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Cervino NG, Elias-Costa AJ, Iglesias PP, Yovanovich CAM, Faivovich J. Insights into the evolution of photoreceptor oil droplets in frogs and toads. Proc Biol Sci 2024; 291:20241388. [PMID: 39079666 PMCID: PMC11288682 DOI: 10.1098/rspb.2024.1388] [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: 01/08/2024] [Revised: 06/23/2024] [Accepted: 07/02/2024] [Indexed: 08/03/2024] Open
Abstract
Photoreceptor oil droplets (ODs) are spherical organelles placed most commonly within the inner segment of the cone photoreceptors. Comprising neutral lipids, ODs can be either non-pigmented or pigmented and have been considered optically functional in various studies. Among living amphibians, ODs were only reported to occur in frogs and toads (Anura), while they are absent in salamanders and caecilians. Nonetheless, the limited understanding of their taxonomic distribution in anurans impedes a comprehensive assessment of their evolution and relationship with visual ecology. We studied the retinae of 134 anuran species, extending the knowledge of the distribution of ODs to 46 of the 58 currently recognized families, and providing a new perspective on this group that complements the available information from other vertebrates. The occurrence of ODs in anurans shows a strong phylogenetic signal, and our findings revealed that ODs evolved at least six times during the evolutionary history of the group, independently from other vertebrates. Although no evident correlation was found between OD occurrence, adult habits and diel activity, it is inferred that each independent origin involves distinct scenarios in the evolution of ODs concerning photic habits. Furthermore, our results revealed significant differences in the size of the ODs between nocturnal and arrhythmic anurans relative to the length of the cones' outer segment.
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Affiliation(s)
- Nadia G. Cervino
- División Herpetología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ – CONICET, Av. Ángel Gallardo 470, Buenos AiresC1405DJR, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresC1428EGA, Argentina
| | - Agustín J. Elias-Costa
- División Herpetología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ – CONICET, Av. Ángel Gallardo 470, Buenos AiresC1405DJR, Argentina
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin10115, Germany
| | - Patricia P. Iglesias
- CONICET--Agencia INTA General Acha, Estación Experimental Anguil, Avellaneda 530 General Acha, La PampaL8200AEL, Argentina
| | - Carola A. M. Yovanovich
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão No. 101, São Paulo05508-090, Brazil
- Department of Biology, Lund University, Sölvegatan 35, Lund22362, Sweden
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ – CONICET, Av. Ángel Gallardo 470, Buenos AiresC1405DJR, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresC1428EGA, Argentina
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Boyette JL, Bell RC, Fujita MK, Thomas KN, Streicher JW, Gower DJ, Schott RK. Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs. Mol Biol Evol 2024; 41:msae090. [PMID: 38736374 PMCID: PMC11181710 DOI: 10.1093/molbev/msae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024] Open
Abstract
Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.
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Affiliation(s)
- John L Boyette
- Department of Biological Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Biology, Berry College, Rome, GA, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Kate N Thomas
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
- Natural History Museum, London, UK
| | | | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA
- Department of Biology & Centre for Vision Research, York University, Toronto, ON, Canada
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3
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Morrow A, Smale L, Meek PD, Lundrigan B. Tradeoffs in the sensory brain between diurnal and nocturnal rodents. BRAIN, BEHAVIOR AND EVOLUTION 2024; 99:000538090. [PMID: 38569487 PMCID: PMC11346379 DOI: 10.1159/000538090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
INTRODUCTION Transitions in temporal niche have occurred many times over the course of mammalian evolution. These are associated with changes in sensory stimuli available to animals, particularly with visual cues, because levels of light are so much higher during the day than night. This relationship between temporal niche and available sensory stimuli elicits the expectation that evolutionary transitions between diurnal and nocturnal lifestyles will be accompanied by modifications of sensory systems that optimize the ability of animals to receive, process, and react to important stimuli in the environment. METHODS This study examines the influence of temporal niche on investment in sensory brain tissue of 13 rodent species (five diurnal; eight nocturnal). Animals were euthanized and the brain immediately frozen on dry ice; olfactory bulbs were subsequently dissected and weighed, and the remaining brain was weighed, sectioned, and stained. Stereo Investigator was used to calculate volumes of four sensory regions that function in processing visual (lateral geniculate nucleus, superior colliculus) and auditory (medial geniculate nucleus, inferior colliculus) information. A phylogenetic framework was used to assess the influence of temporal niche on the relative sizes of these brain structures and of olfactory bulb weights. RESULTS Compared to nocturnal species, diurnal species had larger visual regions, whereas nocturnal species had larger olfactory bulbs than their diurnal counterparts. Of the two auditory structures examined, one (medial geniculate nucleus) was larger in diurnal species, while the other (inferior colliculus) did not differ significantly with temporal niche. CONCLUSION Our results indicate a possible indirect association between temporal niche and auditory investment and suggest probable tradeoffs of investment between olfactory and visual areas of the brain, with diurnal species investing more in processing visual information and nocturnal species investing more in processing olfactory information.
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Affiliation(s)
- Andrea Morrow
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution, Michigan State University, East Lansing, MI, USA
| | - Laura Smale
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution, Michigan State University, East Lansing, MI, USA
- Department of Psychology, Michigan State University, East Lansing, MI, USA
- Neuroscience Program, Michigan State University, East Lansing, MI, USA
| | - Paul Douglas Meek
- Vertebrate Pest Research Unit, New South Wales Department of Primary Industries, Coffs Harbour, NSW, Australia
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Barbara Lundrigan
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution, Michigan State University, East Lansing, MI, USA
- Michigan State University Museum, East Lansing, MI, USA
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4
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Schott RK, Fujita MK, Streicher JW, Gower DJ, Thomas KN, Loew ER, Bamba Kaya AG, Bittencourt-Silva GB, Guillherme Becker C, Cisneros-Heredia D, Clulow S, Davila M, Firneno TJ, Haddad CFB, Janssenswillen S, Labisko J, Maddock ST, Mahony M, Martins RA, Michaels CJ, Mitchell NJ, Portik DM, Prates I, Roelants K, Roelke C, Tobi E, Woolfolk M, Bell RC. Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments. Mol Biol Evol 2024; 41:msae049. [PMID: 38573520 PMCID: PMC10994157 DOI: 10.1093/molbev/msae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.
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Affiliation(s)
- Ryan K Schott
- Department of Biology and Centre for Vision Research, York University, Toronto, Ontario, Canada
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | | | | | - Kate N Thomas
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
- Natural History Museum, London, UK
| | - Ellis R Loew
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | | | - C Guillherme Becker
- Department of Biology and One Health Microbiome Center, Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Diego Cisneros-Heredia
- Laboratorio de Zoología Terrestre, Instituto de Biodiversidad Tropical IBIOTROP, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Simon Clulow
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mateo Davila
- Laboratorio de Zoología Terrestre, Instituto de Biodiversidad Tropical IBIOTROP, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Thomas J Firneno
- Department of Biological Sciences, University of Denver, Denver, USA
| | - Célio F B Haddad
- Department of Biodiversity and Center of Aquaculture—CAUNESP, I.B., São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Sunita Janssenswillen
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jim Labisko
- Natural History Museum, London, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
| | - Simon T Maddock
- Natural History Museum, London, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Michael Mahony
- Department of Biological Sciences, The University of Newcastle, Newcastle 2308, Australia
| | - Renato A Martins
- Programa de Pós-graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Daniel M Portik
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Ivan Prates
- Department of Biology, Lund University, Lund, Sweden
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Corey Roelke
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Center for Conservation and Sustainability, Smithsonian National Zoo and Conservation Biology Institute, Gamba, Gabon
| | - Maya Woolfolk
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
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5
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Cox DTC, Gaston KJ. Cathemerality: a key temporal niche. Biol Rev Camb Philos Soc 2024; 99:329-347. [PMID: 37839797 DOI: 10.1111/brv.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Given the marked variation in abiotic and biotic conditions between day and night, many species specialise their physical activity to being diurnal or nocturnal, and it was long thought that these strategies were commonly fairly fixed and invariant. The term 'cathemeral', was coined in 1987, when Tattersall noted activity in a Madagascan primate during the hours of both daylight and darkness. Initially thought to be rare, cathemerality is now known to be a quite widespread form of time partitioning amongst arthropods, fish, birds, and mammals. Herein we provide a synthesis of present understanding of cathemeral behaviour, arguing that it should routinely be included alongside diurnal and nocturnal strategies in schemes that distinguish and categorise species across taxa according to temporal niche. This synthesis is particularly timely because (i) the study of animal activity patterns is being revolutionised by new and improved technologies; (ii) it is becoming apparent that cathemerality covers a diverse range of obligate to facultative forms, each with their own common sets of functional traits, geographic ranges and evolutionary history; (iii) daytime and nighttime activity likely plays an important but currently neglected role in temporal niche partitioning and ecosystem functioning; and (iv) cathemerality may have an important role in the ability of species to adapt to human-mediated pressures.
