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van den Berg CP, Condon ND, Conradsen C, White TE, Cheney KL. Automated workflows using Quantitative Colour Pattern Analysis (QCPA): a guide to batch processing and downstream data analysis. Evol Ecol 2024; 38:387-397. [PMID: 38946730 PMCID: PMC11208187 DOI: 10.1007/s10682-024-10291-7] [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: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024]
Abstract
Animal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We also provide a complimentary set of useful R scripts for downstream data extraction and analysis. The presented batch processing extension will empower users to further utilise the analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern spaces and developing ever-richer frameworks for analysing organismal colouration accounting for visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-024-10291-7.
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Affiliation(s)
- Cedric P. van den Berg
- School of the Environment, The University of Queensland, Brisbane, QLD 4072 Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050 Australia
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ UK
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Cara Conradsen
- School of the Environment, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Thomas E. White
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2050 Australia
| | - Karen L. Cheney
- School of the Environment, The University of Queensland, Brisbane, QLD 4072 Australia
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2
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Yang Y, Axelrod CJ, Grant E, Earl SR, Urquhart EM, Talbert K, Johnson LE, Walker Z, Hsiao K, Stone I, Carlson BA, López-Sepulcre A, Gordon SP. Evolutionary divergence of developmental plasticity and learning of mating tactics in Trinidadian guppies. J Anim Ecol 2023. [PMID: 38156548 DOI: 10.1111/1365-2656.14043] [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: 08/30/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023]
Abstract
Behavioural plasticity is a major driver in the early stages of adaptation, but its effects in mediating evolution remain elusive because behavioural plasticity itself can evolve. In this study, we investigated how male Trinidadian guppies (Poecilia reticulata) adapted to different predation regimes diverged in behavioural plasticity of their mating tactic. We reared F2 juveniles of high- or low-predation population origins with different combinations of social and predator cues and assayed their mating behaviour upon sexual maturity. High-predation males learned their mating tactic from conspecific adults as juveniles, while low-predation males did not. High-predation males increased courtship when exposed to chemical predator cues during development; low-predation males decreased courtship in response to immediate chemical predator cues, but only when they were not exposed to such cues during development. Behavioural changes induced by predator cues were associated with developmental plasticity in brain morphology, but changes acquired through social learning were not. We thus show that guppy populations diverged in their response to social and ecological cues during development, and correlational evidence suggests that different cues can shape the same behaviour via different neural mechanisms. Our study demonstrates that behavioural plasticity, both environmentally induced and socially learnt, evolves rapidly and shapes adaptation when organisms colonize ecologically divergent habitats.
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Affiliation(s)
- Yusan Yang
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Caleb J Axelrod
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Ecology and Evolution, Cornell University, Ithaca, New York, USA
| | - Elly Grant
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shayna R Earl
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Biology, University of Louisville, Louisville, Kentucky, USA
| | - Ellen M Urquhart
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Katie Talbert
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Ecology and Evolution, Cornell University, Ithaca, New York, USA
| | - Lauren E Johnson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Zakiya Walker
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kyle Hsiao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Isabel Stone
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Bruce A Carlson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Andrés López-Sepulcre
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Ecology and Evolution, Cornell University, Ithaca, New York, USA
| | - Swanne P Gordon
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Ecology and Evolution, Cornell University, Ithaca, New York, USA
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3
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Rieseberg L, Warschefsky E, Ortiz-Barrientos D, Kane NC, Thresher K, Sibbett B. Editorial 2023. Mol Ecol 2023; 32:1-25. [PMID: 36573261 DOI: 10.1111/mec.16815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/28/2022]
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Qiu S, Yong L, Wilson A, Croft DP, Graham C, Charlesworth D. Partial sex linkage and linkage disequilibrium on the guppy sex chromosome. Mol Ecol 2022; 31:5524-5537. [PMID: 36005298 PMCID: PMC9826361 DOI: 10.1111/mec.16674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 01/11/2023]
Abstract
The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex-linkage has evolved across about 3 Mb surrounding this fish's sex-determining locus, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger "evolutionary strata". Sequences of the guppy genome show that Y is very similar to the X chromosome. Knowing which parts of the Y are completely nonrecombining, and whether there is indeed a large completely nonrecombining region, are important for understanding its evolution. Here, we describe analyses of PoolSeq data in samples from within multiple natural populations from Trinidad, yielding new results that support previous evidence for occasional recombination between the guppy Y and X. We detected recent demographic changes, notably that downstream populations have higher synonymous site diversity than upstream ones and other expected signals of bottlenecks. We detected evidence of associations between sequence variants and the sex-determining locus, rather than divergence under a complete lack of recombination. Although recombination is infrequent, it is frequent enough that associations with SNPs can suggest the region in which the sex-determining locus must be located. Diversity is elevated across a physically large region of the sex chromosome, conforming to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. However, no consistently male-specific variants were found, supporting the suggestion that any completely sex-linked region may be very small.
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Affiliation(s)
- Suo Qiu
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Lengxob Yong
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynUK,Marine Resources Research InstituteSouth Carolina Department of Natural ResourcesCharlestonSouth CarolinaUSA
| | - Alastair Wilson
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | - Darren P. Croft
- Centre for Research in Animal Behaviour, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Chay Graham
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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Heckley AM, Pearce AE, Gotanda KM, Hendry AP, Oke KB. Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution. J Evol Biol 2022; 35:1414-1431. [PMID: 36098479 DOI: 10.1111/jeb.14086] [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: 10/28/2021] [Revised: 04/29/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive - but not significant - trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary 'replicates' can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.
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Affiliation(s)
- Alexis M Heckley
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Allegra E Pearce
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Kiyoko M Gotanda
- Department of Biology, Université Sherbrooke, Sherbrooke, Quebec, Canada.,Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Krista B Oke
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
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Fuller RC. Revisiting old truths: The evolution of male coloration in guppies as a function of predation. Mol Ecol 2022; 31:1333-1336. [PMID: 35100465 DOI: 10.1111/mec.16376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
The Trinidadian guppy, Poecilia reticulata, is a long-studied model for the evolution of trade-offs in male nuptial coloration as a function of female mating preferences versus predation risk. Previous work suggests that female mating preferences favor the evolution of increased conspicuous male coloration in low predation populations. In contrast, high predation risk shifts the balance towards reduced conspicuous coloration. In a From the Cover article in this issue of Molecular Ecology, Yong, Croft, Troscianko, Ramnarine, and Wilson (2021) use visual detection models to estimate the 'conspicuousness' of male color patterns as seen by guppies and their predators. The study fails to find robust patterns of increased conspicuousness in low predation populations. Only one of eight measures of conspicuousness showed parallel changes between high and low predation regimes, forcing us to re-consider the validity and repeatability of this classic example of parallel evolution.
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Affiliation(s)
- Rebecca C Fuller
- Department of Evolution, Ecology, and Behavior, University of Illinois, Champaign, IL, 61820, USA
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