D. Noble, Patrice Pottier, M. Lagisz, Samantha Burke, S. Drobniak, R. E. O’Dea, S Nakagawa
Meta-analysis is a powerful tool used to generate quantitatively informed answers to pressing global challenges. By distilling data from broad sets of research designs and study systems into standardised effect sizes, meta-analyses provide physiologists with opportunities to estimate overall effect sizes and understand the drivers of effect variability. Despite this ambition, research designs in the field of comparative physiology can appear, at the outset, as being vastly different to each other because of 'nuisance heterogeneity' (e.g. different temperatures or treatment dosages used across studies). Methodological differences across studies have led many to believe that meta-analysis is an exercise in comparing 'apples with oranges'. Here, we dispel this myth by showing how standardised effect sizes can be used in conjunction with multilevel meta-regression models to both account for the factors driving differences across studies and make them more comparable. We assess the prevalence of nuisance heterogeneity in the comparative physiology literature - showing it is common and often not accounted for in analyses. We then formalise effect size measures (e.g. the temperature coefficient, Q10) that provide comparative physiologists with a means to remove nuisance heterogeneity without the need to resort to more complex statistical models that may be harder to interpret. We also describe more general approaches that can be applied to a variety of different contexts to derive new effect sizes and sampling variances, opening up new possibilities for quantitative synthesis. By using effect sizes that account for components of effect heterogeneity, in combination with existing meta-analytic models, comparative physiologists can explore exciting new questions while making results from large-scale data sets more accessible, comparable and widely interpretable.
{"title":"Meta-analytic approaches and effect sizes to account for 'nuisance heterogeneity' in comparative physiology.","authors":"D. Noble, Patrice Pottier, M. Lagisz, Samantha Burke, S. Drobniak, R. E. O’Dea, S Nakagawa","doi":"10.1242/jeb.243225","DOIUrl":"https://doi.org/10.1242/jeb.243225","url":null,"abstract":"Meta-analysis is a powerful tool used to generate quantitatively informed answers to pressing global challenges. By distilling data from broad sets of research designs and study systems into standardised effect sizes, meta-analyses provide physiologists with opportunities to estimate overall effect sizes and understand the drivers of effect variability. Despite this ambition, research designs in the field of comparative physiology can appear, at the outset, as being vastly different to each other because of 'nuisance heterogeneity' (e.g. different temperatures or treatment dosages used across studies). Methodological differences across studies have led many to believe that meta-analysis is an exercise in comparing 'apples with oranges'. Here, we dispel this myth by showing how standardised effect sizes can be used in conjunction with multilevel meta-regression models to both account for the factors driving differences across studies and make them more comparable. We assess the prevalence of nuisance heterogeneity in the comparative physiology literature - showing it is common and often not accounted for in analyses. We then formalise effect size measures (e.g. the temperature coefficient, Q10) that provide comparative physiologists with a means to remove nuisance heterogeneity without the need to resort to more complex statistical models that may be harder to interpret. We also describe more general approaches that can be applied to a variety of different contexts to derive new effect sizes and sampling variances, opening up new possibilities for quantitative synthesis. By using effect sizes that account for components of effect heterogeneity, in combination with existing meta-analytic models, comparative physiologists can explore exciting new questions while making results from large-scale data sets more accessible, comparable and widely interpretable.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72800652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rafael A Lara, Lukas Breitzler, Ieng Hou Lau, Flora Gordillo-Martínez, Fangyi Chen, P. Fonseca, A. Bass, Raquel O. Vasconcelos
Anthropogenic noise can be hazardous for the auditory system and wellbeing of animals, including humans. However, very limited information is known on how this global environmental pollutant affects auditory function and inner ear sensory receptors in early ontogeny. The zebrafish (Danio rerio) is a valuable model in hearing research, including to investigate developmental processes of the vertebrate inner ear. We tested the effects of chronic exposure to white noise in larval zebrafish on inner ear saccular sensitivity and morphology at 3 and 5 days post fertilization (dpf), as well as on auditory-evoked swimming responses using the prepulse inhibition paradigm (PPI) at 5 dpf. Noise-exposed larvae showed significant increase in microphonic potential thresholds at low frequencies, 100 and 200 Hz, while PPI revealed a hypersensitisation effect and similar threshold shift at 200 Hz. Auditory sensitivity changes were accompanied by a decrease in saccular hair cell number and epithelium area. In aggregate, the results reveal noise-induced effects on inner ear structure-function in a larval fish paralleled by a decrease in auditory-evoked sensorimotor responses. More broadly, this study highlights the importance of investigating the impact of environmental noise on early development of sensory and behavioural responsiveness to acoustic stimuli.