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Affiliation(s)
- Daniel T C Cox
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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Rutschmann A, Perry C, Le Galliard JF, Dupoué A, Lourdais O, Guillon M, Brusch G, Cote J, Richard M, Clobert J, Miles DB. Ecological responses of squamate reptiles to nocturnal warming. Biol Rev Camb Philos Soc 2024; 99:598-621. [PMID: 38062628 DOI: 10.1111/brv.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 03/06/2024]
Abstract
Nocturnal temperatures are increasing at a pace exceeding diurnal temperatures in most parts of the world. The role of warmer nocturnal temperatures in animal ecology has received scant attention and most studies focus on diurnal or daily descriptors of thermal environments' temporal trends. Yet, available evidence from plant and insect studies suggests that organisms can exhibit contrasting physiological responses to diurnal and nocturnal warming. Limiting studies to diurnal trends can thus result in incomplete and misleading interpretations of the ability of species to cope with global warming. Although they are expected to be impacted by warmer nocturnal temperatures, insufficient data are available regarding the night-time ecology of vertebrate ectotherms. Here, we illustrate the complex effects of nocturnal warming on squamate reptiles, a keystone group of vertebrate ectotherms. Our review includes discussion of diurnal and nocturnal ectotherms, but we mainly focus on diurnal species for which nocturnal warming affects a period dedicated to physiological recovery, and thus may perturb activity patterns and energy balance. We first summarise the physical consequences of nocturnal warming on habitats used by squamate reptiles. Second, we describe how such changes can alter the energy balance of diurnal species. We illustrate this with empirical data from the asp viper (Vipera aspis) and common wall lizard (Podarcis muralis), two diurnal species found throughout western Europe. Third, we make use of a mechanistic approach based on an energy-balance model to draw general conclusions about the effects of nocturnal temperatures. Fourth, we examine how warmer nights may affect squamates over their lifetime, with potential consequences on individual fitness and population dynamics. We review quantitative evidence for such lifetime effects using recent data derived from a range of studies on the European common lizard (Zootoca vivipara). Finally, we consider the broader eco-evolutionary ramifications of nocturnal warming and highlight several research questions that require future attention. Our work emphasises the importance of considering the joint influence of diurnal and nocturnal warming on the responses of vertebrate ectotherms to climate warming.
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Affiliation(s)
- Alexis Rutschmann
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS UAR2029, 02 route du CNRS, Moulis, 09200, France
| | - Constant Perry
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS UAR2029, 02 route du CNRS, Moulis, 09200, France
| | - Jean-François Le Galliard
- Sorbonne Université, CNRS, UMR 7618, IRD, INRAE, Institut d'écologie et des sciences de l'environnement (iEES Paris), Tours 44-45, 4 Place Jussieu, Paris, 75005, France
- Département de Biologie, Ecole Normale Supérieure, PSL Research University, CNRS, UMS 3194, Centre de Recherche en écologie expérimentale et Prédictive (CEREEP-Ecotron IleDeFrance), 78 rue du château, Saint-Pierre-Lès-Nemours, 77140, France
| | - Andréaz Dupoué
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, 1625 Rte de Sainte-Anne, Plouzané, 29280, France
| | - Olivier Lourdais
- Centre d'Etudes Biologiques de Chizé, CNRS UMR 7372-Université de La Rochelle, 405 Route de Prissé la Charrière, Villiers-en-Bois, 79630, France
- School of Life Sciences, Arizona State University, Life Sciences Center Building, 427E Tyler Mall, Tempe, AZ, 85281, USA
| | - Michaël Guillon
- Centre d'Etudes Biologiques de Chizé, CNRS UMR 7372-Université de La Rochelle, 405 Route de Prissé la Charrière, Villiers-en-Bois, 79630, France
- Cistude Nature, Chemin du Moulinat-33185, Le Haillan, France
| | - George Brusch
- Department of Biological Sciences, California State University San Marcos, 333 S. Twin Oaks Valley Rd., San Marcos, CA, 92096, USA
| | - Julien Cote
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Université Toulouse 3 Paul Sabatier, CNRS, IRD, 118 Rte de Narbonne, Toulouse, 31077, France
| | - Murielle Richard
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS UAR2029, 02 route du CNRS, Moulis, 09200, France
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS UAR2029, 02 route du CNRS, Moulis, 09200, France
| | - Donald B Miles
- Department of Biological Sciences, 131 Life Science Building, Ohio University, Athens, OH, 45701, USA
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7
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Gerber BD, Devarajan K, Farris ZJ, Fidino M. A model-based hypothesis framework to define and estimate the diel niche via the 'Diel.Niche' R package. J Anim Ecol 2024; 93:132-146. [PMID: 38213300 DOI: 10.1111/1365-2656.14035] [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: 06/23/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024]
Abstract
How animals use the diel period (24-h light-dark cycle) is of fundamental importance to understand their niche. While ecological and evolutionary literature abound with discussion of diel phenotypes (e.g. diurnal, nocturnal, crepuscular, cathemeral), they lack clear and explicit quantitative definitions. As such, inference can be confounded when evaluating hypotheses of animal diel niche switching or plasticity across studies because researchers may be operating under different definitions of diel phenotypes. We propose quantitative definitions of diel phenotypes using four alternative hypothesis sets (maximizing, traditional, general and selection) aimed at achieving different objectives. Each hypothesis set is composed of mutually exclusive hypotheses defined based on the activity probabilities in the three fundamental periods of light availability (twilight, daytime and night-time). We develop a Bayesian modelling framework that compares diel phenotype hypotheses using Bayes factors and estimates model parameters using a multinomial model with linear inequality constraints. Model comparison, parameter estimation and visualizing results can be done in the Diel.Niche R package. A simplified R Shiny web application is also available. We provide extensive simulation results to guide researchers on the power to discriminate among hypotheses for a range of sample sizes (10-1280). We also work through several examples of using data to make inferences on diel activity, and include online vignettes on how to use the Diel.Niche package. We demonstrate how our modelling framework complements other analyses, such as circular kernel density estimators and animal movement modelling. Our aim is to encourage standardization of the language of diel activity and bridge conceptual frameworks and hypotheses in diel research with data and models. Lastly, we hope more research focuses on the ecological and conservation importance of understanding how animals use diel time.
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Affiliation(s)
- Brian D Gerber
- Department of Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
| | - Kadambari Devarajan
- Department of Natural Resources Science, University of Rhode Island, Kingston, Rhode Island, USA
| | - Zach J Farris
- Department of Public Health and Exercise Science, Appalachian State University, Boone, North Carolina, USA
| | - Mason Fidino
- Conservation & Science Department, Lincoln Park Zoo, Chicago, Illinois, USA
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8
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [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: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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9
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Wan YC, Navarrete Méndez MJ, O'Connell LA, Uricchio LH, Roland AB, Maan ME, Ron SR, Betancourth-Cundar M, Pie MR, Howell KA, Richards-Zawacki CL, Cummings ME, Cannatella DC, Santos JC, Tarvin RD. Selection on Visual Opsin Genes in Diurnal Neotropical Frogs and Loss of the SWS2 Opsin in Poison Frogs. Mol Biol Evol 2023; 40:msad206. [PMID: 37791477 PMCID: PMC10548314 DOI: 10.1093/molbev/msad206] [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] [Indexed: 10/05/2023] Open
Abstract
Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here, we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their behavior. Our analyses show that assessments of opsin diversification in across taxa could expand our understanding of the role of sensory system evolution in ecological adaptation.
