{"title":"A Critical Evaluation of Network Approaches for Studying Species Interactions","authors":"Nico Blüthgen, Michael Staab","doi":"10.1146/annurev-ecolsys-102722-021904","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102722-021904","url":null,"abstract":"Ecological networks of species interactions are popular and provide powerful analytical tools for understanding variation in community structure and ecosystem functioning. However, network analyses and commonly used metrics such as nestedness and connectance have also attracted criticism. One major concern is that observed patterns are misinterpreted as niche properties such as specialization, whereas they may instead merely reflect variation in sampling, abundance, and/or diversity. As a result, studies potentially draw flawed conclusions about ecological function, stability, or coextinction risks. We highlight potential biases in analyzing and interpreting species-interaction networks and review the solutions available to overcome them, among which we particularly recommend the use of null models that account for species abundances. We show why considering variation across species and networks is important for understanding species interactions and their consequences. Network analyses can advance knowledge on the principles of species interactions but only when judiciously applied.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"178 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141785659","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}
Bethany A. Bradley, Evelyn M. Beaury, Belinda Gallardo, Inés Ibáñez, Catherine Jarnevich, Toni Lyn Morelli, Helen R. Sofaer, Cascade J.B. Sorte, Montserrat Vilà
{"title":"Observed and Potential Range Shifts of Native and Nonnative Species with Climate Change","authors":"Bethany A. Bradley, Evelyn M. Beaury, Belinda Gallardo, Inés Ibáñez, Catherine Jarnevich, Toni Lyn Morelli, Helen R. Sofaer, Cascade J.B. Sorte, Montserrat Vilà","doi":"10.1146/annurev-ecolsys-102722-013135","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102722-013135","url":null,"abstract":"There is broad concern that the range shifts of global flora and fauna will not keep up with climate change, increasing the likelihood of population declines and extinctions. Many populations of nonnative species already have advantages over native species, including widespread human-aided dispersal and release from natural enemies. But do nonnative species also have an advantage with climate change? Here, we review observed and potential range shifts for native and nonnative species globally. We show that nonnative species are expanding their ranges 100 times faster than native species, reflecting both traits that enable rapid spread and ongoing human-mediated introduction. We further show that nonnative species have large potential ranges and range expansions with climate change, likely due to a combination of widespread introduction and broader climatic tolerances. With faster spread rates and larger potential to persist or expand, nonnative populations have a decided advantage in a changing climate.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"58 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141504267","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}
Hélène Morlon, Jérémy Andréoletti, Joëlle Barido-Sottani, Sophia Lambert, Benoît Perez-Lamarque, Ignacio Quintero, Viktor Senderov, Pierre Veron
{"title":"Phylogenetic Insights into Diversification","authors":"Hélène Morlon, Jérémy Andréoletti, Joëlle Barido-Sottani, Sophia Lambert, Benoît Perez-Lamarque, Ignacio Quintero, Viktor Senderov, Pierre Veron","doi":"10.1146/annurev-ecolsys-102722-020508","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102722-020508","url":null,"abstract":"Species diversification—the balance between speciation and extinction—is fundamental to our understanding of how species richness varies in space and time and throughout the Tree of Life. Phylogenetic approaches provide insights into species diversification by enabling support for alternative diversification scenarios to be compared and speciation and extinction rates to be estimated. Here, we review the current toolkit available for conducting such analyses. We first highlight how modeling efforts over the past decade have fostered a notable transition from overly simplistic evolutionary scenarios to a more nuanced understanding of how and why diversification rates vary through time and across lineages. Using the latitudinal diversity gradient as a case study, we then illustrate the impact that modeling choices can have on the results obtained. Finally, we review recent progress in two areas that are still lagging behind: phylogenetic insights into microbial diversification and the speciation process.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"149 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141504235","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":"Patterns and Evolutionary Consequences of Pleiotropy","authors":"Jianzhi Zhang","doi":"10.1146/annurev-ecolsys-022323-083451","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-022323-083451","url":null,"abstract":"Pleiotropy refers to the phenomenon of one gene or one mutation affecting multiple phenotypic traits. While the concept of pleiotropy is as old as Mendelian genetics, functional genomics has finally allowed the first glimpses of the extent of pleiotropy for a large fraction of genes in a genome. After describing conceptual and operational difficulties in quantifying pleiotropy and the pros and cons of various methods for measuring pleiotropy, I review empirical data on pleiotropy, which generally show an L-shaped distribution of the degree of pleiotropy (i.e., the number of traits affected), with most genes having low pleiotropy. I then review the current understanding of the molecular basis of pleiotropy. In the rest of the review, I discuss evolutionary consequences of pleiotropy, focusing on advances in topics including the cost of complexity, regulatory versus coding evolution, environmental pleiotropy and adaptation, evolution of ageing and other seemingly harmful traits, and evolutionary resolution of pleiotropy.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"182 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135933023","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":"How Whales Dive, Feast, and Fast: The Ecophysiological Drivers and Limits of Foraging in the Evolution of Cetaceans","authors":"J. Goldbogen, N. Pyenson, P. Madsen","doi":"10.1146/annurev-ecolsys-102220-025458","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102220-025458","url":null,"abstract":"Whales are an extraordinary study group for questions about ecology and evolution because their combinations of extreme body sizes and unique foraging strategies are unparalleled among animals. From a terrestrial ancestry, whales evolved specialized oceanic foraging mechanisms that characterize the two main groups of living cetaceans: echolocation by toothed whales and bulk filter feeding by baleen whales. In toothed whales, lineage-specific increases in body size, enhanced diving capacity, and echolocation enable them to hunt the most abundant prey on the planet: deep-sea fish and cephalopods. Even greater body size increases, along with filter feeding and fasting capacity, permit large baleen whales to migrate long distances and exploit epipelagic patches of schooling prey, such as krill or fish, which are highly abundant but ephemeral. For both groups, prey abundance and distribution limits foraging performance, yielding divergent energetic niches that have shaped their convergent evolution to gigantism. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"66 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73380879","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}
