1
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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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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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3
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Recknagel H, Leitão HG, Elmer KR. Genetic basis and expression of ventral colour in polymorphic common lizards. Mol Ecol 2024; 33:e17278. [PMID: 38268086 DOI: 10.1111/mec.17278] [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: 09/12/2022] [Revised: 12/15/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024]
Abstract
Colour is an important visual cue that can correlate with sex, behaviour, life history or ecological strategies, and has evolved divergently and convergently across animal lineages. Its genetic basis in non-model organisms is rarely known, but such information is vital for determining the drivers and mechanisms of colour evolution. Leveraging genetic admixture in a rare contact zone between oviparous and viviparous common lizards (Zootoca vivipara), we show that females (N = 558) of the two otherwise morphologically indistinguishable reproductive modes differ in their ventral colouration (from pale to vibrant yellow) and intensity of melanic patterning. We find no association between female colouration and reproductive investment, and no evidence for selection on colour. Using a combination of genetic mapping and transcriptomic evidence, we identified two candidate genes associated with ventral colour differentiation, DGAT2 and PMEL. These are genes known to be involved in carotenoid metabolism and melanin synthesis respectively. Ventral melanic spots were associated with two genomic regions, including a SNP close to protein tyrosine phosphatase (PTP) genes. Using genome re-sequencing data, our results show that fixed coding mutations in the candidate genes cannot account for differences in colouration. Taken together, our findings show that the evolution of ventral colouration and its associations across common lizard lineages is variable. A potential genetic mechanism explaining the flexibility of ventral colouration may be that colouration in common lizards, but also across squamates, is predominantly driven by regulatory genetic variation.
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Affiliation(s)
- Hans Recknagel
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Henrique G Leitão
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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4
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Recknagel H, Harvey WT, Layton M, Elmer KR. Common lizard microhabitat selection varies by sex, parity mode, and colouration. BMC Ecol Evol 2023; 23:47. [PMID: 37667183 PMCID: PMC10478496 DOI: 10.1186/s12862-023-02158-2] [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: 01/25/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Animals select and interact with their environment in various ways, including to ensure their physiology is at its optimal capacity, access to prey is possible, and predators can be avoided. Often conflicting, the balance of choices made may vary depending on an individual's life-history and condition. The common lizard (Zootoca vivipara) has egg-laying and live-bearing lineages and displays a variety of dorsal patterns and colouration. How colouration and reproductive mode affect habitat selection decisions on the landscape is not known. In this study, we first tested if co-occurring male and female viviparous and oviparous common lizards differ in their microhabitat selection. Second, we tested if the dorsal colouration of an individual lizard matched its basking site choice within the microhabitat where it was encountered, which could be related to camouflage and crypsis. RESULTS We found that site use differed from the habitat otherwise available, suggesting lizards actively choose the composition and structure of their microhabitat. Females were found in areas with more wood and less bare ground compared to males; we speculate that this may be for better camouflage and reducing predation risk during pregnancy, when females are less mobile. Microhabitat use also differed by parity mode: viviparous lizards were found in areas with more density of flowering plants, while oviparous lizards were found in areas that were wetter and had more moss. This may relate to differing habitat preferences of viviparous vs. oviparous for clutch lay sites. We found that an individual's dorsal colouration matched that of the substrate of its basking site. This could indicate that individuals may choose their basking site to optimise camouflage within microhabitat. Further, all individuals were found basking in areas close to cover, which we expect could be used to escape predation. CONCLUSIONS Our study suggests that common lizards may actively choose their microhabitat and basking site, balancing physiological requirements, escape response and camouflage as a tactic for predator avoidance. This varies for parity modes, sexes, and dorsal colourations, suggesting that individual optimisation strategies are influenced by inter-individual variation within populations as well as determined by evolutionary differences associated with life history.
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Affiliation(s)
- Hans Recknagel
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Biotechnical Faculty, Department of Biology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - William T Harvey
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Megan Layton
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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5
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Libro P, Chiocchio A, De Rysky E, Di Martino J, Bisconti R, Castrignanò T, Canestrelli D. De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage. Sci Data 2023; 10:330. [PMID: 37244908 DOI: 10.1038/s41597-023-02217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/09/2023] [Indexed: 05/29/2023] Open
Abstract
Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we assembled and annotated the first de novo transcriptome of the head tissues of Salamandra salamandra from individuals, representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully assembled and annotated. The high-quality of the assembly was confirmed by three assembly validators. The alignment of contigs against the de novo transcriptome led to a mapping percentage higher than 94%. The homology annotation with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NR, Swiss-Prot and TrEMBL. The domain and site protein prediction led to 9850 GO-annotated contigs. This de novo transcriptome represents reliable reference for comparative gene expression studies between alternative behavioral types, for comparative gene expression studies within Salamandra, and for whole transcriptome and proteome studies in amphibians.
