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
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.
{"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":null,"pages":null},"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}
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 CO2 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.
{"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":null,"pages":null},"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}
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.
{"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":null,"pages":null},"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}
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
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.
{"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":null,"pages":null},"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}
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
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.
{"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":null,"pages":null},"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}
Bram Vanschoenwinkel, Luiza F A de Paula, Joren M Snoeks, Tom Van der Stocken, Falko T Buschke, Stefan Porembski, Fernando A O Silveira
Islands are fundamental model systems in ecology, biogeography, and evolutionary biology. However, terrestrial islands, unlike their aquatic counterparts, have received comparatively less attention. Among these land islands, inselbergs (i.e. isolated rock outcrops with diverse lithologies and a modest topographical prominence) stand out as iconic examples distributed worldwide across global biomes. Due to their durable lithology, inselbergs change slowly, persisting for tens of millions of years. In this review, we propose a biological definition for inselbergs that captures three fundamental characteristics of inselbergs from the perspective of biota. These are old age, isolation and the presence of unique microhabitats that are rare or absent in the surrounding matrix, fostering distinct communities often with unique and endemic biota. We synthesise the state of the art and formulate a set of testable hypotheses to deepen our understanding of the origins and maintenance of diversity on inselbergs, which are increasingly exposed to anthropogenic threats. By offering different habitats compared to the surrounding habitat matrix (e.g. moist microhabitats in dryland landscapes and xeric environments in humid tropical landscapes), inselbergs may allow specific lineages to thrive beyond their typical geographical limits. Particularly in drylands and degraded landscapes, inselbergs may not just provide different habitats but also act as ecological refuges or evolutionary refugia by providing a wider range of potential microhabitats than the surrounding matrix, enhancing resilience and promoting regional biodiversity. The central role of the matrix ensures that the ecological and evolutionary dynamics of inselbergs differ from those of true islands such as oceanic islands. Given that inselberg biota coexist within a terrestrial matrix, interactions between inselberg and matrix populations impact each other significantly. Over evolutionary timescales, matrix species may contract to inselberg refugia, preserving lineages while cycles of isolation and reconnection may drive speciation via a species pump. Although inselberg biodiversity has been studied predominantly from an island biogeography perspective, we argue that depending on the spatial scale, habitat specificity and mobility of the organisms considered, a range of different theories and paradigms can help explain the biogeography and local distribution patterns of different taxonomic and functional groups of inselberg species.
{"title":"The ecological and evolutionary dynamics of inselbergs.","authors":"Bram Vanschoenwinkel, Luiza F A de Paula, Joren M Snoeks, Tom Van der Stocken, Falko T Buschke, Stefan Porembski, Fernando A O Silveira","doi":"10.1111/brv.13150","DOIUrl":"https://doi.org/10.1111/brv.13150","url":null,"abstract":"<p><p>Islands are fundamental model systems in ecology, biogeography, and evolutionary biology. However, terrestrial islands, unlike their aquatic counterparts, have received comparatively less attention. Among these land islands, inselbergs (i.e. isolated rock outcrops with diverse lithologies and a modest topographical prominence) stand out as iconic examples distributed worldwide across global biomes. Due to their durable lithology, inselbergs change slowly, persisting for tens of millions of years. In this review, we propose a biological definition for inselbergs that captures three fundamental characteristics of inselbergs from the perspective of biota. These are old age, isolation and the presence of unique microhabitats that are rare or absent in the surrounding matrix, fostering distinct communities often with unique and endemic biota. We synthesise the state of the art and formulate a set of testable hypotheses to deepen our understanding of the