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Archaeocytes in sponges: simple cells of complicated fate. 海绵中的古细胞:命运复杂的简单细胞。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-12 DOI: 10.1111/brv.13162
Alexander Ereskovsky, Nikolai P Melnikov, Andrey Lavrov
{"title":"Archaeocytes in sponges: simple cells of complicated fate.","authors":"Alexander Ereskovsky, Nikolai P Melnikov, Andrey Lavrov","doi":"10.1111/brv.13162","DOIUrl":"https://doi.org/10.1111/brv.13162","url":null,"abstract":"<p><p>Archaeocytes are considered a key cell type in sponges (Porifera). They are believed to be multifunctional cells performing various functions, from nutrient digestion to acting as adult stem cells (ASCs). Thus, archaeocytes are mentioned in discussions on various aspects of sponge biology. As presumed ASCs of an early-diverged animal taxon, archaeocytes are of great fundamental interest for further progress in understanding tissue functioning in metazoans. However, the term 'archaeocyte' is rather ambiguous in its usage and understanding, and debates surrounding archaeocytes have persisted for over a century, reflecting the ongoing complexity of understanding their nature. This article presents a comprehensive revision of the archaeocyte concept, including both its historical development and biological features (i.e. taxonomic distribution, characteristics, and functions). The term 'archaeocyte' and its central aspects were introduced as early as the end of the 19th century based on data mainly from demosponges. Remarkably, despite the general lack of comparative and non-histological data, these early studies already regarded archaeocytes as the ASCs of sponges. These early views were readily inherited by subsequent studies, often without proper verification, shaping views on many aspects of sponge biology for more than a century. Taking into account all available data, we propose considering the archaeocytes as a cell type specific to the class Demospongiae. Clear homologues of archaeocytes are absent in other sponge classes. In demosponges, the term 'archaeocytes' refers to mesohyl cells that have an amoeboid shape, nucleolated nuclei, and non-specific inclusions in the cytoplasm. The absence of specific traits makes the archaeocytes a loosely defined and probably heterogeneous cell population, rendering the exhaustive characterisation of the 'true' archaeocyte population impossible. At the same time, the molecular characterisation of archaeocytes is only beginning to develop. Stemness and almost unlimited potency have always been at the core of the traditional archaeocyte concept. However, currently, the most consistent data on archaeocyte stem cell function come only from developing gemmules of freshwater sponges. For tissues of adult demosponges, the data favour a two-component stem cell system, in which archaeocytes may cooperate with another stem cell population, choanocytes. Simultaneously, cells with archaeocyte morphology function as macrophages in demosponges, participating in the food digestion cycle and immune defence. Such cells should be denoted with the more neutral term 'nucleolar amoebocytes', as the term 'archaeocyte' not only describes the morphology of a cell but also introduces the proposition of its stem nature. Thus, the future usage of the term 'archaeocyte' should be limited to cases where a cell is shown or at least presumed to be a stem cell.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Meta-analysis of the acoustic adaptation hypothesis reveals no support for the effect of vegetation structure on acoustic signalling across terrestrial vertebrates. 对声学适应假说的元分析表明,植被结构对陆生脊椎动物的声学信号没有影响。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-12 DOI: 10.1111/brv.13163
Bárbara Freitas, Pietro B D'Amelio, Borja Milá, Christophe Thébaud, Tim Janicke
{"title":"Meta-analysis of the acoustic adaptation hypothesis reveals no support for the effect of vegetation structure on acoustic signalling across terrestrial vertebrates.","authors":"Bárbara Freitas, Pietro B D'Amelio, Borja Milá, Christophe Thébaud, Tim Janicke","doi":"10.1111/brv.13163","DOIUrl":"https://doi.org/10.1111/brv.13163","url":null,"abstract":"<p><p>Acoustic communication plays a prominent role in various ecological and evolutionary processes involving social interactions. The properties of acoustic signals are thought to be influenced not only by the interaction between signaller and receiver but also by the acoustic characteristics of the environment through which the signal is transmitted. This