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Affiliation(s)
- Yin Chen Wan
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - María José Navarrete Méndez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Lawrence H Uricchio
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Biology, Tufts University, Medford, MA, USA
| | - Alexandre-Benoit Roland
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), UMR5169 CNRS, Toulouse University, Toulouse, France
| | - Martine E Maan
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Santiago R Ron
- Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Marcio R Pie
- Department of Zoology, Universidade Federal do Paraná, Curitiba, Brazil
- Biology Department, Edge Hill University, Ormskirk, United Kingdom
| | - Kimberly A Howell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Molly E Cummings
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - David C Cannatella
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Biodiversity Center, University of Texas at Austin, Austin, TX, USA
| | - Juan C Santos
- Department of Biological Sciences, St. John's University, New York City, NY, USA
| | - Rebecca D Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
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10
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Wiens JJ. Trait-based species richness: ecology and macroevolution. Biol Rev Camb Philos Soc 2023; 98:1365-1387. [PMID: 37015839 DOI: 10.1111/brv.12957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA
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11
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Emberts Z, Wiens JJ. Why are animals conspicuously colored? Evolution of sexual versus warning signals in land vertebrates. Evolution 2022; 76:2879-2892. [PMID: 36221224 DOI: 10.1111/evo.14636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/16/2022] [Accepted: 09/02/2022] [Indexed: 01/22/2023]
Abstract
Conspicuous colors (e.g., red, yellow, blue) have evolved numerous times across animals. But the function of this coloration can differ radically among species. Many species use this coloration as a sexual signal to conspecifics, whereas others use it as a warning signal to predators. Why do different species evolve conspicuous coloration in association with one function as opposed to the other? We address this question in terrestrial vertebrates (tetrapods) using phylogenetic approaches, and test whether day-night activities of species help determine these patterns. Using phylogenetic logistic regression, we found that conspicuous, sexually dimorphic coloration is significantly associated with diurnal lineages (e.g., many birds and lizards). By contrast, the evolution of warning signals was significantly associated with large-scale clades that were ancestrally nocturnal (e.g., snakes, amphibians), regardless of the current diel activity of species. Overall, we show that the evolution of conspicuous coloration as warning signals or sexual signals is influenced by the ecology of species, both recently and in the ancient past.
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Affiliation(s)
- Zachary Emberts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721.,Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
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12
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Mitra AT, Womack MC, Gower DJ, Streicher JW, Clark B, Bell RC, Schott RK, Fujita MK, Thomas KN. Ocular lens morphology is influenced by ecology and metamorphosis in frogs and toads. Proc Biol Sci 2022; 289:20220767. [PMID: 36382525 PMCID: PMC9667364 DOI: 10.1098/rspb.2022.0767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution.
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Affiliation(s)
- Amartya T. Mitra
- Division of Biosciences, University College London, London, UK
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Molly C. Womack
- Department of Biology, Utah State University, Logan, UT 84322, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
| | - David J. Gower
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | | | - Brett Clark
- Imaging and Analysis Centre, The Natural History Museum, London SW7 5BD, UK
| | - Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Ryan K. Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
- Department of Biology and Centre for Vision Research, York University, Toronto, Ontario, Canada
| | - Matthew K. Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kate N. Thomas
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
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13
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Cunningham CX, Nuñez TA, Hentati Y, Sullender B, Breen C, Ganz TR, Kreling SES, Shively KA, Reese E, Miles J, Prugh LR. Permanent daylight saving time would reduce deer-vehicle collisions. Curr Biol 2022; 32:4982-4988.e4. [PMID: 36327981 DOI: 10.1016/j.cub.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/12/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
Overlap between wildlife and human activity is key to causing wildlife-vehicle collisions, a globally pervasive and growing source of wildlife mortality.1,2 Policies regarding clock time often involve abrupt seasonal shifts in human activity, potentially influencing rates of human-wildlife conflict. Here, we harness the biannual shift between standard and daylight saving time as a natural experiment to reveal how the timing of human activity influences deer-vehicle collisions. Based on 1,012,465 deer-vehicle collisions and 96 million hourly traffic observations across the United States, we show that collisions are 14 times more frequent 2 hours after sunset than before sunset, highlighting the importance of traffic during dark hours as a key determinant of deer-vehicle collision risk. The switch from daylight saving to standard time in autumn causes peak traffic volumes to shift from before sunset to after sunset, leading to a 16% spike in deer-vehicle collisions. By reducing traffic after dark, our model predicts that year-round daylight saving time would prevent 36,550 deer (Odocoileus sp.) deaths, 33 human deaths, 2,054 human injuries, and US$1.19 billion in collision costs annually. In contrast, permanent standard time is predicted to increase collisions by an even larger magnitude, incurring an additional US$2.39 billion in costs. By targeting the temporal dimension of wildlife-vehicle collisions, strategies such as year-round daylight saving time that reduce traffic during dark hours, especially during the breeding season of abundant ungulates, would yield substantial benefits for wildlife conservation and reduce the social and economic costs of deer-vehicle collisions.
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Affiliation(s)
- Calum X Cunningham
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA.
| | - Tristan A Nuñez
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Yasmine Hentati
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Ben Sullender
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Catherine Breen
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Taylor R Ganz
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Samantha E S Kreling
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Kayla A Shively
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Ellie Reese
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Jeff Miles
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Laura R Prugh
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
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14
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Roberts SM, Stuart‐Fox D, Medina I. The evolution of conspicuousness in frogs: When to signal toxicity? J Evol Biol 2022; 35:1455-1464. [PMID: 36129907 PMCID: PMC9825868 DOI: 10.1111/jeb.14092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 01/11/2023]
Abstract
Many organisms use conspicuous colour patterns to advertise their toxicity or unpalatability, a strategy known as aposematism. Despite the recognized benefits of this anti-predator tactic, not all chemically defended species exhibit warning coloration. Here, we use a comparative approach to investigate which factors predict the evolution of conspicuousness in frogs, a group in which conspicuous coloration and toxicity have evolved multiple times. We extracted colour information from dorsal and ventral photos of 594 frog species for which chemical defence information was available. Our results show that chemically defended and diurnal species have higher internal chromatic contrast, both ventrally and dorsally, than chemically undefended and/or nocturnal species. Among species that are chemically defended, conspicuous coloration is more likely to occur if species are diurnal. Our results also suggest that the evolution of conspicuous colour is more likely to occur in chemically defended prey with smaller body size. We discuss potential explanations for this association and suggest that prey profitability (related to body size) could be an important force driving the macroevolution of warning signals.
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Affiliation(s)
| | - Devi Stuart‐Fox
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Iliana Medina
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
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15
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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16
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Thomas KN, Rich C, Quock RC, Streicher JW, Gower DJ, Schott RK, Fujita MK, Douglas RH, Bell RC. Diversity and evolution of amphibian pupil shapes. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape.
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Affiliation(s)
- Kate N Thomas
- Department of Life Sciences, The Natural History Museum , London SW7 5BD , UK
| | - Caitlyn Rich
- Department of Herpetology, California Academy of Sciences , San Francisco, CA 94118 , USA
| | - Rachel C Quock
- Department of Herpetology, California Academy of Sciences , San Francisco, CA 94118 , USA
- Department of Biology, San Francisco State University , San Francisco, CA 94132 , USA
| | - Jeffrey W Streicher
- Department of Life Sciences, The Natural History Museum , London SW7 5BD , UK
| | - David J Gower
- Department of Life Sciences, The Natural History Museum , London SW7 5BD , UK
| | - Ryan K Schott
- Department of Biology & Centre for Vision Research, York University , Toronto M3J 1P3 , Canada
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC, 20560-0162 , USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington , Arlington, TX 76019 , USA
| | - Ron H Douglas
- Division of Optometry & Visual Science, School of Health Sciences, City, University of London , Northampton Square, London EC1V 0HB , UK
| | - Rayna C Bell
- Department of Herpetology, California Academy of Sciences , San Francisco, CA 94118 , USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC, 20560-0162 , USA
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17
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Espíndola-Hernández P, Mueller JC, Kempenaers B. Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes. G3 GENES|GENOMES|GENETICS 2022; 12:6595023. [PMID: 35640557 PMCID: PMC9339318 DOI: 10.1093/g3journal/jkac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
Abstract
Understanding the targets of selection associated with changes in behavioral traits represents an important challenge of current evolutionary research. Owls (Strigiformes) are a diverse group of birds, most of which are considered nocturnal raptors. However, a few owl species independently adopted a diurnal lifestyle in their recent evolutionary history. We searched for signals of accelerated rates of evolution associated with a diurnal lifestyle using a genome-wide comparative approach. We estimated substitution rates in coding and noncoding conserved regions of the genome of seven owl species, including three diurnal species. Substitution rates of the noncoding elements were more accelerated than those of protein-coding genes. We identified new, owl-specific conserved noncoding elements as candidates of parallel evolution during the emergence of diurnality in owls. Our results shed light on the molecular basis of adaptation to a new niche and highlight the importance of regulatory elements for evolutionary changes in behavior. These elements were often involved in the neuronal development of the brain.