{"title":"Noise-induced hearing loss correlates with inner ear hair cell decrease in larval zebrafish.","authors":"Rafael A Lara, Lukas Breitzler, Ieng Hou Lau, Flora Gordillo-Martínez, Fangyi Chen, P. Fonseca, A. Bass, Raquel O. Vasconcelos","doi":"10.1242/jeb.243743","DOIUrl":"https://doi.org/10.1242/jeb.243743","url":null,"abstract":"Anthropogenic noise can be hazardous for the auditory system and wellbeing of animals, including humans. However, very limited information is known on how this global environmental pollutant affects auditory function and inner ear sensory receptors in early ontogeny. The zebrafish (Danio rerio) is a valuable model in hearing research, including to investigate developmental processes of the vertebrate inner ear. We tested the effects of chronic exposure to white noise in larval zebrafish on inner ear saccular sensitivity and morphology at 3 and 5 days post fertilization (dpf), as well as on auditory-evoked swimming responses using the prepulse inhibition paradigm (PPI) at 5 dpf. Noise-exposed larvae showed significant increase in microphonic potential thresholds at low frequencies, 100 and 200 Hz, while PPI revealed a hypersensitisation effect and similar threshold shift at 200 Hz. Auditory sensitivity changes were accompanied by a decrease in saccular hair cell number and epithelium area. In aggregate, the results reveal noise-induced effects on inner ear structure-function in a larval fish paralleled by a decrease in auditory-evoked sensorimotor responses. More broadly, this study highlights the importance of investigating the impact of environmental noise on early development of sensory and behavioural responsiveness to acoustic stimuli.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"102 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88687044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Looking to the future: Building New Paradigms in Comparative Physiology and Biomechanics.","authors":"C. Franklin, S. Patek, P. Wright","doi":"10.1242/jeb.244096","DOIUrl":"https://doi.org/10.1242/jeb.244096","url":null,"abstract":"","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"116 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85643899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Naomi F. Green, Emily Guevara, D. Osorio, J. Endler, N. Marshall, M. Vorobyev, K. L. Cheney
ABSTRACT Animals use colour vision in a range of behaviours. Visual performance is limited by thresholds, which are set by noise in photoreceptors and subsequent neural processing. The receptor noise limited (RNL) model of colour discrimination is widely used for modelling colour vision and accounts well for experimental data from many species. In one of the most comprehensive tests yet of colour discrimination in a non-human species, we used Ishihara-style stimulus patterns to examine thresholds for 21 directions at five locations in colour space for the fish Rhinecanthus aculeatus. Thresholds matched RNL model predictions most closely for stimuli near the achromatic point, but exceeded predictions (indicating a decline in sensitivity) with distance from this point. Thresholds were also usually higher for saturation than for hue differences. These changes in colour threshold with colour space location and direction may give insight into photoreceptor non-linearities and post-receptoral mechanisms of colour vision in fish. Our results highlight the need for a cautious interpretation of the RNL model – especially for modelling colours that differ from one another in saturation (rather than hue), and for highly saturated colours distant from the achromatic point in colour space.