conjecture forms the core of the so-called \"acoustic adaptation hypothesis\" (AAH), which posits that vegetation structure affects frequency and temporal parameters of acoustic signals emitted by a signaller as a function of their acoustic degradation properties. Specifically, animals in densely vegetated \"closed habitats\" are expected to produce longer acoustic signals with lower repetition rates and lower frequencies (minimum, mean, maximum, and peak) compared to those inhabiting less-vegetated \"open habitats\". To date, this hypothesis has received mixed results, with the level of support depending on the taxonomic group and the methodology used. We conducted a systematic literature search of empirical studies testing for an effect of vegetation structure on acoustic signalling and assessed the generality of the AAH using a meta-analytic approach based on 371 effect sizes from 75 studies and 57 taxa encompassing birds, mammals and amphibians. Overall, our results do not provide consistent support for the AAH, neither in within-species comparisons (suggesting no overall phenotypically plastic response of acoustic signalling to vegetation structure) nor in among-species comparisons (suggesting no overall evolutionary response). However, when considering birds only, we found weak support for the AAH in within-species comparisons, which was mainly driven by studies that measured frequency bandwidth, suggesting that this variable may exhibit a phenotypically plastic response to vegetation structure. For among-species comparisons in birds, we also found support for the AAH, but this effect was not significant after excluding comparative studies that did not account for phylogenetic non-independence. Collectively, our synthesis does not support a universal role of vegetation structure in the evolution of acoustic communication. We highlight the need for more empirical work on currently under-studied taxa such as amphibians, mammals, and insects. Furthermore, we propose a framework for future research on the AAH. We specifically advocate for a more detailed and quantitative characterisation of habitats to identify frequencies with the highest detection probability and to determine if frequencies with greater detection distances are preferentially used. Finally, we stress that empirical tests of the AAH should focus on signals that are selected for increased transmission distance.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of eodiscinid trilobites. 三叶虫的发育。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-10 DOI: 10.1111/brv.13159
Tao Dai, Xingliang Zhang
{"title":"Development of eodiscinid trilobites.","authors":"Tao Dai, Xingliang Zhang","doi":"10.1111/brv.13159","DOIUrl":"https://doi.org/10.1111/brv.13159","url":null,"abstract":"<p><p>A comprehensive review of a full developmental sequence of eodiscinid trilobites reported in recent decades from Cambrian Series 2 and 3 strata is presented. These mostly articulated specimens exhibit detailed morphologies with preservation of even delicate structures at different growth stages, such as the bacculae, axial pores, spine pores, pygidial marginal spines and line coaptative structures. Their trunk segmentation schedules displayed a consistent developmental mode in segment generation and liberation, that is tagmosis and somitogenesis occurred heterochronously after each moulting event, providing clues regarding the potential developmental strategy in isopygous and even macropygous trilobites. The fact that the rate of segmentation obviously exceeds that of articulation results in a seemingly prolonged process of the formation of thoracic segments, which might explain why eodiscinid trilobites have a fixed and limited number of thoracic segments. In addition, the relationship between enrollment mechanism and trunk segmentation during eodiscinid ontogeny confirms this highly unusual growth pattern among the Trilobita, revealing why these early-diverging trilobites controlled the rate of segment increase and release during their life cycles, and is thus of interest with regard to the evolution of arthropod body patterning.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Shedding light on biodiversity: reviewing existing knowledge and exploring hypothesised impacts of agrophotovoltaics. 照亮生物多样性:回顾现有知识,探索假设的农用光伏发电影响。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-10 DOI: 10.1111/brv.13165
Rachel Schwarz, Yaron Ziv
