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Monteiro JPC, Pröhl H, Lyra ML, Brunetti AE, de Nardin EC, Condez TH, Haddad CFB, Rodríguez A. Expression patterns of melanin-related genes are linked to crypsis and conspicuousness in a pumpkin toadlet. Mol Ecol 2024:e17458. [PMID: 38970414 DOI: 10.1111/mec.17458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Colour signals play pivotal roles in different communication systems, and the evolution of these characters has been associated with behavioural ecology, integumentary production processes and perceptual mechanisms of the species involved. Here, we present the first insight into the molecular and histological basis of skin colour polymorphism within a miniaturized species of pumpkin toadlet, potentially representing the lowest size threshold for colour polytypism in tetrapods. Brachycephalus actaeus exhibits a coloration ranging from cryptic green to conspicuous orange skin, and our findings suggest that colour morphs differ in their capability to be detected by potential predators. We also found that the distribution and abundance of chromatophores are variable in the different colour morphs. The expression pattern of coloration related genes was predominantly associated with melanin synthesis (including dct, edn1, mlana, oca2, pmel, slc24a5, tyrp1 and wnt9a). Up-regulation of melanin genes in grey, green and brown skin was associated with higher melanophore abundance than in orange skin, where xanthophores predominate. Our findings provide a significant foundation for comparing and understanding the diverse pathways that contribute to the evolution of pigment production in the skin of amphibians.
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Affiliation(s)
- Juliane P C Monteiro
- Post-Graduate Program in Biodiversity, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
| | - Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
| | - Mariana L Lyra
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Andrés E Brunetti
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Institute of Subtropical Biology (IBS, UNaM-CONICET), Posadas, Misiones, Argentina
- Department of Insect Symbiosis, Max Planck Institute of Chemical Ecology, Jena, Thuringia, Germany
| | - Eli C de Nardin
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Thais H Condez
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Célio F B Haddad
- Department of Biodiversity and Aquaculture Center (CAUNESP), Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
- Center for Research on Biodiversity Dynamics and Climate Change, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Hannover, Lower Saxony, Germany
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2
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Rubio AO, Stuckert AMM, Geralds B, Nielsen R, MacManes MD, Summers K. What Makes a Mimic? Orange, Red, and Black Color Production in the Mimic Poison Frog (Ranitomeya imitator). Genome Biol Evol 2024; 16:evae123. [PMID: 38874406 PMCID: PMC11255871 DOI: 10.1093/gbe/evae123] [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: 09/03/2023] [Revised: 05/08/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
Aposematic organisms rely on their conspicuous appearance to signal that they are defended and unpalatable. Such phenotypes are strongly tied to survival and reproduction. Aposematic colors and patterns are highly variable; however, the genetic, biochemical, and physiological mechanisms producing this conspicuous coloration remain largely unidentified. Here, we identify genes potentially affecting color variation in two color morphs of Ranitomeya imitator: the orange-banded Sauce and the redheaded Varadero morphs. We examine gene expression in black and orange skin patches from the Sauce morph and black and red skin patches from the Varadero morph. We identified genes differentially expressed between skin patches, including those that are involved in melanin synthesis (e.g. mlana, pmel, tyrp1), iridophore development (e.g. paics, ppat, ak1), pteridine synthesis (e.g. gch1, pax3-a, xdh), and carotenoid metabolism (e.g. dgat2, rbp1, scarb2). In addition, using weighted correlation network analysis, we identified the top 50 genes with high connectivity from the most significant network associated with gene expression differences between color morphs. Of these 50 genes, 13 were known to be related to color production (gch1, gmps, gpr143, impdh1, mc1r, pax3-a, pax7, ppat, rab27a, rlbp1, tfec, trpm1, xdh).
