Biological Reviews最新文献

{"title":"Multi-response phylogenetic mixed models: concepts and application.","authors":"Ben Halliwell, Barbara R Holland, Luke A Yates","doi":"10.1111/brv.70001","DOIUrl":"https://doi.org/10.1111/brv.70001","url":null,"abstract":"<p><p>The scale and resolution of trait databases and molecular phylogenies is increasing rapidly. These resources permit many open questions in comparative biology to be addressed with the right statistical tools. Multi-response (MR) phylogenetic mixed models (PMMs) offer great potential for multivariate analyses of trait evolution. While flexible and powerful, these methods are not often employed by researchers in ecology and evolution, reflecting a specialised and technical literature that creates barriers to usage for many biologists. Here we present a practical and accessible guide to MR-PMMs. We begin with a review of single-response (SR) PMMs to introduce key concepts and outline the limitations of this approach for characterising patterns of trait coevolution. We emphasise MR-PMMs as a preferable approach for analyses involving multiple species traits, due to the explicit decomposition of trait covariances. We discuss multilevel models, multivariate models of evolution, and extensions to non-Gaussian response traits. We highlight techniques for causal inference using graphical models, as well as advanced topics including prior specification and latent factor models. Using simulated data and visual examples, we discuss interpretation, prediction, and model validation. We implement many of the techniques discussed in example analyses of plant functional traits to demonstrate the general utility of MR-PMMs in handling complex real-world data sets. Finally, we discuss the emerging synthesis of comparative techniques made possible by MR-PMMs, highlight strengths and weaknesses, and offer practical recommendations to analysts. To complement this material, we provide online tutorials including side-by-side model implementations in two popular R packages, MCMCglmm and brms.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794157","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}

{"title":"Past aridity and dust drove biodiversity crises and altered pollination in the ancient gymnosperm Ephedra (Gnetales).","authors":"Natasha Barbolini, Niels Meijer, Carina Hoorn, Guillaume Dupont-Nivet, Fang Han, Ashley Krüger, Qin Yuan, Alexander Rohrmann, Kristina Bolinder, Catarina Rydin","doi":"10.1111/brv.70019","DOIUrl":"https://doi.org/10.1111/brv.70019","url":null,"abstract":"<p><p>The long-term effects of present-day climate change on pollination are unquantified. However, distinguishing climatic drivers of ancient changes in pollination could provide valuable insights into biotic responses to near-future climate states. Herein, we show that pollination in a group of gymnosperm shrubs (Ephedra L., Gnetales) was irrevocably altered by the Cenozoic expansion of drylands on two different continents. In Asia, increased continentality during the mid-Eocene drove aridification and strong, dust-carrying storms that promoted a shift to prevailing wind pollination in the core clade of Ephedra. Surface uplift in the North American interior together with global cooling caused the expansion of aeolian deposition and placed similar evolutionary pressures on ephedras there, beginning in the latest Eocene and continuing across the Eocene-Oligocene transition (EOT). These climatic changes fundamentally altered the abundance and evolution of this ancient plant lineage on both continents and determined pollination mechanisms in the core clade of Ephedra today. Based on fossil evidence, this review demonstrates how climate change may have major and permanent impacts on plant-pollinator networks, as well as demonstrates possible evolutionary consequences of near-future climate scenarios for which we have no modern analogue.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143801974","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}

{"title":"Unravelling the regulatory network behind chitin degradation in Serratia marcescens.","authors":"Wouter Demeester, Brecht De Paepe, Chiara Guidi, Marjan De Mey","doi":"10.1111/brv.70020","DOIUrl":"https://doi.org/10.1111/brv.70020","url":null,"abstract":"<p><p>Chitin degradation plays a crucial role in bacterial nutrient recycling and is performed by specialised, chitinolytic microorganisms such as Serratia marcescens, which is known to excel at this biological process. While its chitinolytic enzymes have been studied in detail, the underlying regulatory systems that allow such proficiency at chitin utilisation remain elusive. This review addresses different aspects of chitin degradation by Serratia marcescens. Together with a summary of the necessary enzymes and transport systems for extracellular chitin degradation, we focus on the strategies employed by Serratia marcescens for optimal use of different carbon sources in the presence of chitin. A complex, multi-layered, regulatory network results in 'bet-hedging', involving the formation of phenotypically bistable populations that facilitate a rapid transition towards chitin degradation when required. For the first time, a model of chitin degradation by Serratia marcescens is proposed, and aspects that currently remain elusive are highlighted. Hence, this review provides the basis for further investigations to reach a holistic understanding of this intriguing and important biological system.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778726","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}