{"title":"Shedding light on biodiversity: reviewing existing knowledge and exploring hypothesised impacts of agrophotovoltaics.","authors":"Rachel Schwarz, Yaron Ziv","doi":"10.1111/brv.13165","DOIUrl":"https://doi.org/10.1111/brv.13165","url":null,"abstract":"<p><p>The growing demand for energy and the shift towards green energy solutions have led to the conversion of open spaces and agricultural fields into photovoltaic (PV) power plants, exacerbating the \"food-energy-environment\" trilemma. Agrophotovoltaics (APVs), a dual-use system combining agriculture and energy production on the same land, presents a potential solution to this challenge. While the environmental impacts of ground-mounted utility-scale PV (USPV) power plants and the effects of APV systems on agricultural yields have been extensively studied and reviewed, the implications for wildlife and biodiversity remain largely unexplored. This knowledge gap is pressing, given the accelerated global adoption of APV systems and the urgency of understanding their broader ecological consequences. In this concise review, we synthesise existing literature on the impacts of USPV installations on biodiversity and the effects of APV on crop production. Building on these foundations, we propose novel hypotheses concerning the potential pathways and mechanisms through which APV systems may influence biodiversity. We explore the complex interactions between agroecosystems and natural ecosystems, examining both direct and indirect effects. Our review culminates in a set of key research questions designed to guide future studies on the biodiversity outcomes of APV deployment. Future research should comprehensively address factors such as habitat type, climate, spatial scale, technology, and agricultural practices, as well as the overarching impacts of climate change. By highlighting the importance of these variables, we aim to facilitate a nuanced understanding of how APV systems can either support or undermine biodiversity. This work not only underscores the critical need for empirical studies in this emerging field but also sets the stage for more informed and sustainable implementation of APV technologies.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The underlying causes of differential migration: assumptions, hypotheses, and predictions. 差异化迁移的根本原因:假设、假说和预测。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-10 DOI: 10.1111/brv.13160
Neil Paprocki, Courtney J Conway
{"title":"The underlying causes of differential migration: assumptions, hypotheses, and predictions.","authors":"Neil Paprocki, Courtney J Conway","doi":"10.1111/brv.13160","DOIUrl":"https://doi.org/10.1111/brv.13160","url":null,"abstract":"<p><p>Mechanisms governing the migratory decisions of birds have long fascinated ecologists and sparked considerable debate. Identifying factors responsible for variation in migration distance, also known as differential migration, has been a popular approach to understanding the mechanisms underlying migratory behaviour more generally. However, research progress has been slowed by the continued testing of overlapping, non-mechanistic, and circular predictions among a small set of historically entrenched hypotheses. We highlight the body size hypothesis and suggest that the predictions commonly tested have impeded progress because body size relationships with migration distance are predictions made by several distinct hypotheses with contrasting mechanisms. The cost of migration itself has not been adequately accounted for in most hypotheses, and we propose two flight efficiency hypotheses with time- and energy-minimizing mechanisms that allow individuals to mitigate the risks inherent to longer migrations. We also advance two conceptual versions of the social dominance hypothesis based on two distinct underlying mechanisms related to distance minimization and food maximization that will help clarify the role of competition in driving migratory decisions. Overall, we describe and refine 12 mechanistic hypotheses proposed to explain differential migration (along with several other special-case hypotheses), seven of which have underlying mechanisms related to food limitation as past research has identified this to be an important driver of differential migration. We also thoroughly reviewed 145 publications to assess the amount of support for 10 critical assumptions underlying alternative hypotheses for differential migration in birds. Our review reveals that surprisingly few studies explicitly evaluate assumptions within a differential migration context. Generating and testing strong predictions and