origins and maintenance of diversity on inselbergs, which are increasingly exposed to anthropogenic threats. By offering different habitats compared to the surrounding habitat matrix (e.g. moist microhabitats in dryland landscapes and xeric environments in humid tropical landscapes), inselbergs may allow specific lineages to thrive beyond their typical geographical limits. Particularly in drylands and degraded landscapes, inselbergs may not just provide different habitats but also act as ecological refuges or evolutionary refugia by providing a wider range of potential microhabitats than the surrounding matrix, enhancing resilience and promoting regional biodiversity. The central role of the matrix ensures that the ecological and evolutionary dynamics of inselbergs differ from those of true islands such as oceanic islands. Given that inselberg biota coexist within a terrestrial matrix, interactions between inselberg and matrix populations impact each other significantly. Over evolutionary timescales, matrix species may contract to inselberg refugia, preserving lineages while cycles of isolation and reconnection may drive speciation via a species pump. Although inselberg biodiversity has been studied predominantly from an island biogeography perspective, we argue that depending on the spatial scale, habitat specificity and mobility of the organisms considered, a range of different theories and paradigms can help explain the biogeography and local distribution patterns of different taxonomic and functional groups of inselberg species.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337715","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}
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
真核生物基因组中的 DNA 不断受到来自外源和内源的攻击,导致 DNA 损伤,这被认为是老化的主要分子驱动因素。幸运的是,基因组和中心外显子组受到丰富的外周非编码 DNA 的保护,免受这些攻击。非编码 DNA 可编码小型非编码 RNA,在细胞质中使外来核酸失活,并在细胞核中对这些攻击进行物理阻断。在这种阻断过程中对非编码 DNA 造成的损伤会通过核孔复合体以染色体外环状 DNA(eccDNA)的形式被清除。因此,非编码 DNA 是外显子组抵御 DNA 损伤的一道防线。非编码 DNA/异染色质的总量会随着年龄的增长而减少,从而导致物理阻断和 eccDNA 排阻的减少,因此在衰老过程中和与年龄相关的疾病中,DNA 损伤在细胞核中的积累会增加。在此,我们总结了支持非编码 DNA 在健康和病理状态下发挥保护作用的最新证据,并认为 DNA 损伤是老化和与年龄相关的遗传疾病的近因。旨在加强非编码 DNA/异染色质保护作用的策略有可能为动态基因组和外显子组提供更好的系统保护,使其免受各种攻击,减轻 DNA 损伤对外显子组造成的负担,从而延缓衰老,抵御与年龄相关的遗传疾病,促进个人更健康的生活。
{"title":"Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases.","authors":"Guo-Hua Qiu, Mingjun Fu, Xintian Zheng, Cuiqin Huang","doi":"10.1111/brv.13151","DOIUrl":"https://doi.org/10.1111/brv.13151","url":null,"abstract":"<p><p>DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337711","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}
<p><p>Anticipating future biosecurity threats to prevent their occurrence is the most cost-effective strategy to manage invasive alien species. Yet, biological invasions are complex, highly uncertain processes. High uncertainty drives decision-making away from strategic preventative measures and towards operational outcomes aimed at post-invasion management. The limited success of preventative measures in curbing biological invasions reflects this short-term mindset and decision-makers should instead apply strategic foresight to imagine futures where biosecurity threats are minimised. Here, four major futures thinking tools (environmental scanning, driver-mapping, horizon scanning, and scenario planning) that describe probable, possible, plausible and preferable futures are assessed in terms of their potential to support both research and policy addressing biological invasions. Environmental scanning involves surveying existing data sources to detect signals of emerging alien species through knowledge of changes in either the likelihood or consequences of biological invasions. Several approaches are widely used for biosecurity including automated scans of digital media, consensus-based expert scoring, and prediction markets. Automated systems can be poor at detecting weak signals because of the large volume of 'noise' they generate while expert scoring relies on prior knowledge and so fails to identify unknown unknowns which is also true of prediction markets that work well for quite specific known risks. Driver-mapping uses expert consensus to identify the political, economic, societal, technological, legislative, and environmental forces shaping the future and is a critical component of strategic foresight that has rarely been applied to biological invasions. Considerable potential exists to extend this approach to develop system maps to identify where biosecurity interventions may be most effective and to explore driver complexes to determine megatrends shaping the future of biological invasions. Horizon scanning is a systematic outlook of potential threats and future developments to detect weak signals of emerging issues that exist at the margins of current thinking. Applications have been strongly focused on emerging issues related to research and technological challenges relevant to biosecurity and invasion science. However, most of these emerging issues are already well known in current-day research. Because horizon scanning is based on expert consensus, it needs to embrace a diversity of cultural, gender, and disciplinary diversity more adequately to ensure participants think intuitively and outside of their own subject boundaries. Scenario planning constructs storylines that describe alternative ways the political, economic, social, technological, legislative, and environmental situation might develop in the future. Biological invasion scenario planning has favoured structured approaches such as standardised archetypes and uncertainty ma