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Affiliation(s)
- Pamela Espíndola-Hernández
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
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18
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Slavenko A, Dror L, Camaiti M, Farquhar JE, Shea GM, Chapple DG, Meiri S. Evolution of diel activity patterns in skinks (Squamata: Scincidae), the world's second-largest family of terrestrial vertebrates. Evolution 2022; 76:1195-1208. [PMID: 35355258 PMCID: PMC9322454 DOI: 10.1111/evo.14482] [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] [Received: 09/11/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/21/2023]
Abstract
Many animals have strict diel activity patterns, with unique adaptations for either diurnal or nocturnal activity. Diel activity is phylogenetically conserved, yet evolutionary shifts in diel activity occur and lead to important changes in an organism's morphology, physiology, and behavior. We use phylogenetic comparative methods to examine the evolutionary history of diel activity in skinks, one of the largest families of terrestrial vertebrates. We examine how diel patterns are associated with microhabitat, ambient temperatures, and morphology. We found support for a nondiurnal ancestral skink. Strict diurnality in crown group skinks only evolved during the Paleogene. Nocturnal habits are associated with fossorial activity, limb reduction and loss, and warm temperatures. Our results shed light on the evolution of diel activity patterns in a large radiation of terrestrial ectotherms and reveal how both intrinsic biotic and extrinsic abiotic factors can shape the evolution of animal activity patterns.
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Affiliation(s)
- Alex Slavenko
- School of BiosciencesUniversity of SheffieldSheffieldSouth YorkshireUnited Kingdom
| | - Liat Dror
- School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Marco Camaiti
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Jules E. Farquhar
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Glenn M. Shea
- Sydney School of Veterinary Science B01University of SydneyNew South WalesAustralia,Australian Museum Research InstituteThe Australian MuseumSydneyNew South WalesAustralia
| | - David G. Chapple
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Shai Meiri
- School of ZoologyTel Aviv UniversityTel AvivIsrael,The Steinhardt Museum of Natural HistoryTel AvivIsrael
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19
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Jiang Y, Chen C, Liao W. Anuran interorbital distance variation: the role of ecological and behavioral factors. Integr Zool 2022; 17:777-786. [PMID: 35512218 DOI: 10.1111/1749-4877.12653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eye position varies significantly among taxonomic levels, and this variation is often shaped by ecological and behavioral factors. Eye position is often positively associated with interorbital distance where species with broad visual fields possess a large distance between the left and right eye. Selective pressures underlying the evolution of the eye position are especially studied in birds and mammals. However, selective pressures underling the evolution of anuran eye position which can be indicated by interorbital distance keep unknown. Here, we investigated the effects of ecological (e.g., habitat type, light availability) and behavioral factors (e.g., activity pattern, foraging mobility, and defensive strategy) on variations in interorbital distance among 260 anuran species in China. Our results showed that variations of the interorbital distance can be significantly predicted by the activity pattern. Nocturnal species had larger interorbital distance than both nocturnal and diurnal species. We also found that foraging mobility and defensive strategy affected markedly variation of interorbital distance. Species having slower foraging mobility and possessing poison glands had larger interorbital distance than species having faster foraging mobility and possessing non-position glands. Light availability tended to be associated with variation of interorbital distance, indicating that species living weak light tending to possess larger interorbital distance. However, variations of the interorbital space were not associated with habitat type in anurans. Our findings suggest that anuran behaviors play key roles in shaping visual fields and eye position, and thus affecting the evolution of interorbital distance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ying Jiang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong, China.,Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong, China
| | - Chuan Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong, China.,Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong, China
| | - Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong, China.,Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong, China
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20
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Rivera K, Fidino M, Farris ZJ, Magle SB, Murphy A, Gerber BD. Rethinking habitat occupancy modeling and the role of diel activity in an anthropogenic world. Am Nat 2022; 200:556-570. [DOI: 10.1086/720714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Thomas KN, Gower DJ, Streicher JW, Bell RC, Fujita MK, Schott RK, Liedtke HC, Haddad CFB, Becker CG, Cox CL, Martins RA, Douglas RH. Ecology drives patterns of spectral transmission in the ocular lenses of frogs and salamanders. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kate N. Thomas
- Department of Life Sciences The Natural History Museum London UK
| | - David J. Gower
- Department of Life Sciences The Natural History Museum London UK
| | | | - Rayna C. Bell
- Department of Herpetology California Academy of Sciences San Francisco CA USA
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
| | - Matthew K. Fujita
- Department of Biology Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington TX USA
| | - Ryan K. Schott
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
- Department of Biology York University Toronto ON Canada
| | - H. Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Célio F. B. Haddad
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP) I.B. Universidade Estadual Paulista Rio Claro Brazil
| | - C. Guilherme Becker
- Department of Biology The Pennsylvania State University University Park PA USA
| | - Christian L. Cox
- Department of Biological Sciences Institute for the Environment Florida International University Miami FL USA
| | - Renato A. Martins
- Programa de Pós‐graduação em Conservação da Fauna Universidade Federal de São Carlos São Carlos Brazil
| | - Ron H. Douglas
- Division of Optometry & Visual Science, School of Health Sciences City, University of London London UK
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22
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Schott RK, Perez L, Kwiatkowski MA, Imhoff V, Gumm JM. Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection. Ecol Evol 2022; 12:e8595. [PMID: 35154658 PMCID: PMC8820127 DOI: 10.1002/ece3.8595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 01/12/2023] Open
Abstract
Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and had conserved substitutions that may be related to dim-light adaptation. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. We also found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes suggesting the possibility of sex-specific visual adaptation. Taken together, our results indicate that ecological factors, such as habitat and life history, as well as behavior, may be driving changes to anuran visual systems.
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Affiliation(s)
- Ryan K. Schott
- Department of BiologyYork UniversityTorontoOntarioCanada
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Leah Perez
- Department of BiologyStephen F. Austin State UniversityNacogdochesTexasUSA
| | | | - Vance Imhoff
- Southern Nevada Fish and Wildlife OfficeUS Fish and Wildlife ServiceLas VegasNevadaUSA
| | - Jennifer M. Gumm
- Department of BiologyStephen F. Austin State UniversityNacogdochesTexasUSA
- Ash Meadows Fish Conservation FacilityUS Fish and Wildlife ServiceAmargosa ValleyNevadaUSA
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23
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Wcislo WT. A Dual Role for Behavior in Evolution and Shaping Organismal Selective Environments. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012921-052523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The hypothesis that evolved behaviors play a determining role in facilitating and impeding the evolution of other traits has been discussed for more than 100 years with little consensus beyond an agreement that the ideas are theoretically plausible in accord with the Modern Synthesis. Many recent reviews of the genomic, epigenetic, and developmental mechanisms underpinning major behavioral transitions show how facultative expression of novel behaviors can lead to the evolution of obligate behaviors and structures that enhance behavioral function. Phylogenetic and genomic studies indicate that behavioral traits are generally evolutionarily more labile than other traits and that they help shape selective environments on the latter traits. Adaptive decision-making to encounter resources and avoid stress sources requires specific sensory inputs, which behaviorally shape selective environments by determining those features of the external world that are biologically relevant. These recent findings support the hypothesis of a dual role for behavior in evolution and are consistent with current evolutionary theory.
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Affiliation(s)
- William T. Wcislo
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Republic of Panama
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24
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Moreira MO, Qu YF, Wiens JJ. Large-scale evolution of body temperatures in land vertebrates. Evol Lett 2021; 5:484-494. [PMID: 34621535 PMCID: PMC8484719 DOI: 10.1002/evl3.249] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/07/2022] Open
Abstract
Body temperature is a crucial variable in animals that affects nearly every aspect of their lives. Here we analyze for the first time largescale patterns in the evolution of body temperatures across terrestrial vertebrates (tetrapods: including amphibians, mammals, birds and other reptiles). Despite the traditional view that endotherms (birds and mammals) have higher body temperatures than ectotherms, we find they are not significantly different. However, rates of body-temperature evolution are significantly different, with lower rates in endotherms than ectotherms, and the highest rates in amphibians. We find that body temperatures show strong phylogenetic signal and conservatism over 350 million years of evolutionary history in tetrapods, and some lineages appear to have retained similar body temperatures over time for hundreds of millions of years. Although body temperatures are often unrelated to climate in tetrapods, we find that body temperatures are significantly related to day-night activity patterns. Specifically, body temperatures are generally higher in diurnal species than nocturnal species, both across ectotherms and, surprisingly, across endotherms also. Overall, our results suggest that body temperatures are significantly linked to phylogeny and diel-activity patterns within and among tetrapod groups, rather than just climate and the endotherm-ectotherm divide.