{"title":"Combating desertification: comprehensive strategies, challenges, and future directions for sustainable solutions.","authors":"Waqar Islam, Fanjiang Zeng, Junaid Ali Siddiqui, Zhang Zhihao, Yi Du, Yulin Zhang, Mohammed O Alshaharni, Khalid Ali Khan","doi":"10.1111/brv.70015","DOIUrl":"https://doi.org/10.1111/brv.70015","url":null,"abstract":"<p><p>Desertification, a process through which once fertile and productive land is degraded into barren, arid desert, represents a significant environmental challenge with widespread consequences for ecosystems and human populations globally. This review explores the fundamental causes of desertification, its profound environmental and socio-economic impacts, and the strategies employed to combat it. We address the diverse range of approaches aimed at mitigating the effects of desertification, in particular the importance of sustainable land management practices, such as reforestation and soil conservation. We also examine the numerous obstacles to the practical implementation of these strategies and potential future directions for more effective management. In addition, we highlight the role of policy frameworks, governmental interventions, and international cooperation as essential components in addressing this pressing issue. As desertification continues to threaten both ecosystems and livelihoods in vulnerable regions, a comprehensive understanding of the strategies, challenges, and potential solutions will be crucial for ensuring the resilience of affected communities and the preservation of biodiversity. By fostering sustainable land-use practices and promoting global cooperation, we can pave the way for more resilient ecosystems and improved well-being for populations facing the severe consequences of land degradation.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778722","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}

{"title":"Advancements in ecological niche models for forest adaptation to climate change: a comprehensive review.","authors":"Wenhuan Xu, Dawei Luo, Kate Peterson, Yueru Zhao, Yue Yu, Zhengyang Ye, Jiejie Sun, Ke Yan, Tongli Wang","doi":"10.1111/brv.70023","DOIUrl":"https://doi.org/10.1111/brv.70023","url":null,"abstract":"<p><p>Climate change poses significant challenges to the health and functions of forest ecosystems. Ecological niche models have emerged as crucial tools for understanding the impact of climate change on forests at the population, species, and ecosystem levels. These models also play a pivotal role in developing adaptive forest conservation and management strategies. Recent advancements in niche model development have led to enhanced prediction accuracy and broadened applications of niche models, driven using high-quality climate data, improved model algorithms, and the application of landscape genomic information. In this review, we start by elucidating the concept and rationale behind niche models in the context of forestry adaptation to climate change. We then provide an overview of the advancements in occurrence-based, trait-based, and genomics-based models, contributing to a more comprehensive understanding of species responses to climate change. In addition, we summarize findings from 338 studies to highlight the progress made in niche models for forest tree species, including data sources, model algorithms, future climate scenarios used and diverse applications. To assist researchers and practitioners, we provide an exemplar data set and accompanying source code as a tutorial, demonstrating the integration of population genetics into niche models. This paper aims to provide a concise yet comprehensive overview of the continuous advancements and refinements of niche models, serving as a valuable resource for effectively addressing the challenges posed by a changing climate.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778716","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}