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Affiliation(s)
- Pietro Libro
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Andrea Chiocchio
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Erika De Rysky
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Jessica Di Martino
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Roberta Bisconti
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
| | - Tiziana Castrignanò
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy.
| | - Daniele Canestrelli
- Università degli Studi della Tuscia, Dipartimento di Scienze ecologiche e Biologiche, Largo dell'Università snc, 01100, Viterbo, Italy
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6
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Jin Y, Aguilar-Gómez D, Y C Brandt D, Square TA, Li J, Liu Z, Wang T, Sudmant PH, Miller CT, Nielsen R. Population Genomics of Variegated Toad-Headed Lizard Phrynocephalus versicolor and Its Adaptation to the Colorful Sand of the Gobi Desert. Genome Biol Evol 2022; 14:6604964. [PMID: 35679302 PMCID: PMC9260186 DOI: 10.1093/gbe/evac076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The variegated toad-headed agama, Phrynocephalus versicolor, lives in the arid landscape of the Chinese Gobi Desert. We analyzed populations from three different locations which vary in substrate color and altitude: Heishankou (HSK), Guazhou County (GZ), and Ejin Banner (EJN). The substrate color is either light-yellow (GZ-y), yellow (EJN-y), or black (HSK-b); the corresponding lizard population colors largely match their substrate in the degree of melanism. We assembled the P. versicolor genome and sequenced over 90 individuals from the three different populations. Genetic divergence between populations corresponds to their geographic distribution. We inferred the genetic relationships among these populations and used selection scans and differential expression to identify genes that show signatures of selection. Slc2a11 and akap12, among other genes, are highly differentiated and may be responsible for pigment adaptation to substrate color in P. versicolor.
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Affiliation(s)
| | | | - Débora Y C Brandt
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jiasheng Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China
| | - Zhengxia Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China
| | - Tao Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Peter H Sudmant
- Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA,Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Rasmus Nielsen
- Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA,Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
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7
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Rossi V, Unitt R, McNamara M, Zorzin R, Carnevale G. Skin patterning and internal anatomy in a fossil moonfish from the Eocene Bolca Lagerstätte illuminate the ecology of ancient reef fish communities. PALAEONTOLOGY 2022; 65:e12600. [PMID: 35915728 PMCID: PMC9324815 DOI: 10.1111/pala.12600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/07/2022] [Indexed: 06/15/2023]
Abstract
Colour patterning in extant animals can be used as a reliable indicator of their biology and, in extant fish, can inform on feeding strategy. Fossil fish with preserved colour patterns may thus illuminate the evolution of fish behaviour and community structure, but are understudied. Here we report preserved melanin-based integumentary colour patterning and internal anatomy of the fossil moonfish Mene rhombea (Menidae) from the Bolca Lagerstätte (Eocene (Ypresian), north-east Italy). The melanosome-based longitudinal stripes of M. rhombea differ from the dorsal rows of black spots in its extant relative M. maculata, suggesting that the ecology of moonfish has changed during the Cenozoic. Extant moonfish are coastal schooling fish that feed on benthic invertebrates, but the longitudinal stripes and stomach contents with fish remains in M. rhombea suggest unstructured open marine ecologies and a piscivorous diet. The localized distribution of extant moonfish species in the Indo-Pacific Ocean may reflect, at least in part, tectonically-driven reorganization of global oceanographic patterns during the Cenozoic. It is likely that shifts in habitat and colour patterning genes promoted colour pattern evolution in the menid lineage.
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Affiliation(s)
- Valentina Rossi
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkT23 TK30Ireland
- Museo di Scienze Naturali dell’Alto AdigeBolzano39100Italy
- Environmental Research InstituteUniversity College CorkCorkT23 XE10Ireland
| | - Richard Unitt
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkT23 TK30Ireland
- Environmental Research InstituteUniversity College CorkCorkT23 XE10Ireland
| | - Maria McNamara
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkT23 TK30Ireland
- Environmental Research InstituteUniversity College CorkCorkT23 XE10Ireland
| | - Roberto Zorzin
- Sezione di Geologia e PaleontologiaMuseo Civico di Storia Naturale di VeronaLungadige Porta Vittoria 937129VeronaItaly
| | - Giorgio Carnevale
- Dipartimento di Scienze della TerraUniversità degli Studi di TorinoVia Valperga Caluso 3510125TorinoItaly
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8
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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: 5] [Impact Index Per Article: 1.7] [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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9
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Lou RN, Jacobs A, Wilder A, Therkildsen NO. A beginner's guide to low-coverage whole genome sequencing for population genomics. Mol Ecol 2021; 30:5966-5993. [PMID: 34250668 DOI: 10.1111/mec.16077] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/26/2022]
Abstract
Low-coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost-effective approach for population genomic studies in both model and non-model species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account for genotype uncertainty. A growing number of such tools have become available, but it can be difficult to get an overview of what types of analyses can be performed reliably with lcWGS data, and how the distribution of sequencing effort between the number of samples analyzed and per-sample sequencing depths affects inference accuracy. In this introductory guide to lcWGS, we first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. We then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, we use both simulated and empirical data to assess the accuracy of allele frequency and genetic diversity estimation, detection of population structure, and selection scans under different sequencing strategies. Our results show that spreading a given amount of sequencing effort across more samples with lower depth per sample consistently improves the accuracy of most types of inference, with a few notable exceptions. Finally, we assess the potential for using imputation to bolster inference from lcWGS data in non-model species, and discuss current limitations and future perspectives for lcWGS-based population genomics research. With this overview, we hope to make lcWGS more approachable and stimulate its broader adoption.