{"title":"Colour discrimination thresholds vary throughout colour space in a reef fish (Rhinecanthus aculeatus)","authors":"Naomi F. Green, Emily Guevara, D. Osorio, J. Endler, N. Marshall, M. Vorobyev, K. L. Cheney","doi":"10.1242/jeb.243533","DOIUrl":"https://doi.org/10.1242/jeb.243533","url":null,"abstract":"ABSTRACT Animals use colour vision in a range of behaviours. Visual performance is limited by thresholds, which are set by noise in photoreceptors and subsequent neural processing. The receptor noise limited (RNL) model of colour discrimination is widely used for modelling colour vision and accounts well for experimental data from many species. In one of the most comprehensive tests yet of colour discrimination in a non-human species, we used Ishihara-style stimulus patterns to examine thresholds for 21 directions at five locations in colour space for the fish Rhinecanthus aculeatus. Thresholds matched RNL model predictions most closely for stimuli near the achromatic point, but exceeded predictions (indicating a decline in sensitivity) with distance from this point. Thresholds were also usually higher for saturation than for hue differences. These changes in colour threshold with colour space location and direction may give insight into photoreceptor non-linearities and post-receptoral mechanisms of colour vision in fish. Our results highlight the need for a cautious interpretation of the RNL model – especially for modelling colours that differ from one another in saturation (rather than hue), and for highly saturated colours distant from the achromatic point in colour space.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86038328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eric Ste-Marie, Y. Watanabe, J. Semmens, M. Marcoux, N. Hussey
Field metabolic rate (FMR) is a holistic measure of metabolism representing the routine energy utilization of a species living within a specific ecological context, thus providing insight into its ecology, fitness and resilience to environmental stressors. For animals which cannot be easily observed in the wild, FMR can also be used in concert with dietary data to quantitatively assess their role as consumers, improving understanding of the trophic linkages that structure food webs and allowing for informed management decisions. Here we modeled the FMR of Greenland sharks (Somniosus microcephalus) equipped with biologger packages or pop-up archival satellite tags (PSATs) in two coastal inlets of Baffin Island (Nunavut) using metabolic scaling relationships for mass, temperature and activity. We estimated that Greenland sharks had an overall mean FMR of 21.67±2.30 mgO2h-1kg-0.84 (n=30; 1-4 day accelerometer package deployments) while residing inside these cold-water fjord systems in the late summer, and 25.48±0.47 mgO2h-1kg-0.84 (n=6; PSATs) over an entire year. When considering prey consumption rate, an average shark in these systems (224kg) requires a maintenance ration of 61-193g of fish or marine mammal prey daily. As a lethargic polar species, these low FMR estimates, and corresponding prey consumption estimates suggest Greenland sharks require very little energy to sustain themselves under natural conditions. These data provide the first characterization of the energetics and consumer role of this vulnerable and understudied species in the wild, essential given growing pressures from climate change and expanding commercial fisheries in the Arctic.