critical assumptions underlying mechanisms of alternative hypotheses will improve our ability to differentiate among these explanations of differential migration. Additionally, future intraspecific progress will be greatest if investigators continue to focus on mechanisms underlying variation in migration distance within rather than among demographic classes, as previous research has found differing mechanisms to be responsible for differential migration among demographic classes. Interspecifically, a thorough comparative analysis that seeks to explain variation in migration distance among species would broaden both our understanding of the mechanisms regulating current differential migration patterns and those that led to the evolution of migration more generally. Collectively, we provide a framework that, together with advances in animal-borne tracking and other technology, can be used to advance our understanding of the causes of differential migration distance, and migratory decisions more generally.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molluscan systematics: historical perspectives and the way ahead. 软体动物系统学:历史展望与未来之路。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-06 DOI: 10.1111/brv.13157
Biyang Xu, Lingfeng Kong, Jin Sun, Junlong Zhang, Yang Zhang, Hao Song, Qi Li, Juan E Uribe, Kenneth M Halanych, Chenyang Cai, Yun-Wei Dong, Shi Wang, Yuanning Li
{"title":"Molluscan systematics: historical perspectives and the way ahead.","authors":"Biyang Xu, Lingfeng Kong, Jin Sun, Junlong Zhang, Yang Zhang, Hao Song, Qi Li, Juan E Uribe, Kenneth M Halanych, Chenyang Cai, Yun-Wei Dong, Shi Wang, Yuanning Li","doi":"10.1111/brv.13157","DOIUrl":"https://doi.org/10.1111/brv.13157","url":null,"abstract":"<p><p>Mollusca, the second-most diverse animal phylum, is estimated to have over 100,000 living species with great genetic and phenotypic diversity, a rich fossil record, and a considerable evolutionary significance. Early work on molluscan systematics was grounded in morphological and anatomical studies. With the transition from oligo gene Sanger sequencing to cutting-edge genomic sequencing technologies, molecular data has been increasingly utilised, providing abundant information for reconstructing the molluscan phylogenetic tree. However, relationships among and within most major lineages of Mollusca have long been contentious, often due to limited genetic markers, insufficient taxon sampling and phylogenetic conflict. Fortunately, remarkable progress in molluscan systematics has been made in recent years, which has shed light on how major molluscan groups have evolved. In this review of molluscan systematics, we first synthesise the current understanding of the molluscan Tree of Life at higher taxonomic levels. We then discuss how micromolluscs, which have adult individuals with a body size smaller than 5 mm, offer unique insights into Mollusca's vast diversity and deep phylogeny. Despite recent advancements, our knowledge of molluscan systematics and phylogeny still needs refinement. Further advancements in molluscan systematics will arise from integrating comprehensive data sets, including genome-scale data, exceptional fossils, and digital morphological data (including internal structures). Enhanced access to these data sets, combined with increased collaboration among morphologists, palaeontologists, evolutionary developmental biologists, and molecular phylogeneticists, will significantly advance this field.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Insect immunity in the Anthropocene. 人类世的昆虫免疫力。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-11-05 DOI: 10.1111/brv.13158
Md Kawsar Khan, Jens Rolff
{"title":"Insect immunity in the Anthropocene.","authors":"Md Kawsar Khan, Jens Rolff","doi":"10.1111/brv.13158","DOIUrl":"https://doi.org/10.1111/brv.13158","url":null,"abstract":"<p><p>Anthropogenic activities result in global change, including climate change, landscape degradation and pollution, that can alter insect physiology and immune defences. These changes may have contributed to global insect decline and the dynamics of insect-transmitted diseases. The ability of insects to mount immune responses upon infection is crucial for defence against pathogens and parasites. Suppressed immune defences reduce fitness by causing disease-driven mortality and elevated immune responses reduce energy available to invest in other fitness traits such as reproduction. Understanding the impact of anthropogenic factors on insect-pathogen interactions is