{"title":"Trouble on the horizon: anticipating biological invasions through futures thinking.","authors":"Philip E Hulme","doi":"10.1111/brv.13149","DOIUrl":"https://doi.org/10.1111/brv.13149","url":null,"abstract":"<p><p>Anticipating future biosecurity threats to prevent their occurrence is the most cost-effective strategy to manage invasive alien species. Yet, biological invasions are complex, highly uncertain processes. High uncertainty drives decision-making away from strategic preventative measures and towards operational outcomes aimed at post-invasion management. The limited success of preventative measures in curbing biological invasions reflects this short-term mindset and decision-makers should instead apply strategic foresight to imagine futures where biosecurity threats are minimised. Here, four major futures thinking tools (environmental scanning, driver-mapping, horizon scanning, and scenario planning) that describe probable, possible, plausible and preferable futures are assessed in terms of their potential to support both research and policy addressing biological invasions. Environmental scanning involves surveying existing data sources to detect signals of emerging alien species through knowledge of changes in either the likelihood or consequences of biological invasions. Several approaches are widely used for biosecurity including automated scans of digital media, consensus-based expert scoring, and prediction markets. Automated systems can be poor at detecting weak signals because of the large volume of 'noise' they generate while expert scoring relies on prior knowledge and so fails to identify unknown unknowns which is also true of prediction markets that work well for quite specific known risks. Driver-mapping uses expert consensus to identify the political, economic, societal, technological, legislative, and environmental forces shaping the future and is a critical component of strategic foresight that has rarely been applied to biological invasions. Considerable potential exists to extend this approach to develop system maps to identify where biosecurity interventions may be most effective and to explore driver complexes to determine megatrends shaping the future of biological invasions. Horizon scanning is a systematic outlook of potential threats and future developments to detect weak signals of emerging issues that exist at the margins of current thinking. Applications have been strongly focused on emerging issues related to research and technological challenges relevant to biosecurity and invasion science. However, most of these emerging issues are already well known in current-day research. Because horizon scanning is based on expert consensus, it needs to embrace a diversity of cultural, gender, and disciplinary diversity more adequately to ensure participants think intuitively and outside of their own subject boundaries. Scenario planning constructs storylines that describe alternative ways the political, economic, social, technological, legislative, and environmental situation might develop in the future. Biological invasion scenario planning has favoured structured approaches such as standardised archetypes and uncertainty ma","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277502","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}
How tissues develop distinct structures remains poorly understood. We propose herein the Lego hypothesis of tissue morphogenesis, which states that during tissue morphogenesis, the topographical properties of cell surface adhesion molecules can be dynamically altered and polarised by regulating the spatiotemporal expression and localization of orientational cell adhesion (OCA) molecules cell-autonomously and non-cell-autonomously, thus modulating cells into unique Lego pieces for self-assembling into distinct cytoarchitectures. This concept can be exemplified by epithelial morphogenesis, in which cells are coalesced into a sheet by many types of adhesions. Among them, parallel OCAs (pOCAs) at the lateral cell membranes are essential for configuring cells in parallel. Major pOCAs include Na+/K+-ATPase-mediated adhesions, Crumbs-mediated adhesions, tight junctions, adherens junctions, and desmosomes. These pOCAs align in stereotypical orders along the apical-to-basal axis, and their absolute positioning is also regulated. Such spatial organization of pOCAs underlies proper epithelial morphogenesis. Thus, a key open question about tissue morphogenesis is how to regulate OCAs to make compatible adhesive cellular Lego pieces for tissue construction.