{"title":"Soil extracellular enzymes as drivers of soil carbon storage under nitrogen addition.","authors":"Xiao Chen, Junji Cao, Robert L Sinsabaugh, Daryl L Moorhead, Richard D Bardgett, Nicolas Fanin, Andrew T Nottingham, Xunhua Zheng, Ji Chen","doi":"10.1111/brv.70021","DOIUrl":"https://doi.org/10.1111/brv.70021","url":null,"abstract":"<p><p>Enhanced anthropogenic nitrogen (N) inputs to ecosystems may have substantial impacts on microbially mediated soil organic carbon (SOC) cycling. One way to link species-rich soil microbial communities with SOC cycling processes is via soil extracellular enzyme activities (EEAs). However, the effects of N addition on EEAs and the associated driving factors remain poorly understood. By conducting a meta-analysis, we find that N addition increases hydrolytic C-degrading EEAs that target simple polysaccharides decomposition by 12.8%, but decreases oxidative C-degrading EEAs that degrade complex phenolic macromolecules by 11.9%. The net effect of N addition on SOC storage is determined by the shifts between these two types of C-degrading EEAs, and the impacts varied across different ecosystem types. These insights highlight the crucial but understudied roles of hydrolytic and oxidative C-degrading EEAs on SOC dynamics with ongoing enhanced anthropogenic N loading. Understanding the mechanisms behind these C-degrading EEAs could help optimize SOC sequestration and inform climate mitigation strategies across different ecosystems.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771066","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}

{"title":"Lords of the flies: dipteran migrants are diverse, abundant and ecologically important.","authors":"Will L Hawkes, Myles H M Menz, Karl R Wotton","doi":"10.1111/brv.70017","DOIUrl":"https://doi.org/10.1111/brv.70017","url":null,"abstract":"<p><p>Insect migrants are hugely abundant, with recent studies identifying the megadiverse order Diptera as the major component of many migratory assemblages. Despite this, their migratory behaviour has been widely overlooked in favour of more 'charismatic' migrant insects such as butterflies, dragonflies, and moths. Herein we review the available literature on dipteran migration to determine its prevalence, identify key migratory routes and elucidate areas that may prove fruitful for future research. Using 13 lines of evidence to determine migratory behaviour, we determined that species from 60 out of 130 dipteran families show evidence of migration, with Syrphidae fulfilling 12 of these criteria, followed by the Tephritidae with 10. By contrast, 22 families met just two criteria or fewer, underlining the need for more research into the migratory characteristics of these groups. In total, 592 species of Diptera were identified as potentially migratory, making them the most speciose group of insect migrants yet described. Despite this, only 0.5% of dipteran species were found to be migrants, a figure rising to 3% for the Syrphidae, a percentage mirrored by other migratory taxa such as butterflies, noctuid moths, and bats. Research was biased to locations in Europe (49% of publications) and while vast regions remain understudied, our review identified major flyways used by dipteran migrants across all biogeographic realms. Finally, we highlight an unsurpassed level of ecological diversity within dipteran migrants, including ecological roles of huge economic value. Overall, this review highlights how little is known about dipteran migration and how vital their migratory behaviour may be to the health of global ecosystems.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750416","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}

{"title":"Global impacts of exotic eucalypt plantations on wildlife.","authors":"Maider Iglesias-Carrasco, Jeannette Torres, Adalid Cruz-Dubon, Ulrika Candolin, Bob B M Wong, Guillermo Velo-Antón","doi":"10.1111/brv.70022","DOIUrl":"https://doi.org/10.1111/brv.70022","url":null,"abstract":"<p><p>The establishment of exotic tree plantations poses a pervasive threat to wildlife across the globe. Among the most important tree species used for forestry purposes worldwide are members of the genus Eucalyptus, which have now been established in at least 107 countries outside of their native range. When introduced into non-native areas, eucalypt plantations are associated with myriad novel challenges for native fauna, and have often been associated with reductions in the biodiversity of local communities. However, similar to other anthropogenic habitats, eucalypt plantations can also create novel opportunities for species that can allow them to survive and thrive in these novel environments. In this review, we use eucalypt plantations as a case study for understanding the ecological and evolutionary responses of wildlife to anthropogenic habitat loss and change. We begin by summarising the main avenues of research addressing the study of wildlife responses at the individual, community, and ecosystem levels, and highlight critical research gaps. We also consider the characteristics of different types of eucalypt plantations and how such attributes are linked with the ability of animals to respond appropriately to the establishment of plantations, and summarise important considerations for the conservation of animal communities in these human-altered habitats.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750407","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}