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Affiliation(s)
- Runyang Nicolas Lou
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Arne Jacobs
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Aryn Wilder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Nina O Therkildsen
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
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10
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Brejcha J, kodejš K, Benda P, Jablonski D, Holer T, Chmelař J, Moravec J. Variability of colour pattern and genetic diversity of Salamandra salamandra (Caudata: Salamandridae) in the Czech Republic. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jindřich Brejcha
- Department of Zoology, National Museum, Praha-Horní Počernice, Czech Republic; e-mail:
| | - Karel kodejš
- Department of Zoology, National Museum, Praha-Horní Počernice, Czech Republic; e-mail:
| | - Pavel Benda
- Bohemian Switzerland National Park, Krásná Lípa, Czech Republic
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Holer
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha-Suchdol, Czech Republic
| | - Jan Chmelař
- Department of Zoology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Jiří Moravec
- Department of Zoology, National Museum, Praha-Horní Počernice, Czech Republic; e-mail:
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11
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Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies. Heredity (Edinb) 2021; 126:776-789. [PMID: 33536637 PMCID: PMC8102559 DOI: 10.1038/s41437-021-00405-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted, leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in the adjacent Montes de Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.
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Decoding the Evolution of Melanin in Vertebrates. Trends Ecol Evol 2021; 36:430-443. [DOI: 10.1016/j.tree.2020.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 02/08/2023]
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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Burgon JD, Vences M, Steinfartz S, Bogaerts S, Bonato L, Donaire-Barroso D, Martínez-Solano I, Velo-Antón G, Vieites DR, Mable BK, Elmer KR. Phylogenomic inference of species and subspecies diversity in the Palearctic salamander genus Salamandra. Mol Phylogenet Evol 2020; 157:107063. [PMID: 33387650 DOI: 10.1016/j.ympev.2020.107063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 02/09/2023]
Abstract
The salamander genus Salamandra is widespread across Europe, North Africa, and the Near East and is renowned for its conspicuous and polymorphic colouration and diversity of reproductive modes. The phylogenetic relationships within the genus, and especially in the highly polymorphic species S. salamandra, have been very challenging to elucidate, leaving its real evolutionary history and classification at species and subspecies levels a topic of debate and contention. However, the distribution of diversity and species delimitation within the genus are critically important for identifying evolutionarily significant units for conservation and management, especially in light of threats posed by the pathogenic chytrid fungus Batrachochytrium salamandrivorans that is causing massive declines of S. salamandra populations in central Europe. Here, we conducted a phylogenomic analysis from across the taxonomic and geographic breadth of the genus Salamandra in its entire range. Bayesian, maximum likelihood and network-based phylogenetic analyses of up to 4905 ddRADseq-loci (294,300 nucleotides of sequence) supported the distinctiveness of all currently recognised species (Salamandra algira, S. atra, S. corsica, S. infraimmaculata, S. lanzai, and S. salamandra), and all five species for which we have multiple exemplars were confirmed as monophyletic. Within S. salamandra, two main clades can be distinguished: one clade with the Apenninic subspecies S. s. gigliolii nested within the Iberian S. s. bernardezi/fastuosa; and a second clade comprising all other Iberian, Central and East European subspecies. Our analyses revealed that some of the currently recognized subspecies of S. salamandra are paraphyletic and may require taxonomic revision, with the Central- and Eastern-European subspecies all being poorly differentiated at the analysed genomic markers. Salamandra s. longirostris - sometimes considered a separate species - was nested within S. salamandra, consistent with its subspecies status. The relationships identified within and between Salamandra species provide valuable context for future systematic and biogeographic studies, and help elucidate critical evolutionary units for conservation and taxonomy.
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Affiliation(s)
- James D Burgon
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | - Sebastian Steinfartz
- Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| | | | - Lucio Bonato
- Department of Biology, University of Padova, Via Bassi 58B, 35131 Padova, Italy
| | - David Donaire-Barroso
- Asociación Herpetológica Fretum Gaditanum, Calle Mar Egeo 7, 11407 Jerez de la Frontera, Spain
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), C./ José Gutiérrez Abascal n°2, 28006 Madrid, Spain
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas n° 7, 4485-661 Vairão, Portugal; Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, 36310 Vigo, Spain
| | - David R Vieites
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), C./ José Gutiérrez Abascal n°2, 28006 Madrid, Spain
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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