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Affiliation(s)
- Matthew O Moreira
- Center for Environmental and Marine Studies, Department of Biology University of Aveiro Aveiro Portugal.,Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA
| | - Yan-Fu Qu
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences Nanjing Normal University Nanjing Jiangsu China
| | - John J Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona USA
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25
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Chen C, Jiang Y, Jin L, Liao WB. No Evidence for Effects of Ecological and Behavioral Factors on Eye Size Evolution in Anurans. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.755818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Eye size varies markedly among taxonomic levels, and this variation is often related to the patterns shaped by phylogeny and ecological and behavioral factors. The selective pressures underlying eye size evolution are especially studied in fishes, anurans, birds, and mammals. However, selective pressures underlying the eye size evolution in anurans have inconsistent scaling rules. Here, we investigated the links between eye size and both ecological (e.g., light availability and habitat type) and behavioral factors (e.g., activity time, foraging mobility, defensive strategy, and mating system) among 252 species of anurans by using phylogenetically controlled generalized least-squared (PGLS) regression. Results show that anuran eye size scales hypo-allometrically with body size. However, eye size was not significantly influenced by ecological and behavioral factors, including habitat type, activity time, light availability, foraging mobility, defensive strategy, and mating system. Therefore, neither ecology nor behavior plays a key role in promoting eye size evolution in frogs.
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26
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Gray HM, Green DM, Ibáñez R. Diurnal Calling in a Nocturnal Frog: Exceptional Calling Activity of Túngara Frogs (Engystomops pustulosus) on the Panamanian Island of Taboga. HERPETOLOGICA 2021. [DOI: 10.1655/herpetologica-d-20-00057.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Styga JM, Welsh DP. Spawning substrate shift associated with the evolution of a female sexual characteristic in a family of fishes. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Because ‘primary’ sexual characteristics (i.e. those directly associated with reproduction) can be extremely variable, evolve quickly, and can be impacted by both natural and sexual selection, they are often considered excellent model systems in which to study evolution. Here, we explore the evolution of the anal sheath, a trait hypothesized to facilitate the release and proper placement of eggs on the spawning substrate, and its relationship to spawning habitat and maximum body size in a family of fish (Fundulidae). In addition to using phylogenetically informed statistics to determine the role of preferred spawning habitat and maximum body size on the evolution of anal sheath length, we reconstruct the evolutionary history of the anal sheath and preferred spawning habitat. We then test for significant phylogenetic signal and evolutionary rate shifts in the size of the anal sheath and the preferred spawning habitat. Our results indicate that preferred spawning habitat, and not maximum body length, significantly influences anal sheath size, which is associated with a significant phylogenetic signal, and an evolutionary rate similar to that of preferred spawning substrate. We discuss these results in terms of potential evolutionary mechanisms driving anal sheath length.
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Affiliation(s)
| | - Daniel P Welsh
- Fitchburg State University, Department of Biology and Chemistry, Fitchburg, MA, USA
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28
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Cox DTC, Gardner AS, Gaston KJ. Diel niche variation in mammals associated with expanded trait space. Nat Commun 2021; 12:1753. [PMID: 33741946 PMCID: PMC7979707 DOI: 10.1038/s41467-021-22023-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/08/2021] [Indexed: 01/28/2023] Open
Abstract
Mammalian life shows huge diversity, but most groups remain nocturnal in their activity pattern. A key unresolved question is whether mammal species that have diversified into different diel niches occupy unique regions of functional trait space. For 5,104 extant mammals we show here that daytime-active species (cathemeral or diurnal) evolved trait combinations along different gradients from those of nocturnal and crepuscular species. Hypervolumes of five major functional traits (body mass, litter size, diet, foraging strata, habitat breadth) reveal that 30% of diurnal trait space is unique, compared to 55% of nocturnal trait space. Almost half of trait space (44%) of species with apparently obligate diel niches is shared with those that can switch, suggesting that more species than currently realised may be somewhat flexible in their activity patterns. Increasingly, conservation measures have focused on protecting functionally unique species; for mammals, protecting functional distinctiveness requires a focus across diel niches.
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Affiliation(s)
- D T C Cox
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - A S Gardner
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - K J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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29
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Jerem P, Mathews F. Trends and knowledge gaps in field research investigating effects of anthropogenic noise. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:115-129. [PMID: 32277776 DOI: 10.1111/cobi.13510] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/17/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic noise is a globally widespread sensory pollutant, recognized as having potentially adverse effects on function, demography, and physiology in wild animals. Human population growth and associated changes in urbanization, transportation, and resource extraction all contribute to anthropogenic noise and are predicted to increase in the coming decades. Wildlife exposure to anthropogenic noise is expected to rise correspondingly. Data collected through field research are uniquely important in advancing understanding of the real-world repercussions of human activity on wildlife. We, therefore, performed a systematic review of literature published from 2008 to 2018 that reported on field investigations of anthropogenic noise impacts. We evaluated publication metrics (e.g., publication rates and journal type), geographical distribution of studies, study subject, and methods used. Research activity increased markedly over the assessment period. However, there was a pronounced geographical bias in research, with most being conducted in North America or Europe, and a notable focus on terrestrial environments. Fewer than one-fifth of terrestrial studies were located in rural areas likely to experience urbanization by 2030, meaning data on ecosystems most likely to be affected by future changes are not being gathered. There was also bias in the taxonomic groups investigated. Most research was conducted on birds and aquatic mammals, whereas terrestrial mammals, reptiles, amphibians, fish, and invertebrates received limited attention. Almost all terrestrial studies examined diurnal species, despite evidence that nocturnality is the prevailing animal activity pattern. Nearly half the studies investigated effects of road or urban noise; the bulk of research was restricted to functional, rather than physiological or demographic consequences. Few experimental studies addressed repercussions of long-term exposure to anthropogenic noise or long-term postexposure effects, and multiple noise types or levels were rarely compared. Tackling these knowledge gaps will be vital for successful management of the effects of increasing wildlife exposure to anthropogenic noise.
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Affiliation(s)
- Paul Jerem
- Department of Evolution, Behaviour and Environment, University of Sussex, John Maynard Smith Building, Falmer, Brighton, BN1 9QG, U.K
| | - Fiona Mathews
- Department of Evolution, Behaviour and Environment, University of Sussex, John Maynard Smith Building, Falmer, Brighton, BN1 9QG, U.K
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30
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Coates TD. Circadian activity of the swamp rat (Rattus lutreolus) in South Central Victoria. AUSTRALIAN MAMMALOGY 2021. [DOI: 10.1071/am19048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The swamp rat (Rattus lutreolus) is one of the few Australian terrestrial mammals that is commonly active between dawn and dusk. The species has typically been considered cathemeral (active throughout the diel cycle) with variation in circadian activity dependant on proximate factors such as the risk of predation or competition with closely related taxa. Data from camera trapping over 8 years and across 79 sites in South Central Victoria confirmed the species was effectively diurnal throughout the region and that night activity was relatively uncommon. Activity generally tracked daily temperature cycles; lowest in the period prior to dawn and highest in the middle of the afternoon and is consistent with an energy conservation strategy linked to the species’ unusual diet. Other rodent taxa, including two widespread exotic species were strictly nocturnal yet there was little evidence to suggest that R. lutreolus activity was influenced by the presence or absence of other murids or the risk of predation.
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31
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Callaghan CT, Rowley JJL. A continental assessment of diurnality in frog calling behaviour. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Corey T. Callaghan
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences UNSW Sydney SydneyNew South WalesAustralia
- Ecology & Evolution Research Centre School of Biological, Earth and Environmental Sciences UNSW Sydney SydneyNew South WalesAustralia
| | - Jodi J. L. Rowley
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences UNSW Sydney SydneyNew South WalesAustralia
- Australian Museum Research Institute Australian Museum Sydney New South Wales Australia
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32
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Espíndola-Hernández P, Mueller JC, Carrete M, Boerno S, Kempenaers B. Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls. Genome Biol Evol 2020; 12:1895-1908. [PMID: 32770228 PMCID: PMC7566403 DOI: 10.1093/gbe/evaa166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.