{"title":"Relevance of state-behaviour feedbacks for animal welfare.","authors":"Camille M Montalcini, Charles C Driver, Michael T Mendl","doi":"10.1111/brv.70016","DOIUrl":"https://doi.org/10.1111/brv.70016","url":null,"abstract":"<p><p>An animal's behaviour and its state, including its health and affective state, are dynamic and tightly coupled, influencing each other over time. Although both are relevant to the animal's welfare, there has been limited research on their dynamics in welfare studies. Here we aim to: (i) review evidence for feedbacks between state and behaviour that could have beneficial or detrimental consequences for farm animal welfare; (ii) propose ways in which an understanding of such feedbacks could be used to enhance welfare; and (iii) provide practical guidance. We include as state variables any features that could influence the costs and benefits of an animal's behavioural actions, including individual characteristics and aspects of its social environment. We find evidence supporting positive state-behaviour feedback loops in various livestock species, suggesting that these loops could be common in farm settings and have significant welfare implications, such as leading to abnormal behaviours and persistent negative affective states. We suggest (i) estimating within-individual feedback loops to extract individual characteristics for studying differences in welfare; (ii) identifying scenarios where change accelerated by positive feedbacks pushes an animal (or a group of animals) to a new state, also called tipping points; and (iii) generating positive feedback loops to elicit and maintain positive affective states. We end by encouraging use of dynamic models that integrate longitudinal data on animals' behaviour and state to enable exploration of their dynamics, and we provide a practical guide with annotated R code for support. Since the principles and ideas discussed here are relevant to any animals under human care, this approach could foster new perspectives for improving the welfare of all captive animals.</p>","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690624","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}

{"title":"Assembling the Pecos River fish fauna: barrier displacement on the Southern Great Plains, North America.","authors":"Christopher W Hoagstrom, Stephen R Davenport, Megan J Osborne","doi":"10.1111/brv.70012","DOIUrl":"https://doi.org/10.1111/brv.70012","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Barrier displacement by river capture is an important mechanism for the assembly of freshwater fish faunas. The production of increasingly comprehensive and rigorously dated phylogentic trees for major clades of fishes, along with improved resolution in historical geomorphology, provide an unprecedented opportunity to develop thorough biogeographical scenarios of faunal assembly that synthesise existing knowledge and provide detailed context for future study. The Pecos River of southwestern North America is a textbook example of drainage formation by river capture and provides a straightforward case of freshwater fish faunal assembly by river capture. Fishes ultimately confined to the middle section of the Pecos River (Capitan area of endemism) have their closest relatives in the Brazos, Colorado (Texas), and Red rivers, which served as ancient dispersal corridors from the Mississippi River drainage. The Capitan area of endemism developed in association with two dissolution basins that, in the Late Miocene, captured headwaters of these rivers. In the Late Pliocene or Early Pleistocene, the endorheic middle Pecos River (Capitan area of endemism) was captured by or overflowed into a tributary to the Río Grande, which became the lower Pecos River. The nascent lower Pecos River also harboured an endemic-fish assemblage as part of a nexus of springfed rivers (ancestral Río Grande, Devils River, lower Pecos River) that comprised the Devils area of endemism. Even after a through-flowing Pecos River linked the Capitan and Devils areas of endemism, many endemic species remained only within their original area of endemism, giving the Pecos River a composite fish fauna. The Río Grande connection later allowed fishes dispersing along the Gulf of Mexico coast, aided by Late Pleistocene sea-level falls and glacial outbursts, not only to populate the Río Grande, but also to disperse up the Pecos River. Incision of the lower Río Grande valley and uplift in the Sangre de Cristo Mountains empowered the Pecos River to capture headwater streams from the adjacent South Canadian River and middle Río Grande, bringing in additional fishes. More recently, humans introduced at least 50 species to the drainage, while human impacts fragmented the native fauna. Non-native versus native status remains uncertain for several species (e.g. Miniellus stramineus) and multiple lineages of diverse origin may exist for some widespread, polytypic species like Cyprinella lutrensis and Pimephales promelas. The composite fish fauna of the Pecos River is a biogeographical anomaly explainable by the complex geomorphological history that produced it. As such, it provides a unique opportunity for studies of fish-assemblage evolutionary ecology. Also, its historical association with neighbouring drainages helps clarify their biogeography (as detailed here). Further broadening of this synthesis could support biogeographical scenarios at large spatial scales, illustrating the potential th","PeriodicalId":133,"journal":{"name":"Biological Reviews","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668529","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}