{"title":"Life in the slow lane: Field Metabolic Rate and Prey Consumption Rate of the Greenland Shark (Somniosus microcephalus) modeled using Archival Biologgers.","authors":"Eric Ste-Marie, Y. Watanabe, J. Semmens, M. Marcoux, N. Hussey","doi":"10.1242/jeb.242994","DOIUrl":"https://doi.org/10.1242/jeb.242994","url":null,"abstract":"Field metabolic rate (FMR) is a holistic measure of metabolism representing the routine energy utilization of a species living within a specific ecological context, thus providing insight into its ecology, fitness and resilience to environmental stressors. For animals which cannot be easily observed in the wild, FMR can also be used in concert with dietary data to quantitatively assess their role as consumers, improving understanding of the trophic linkages that structure food webs and allowing for informed management decisions. Here we modeled the FMR of Greenland sharks (Somniosus microcephalus) equipped with biologger packages or pop-up archival satellite tags (PSATs) in two coastal inlets of Baffin Island (Nunavut) using metabolic scaling relationships for mass, temperature and activity. We estimated that Greenland sharks had an overall mean FMR of 21.67±2.30 mgO2h-1kg-0.84 (n=30; 1-4 day accelerometer package deployments) while residing inside these cold-water fjord systems in the late summer, and 25.48±0.47 mgO2h-1kg-0.84 (n=6; PSATs) over an entire year. When considering prey consumption rate, an average shark in these systems (224kg) requires a maintenance ration of 61-193g of fish or marine mammal prey daily. As a lethargic polar species, these low FMR estimates, and corresponding prey consumption estimates suggest Greenland sharks require very little energy to sustain themselves under natural conditions. These data provide the first characterization of the energetics and consumer role of this vulnerable and understudied species in the wild, essential given growing pressures from climate change and expanding commercial fisheries in the Arctic.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75528920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dominique G. Roche, G. Raby, T. Norin, R. Ern, H. Scheuffele, M. Skeeles, Rachael Morgan, Anna H. Andreassen, J. Clements, Sarahdghyn Louissaint, F. Jutfelt, T. Clark, S. Binning
In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10 years. Nineteen per cent of studies on the three paradigms had open data, and 3.2% had open code. Similarly, 12.1% of studies in the journals we examined had open data, and 3.1% had open code. Previous research indicates that only 50% of shared datasets are complete and re-usable, suggesting that fewer than 10% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.
在最近的一篇社论中，《实验生物学杂志》(Journal of Experimental Biology)主编认为，需要建立共识、数据共享和更好地跨学科整合，以应对气候变化带来的紧迫科学挑战。我们同意并扩大跨学科整合和透明度的重要性，以改善共识的建立和推进实验生物学中的气候变化研究。我们通过回顾过去10年来在比较生理学和行为生态学的主要期刊上发表的与三种有争议的范式的实证研究相关的开放数据和分析代码，调查了实验生物学中可重复的研究实践。在这三种范式的研究中，19%的研究有开放数据，3.2%的研究有开放代码。同样，在我们研究的期刊中，12.1%的研究有开放数据，3.1%有开放代码。先前的研究表明，只有50%的共享数据集是完整的和可重复使用的，这表明只有不到10%的实验生物学研究拥有可用的开放数据。令人鼓舞的是，我们的研究结果表明，随着时间的推移，可重复的研究实践正在增加，近年来一些期刊的数据共享率达到75%。实验生物学中严谨的实证研究是理解气候变化影响生物机制的关键，并最终促进以证据为基础的保护政策和实践。我们认为，更多地采用开放科学实践，特别是关注FAIR(可查找、可访问、可互操作、可重用)数据和代码，代表了一种急需的范式转变，即提高透明度、跨学科整合和建立共识，以最大限度地发挥实验生物学家在解决环境变化对生物体的影响方面的贡献。
{"title":"Paths towards greater consensus building in experimental biology.","authors":"Dominique G. Roche, G. Raby, T. Norin, R. Ern, H. Scheuffele, M. Skeeles, Rachael Morgan, Anna H. Andreassen, J. Clements, Sarahdghyn Louissaint, F. Jutfelt, T. Clark, S. Binning","doi":"10.1242/jeb.243559","DOIUrl":"https://doi.org/10.1242/jeb.243559","url":null,"abstract":"In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10 years. Nineteen per cent of studies on the three paradigms had open data, and 3.2% had open code. Similarly, 12.1% of studies in the journals we examined had open data, and 3.1% had open code. Previous research indicates that only 50% of shared datasets are complete and re-usable, suggesting that fewer than 10% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86816775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rebecca S Raynal, D. Noble, J. Riley, A. Senior, D. Warner, G. While, L. Schwanz
During the vulnerable stages of early life, most ectothermic animals experience hourly and diel fluctuations in temperature as air temperatures change. While we know a great deal about how different constant temperatures impact the phenotypes of developing ectotherms, we know remarkably little about the impacts of temperature fluctuations on the development of ectotherms. In this study, we used a meta-analytic approach to compare the mean and variance of phenotypic outcomes from constant and fluctuating incubation temperatures across reptile species. We found that fluctuating temperatures provided a small benefit (higher hatching success and shorter incubation durations) at cool mean temperatures compared with constant temperatures, but had a negative effect at warm mean temperatures. In addition, more extreme temperature fluctuations led to greater reductions in embryonic survival compared with moderate temperature fluctuations. Within the limited data available from species with temperature-dependent sex determination, embryos had a higher chance of developing as female when developing in fluctuating temperatures compared with those developing in constant temperatures. With our meta-analytic approach, we identified average mean nest temperatures across all taxa where reptiles switch from receiving benefits to incurring costs when incubation temperatures fluctuate. More broadly, our study indicates that the impact of fluctuating developmental temperature on some phenotypes in ectothermic taxa are likely to be predictable via integration of developmental temperature profiles with thermal performance curves.
