinus canaria), which carries an autosomal recessive mutation that renders its plumage pure white, provides a unique opportunity to investigate mechanisms of carotenoid coloration. We carried out detailed genomic and biochemical analyses comparing the white recessive with yellow and red breeds of canaries. Biochemical analysis revealed that carotenoids are absent or at very low concentrations in feathers and several tissues of white recessive canaries, consistent with a genetic defect in carotenoid uptake. Using a combination of genetic mapping approaches, we show that the white recessive allele is due to a splice donor site mutation in the scavenger receptor B1 (SCARB1; also known as SR-B1) gene. This mutation results in abnormal splicing, with the most abundant transcript lacking exon 4. Through functional assays, we further demonstrate that wild-type SCARB1 promotes cellular uptake of carotenoids but that this function is lost in the predominant mutant isoform in white recessive canaries. Our results indicate that SCARB1 is an essential mediator of the expression of carotenoid-based coloration in birds, and suggest a potential link between visual displays and lipid metabolism.
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Sætre GP, Cuevas A, Hermansen JS, Elgvin TO, Fernández LP, Sæther SA, Cascio Sætre CL, Eroukhmanoff F. Rapid polygenic response to secondary contact in a hybrid species. Proc Biol Sci 2017; 284:20170365. [PMID: 28446700 PMCID: PMC5413929 DOI: 10.1098/rspb.2017.0365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/22/2017] [Indexed: 12/26/2022] Open
Abstract
Secondary contact between closely related species can have genetic consequences. Competition for essential resources may lead to divergence in heritable traits that reduces interspecific competition leading to increased rate of genetic divergence. Conversely, hybridization and backcrossing can lead to genetic convergence. Here, we study a population of a hybrid species, the Italian sparrow (Passer italiae), before and after it came into secondary contact with one of its parent species, the Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate strong consequences of interspecific competition: Italian sparrows were kept away from a popular feeding site by its parent species, resulting in poorer body condition and a significant drop in population size. Although no significant morphological change could be detected, after only 3 years of sympatry, the Italian sparrows had diverged significantly from the Spanish sparrows across a set of 81 protein-coding genes. These temporal genetic changes are mirrored by genetic divergence observed in older sympatric Italian sparrow populations within the same area of contact. Compared with microallopatric birds, sympatric ones are genetically more diverged from Spanish sparrows. Six significant outlier genes in the temporal and spatial comparison (i.e. showing the greatest displacement) have all been found to be associated with learning and neural development in other bird species.
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Affiliation(s)
- Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Jo S Hermansen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Tore O Elgvin
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Laura Piñeiro Fernández
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Stein A Sæther
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
- Norwegian Institute for Nature Research (NINA), PO Box 5685, Sluppen, 7485 Trondheim, Norway
| | - Camilla Lo Cascio Sætre
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Fabrice Eroukhmanoff
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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dos Santos MDS, Kretschmer R, Frankl-Vilches C, Bakker A, Gahr M, O´Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary. PLoS One 2017; 12:e0170997. [PMID: 28129381 PMCID: PMC5271350 DOI: 10.1371/journal.pone.0170997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.
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Affiliation(s)
| | - Rafael Kretschmer
- Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Patricia C. M. O´Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Belém, Brazil
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Kapusta A, Suh A. Evolution of bird genomes-a transposon's-eye view. Ann N Y Acad Sci 2016; 1389:164-185. [DOI: 10.1111/nyas.13295] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics; University of Utah School of Medicine; Salt Lake City Utah
| | - Alexander Suh
- Department of Evolutionary Biology (EBC); Uppsala University; Uppsala Sweden
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A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq. Sci Rep 2016; 6:20957. [PMID: 26864856 PMCID: PMC4750092 DOI: 10.1038/srep20957] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/14/2016] [Indexed: 01/20/2023] Open
Abstract
Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.
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Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ, Minx P, Stager M, Betuel A, Cheviron ZA, Warren WC, Gonser RA, Balakrishnan CN. Divergence and Functional Degradation of a Sex Chromosome-like Supergene. Curr Biol 2016; 26:344-50. [PMID: 26804558 DOI: 10.1016/j.cub.2015.11.069] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/12/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022]
Abstract
A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e., "supergenes" [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3-5]. Morph is determined by alternative alleles at a balanced >100-Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data, we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole-genome sequencing coupled with population- and phylogenomic data to show that alternate supergene alleles are highly divergent at over 1,000 genes and that these alleles originated prior to the split of Z. albicollis from its sister species and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the "white" allele may be degrading, similar to neo-Y/W sex chromosomes. We further show that the "tan" allele has surprisingly low levels of genetic diversity yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism.
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Affiliation(s)
- Elaina M Tuttle
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA.
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305-5020, USA
| | - Marisa L Korody
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
| | - Michael S Brewer
- Department of Biology, East Carolina University, Howell Science Complex, Greenville, NC 27858, USA
| | - Daniel J Newhouse
- Department of Biology, East Carolina University, Howell Science Complex, Greenville, NC 27858, USA
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Maria Stager
- Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Adam Betuel
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
| | - Zachary A Cheviron
- Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Rusty A Gonser
- Department of Biology and The Center for Genomic Advocacy, Indiana State University, 600 Chestnut Street, Terre Haute, IN 47809, USA
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Mueller JC, Kuhl H, Timmermann B, Kempenaers B. Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals. Mol Ecol Resour 2015. [PMID: 26220359 DOI: 10.1111/1755-0998.12450] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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de Oliveira Furo I, Kretschmer R, O’Brien PC, Ferguson-Smith MA, de Oliveira EHC. Chromosomal Diversity and Karyotype Evolution in South American Macaws (Psittaciformes, Psittacidae). PLoS One 2015; 10:e0130157. [PMID: 26087053 PMCID: PMC4472783 DOI: 10.1371/journal.pone.0130157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/18/2015] [Indexed: 11/18/2022] Open
Abstract
Most species of macaws, which represent the largest species of Neotropical Psittacidae, characterized by their long tails and exuberant colours, are endangered, mainly because of hunting, illegal trade and habitat destruction. Long tailed species seem to represent a monophyletic group within Psittacidae, supported by cytogenetic data. Hence, these species show karyotypes with predominance of biarmed macrochromosomes, in contrast to short tailed species, with a predominance of acro/telocentric macrochromosomes. Because of their similar karyotypes, it has been proposed that inversions and translocations may be the main types of rearrangements occurring during the evolution of this group. However, only one species of macaw, Ara macao, that has had its genome sequenced was analyzed by means of molecular cytogenetics. Hence, in order to verify the rearrangements, we analyzed the karyotype of two species of macaws, Ara chloropterus and Anodorhynchus hyacinthinus, using cross-species chromosome painting with two different sets of probes from chicken and white hawk. Both intra- and interchromosomal rearrangements were observed. Chicken probes revealed the occurrence of fusions, fissions and inversions in both species, while the probes from white hawk determined the correct breakpoints or chromosome segments involved in the rearrangements. Some of these rearrangements were common for both species of macaws (fission of GGA1 and fusions of GGA1p/GGA4q, GGA6/GGA7 and GGA8/GGA9), while the fissions of GGA 2 and 4p were found only in A. chloropterus. These results confirm that despite apparent chromosomal similarity, macaws have very diverse karyotypes, which differ from each other not only by inversions and translocations as postulated before, but also by fissions and fusions.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Programa de Pós Graduação em Genética e Biologia Molecular, Instituto de Ciências Biológicas Universidade Federal do Pará, Belém, PA, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
| | - Rafael Kretschmer
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Patrícia C. O’Brien
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA-Brazil
- * E-mail:
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