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Affiliation(s)
- Andrew O Rubio
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Adam M M Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - BreAnn Geralds
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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3
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Stuckert AMM, Chouteau M, McClure M, LaPolice TM, Linderoth T, Nielsen R, Summers K, MacManes MD. The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 2024; 33:e17438. [PMID: 38923007 DOI: 10.1111/mec.17438] [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: 07/13/2023] [Revised: 04/22/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which mimicry is produced in poison frogs. We assembled a 6.02-Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four colour morphs of Ranitomeya imitator and two colour morphs from both R. fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes differentially expressed throughout development, many of them related to melanophores/melanin, iridophore development and guanine synthesis. We also identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in colour between morphs of these species, and identify several plausible candidates for colouration in vertebrates (e.g. cd36, ep-cadherin and perlwapin). Finally, we hypothesise that keratin genes (e.g. krt8) are important for producing different structural colours within these frogs.
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Affiliation(s)
- Adam M M Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), CNRS, IFREMER, Université de Guyane, Cayenne, France
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), CNRS, IFREMER, Université de Guyane, Cayenne, France
| | - Troy M LaPolice
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Kosch TA, Torres-Sánchez M, Liedtke HC, Summers K, Yun MH, Crawford AJ, Maddock ST, Ahammed MS, Araújo VLN, Bertola LV, Bucciarelli G, Carné A, Carneiro CM, Chan KO, Chen Y, Crottini A, da Silva JM, Denton RD, Dittrich C, Themudo GE, Farquharson KA, Forsdick NJ, Gilbert E, Jing C, Katzenback BA, Kotharambath R, Levis NA, Márquez R, Mazepa G, Mulder KP, Müller H, O’Connell MJ, Orozco-terWengel P, Palomar G, Petzold A, Pfennig DW, Pfennig KS, Reichert MS, Robert J, Scherz MD, Siu-Ting K, Snead AA, Stöck M, Stuckert AMM, Stynoski JL, Tarvin RD, Valero KCW. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601086. [PMID: 39005434 PMCID: PMC11244923 DOI: 10.1101/2024.06.27.601086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.
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Affiliation(s)
- Tiffany A. Kosch
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia
| | - María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Kyle Summers
- Biology Department, East Carolina University, Greenville, NC, USA 27858
| | - Maximina H. Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
- Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Simon T. Maddock
- School of Natural and Environmental Sciences, Newcastle University, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Seychelles
| | | | - Victor L. N. Araújo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Lorenzo V. Bertola
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD 4810, Australia
| | - Gary Bucciarelli
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, USA
| | - Albert Carné
- Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Céline M. Carneiro
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kin O. Chan
- University of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas 66045, USA
| | - Ying Chen
- Biology Department, Queen’s University, Ontario, Canada
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169– 007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jessica M. da Silva
- Evolutionary Genomics and Wildlife Management, Foundatonal Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands 7735, Cape Town, South Africa
- Centre for Evolutionary Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa
| | - Robert D. Denton
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Carolin Dittrich
- Rojas Lab, Konrad-Lorenz-Institute of Ethology, Department of Life Science, University of Veterinary Medicine, Vienna, Austria
| | - Gonçalo Espregueira Themudo
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos, Portugal
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Edward Gilbert
- School of Natural Sciences, The University of Hull, Hull, HU6 7RX, United Kingdom
- Energy and Environment Institute, The University of Hull, Hull, HU6 7RX, United Kingdom
| | - Che Jing
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | | | - Ramachandran Kotharambath
- Herpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, 671320, India
| | - Nicholas A. Levis
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roberto Márquez
- Department of Biological Sciences, Virginia Tech. Blacksburg, VA 24060, USA
| | - Glib Mazepa
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Kevin P. Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hendrik Müller
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, D-06108 Halle (Saale), Germany
| | - Mary J. O’Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Museum Avenue, CF10 3AX Cardiff, United Kingdom
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology; Faculty of Biological Sciences; Complutense University of Madrid, Madrid, Spain
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str.24-25, 14476 Potsdam, Germany
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karin S. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael S. Reichert
- Department of Integrative Biology, Oklahoma State University, Stillwater OK, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Karen Siu-Ting