{"title":"Impact of fluctuating developmental temperatures on phenotypic traits in reptiles: a meta-analysis.","authors":"Rebecca S Raynal, D. Noble, J. Riley, A. Senior, D. Warner, G. While, L. Schwanz","doi":"10.1242/jeb.243369","DOIUrl":"https://doi.org/10.1242/jeb.243369","url":null,"abstract":"During the vulnerable stages of early life, most ectothermic animals experience hourly and diel fluctuations in temperature as air temperatures change. While we know a great deal about how different constant temperatures impact the phenotypes of developing ectotherms, we know remarkably little about the impacts of temperature fluctuations on the development of ectotherms. In this study, we used a meta-analytic approach to compare the mean and variance of phenotypic outcomes from constant and fluctuating incubation temperatures across reptile species. We found that fluctuating temperatures provided a small benefit (higher hatching success and shorter incubation durations) at cool mean temperatures compared with constant temperatures, but had a negative effect at warm mean temperatures. In addition, more extreme temperature fluctuations led to greater reductions in embryonic survival compared with moderate temperature fluctuations. Within the limited data available from species with temperature-dependent sex determination, embryos had a higher chance of developing as female when developing in fluctuating temperatures compared with those developing in constant temperatures. With our meta-analytic approach, we identified average mean nest temperatures across all taxa where reptiles switch from receiving benefits to incurring costs when incubation temperatures fluctuate. More broadly, our study indicates that the impact of fluctuating developmental temperature on some phenotypes in ectothermic taxa are likely to be predictable via integration of developmental temperature profiles with thermal performance curves.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"2007 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78575624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Schwanz, A. Gunderson, Maider Iglesias‐Carrasco, Michele A. Johnson, J. Kong, J. Riley, N. Wu
Comparative analyses have a long history of macro-ecological and -evolutionary approaches to understand structure, function, mechanism and constraint. As the pace of science accelerates, there is ever-increasing access to diverse types of data and open access databases that are enabling and inspiring new research. Whether conducting a species-level trait-based analysis or a formal meta-analysis of study effect sizes, comparative approaches share a common reliance on reliable, carefully curated databases. Unlike many scientific endeavors, building a database is a process that many researchers undertake infrequently and in which we are not formally trained. This Commentary provides an introduction to building databases for comparative analyses and highlights challenges and solutions that the authors of this Commentary have faced in their own experiences. We focus on four major tips: (1) carefully strategizing the literature search; (2) structuring databases for multiple use; (3) establishing version control within (and beyond) your study; and (4) the importance of making databases accessible. We highlight how one's approach to these tasks often depends on the goal of the study and the nature of the data. Finally, we assert that the curation of single-question databases has several disadvantages: it limits the possibility of using databases for multiple purposes and decreases efficiency due to independent researchers repeatedly sifting through large volumes of raw information. We argue that curating databases that are broader than one research question can provide a large return on investment, and that research fields could increase efficiency if community curation of databases was established.