{"title":"The Lego hypothesis of tissue morphogenesis: stereotypic organization of parallel orientational cell adhesions for epithelial self-assembly.","authors":"Lili Zhang, Xiangyun Wei","doi":"10.1111/brv.13147","DOIUrl":"https://doi.org/10.1111/brv.13147","url":null,"abstract":"<p><p>How tissues develop distinct structures remains poorly understood. We propose herein the Lego hypothesis of tissue morphogenesis, which states that during tissue morphogenesis, the topographical properties of cell surface adhesion molecules can be dynamically altered and polarised by regulating the spatiotemporal expression and localization of orientational cell adhesion (OCA) molecules cell-autonomously and non-cell-autonomously, thus modulating cells into unique Lego pieces for self-assembling into distinct cytoarchitectures. This concept can be exemplified by epithelial morphogenesis, in which cells are coalesced into a sheet by many types of adhesions. Among them, parallel OCAs (pOCAs) at the lateral cell membranes are essential for configuring cells in parallel. Major pOCAs include Na<sup>+</sup>/K<sup>+</sup>-ATPase-mediated adhesions, Crumbs-mediated adhesions, tight junctions, adherens junctions, and desmosomes. These pOCAs align in stereotypical orders along the apical-to-basal axis, and their absolute positioning is also regulated. Such spatial organization of pOCAs underlies proper epithelial morphogenesis. Thus, a key open question about tissue morphogenesis is how to regulate OCAs to make compatible adhesive cellular Lego pieces for tissue construction.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277501","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}
Fabio Bulleri, Nadine Schubert, Jason M. Hall-Spencer, Daniela Basso, Heidi L. Burdett, Ronaldo B. Francini-Filho, Jacques Grall, Paulo A. Horta, Nicholas A. Kamenos, Sophie Martin, Matteo Nannini, Pedro Neves, Irene Olivé, Viviana Peña, Federica Ragazzola, Cláudia Ribeiro, Eli Rinde, Marina Sissini, Fernando Tuya, João Silva
Rhodolith beds are diverse and globally distributed habitats. Nonetheless, the role of rhodoliths in structuring the associated species community through a hierarchy of positive interactions is yet to be recognised. In this review, we provide evidence that rhodoliths can function as foundation species of multi-level facilitation cascades and, hence, are fundamental for the persistence of hierarchically structured communities within coastal oceans. Rhodoliths generate facilitation cascades by buffering physical stress, reducing consumer pressure and enhancing resource availability. Due to large variations in their shape, size and density, a single rhodolith bed can support multiple taxonomically distant and architecturally distinct habitat-forming species, such as primary producers, sponges or bivalves, thus encompassing a broad range of functional traits and providing a wealth of secondary microhabitat and food resources. In addition, rhodoliths are often mobile, and thus can redistribute associated species, potentially expanding the distribution of species with short-distance dispersal abilities. Key knowledge gaps we have identified include: the experimental assessment of the role of rhodoliths as basal facilitators; the length and temporal stability of facilitation cascades; variations in species interactions within cascades across environmental gradients; and the role of rhodolith beds as climate refugia. Addressing these research priorities will allow the development of evidence-based policy decisions and elevate rhodolith beds within marine conservation strategies.
{"title":"Positive species interactions structure rhodolith bed communities at a global scale","authors":"Fabio Bulleri, Nadine Schubert, Jason M. Hall-Spencer, Daniela Basso, Heidi L. Burdett, Ronaldo B. Francini-Filho, Jacques Grall, Paulo A. Horta, Nicholas A. Kamenos, Sophie Martin, Matteo Nannini, Pedro Neves, Irene Olivé, Viviana Peña, Federica Ragazzola, Cláudia Ribeiro, Eli Rinde, Marina Sissini, Fernando Tuya, João Silva","doi":"10.1111/brv.13148","DOIUrl":"https://doi.org/10.1111/brv.13148","url":null,"abstract":"Rhodolith beds are diverse and globally distributed habitats. Nonetheless, the role of rhodoliths in structuring the associated species community through a hierarchy of positive interactions is yet to be recognised. In this review, we provide evidence that rhodoliths can function as foundation species of multi-level facilitation cascades and, hence, are fundamental for the persistence of hierarchically structured communities within coastal oceans. Rhodoliths generate facilitation cascades by buffering physical stress, reducing consumer pressure and enhancing resource availability. Due to large variations in their shape, size and density, a single rhodolith bed can support multiple taxonomically distant and architecturally distinct habitat-forming species, such as primary producers, sponges or bivalves, thus encompassing a broad range of functional traits and providing a wealth of secondary microhabitat and food resources. In addition, rhodoliths are often mobile, and thus can redistribute associated species, potentially expanding the distribution of species with short-distance dispersal abilities. Key knowledge gaps we have identified include: the experimental assessment of the role of rhodoliths as basal facilitators; the length and temporal stability of facilitation cascades; variations in species interactions within cascades across environmental gradients; and the role of rhodolith beds as climate refugia. Addressing these research priorities will allow the development of evidence-based policy decisions and elevate rhodolith beds within marine conservation strategies.","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":null,"pages":null},"PeriodicalIF":10.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258789","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}