- School of Biological Sciences, Queen’s University Belfast, Belfast, BT7 1NN, Northern Ireland, United Kingdom
- Instituto Peruano de Herpetología, Ca. Augusto Salazar Bondy 136, Surco, Lima, Peru
- Herpetology Lab, The Natural History Museum, London, United Kingdom
| | - Anthony A Snead
- Department of Biology, New York University, New York, NY, USA
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany
| | - Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | | | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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Page E, Queste LM, Rosser N, Salazar PA, Nadeau NJ, Mallet J, Srygley RB, McMillan WO, Dasmahapatra KK. Pervasive mimicry in flight behavior among aposematic butterflies. Proc Natl Acad Sci U S A 2024; 121:e2300886121. [PMID: 38408213 PMCID: PMC10945825 DOI: 10.1073/pnas.2300886121] [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: 02/14/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024] Open
Abstract
Flight was a key innovation in the adaptive radiation of insects. However, it is a complex trait influenced by a large number of interacting biotic and abiotic factors, making it difficult to unravel the evolutionary drivers. We investigate flight patterns in neotropical heliconiine butterflies, well known for mimicry of their aposematic wing color patterns. We quantify the flight patterns (wing beat frequency and wing angles) of 351 individuals representing 29 heliconiine and 9 ithomiine species belonging to ten color pattern mimicry groupings. For wing beat frequency and up wing angles, we show that heliconiine species group by color pattern mimicry affiliation. Convergence of down wing angles to mimicry groupings is less pronounced, indicating that distinct components of flight are under different selection pressures and constraints. The flight characteristics of the Tiger mimicry group are particularly divergent due to convergence with distantly related ithomiine species. Predator-driven selection for mimicry also explained variation in flight among subspecies, indicating that this convergence can occur over relatively short evolutionary timescales. Our results suggest that the flight convergence is driven by aposematic signaling rather than shared habitat between comimics. We demonstrate that behavioral mimicry can occur between lineages that have separated over evolutionary timescales ranging from <0.5 to 70 My.
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Affiliation(s)
- Edward Page
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
| | - Lucie M. Queste
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Neil Rosser
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | - Patricio A. Salazar
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, SheffieldS10 2TN, United Kingdom
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Nicola J. Nadeau
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | - Robert B. Srygley
- Smithsonian Tropical Research Institute, Apartado, Panamá0843-03092, Republic of Panama
- Pest Management Research Unit, Agricultural Research Service, United States Department of Agriculture, Sidney, MT59270
| | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Apartado, Panamá0843-03092, Republic of Panama
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6
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Twomey E, Melo-Sampaio P, Schulte LM, Bossuyt F, Brown JL, Castroviejo-Fisher S. Multiple Routes to Color Convergence in a Radiation of Neotropical Poison Frogs. Syst Biol 2023; 72:1247-1261. [PMID: 37561391 PMCID: PMC10924724 DOI: 10.1093/sysbio/syad051] [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: 06/22/2022] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023] Open
Abstract
Convergent evolution is defined as the independent evolution of similar phenotypes in different lineages. Its existence underscores the importance of external selection pressures in evolutionary history, revealing how functionally similar adaptations can evolve in response to persistent ecological challenges through a diversity of evolutionary routes. However, many examples of convergence, particularly among closely related species, involve parallel changes in the same genes or developmental pathways, raising the possibility that homology at deeper mechanistic levels is an important facilitator of phenotypic convergence. Using the genus Ranitomeya, a young, color-diverse radiation of Neotropical poison frogs, we set out to 1) provide a phylogenetic framework for this group, 2) leverage this framework to determine if color phenotypes are convergent, and 3) to characterize the underlying coloration mechanisms to test whether color convergence occurred through the same or different physical mechanisms. We generated a phylogeny for Ranitomeya using ultraconserved elements and investigated the physical mechanisms underlying bright coloration, focusing on skin pigments. Using phylogenetic comparative methods, we identified several instances of color convergence, involving several gains and losses of carotenoid and pterin pigments. We also found a compelling example of nonparallel convergence, where, in one lineage, red coloration evolved through the red pterin pigment drosopterin, and in another lineage through red ketocarotenoids. Additionally, in another lineage, "reddish" coloration evolved predominantly through structural color mechanisms. Our study demonstrates that, even within a radiation of closely related species, convergent evolution can occur through both parallel and nonparallel mechanisms, challenging the assumption that similar phenotypes among close relatives evolve through the same mechanisms.