{"title":"Best practices for building and curating databases for comparative analyses.","authors":"L. Schwanz, A. Gunderson, Maider Iglesias‐Carrasco, Michele A. Johnson, J. Kong, J. Riley, N. Wu","doi":"10.1242/jeb.243295","DOIUrl":"https://doi.org/10.1242/jeb.243295","url":null,"abstract":"Comparative analyses have a long history of macro-ecological and -evolutionary approaches to understand structure, function, mechanism and constraint. As the pace of science accelerates, there is ever-increasing access to diverse types of data and open access databases that are enabling and inspiring new research. Whether conducting a species-level trait-based analysis or a formal meta-analysis of study effect sizes, comparative approaches share a common reliance on reliable, carefully curated databases. Unlike many scientific endeavors, building a database is a process that many researchers undertake infrequently and in which we are not formally trained. This Commentary provides an introduction to building databases for comparative analyses and highlights challenges and solutions that the authors of this Commentary have faced in their own experiences. We focus on four major tips: (1) carefully strategizing the literature search; (2) structuring databases for multiple use; (3) establishing version control within (and beyond) your study; and (4) the importance of making databases accessible. We highlight how one's approach to these tasks often depends on the goal of the study and the nature of the data. Finally, we assert that the curation of single-question databases has several disadvantages: it limits the possibility of using databases for multiple purposes and decreases efficiency due to independent researchers repeatedly sifting through large volumes of raw information. We argue that curating databases that are broader than one research question can provide a large return on investment, and that research fields could increase efficiency if community curation of databases was established.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90152547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The difficulty of quantifying asymmetrical limb movements, compared with symmetrical gaits, has resulted in a dearth of information concerning the mechanics and adaptive benefits of these locomotor patterns. Further, no study has explored the evolutionary history of asymmetrical gaits using phylogenetic comparative techniques. Most foundational work suggests that symmetrical gaits are an ancestral feature and asymmetrical gaits are a more derived feature of mammals, some crocodilians, some turtles, anurans and some fish species. In this study, we searched the literature for evidence of the use of asymmetrical gaits across extant gnathostomes, and from this sample (n=308 species) modeled the evolution of asymmetrical gaits assuming four different scenarios. Our analysis shows strongest support for an evolutionary model where asymmetrical gaits are ancestral for gnathostomes during benthic walking and could be both lost and gained during subsequent gnathostome evolution. We were unable to reconstruct the presence/absence of asymmetrical gaits at the tetrapod, amniote, turtle and crocodilian nodes with certainty. The ability to adopt asymmetrical gaits was likely ancestral for Mammalia but was probably not ancestral for Amphibia and Lepidosauria. The absence of asymmetrical gaits in certain lineages may be attributable to neuromuscular and/or anatomical constraints and/or generally slow movement not associated with these gaits. This finding adds to the growing body of work showing the early gnathostomes and tetrapods may have used a diversity of gaits, including asymmetrical patterns of limb cycling.