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Affiliation(s)
- Pamela Espíndola-Hernández
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Martina Carrete
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Sevilla, Spain
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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33
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Thomas KN, Gower DJ, Bell RC, Fujita MK, Schott RK, Streicher JW. Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology. Proc Biol Sci 2020; 287:20201393. [PMID: 32962540 PMCID: PMC7542830 DOI: 10.1098/rspb.2020.1393] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized to be associated with the evolution of eye size. Anuran eye size was significantly correlated with habitat, with notable decreases in eye investment among fossorial, subfossorial and aquatic species. Relative eye size was also associated with mating habitat and activity pattern. Compared to other vertebrates, anurans have relatively large eyes for their body size, indicating that vision is probably of high importance. Our study reveals the role that ecology and behaviour may have played in the evolution of anuran visual systems and highlights the usefulness of museum specimens, and importance of broad taxonomic sampling, for interpreting macroecological patterns.
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Affiliation(s)
- Kate N Thomas
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA.,Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0162, USA
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34
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Székely D, Cogălniceanu D, Székely P, Denoël M. Adult-Juvenile interactions and temporal niche partitioning between life-stages in a tropical amphibian. PLoS One 2020; 15:e0238949. [PMID: 32925925 PMCID: PMC7489520 DOI: 10.1371/journal.pone.0238949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Divergence in ecological niche offers organisms the opportunity of exploiting different food and habitat resources, scaling down competition and predation both among species, and within different age or size-classes of the same species. In harsh environments, where abiotic factors determine a clustering of resources during short timespans, competition and predation between organisms is likely to be enhanced. This is the case in tropical dry forests, where amphibians have limited opportunities to feed, their activity being restricted to the short rainy season. One way to maximize resource exploitation while avoiding predation risk is by adopting different diel activity patterns. We tested this hypothesis by comparing activity patterns in adults and recently metamorphosed juveniles of Pacific horned frogs (Ceratophrys stolzmanni) during field surveys and in an experimental study. Field surveys showed that the adults are strictly nocturnal, whereas freshly metamorphosed juveniles can be found active above ground at all hours, with a peak activity during daytime. The average body condition index of juveniles found active during the night was higher than that of juveniles found active during the day, suggesting that the weaker individuals may be constrained to being active during the day. On the other hand, in a laboratory experiment, juveniles that were visually exposed to adults moved less than those in the absence of adults. Both field and experimental observations indicate a temporal niche divergence between life stages. The results of the experiment offer support to the hypothesis that the juveniles in this species display an inverse activity pattern compared to adults, which can reduce competitive interactions and predation pressure from the larger conspecifics.
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Affiliation(s)
- Diana Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos - EcoSs Lab, Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| | - Dan Cogălniceanu
- Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, Constanța, Romania
- Asociation Chelonia, București, Romania
| | - Paul Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos - EcoSs Lab, Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
- Asociation Chelonia, București, Romania
- * E-mail:
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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35
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Cicero C, Mason NA, Benedict L, Rising JD. Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows ( Aimophila and Peucaea, Passerellidae). PeerJ 2020; 8:e9249. [PMID: 32596039 PMCID: PMC7307569 DOI: 10.7717/peerj.9249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Nicholas A Mason
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America.,Current affiliation: Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Lauryn Benedict
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States of America
| | - James D Rising
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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36
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Bonebrake TC, Rezende EL, Bozinovic F. Climate Change and Thermoregulatory Consequences of Activity Time in Mammals. Am Nat 2020; 196:45-56. [PMID: 32552099 DOI: 10.1086/709010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Activity times structure the thermal environments experienced by organisms. In mammals, species shift from being nocturnal to diurnal and vice versa, but the thermal consequences of variable activity patterns remain largely unexplored. Here we used theoretical thermoregulatory polygons bounded by estimates of basal metabolic rates (BMR), maximum metabolic rates (MMR), and thermal conductance (C) in small mammals to explore the metabolic consequences of exposure to global-scale daytime and nighttime temperatures. Model predictions indicated higher metabolic scope for activity for nocturnal species at low latitudes and that reduced minimum C and larger body size increased the geographic range in which nocturnality was advantageous. Consistent with predictions, within rodents nocturnal species have low C. However, nocturnal mammals tend to be smaller than diurnal species, likely reflecting the importance of additional factors driving body size. Projections of warming impacts on small mammals suggest that diurnal species could lose habitable space globally. Conversely, warming could lift cool temperature constraints on nocturnal species and increase habitable space, suggesting that a shift toward nocturnal niches might be favored in a warming world. Taken together, these findings demonstrate the importance of energetic considerations for endotherms in managing global change impacts on nocturnal and diurnal species.
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37
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Donner K, Yovanovich CAM. A frog's eye view: Foundational revelations and future promises. Semin Cell Dev Biol 2020; 106:72-85. [PMID: 32466970 DOI: 10.1016/j.semcdb.2020.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Abstract
From the mid-19th century until the 1980's, frogs and toads provided important research models for many fundamental questions in visual neuroscience. In the present century, they have been largely neglected. Yet they are animals with highly developed vision, a complex retina built on the basic vertebrate plan, an accessible brain, and an experimentally useful behavioural repertoire. They also offer a rich diversity of species and life histories on a reasonably restricted physiological and evolutionary background. We suggest that important insights may be gained from revisiting classical questions in anurans with state-of-the-art methods. At the input to the system, this especially concerns the molecular evolution of visual pigments and photoreceptors, at the output, the relation between retinal signals, brain processing and behavioural decision-making.
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Affiliation(s)
- Kristian Donner
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; PB 65 (Viikinkaari 1), 00014, University of Helsinki, Finland.
| | - Carola A M Yovanovich
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil; Rua do Matão, Trav. 14, N°101, São Paulo, SP, 05508-090, Brazil.
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Griffing AH, Gamble T, Bauer AM. Distinct patterns of pigment development underlie convergent hyperpigmentation between nocturnal and diurnal geckos (Squamata: Gekkota). BMC Evol Biol 2020; 20:40. [PMID: 32220231 PMCID: PMC7099784 DOI: 10.1186/s12862-020-01604-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Evolutionary transitions in temporal niche necessitates specialized morphology, physiology, and behaviors. Diurnal, heliothermic squamates (lizards and snakes) that bask require protection from ultraviolet radiation (UV) that can damage internal organs such as the brain, viscera, and gonads. Many smaller squamates have accomplished this protection by hyperpigmentation of the peritoneum and subcutaneous dorsum. Typically, nocturnal species do not require these protections from ultraviolet light. However, some nocturnal species that exhibit extreme crypsis may be exposed to sunlight and UV and require some means of mediating that damage. One such species is Gekko (Ptychozoon) kuhli, a nocturnal, arboreal gecko that uses extreme crypsis to blend in with tree bark. Hiding motionless on tree trunks leaves geckos exposed to sunlight during the day. Thus, we predict that G. kuhli will have independently evolved a hyperpigmented phenotype. To investigate this hypothesized association between temporal niche, behavior, and morphology, we characterized adult subcutaneous pigment for eight gecko species and embryonic pigment accumulation for a subset of four of these species, exhibiting diverse temporal niche and thermoregulatory behaviors. We predicted that nocturnal/potentially-heliothermic G. kuhli would exhibit hyperpigmentation of internal structures like that of diurnal/heliothermic geckos. We further predicted that embryonic pigment accumulation of G. kuhli would resemble that of diurnal/heliothermic as opposed to nocturnal/thigmothermic geckos. RESULTS We found that temporal niche and thermoregulatory behavior predicted the degree of subcutaneous pigment in the eight gecko species examined. We demonstrate that G. kuhli accumulates pigment extremely early in embryonic development, unlike a diurnal/heliothermic gecko species, despite having a similar adult phenotype. CONCLUSIONS The evolution of hyperpigmentation in G. kuhli is likely an adaptation to limit damage from occasional daytime UV exposure caused by crypsis-associated basking behavior. Gekko kuhli achieves its hyperpigmented phenotype through a derived developmental pattern, not seen in any other lizard species investigated to date, suggesting novel temporal differences in the migration and/or differentiation of reptilian neural crest derivatives.
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Affiliation(s)
- Aaron H Griffing
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201, USA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201, USA
- Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI, 53233, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA, 19085, USA.