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Affiliation(s)
- Evan Twomey
- Department of Wildlife/Zoo Animal Biology and Systematics, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
| | - Paulo Melo-Sampaio
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, R. Gen. Herculano Gomes 41, Rio de Janeiro 20941-360, Brazil
| | - Lisa M Schulte
- Department of Wildlife/Zoo Animal Biology and Systematics, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
| | - Franky Bossuyt
- Amphibian Evolution Laboratory, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Jason L Brown
- School of Biological Sciences, Southern Illinois University, 125 Lincoln Dr., Carbondale, IL 62901, USA
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7
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Gonzalez M, Carazzone C. Eco-Metabolomics Applied to the Chemical Ecology of Poison Frogs (Dendrobatoidea). J Chem Ecol 2023; 49:570-598. [PMID: 37594619 PMCID: PMC10725362 DOI: 10.1007/s10886-023-01443-0] [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: 04/14/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
Amphibians are one of the most remarkable sources of unique natural products. Biogenic amines, peptides, bufodienolides, alkaloids, and volatile organic compounds have been characterized in different species. The superfamily Dendrobatoidea represents one of the most enigmatic cases of study in chemical ecology because their skin secretome is composed by a complex mixture (i.e. cocktail) of highly lethal and noxious unique alkaloid structures. While chemical defences from dendrobatoids (families Dendrobatidae and Aromobatidae) have been investigated employing ecological, behavioral, phylogenetic and evolutionary perspectives, studies about the analytical techniques needed to perform the chemical characterization have been neglected for many years. Therefore, our aim is to summarize the current methods applied for the characterization of chemical profiles in dendrobatoids and to illustrate innovative Eco-metabolomics strategies that could be translated to this study model. This approach could be extended to natural products other than alkaloids and implemented for the chemical analysis of different species of dendrobatoids employing both low- and high-resolution mass spectrometers. Here, we overview important biological features to be considered, procedures that could be applied to perform the chemical characterization, steps and tools to perform an Eco-metabolomic analysis, and a final discussion about future perspectives.
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Affiliation(s)
- Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, 4976, Bogotá, AA, Colombia.
- Department of Biology, Stanford University, Palo Alto, CA, 94305, USA.
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, 4976, Bogotá, AA, Colombia.
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8
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de Araujo Miles M, Johnson MJ, Stuckert AMM, Summers K. A histological analysis of coloration in the Peruvian mimic poison frog ( Ranitomeya imitator). PeerJ 2023; 11:e15533. [PMID: 37404476 PMCID: PMC10317021 DOI: 10.7717/peerj.15533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/19/2023] [Indexed: 07/06/2023] Open
Abstract
Aposematism continues to be a phenomenon of central interest in evolutionary biology. The life history of the mimic poison frog, Ranitomeya imitator, relies heavily on aposematism. In order for aposematic signals to be effective, predators must be able to learn to avoid the associated phenotype. However, in R. imitator, aposematism is associated with four different color phenotypes that mimic a complex of congeneric species occurring across the mimic frog's geographic range. Investigations of the underlying mechanics of color production in these frogs can provide insights into how and why these different morphs evolved. We used histological samples to examine divergence in the color production mechanisms used by R. imitator to produce effective aposematic signals across its geographic range. We measured the coverage of melanophores and xanthophores (the area covered by chromatophores divided by total area of the skin section) in each color morph. We find that morphs that produce orange skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce yellow skin. In turn, morphs that produce yellow skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce green skin. Generally, across the morphs, a high ratio of xanthophores to melanophores is associated with colors of brighter spectral reflectance. Together, our results contribute to the understanding of color production in amphibians and document divergence in the histology of a species that is subject to divergent selection associated with aposematism.