{"title":"The evolution of asymmetrical gaits in gnathostome vertebrates.","authors":"E. McElroy, M. Granatosky","doi":"10.1242/jeb.243235","DOIUrl":"https://doi.org/10.1242/jeb.243235","url":null,"abstract":"The difficulty of quantifying asymmetrical limb movements, compared with symmetrical gaits, has resulted in a dearth of information concerning the mechanics and adaptive benefits of these locomotor patterns. Further, no study has explored the evolutionary history of asymmetrical gaits using phylogenetic comparative techniques. Most foundational work suggests that symmetrical gaits are an ancestral feature and asymmetrical gaits are a more derived feature of mammals, some crocodilians, some turtles, anurans and some fish species. In this study, we searched the literature for evidence of the use of asymmetrical gaits across extant gnathostomes, and from this sample (n=308 species) modeled the evolution of asymmetrical gaits assuming four different scenarios. Our analysis shows strongest support for an evolutionary model where asymmetrical gaits are ancestral for gnathostomes during benthic walking and could be both lost and gained during subsequent gnathostome evolution. We were unable to reconstruct the presence/absence of asymmetrical gaits at the tetrapod, amniote, turtle and crocodilian nodes with certainty. The ability to adopt asymmetrical gaits was likely ancestral for Mammalia but was probably not ancestral for Amphibia and Lepidosauria. The absence of asymmetrical gaits in certain lineages may be attributable to neuromuscular and/or anatomical constraints and/or generally slow movement not associated with these gaits. This finding adds to the growing body of work showing the early gnathostomes and tetrapods may have used a diversity of gaits, including asymmetrical patterns of limb cycling.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74933455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Octopus arms are highly flexible structures capable of complex motions and are used in a wide repertoire of behaviors. Movements are generated by the coordinated summation of innervation signals to packed arrays of muscles oriented in different directions and moving based on their anatomical relationships. In this study, we investigated the interplay between muscle biomechanics and anatomical organization in the Octopus vulgaris arm to elucidate their role in different arm movements. We performed isometric and isotonic force measurements on isolated longitudinal (L) and transverse (T) arm muscles and showed that L has a higher rate of activation and relaxation, lower twitch-to-tetanus ratio, and lower passive tension than T muscles, thus prompting their use as faster and slower muscles, respectively. This points to the use of L in more graded responses, such as those involved in precise actions, and T in intense and sustained actions, such as motion stabilization and posture maintenance. Once activated, the arm muscles exert forces that cause deformations of the entire arm, which are determined by the amount, location, properties and orientation of their fibers. Here, we show that, although continuous, the arm manifests a certain degree of morphological specialization, where the arm muscles have a different aspect ratio along the arm. This possibly supports the functional specialization of arm portion observed in various motions, such as fetching and crawling. Hence, the octopus arm as a whole can be seen as a 'reservoir' of possibilities where different types of motion may emerge at the limb level through the co-option of the muscle contractile properties and structural arrangement.
{"title":"How octopus arm muscle contractile properties and anatomical organization contribute to the arm functional specialization.","authors":"L. Zullo, Alessio Di Clemente, Federica Maiole","doi":"10.1242/jeb.243163","DOIUrl":"https://doi.org/10.1242/jeb.243163","url":null,"abstract":"Octopus arms are highly flexible structures capable of complex motions and are used in a wide repertoire of behaviors. Movements are generated by the coordinated summation of innervation signals to packed arrays of muscles oriented in different directions and moving based on their anatomical relationships. In this study, we investigated the interplay between muscle biomechanics and anatomical organization in the Octopus vulgaris arm to elucidate their role in different arm movements. We performed isometric and isotonic force measurements on isolated longitudinal (L) and transverse (T) arm muscles and showed that L has a higher rate of activation and relaxation, lower twitch-to-tetanus ratio, and lower passive tension than T muscles, thus prompting their use as faster and slower muscles, respectively. This points to the use of L in more graded responses, such as those involved in precise actions, and T in intense and sustained actions, such as motion stabilization and posture maintenance. Once activated, the arm muscles exert forces that cause deformations of the entire arm, which are determined by the amount, location, properties and orientation of their fibers. Here, we show that, although continuous, the arm manifests a certain degree of morphological specialization, where the arm muscles have a different aspect ratio along the arm. This possibly supports the functional specialization of arm portion observed in various motions, such as fetching and crawling. Hence, the octopus arm as a whole can be seen as a 'reservoir' of possibilities where different types of motion may emerge at the limb level through the co-option of the muscle contractile properties and structural arrangement.","PeriodicalId":22458,"journal":{"name":"THE EGYPTIAN JOURNAL OF EXPERIMENTAL BIOLOGY","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72818183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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