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Climatic-niche evolution follows similar rules in plants and animals. Nat Ecol Evol 2020; 4:753-763. [PMID: 32203479 DOI: 10.1038/s41559-020-1158-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/24/2020] [Indexed: 12/24/2022]
Abstract
Climatic niches are essential in determining where species can occur and how they will respond to climate change. However, it remains unclear if climatic-niche evolution is similar in plants and animals or is intrinsically different. For example, previous authors have proposed that plants have broader environmental tolerances than animals but are more sensitive to climate change. Here, we test ten predictions about climatic-niche evolution in plants and animals, using phylogenetic and climatic data for 19 plant clades and 17 vertebrate clades (2,087 species total). Surprisingly, we find that for all ten predictions, plants and animals show similar patterns. For example, in both groups, climatic niches change at similar mean rates and species have similar mean niche breadths, and niche breadths show similar relationships with latitude across groups. Our results suggest that there are general 'rules' of climatic-niche evolution that span plants and animals, despite the fundamental differences in their biology. These results may help to explain why plants and animals have similar responses to climate change and why they often have shared species richness patterns, biogeographic regions, biomes and biodiversity hotspots.
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40
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Wiens JJ, Tuschhoff E. Songs versus colours versus horns: what explains the diversity of sexually selected traits? Biol Rev Camb Philos Soc 2020; 95:847-864. [PMID: 32092241 DOI: 10.1111/brv.12593] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 01/25/2020] [Accepted: 02/10/2020] [Indexed: 01/14/2023]
Abstract
Papers on sexual selection often highlight the incredible diversity of sexually selected traits across animals. Yet, few studies have tried to explain why this diversity evolved. Animals use many different types of traits to attract mates and outcompete rivals, including colours, songs, and horns, but it remains unclear why, for example, some taxa have songs, others have colours, and others horns. Here, we first conduct a systematic survey of the basic diversity and distribution of different types of sexually selected signals and weapons across the animal Tree of Life. Based on this survey, we describe seven major patterns in trait diversity and distributions. We then discuss 10 unanswered questions raised by these patterns, and how they might be addressed. One major pattern is that most types of sexually selected signals and weapons are apparently absent from most animal phyla (88%), in contrast to the conventional wisdom that a diversity of sexually selected traits is present across animals. Furthermore, most trait diversity is clustered in Arthropoda and Chordata, but only within certain clades. Within these clades, many different types of traits have evolved, and many types appear to have evolved repeatedly. By contrast, other major arthropod and chordate clades appear to lack all or most trait types, and similar patterns are repeated at smaller phylogenetic scales (e.g. within insects). Although most research on sexual selection focuses on female choice, we find similar numbers of traits (among sampled species) are involved in male contests (44%) and female choice (55%). Overall, these patterns are largely unexplained and unexplored, as are many other fundamental questions about the evolution of these traits. We suggest that understanding the diversity of sexually selected traits may require a shift towards macroevolutionary studies at relatively deep timescales (e.g. tens to hundreds of millions of years ago).
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - E Tuschhoff
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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Wu Y, Wang H. Convergent evolution of bird-mammal shared characteristics for adapting to nocturnality. Proc Biol Sci 2020; 286:20182185. [PMID: 30963837 DOI: 10.1098/rspb.2018.2185] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diapsid lineage (birds) and synapsid lineage (mammals), share a suite of functionally similar characteristics (e.g. endothermy) that are considered to be a result of their convergent evolution, but the candidate selections leading to this convergent evolution are still under debate. Here, we used a newly developed molecular phyloecological approach to reconstruct the diel activity pattern of the common ancestors of living birds. Our results strongly suggest that they had adaptations to nocturnality during their early evolution, which is remarkably similar to that of ancestral mammals. Given their similar adaptation to nocturnality, we propose that the shared traits in birds and mammals may have partly evolved as a result of the convergent evolution of their early ancestors adapting to ecological factors (e.g. low ambient temperature) associated with nocturnality. Finally, a conceptually unifying ecological model on the evolution of endothermy in diverse organisms with an emphasis on low ambient temperature is proposed. We reason that endothermy may evolve as an adaptive strategy to enable organisms to effectively implement various life-cycle activities under relatively low-temperature environments. In particular, a habitat shift from high-temperature to relatively low-temperature environments is identified as a common factor underlying the evolution of endothermy.
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Affiliation(s)
- Yonghua Wu
- 1 School of Life Sciences, Northeast Normal University , 5268 Renmin Street, Changchun 130024 , People's Republic of China.,2 Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , 2555 Jingyue Street, Changchun 130117 , People's Republic of China
| | - Haifeng Wang
- 3 Department of Bioengineering, Stanford University , Stanford, CA 94305 , USA
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Abstract
Acoustic communication is crucial to humans and many other tetrapods, including birds, frogs, crocodilians, and mammals. However, large-scale patterns in its evolution are largely unstudied. Here, we address several fundamental questions about the origins of acoustic communication in terrestrial vertebrates (tetrapods), using phylogenetic methods. We show that origins of acoustic communication are significantly associated with nocturnal activity. We find that acoustic communication does not increase diversification rates, a surprising result given the many speciation-focused studies of frog calls and bird songs. We also demonstrate that the presence of acoustic communication is strongly conserved over time. Finally, we find that acoustic communication evolved independently in most major tetrapod groups, often with remarkably ancient origins (~100-200 million years ago). Overall, we show that the role of ecology in shaping signal evolution applies to surprisingly deep timescales, whereas the role of signal evolution in diversification may not.
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Affiliation(s)
- Zhuo Chen
- College of Life Sciences, Henan Normal University, 453007, Xinxiang, Henan Province, China
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA.
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Yovanovich CAM, Pierotti MER, Kelber A, Jorgewich-Cohen G, Ibáñez R, Grant T. Lens transmittance shapes ultraviolet sensitivity in the eyes of frogs from diverse ecological and phylogenetic backgrounds. Proc Biol Sci 2020; 287:20192253. [PMID: 31910785 PMCID: PMC7003468 DOI: 10.1098/rspb.2019.2253] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The amount of short wavelength (ultraviolet (UV), violet and blue) light that reaches the retina depends on the transmittance properties of the ocular media, especially the lens, and varies greatly across species in all vertebrate groups studied previously. We measured the lens transmittance in 32 anuran amphibians with different habits, geographical distributions and phylogenetic positions and used them together with eye size and pupil shape to evaluate the relationship with diel activity pattern, elevation and latitude. We found an unusually high lens UV transmittance in the most basal species, and a cut-off range that extends into the visible spectrum for the rest of the sample, with lenses even absorbing violet light in some diurnal species. However, other diurnal frogs had lenses that transmit UV light like the nocturnal species. This unclear pattern in the segregation of ocular media transmittance and diel activity is shared with other vertebrates and is consistent with the absence of significant correlations in our statistical analyses. Although we did not detect a significant phylogenetic effect, closely related species tend to have similar transmittances, irrespective of whether they share the same diel pattern or not, suggesting that anuran ocular media transmittance properties might be related to phylogeny.
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Affiliation(s)
- Carola A M Yovanovich
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Michele E R Pierotti
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Almut Kelber
- Department of Biology, Lund University, Lund, Sweden
| | | | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Nguyen HN, Hung CM, Yang MY, Lin SM. Sympatric competitors have driven the evolution of temporal activity patterns in Cnemaspis geckos in Southeast Asia. Sci Rep 2020; 10:27. [PMID: 31913297 PMCID: PMC6949239 DOI: 10.1038/s41598-019-56549-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
It is often assumed that animals' temporal activity patterns are highly conserved throughout evolution. While most geckos are nocturnal, the species in the Cnemaspis genus are mostly diurnal (only a few are nocturnal). This raises a question about the evolution of a diel niche in the Cnemaspis genus. Cnemaspis geckos are distributed across Southeast Asia and are often sympatric with Cyrtodactylus, another widespread gecko genus in the same area. Since both genera are mainly rocky habitat specialists, we hypothesize that Cyrtodactylus may influence the temporal activity pattern of Cnemaspis when they are sympatric through competition. By analyzing habitat data, diel activity, and the existence of sympatric Cyrtodactylus species across the phylogeny of the Cnemaspis genus, we found (1) strong phylogenetic signals in the habitat use trait but not in temporal activity, suggesting that the diel niche of this genus is more labile compared with habitat niche, and (2) a significant association with the temporal activity pattern of Cnemaspis and the sympatry between the two genera, with the former tending to be diurnal when they are sympatric. Originated from a diurnal common ancestor, the release from competition with Cyrtodactylus species might open an opportunity for some Cnemaspis species to shift to nocturnal niches.
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Affiliation(s)
- Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chih-Ming Hung
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Yuan Yang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Si-Min Lin
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan.