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Affiliation(s)
| | | | - Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Kyle Summers
- Biology Department, East Carolina University, Greenville, NC, United States
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10
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Muell MR, Chávez G, Prates I, Guillory WX, Kahn TR, Twomey EM, Rodrigues MT, Brown JL. Phylogenomic analysis of evolutionary relationships in Ranitomeya poison frogs (Family Dendrobatidae) using ultraconserved elements. Mol Phylogenet Evol 2022; 168:107389. [PMID: 35026428 DOI: 10.1016/j.ympev.2022.107389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
The use of genome-scale data in phylogenetics has enabled recent strides in determining the relationships between taxa that are taxonomically problematic because of extensive morphological variation. Here, we employ a phylogenomic approach to infer evolutionary relationships within Ranitomeya (Anura: Dendrobatidae), an Amazonian lineage of poison frogs consisting of 16 species with remarkable diversity in color pattern, range size, and parental care behavior. We infer phylogenies with all described species of Ranitomeya from ultraconserved nuclear genomic elements (UCEs) and also estimate divergence times. Our results differ from previous analyses regarding interspecific relationships. Notably, we find that R. toraro and R. defleri are not sister species but rather distantly related, contrary to previous analyses based on smaller genetic datasets. We recover R. uakarii as paraphyletic, designate certain populations formerly assigned to R. fantastica from Peru as R. summersi, and transfer the French Guianan and eastern Brazilian R. amazonica populations to R. variabilis. By clarifying both inter- and intraspecific relationships within Ranitomeya, our study paves the way for future tests of hypotheses on color pattern evolution and historical biogeography.
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Affiliation(s)
- Morgan R Muell
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Germán Chávez
- Instituto Peruano de Herpetología, Lima, Perú; División de Herpetología - CORBIDI, Lima, Perú
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wilson X Guillory
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Rutgers University Newark, Newark, NJ, USA
| | - Ted R Kahn
- Species Survival Commission (SSC), International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Evan M Twomey
- Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Jason L Brown
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
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11
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Relationship between model noxiousness and mimetic accuracy in myrmecomorphic spiders. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10126-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Stuart-Fox D, Rankin KJ, Lutz A, Elliott A, Hugall AF, McLean CA, Medina I. Environmental gradients predict the ratio of environmentally acquired carotenoids to self-synthesised pteridine pigments. Ecol Lett 2021; 24:2207-2218. [PMID: 34350679 DOI: 10.1111/ele.13850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 07/09/2021] [Indexed: 12/22/2022]
Abstract
Carotenoids are important pigments producing integument colouration; however, their dietary availability may be limited in some environments. Many species produce yellow to red hues using a combination of carotenoids and self-synthesised pteridine pigments. A compelling hypothesis is that pteridines replace carotenoids in environments where carotenoid availability is limited. To test this hypothesis, we quantified concentrations of five carotenoid and six pteridine pigments in multiple skin colours and individuals from 27 species of agamid lizards. We show that environmental gradients predict the ratio of carotenoids to pteridines; carotenoid concentrations are lower and pteridine concentrations higher in arid environments with low vegetation productivity. Both carotenoid and pteridine pigments were present in all species, but only pteridine concentrations explained colour variation among species and there were no correlations between carotenoid and pteridine pigments with a similar hue. These results suggest that in arid environments, where carotenoids are likely limited, species may compensate by synthesising more pteridines but do not necessarily replace carotenoids with pteridines of similar hue.