therefore key to determining the contribution of anthropogenic global change to pathogen-driven global insect decline and the emergence and transmission of insect-borne diseases. Here, we synthesise evidence of the impact of anthropogenic factors on insect immunity. We found evidence that anthropogenic factors, such as insecticides and heavy metals, directly impacting insect immune responses by inhibiting immune activation pathways. Alternatively, factors such as global warming, heatwaves, elevated CO<sub>2</sub> and landscape degradation can indirectly reduce insect immune responses via reducing the energy available for immune function. We further review how anthropogenic factors impact pathogen clearance and contribute to an increase in vector-borne diseases. We discuss the fitness cost of anthropogenic factors via pathogen-driven mortality and reduced reproductive output and how this can contribute to species extinction. We found that most research has determined the impact of a single anthropogenic factor on insect immune responses or pathogen resistance. We recommend studying the combined impact of multiple stressors on immune response and pathogen resistance to understand better how anthropogenic factors affect insect immunity. We conclude by highlighting the importance of initiatives to mitigate the impact of anthropogenic factors on insect immunity, to reduce the spread of vector-borne diseases, and to protect vulnerable ecosystems from emerging diseases.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The cryptonephridial/rectal complex: an evolutionary adaptation for water and ion conservation. 隐鳃/直肠复合体:水和离子保存的进化适应。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-10-22 DOI: 10.1111/brv.13156
Robin Beaven, Barry Denholm
{"title":"The cryptonephridial/rectal complex: an evolutionary adaptation for water and ion conservation.","authors":"Robin Beaven, Barry Denholm","doi":"10.1111/brv.13156","DOIUrl":"https://doi.org/10.1111/brv.13156","url":null,"abstract":"<p><p>Arthropods have integrated digestive and renal systems, which function to acquire and maintain homeostatically the substances they require for survival. The cryptonephridial complex (CNC) is an evolutionary novelty in which the renal organs and gut have been dramatically reorganised. Parts of the renal or Malpighian tubules (MpTs) form a close association with the surface of the rectum, and are surrounded by a novel tissue, the perinephric membrane, which acts to insulate the system from the haemolymph and thus allows tight regulation of ions and water into and out of the CNC. The CNC can reclaim water and solutes from the rectal contents and recycle these back into the haemolymph. Fluid flow in the MpTs runs counter to flow within the rectum. It is this countercurrent arrangement that underpins its powerful recycling capabilities, and represents one of the most efficient water conservation mechanisms in nature. CNCs appear to have evolved multiple times, and are present in some of the largest and most evolutionarily successful insect groups including the larvae of most Lepidoptera and in a major beetle lineage (Cucujiformia + Bostrichoidea), suggesting that the CNC is an important adaptation. Here we review the knowledge of this remarkable organ system gained over the past 200 years. We first focus on the CNCs of tenebrionid beetles, for which we have an in-depth understanding from physiological, structural and ultrastructural studies (primarily in Tenebrio molitor), which are now being extended by studies in Tribolium castaneum enabled by advances in molecular and microscopy approaches established for this species. These recent studies are beginning to illuminate CNC development, physiology and endocrine control. We then take a broader view of arthropod CNCs, phylogenetically mapping their reported occurrence to assess their distribution and likely evolutionary origins. We explore CNCs from an ecological viewpoint, put forward evidence that CNCs may primarily be adaptations for facing the challenges of larval life, and argue that their loss in many aquatic species could point to a primary function in conserving water in terrestrial species. Finally, by considering the functions of renal and digestive epithelia in insects lacking CNCs, as well as the typical architecture of these organs in relation to one another, we propose that ancestral features of these organs predispose them for the evolution of CNCs.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists. 生物声学研究的自动检测:生物学家和计算机科学家的实用指南。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-10-17 DOI: 10.1111/brv.13155