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
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Graipel ME, Bogoni JA, Giehl ELH, Cerezer FO, Cáceres NC, Eizirik E. Melanism evolution in the cat family is influenced by intraspecific communication under low visibility. PLoS One 2019; 14:e0226136. [PMID: 31851714 PMCID: PMC6919575 DOI: 10.1371/journal.pone.0226136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species’ body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.
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Affiliation(s)
- Maurício Eduardo Graipel
- Departamento de Ecologia e Zoologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail:
| | - Juliano André Bogoni
- Laboratório de Ecologia, Manejo e Conservação de Fauna Silvestre (LEMaC), Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Eduardo Luís Hettwer Giehl
- Programa de Pós-Graduação em Ecologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Felipe O. Cerezer
- Programa de Pós-Graduação em Biodiversidade Animal, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Nilton Carlos Cáceres
- Departamento de Ecologia e Evolução, CCNE, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Eduardo Eizirik
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Pinto BJ, Nielsen SV, Gamble T. Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards. Mol Phylogenet Evol 2019; 141:106639. [PMID: 31586687 DOI: 10.1016/j.ympev.2019.106639] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022]
Abstract
Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent "transmutation" of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted to a subset of species. Here, we used de novo eye transcriptomes from five gecko species, and genomes from two additional gecko species, representing the breadth of extant gecko diversity (i.e. 4 of the 7 gecko families, spanning the deepest divergence of crown Gekkota), to show that geckos lost expression of almost the entire suite of necessary rod-cell phototransduction genes in the eye, distinct from all other squamate reptiles. Geckos are the first vertebrate group to have lost their complete rod-cell expression pathway, not just the visual pigment. In addition, all sampled species have also lost expression of the cone-opsin SWS2 visual pigment. These results strongly suggest a single loss of rod cells and subsequent cone-to-rod transmutation that occurred prior to the diversification of extant geckos.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Milwaukee Public Museum, Milwaukee, WI, USA.
| | - Stuart V Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Milwaukee Public Museum, Milwaukee, WI, USA; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA.
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47
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Román-Palacios C, Scholl JP, Wiens JJ. Evolution of diet across the animal tree of life. Evol Lett 2019; 3:339-347. [PMID: 31388444 PMCID: PMC6675143 DOI: 10.1002/evl3.127] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/13/2019] [Accepted: 06/22/2019] [Indexed: 12/24/2022] Open
Abstract
What an animal eats is a fundamental aspect of its biology, but the evolution of diet has not been studied across animal phylogeny. Here, we performed a large‐scale phylogenetic analysis to address three unresolved questions about the evolution of animal diets. (i) Are diets conserved across animal phylogeny? (ii) Does diet influence rates of species proliferation (diversification) among animal phyla? (iii) What was the ancestral diet of animals and major animal clades? We analyzed diet data for 1087 taxa, proportionally sampled among animal phyla based on the relative species richness of phyla. Our survey suggests that across animals, carnivory is most common (∼63%), herbivory less common (∼32%), and omnivory relatively rare (∼3%). Despite considerable controversy over whether ecological traits are conserved or labile, we found strong conservatism in diet over extraordinarily deep timescales. We found that diet is unrelated to rates of species diversification across animal phyla, contrasting with previous studies showing that herbivory increased diversification within some important groups (e.g., crustaceans, insects, and mammals). Finally, we estimated that the ancestor of all animals was most likely carnivorous, as were many major phyla (e.g., arthropods, molluscs, and chordates). Remarkably, our results suggest that many carnivorous species living today may have maintained this diet through a continuous series of carnivorous ancestors for >800 million years.
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Affiliation(s)
| | - Joshua P Scholl
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721
| | - John J Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721
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Scotopic rod vision in tetrapods arose from multiple early adaptive shifts in the rate of retinal release. Proc Natl Acad Sci U S A 2019; 116:12627-12628. [PMID: 31182589 PMCID: PMC6600910 DOI: 10.1073/pnas.1900481116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability of vertebrates to occupy diverse niches has been linked to the spectral properties of rhodopsin, conferring rod-based vision in low-light conditions. More recent insights have come from nonspectral kinetics, including the retinal release rate of the active state of rhodopsin, a key aspect of scotopic vision that shows strong associations with light environments in diverse taxa. We examined the retinal release rates in resurrected proteins across early vertebrates and show that the earliest forms were characterized by much faster rates of retinal release than more recent ancestors. We also show that scotopic vision at the origin of tetrapods is a derived state that arose via at least 4 major shifts in retinal release rate. Our results suggest that early rhodopsin had a function intermediate to that of modern rod and cone pigments and that its well-developed adaptation to low light is a relatively recent innovation since the origin of tetrapods.
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49
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Yovanovich CAM, Pierotti MER, Rodrigues MT, Grant T. A dune with a view: the eyes of a neotropical fossorial lizard. Front Zool 2019; 16:17. [PMID: 31198433 PMCID: PMC6558795 DOI: 10.1186/s12983-019-0320-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Lizards are excellent models to study the adaptations of the visual system to different scenarios, and surface-dwelling representatives have been relatively well studied. In contrast, very little is known about the functional anatomy of the eyes of fossorial lineages, and properties such as the light transmission by the ocular media have never been characterised in any fossorial species. Some lizards in the family Gymnophthalmidae endemic to the sand dunes of North Eastern Brazil have evolved sand-burrowing habits and nocturnal activity. Lizards in the sister group to Gymnophthalmidae, the family Teiidae, have decidedly diurnal and epigeal lifestyles, yet they are equally poorly known in terms of visual systems. We focussed on the eye anatomy, photoreceptor morphology and light transmittance properties of the ocular media and oil droplets in the gymnophthalmid Calyptommatus nicterus and the teiid Ameivula ocellifera. Results The general organisation of the eyes of the fossorial nocturnal C. nicterus and the epigeal diurnal A. ocellifera is remarkably similar. The lenses are highly transmissive to light well into the ultraviolet part of the spectrum. The photoreceptors have the typical cone morphology, with narrow short outer segments and oil droplets. The main difference between the two species is that C. nicterus has only colourless oil droplets, whereas A. ocellifera has colourless as well as green-yellow and pale-orange droplets. Conclusions Our results challenge the assumption that fossorial lizards undergo loss of visual function, a claim that is usually guided by the reduced size and external morphology of their eyes. In the case of C. nicterus, the visual system is well suited for vision in bright light and shows specialisations that improve sensitivity in dim light, suggesting that they might perform some visually-guided behaviour above the surface at the beginning or the end of their daily activity period, when light levels are relatively high in their open dunes habitat. This work highlights how studies on the functional anatomy of sensory systems can provide insights into the habits of secretive species.
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Affiliation(s)
- Carola A M Yovanovich
- 1Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Michele E R Pierotti
- 1Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,2Naos Marine Laboratories, Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - Taran Grant
- 1Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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50
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Scott JE. Macroevolutionary effects on primate trophic evolution and their implications for reconstructing primate origins. J Hum Evol 2019; 133:1-12. [PMID: 31358174 DOI: 10.1016/j.jhevol.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Abstract
The visual-predation hypothesis proposes that certain derived features shared by crown primates reflect an insectivorous ancestry. Critics of this idea have argued that because insectivory is uncommon among extant primates it is unlikely to have been a major influence on early primate evolution. According to this perspective, the low frequency of insectivory indicates that it is an apomorphic deviation from the mostly conserved primate ecological pattern of herbivory. The present study tests two alternative hypotheses that are compatible with an insectivorous ancestor: (1) that trophic evolution was biased, such that herbivory evolved repeatedly with few shifts back to insectivory, and (2) that insectivorous lineages have diversified at a lower rate than herbivorous lineages owing to differential trophic effects on speciation and extinction probabilities. Model-based analysis conducted using trait data for 307 extant primate species indicates that rates of transition into and out of insectivory are similar, rejecting the hypothesis of biased trophic evolution. On the other hand, the hypothesis of asymmetric diversification is supported, with insectivorous lineages having a lower rate of diversification than herbivorous lineages. This correlation is mediated by activity pattern: insectivory occurs mostly in nocturnal lineages, which have a lower diversification rate than diurnal lineages. The frequency of insectivory also appears to have been shaped by repeated transitions into ecological contexts in which insectivory is absent (large body size) or rare (diurnality). These findings suggest that the current distribution of trophic strategies among extant primates is the result of macroevolutionary processes that have favored the proliferation and persistence of herbivory relative to insectivory. This conclusion implies that the low frequency of insectivory is not necessarily evidence against the visual-predation hypothesis.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E. Second St. Pomona, California, 91766-1854, USA.
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