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Affiliation(s)
- Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Katrina J Rankin
- School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Adrian Lutz
- Metabolomics Australia, The University of Melbourne, Parkville, Vic, Australia
| | - Adam Elliott
- School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Andrew F Hugall
- Sciences Department, Museums Victoria, Carlton Gardens, Melbourne, Vic, Australia
| | - Claire A McLean
- School of BioSciences, The University of Melbourne, Parkville, Vic, Australia.,Sciences Department, Museums Victoria, Carlton Gardens, Melbourne, Vic, Australia
| | - Iliana Medina
- School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
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Stuckert AMM, Chouteau M, McClure M, LaPolice TM, Linderoth T, Nielsen R, Summers K, MacManes MD. The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 2021; 30:4039-4061. [PMID: 34145931 PMCID: PMC8457190 DOI: 10.1111/mec.16024] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022]
Abstract
A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid colour and pattern are produced in a Müllerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp R. imitator and two colour morphs from both Ranitomeya fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development and guanine synthesis. Polytypic differences within species may be the result of differences in expression and/or timing of expression, whereas convergence for colour pattern between species does not appear to be due to the same changes in gene expression. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in colour between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colours within these frogs.
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Affiliation(s)
- Adam M. M. Stuckert
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Mathieu Chouteau
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA)Université de Guyane, CNRS, IFREMERCayenneFrance
| | - Troy M. LaPolice
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Tyler Linderoth
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Rasmus Nielsen
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kyle Summers
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
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de Mello PLH, Hime PM, Glor RE. Transcriptomic Analysis of Skin Color in Anole Lizards. Genome Biol Evol 2021; 13:evab110. [PMID: 33988681 PMCID: PMC8290120 DOI: 10.1093/gbe/evab110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 01/23/2023] Open
Abstract
Color and color pattern are critical for animal camouflage, reproduction, and defense. Few studies, however, have attempted to identify candidate genes for color and color pattern in squamate reptiles, a colorful group with over 10,000 species. We used comparative transcriptomic analyses between white, orange, and yellow skin in a color-polymorphic species of anole lizard to 1) identify candidate color and color-pattern genes in squamates and 2) assess if squamates share an underlying genetic basis for color and color pattern variation with other vertebrates. Squamates have three types of chromatophores that determine color pattern: guanine-filled iridophores, carotenoid- or pteridine-filled xanthophores/erythrophores, and melanin-filled melanophores. We identified 13 best candidate squamate color and color-pattern genes shared with other vertebrates: six genes linked to pigment synthesis pathways, and seven genes linked to chromatophore development and maintenance. In comparisons of expression profiles between pigment-rich and white skin, pigment-rich skin upregulated the pteridine pathway as well as xanthophore/erythrophore development and maintenance genes; in comparisons between orange and yellow skin, orange skin upregulated the pteridine and carotenoid pathways as well as melanophore maintenance genes. Our results corroborate the predictions that squamates can produce similar colors using distinct color-reflecting molecules, and that both color and color-pattern genes are likely conserved across vertebrates. Furthermore, this study provides a concise list of candidate genes for future functional verification, representing a first step in determining the genetic basis of color and color pattern in anoles.
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Affiliation(s)
- Pietro Longo Hollanda de Mello
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
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Twomey E, Johnson JD, Castroviejo-Fisher S, Van Bocxlaer I. A ketocarotenoid-based colour polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation. Mol Ecol 2020; 29:2004-2015. [PMID: 32402099 DOI: 10.1111/mec.15466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 01/12/2023]
Abstract
The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog Ranitomeya sirensis is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.
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Affiliation(s)
- Evan Twomey
- Laboratorio de Sistemática de Vertebrados, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Amphibian Evolution Laboratory, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - James D Johnson
- Department of Chemistry, Florida State University, Tallahassee, FL, USA
| | - Santiago Castroviejo-Fisher
- Laboratorio de Sistemática de Vertebrados, Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Ines Van Bocxlaer
- Amphibian Evolution Laboratory, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
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