Arik Kershenbaum, Çağlar Akçay, Lakshmi Babu-Saheer, Alex Barnhill, Paul Best, Jules Cauzinille, Dena Clink, Angela Dassow, Emmanuel Dufourq, Jonathan Growcott, Andrew Markham, Barbara Marti-Domken, Ricard Marxer, Jen Muir, Sam Reynolds, Holly Root-Gutteridge, Sougata Sadhukhan, Loretta Schindler, Bethany R Smith, Dan Stowell, Claudia A F Wascher, Jacob C Dunn
{"title":"Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.","authors":"Arik Kershenbaum, Çağlar Akçay, Lakshmi Babu-Saheer, Alex Barnhill, Paul Best, Jules Cauzinille, Dena Clink, Angela Dassow, Emmanuel Dufourq, Jonathan Growcott, Andrew Markham, Barbara Marti-Domken, Ricard Marxer, Jen Muir, Sam Reynolds, Holly Root-Gutteridge, Sougata Sadhukhan, Loretta Schindler, Bethany R Smith, Dan Stowell, Claudia A F Wascher, Jacob C Dunn","doi":"10.1111/brv.13155","DOIUrl":"https://doi.org/10.1111/brv.13155","url":null,"abstract":"<p><p>Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EthoCRED: a framework to guide reporting and evaluation of the relevance and reliability of behavioural ecotoxicity studies. EthoCRED:指导报告和评估行为生态毒性研究相关性和可靠性的框架。
IF 11 1区 生物学
Biological Reviews Pub Date : 2024-10-12 DOI: 10.1111/brv.13154
Michael G Bertram, Marlene Ågerstrand, Eli S J Thoré, Joel Allen, Sigal Balshine, Jack A Brand, Bryan W Brooks, ZhiChao Dang, Sabine Duquesne, Alex T Ford, Frauke Hoffmann, Henner Hollert, Stefanie Jacob, Werner Kloas, Nils Klüver, Jim Lazorchak, Mariana Ledesma, Gerd Maack, Erin L Macartney, Jake M Martin, Steven D Melvin, Marcus Michelangeli, Silvia Mohr, Stephanie Padilla, Gregory Pyle, Minna Saaristo, René Sahm, Els Smit, Jeffery A Steevens, Sanne van den Berg, Laura E Vossen, Donald Wlodkowic, Bob B M Wong, Michael Ziegler, Tomas Brodin
{"title":"EthoCRED: a framework to guide reporting and evaluation of the relevance and reliability of behavioural ecotoxicity studies.","authors":"Michael G Bertram, Marlene Ågerstrand, Eli S J Thoré, Joel Allen, Sigal Balshine, Jack A Brand, Bryan W Brooks, ZhiChao Dang, Sabine Duquesne, Alex T Ford, Frauke Hoffmann, Henner Hollert, Stefanie Jacob, Werner Kloas, Nils Klüver, Jim Lazorchak, Mariana Ledesma, Gerd Maack, Erin L Macartney, Jake M Martin, Steven D Melvin, Marcus Michelangeli, Silvia Mohr, Stephanie Padilla, Gregory Pyle, Minna Saaristo, René Sahm, Els Smit, Jeffery A Steevens, Sanne van den Berg, Laura E Vossen, Donald Wlodkowic, Bob B M Wong, Michael Ziegler, Tomas Brodin","doi":"10.1111/brv.13154","DOIUrl":"https://doi.org/10.1111/brv.13154","url":null,"abstract":"<p><p>Behavioural analysis has been attracting significant attention as a broad indicator of sub-lethal toxicity and has secured a place as an important subdiscipline in ecotoxicology. Among the most notable characteristics of behavioural research, compared to other established approaches in sub-lethal ecotoxicology (e.g. reproductive and developmental bioassays), are the wide range of study designs being used and the diversity of endpoints considered. At the same time, environmental hazard and risk assessment, which underpins regulatory decisions to protect the environment from potentially harmful chemicals, often recommends that ecotoxicological data be produced following accepted and validated test guidelines. These guidelines typically do not address behavioural changes, meaning that these, often sensitive, effects are not represented in hazard and risk assessments. Here, we propose a new tool, the EthoCRED evaluation method, for assessing the relevance and reliability of behavioural ecotoxicity data, which considers the unique requirements and challenges encountered in this field. This method and accompanying reporting recommendations are designed to serve as an extension of the \"Criteria for Reporting and Evaluating Ecotoxicity Data (CRED)\" project. As such, EthoCRED can both accommodate the wide array of experimental design approaches seen in behavioural ecotoxicology, and could be readily implemented into regulatory frameworks as deemed appropriate by policy makers of different jurisdictions to allow better integration of knowledge gained from behavioural testing into environmental protection. Furthermore, through our reporting recommendations, we aim to improve the reporting of behavioural studies in the peer-reviewed literature, and thereby increase their usefulness to inform chemical regulation.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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