D. Menge, S. Kou‐Giesbrecht, B. Taylor, P. Akana, Ayanna Butler, K. A. Carreras Pereira, S. Cooley, Vanessa M. Lau, Emma L. Lauterbach
{"title":"Terrestrial Phosphorus Cycling: Responses to Climatic Change","authors":"D. Menge, S. Kou‐Giesbrecht, B. Taylor, P. Akana, Ayanna Butler, K. A. Carreras Pereira, S. Cooley, Vanessa M. Lau, Emma L. Lauterbach","doi":"10.1146/annurev-ecolsys-110421-102458","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-110421-102458","url":null,"abstract":"Phosphorus (P) limits productivity in many ecosystems and has the potential to constrain the global carbon sink. The magnitude of these effects depends on how climate change and rising CO2 affect P cycling. Some effects are well established. First, P limitation often constrains CO2 fertilization, and rising CO2 often exacerbates P limitation. Second, P limitation and P constraints to CO2 fertilization are more common in warmer and wetter sites. Models that couple P cycling to vegetation generally capture these outcomes. However, due largely to differences between short-term and long-term dynamics, the patterns observed across climatic gradients do not necessarily indicate how climate change over years to decades will modify P limitation. These annual-to-decadal effects are not well understood. Furthermore, even for the well-understood patterns, much remains to be learned about the quantitative details, mechanisms, and drivers of variability. The interface between empirical and modeling work is particularly ripe for development. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"32 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82893308","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":"The Causes and Consequences of Seed Dispersal","authors":"Noelle G. Beckman, Lauren L. Sullivan","doi":"10.1146/annurev-ecolsys-102320-104739","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102320-104739","url":null,"abstract":"Seed dispersal, or the movement of diaspores away from the parent location, is a multiscale, multipartner process that depends on the interaction of plant life history with vector movement and the environment. Seed dispersal underpins many important plant ecological and evolutionary processes such as gene flow, population dynamics, range expansion, and diversity. We review exciting new directions that the field of seed dispersal ecology and evolution has taken over the past 40 years. We provide an overview of the ultimate causes of dispersal and the consequences of this important process for plant population and community dynamics. We also discuss several emergent unifying frameworks that are being used to study dispersal and describe how they can be integrated to provide a more mechanistic understanding of dispersal. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"71 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75412723","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}
M. Muñoz, L. Frishkoff, Jenna E. Pruett, D. Mahler
{"title":"Evolution of a Model System: New Insights from the Study of Anolis Lizards","authors":"M. Muñoz, L. Frishkoff, Jenna E. Pruett, D. Mahler","doi":"10.1146/annurev-ecolsys-110421-103306","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-110421-103306","url":null,"abstract":"With decades of intensive study, Anolis lizards have emerged as a biological model system. We review how new research on anoles has advanced our understanding of ecology and evolution, challenging long-standing paradigms and opening new areas of inquiry. Recent anole research reveals how changes in behavior can restructure ecological communities and can both stimulate and stymie evolution, sometimes simultaneously. Likewise, investigation of anoles as spatial or phylogenetic evolutionary experiments has documented evolutionary repeatability across spatiotemporal scales, while also illuminating its limits. Current research places anoles as an emerging model for Anthropocene biology, with recent work illustrating how species respond as humans reconfigure natural habitats, alter the climate, and create novel environments and communities through urbanization and species introduction. Combined with ongoing methodological developments in genomics, phylogenetics, and ecology, the growing foundational knowledge of Anolis positions them as a powerful model system in ecology and evolution for years to come. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"39 38","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72420172","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}
Caitlin E. Hicks Pries, R. Ryals, B. Zhu, K. Min, Alexia Cooper, S. Goldsmith, J. Pett‐Ridge, M. Torn, Asmeret Asefaw Berhe
{"title":"The Deep Soil Organic Carbon Response to Global Change","authors":"Caitlin E. Hicks Pries, R. Ryals, B. Zhu, K. Min, Alexia Cooper, S. Goldsmith, J. Pett‐Ridge, M. Torn, Asmeret Asefaw Berhe","doi":"10.1146/annurev-ecolsys-102320-085332","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102320-085332","url":null,"abstract":"Over 70% of soil organic carbon (SOC) is stored at a depth greater than 20 cm belowground. A portion of this deep SOC actively cycles on annual to decadal timescales and is sensitive to global change. However, deep SOC responses to global change likely differ from surface SOC responses because biotic controls on SOC cycling become weaker as mineral controls predominate with depth. Here, we synthesize the current information on deep SOC responses to the global change drivers of warming, shifting precipitation, elevated CO2, and land use and land cover change. Most deep SOC responses can only be hypothesized because few global change studies measure deep soils, and even fewer global change experiments manipulate deep soils. We call on scientists to incorporate deep soils into their manipulations, measurements, and models so that the response of deep SOC can be accounted for in projections of nature-based climate solutions and terrestrial feedbacks to climate change. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"7 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87437616","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":"Background Acoustics in Terrestrial Ecology","authors":"C. D. Francis, J. N. Phillips, J. Barber","doi":"10.1146/annurev-ecolsys-102220-030316","DOIUrl":"https://doi.org/10.1146/annurev-ecolsys-102220-030316","url":null,"abstract":"The way in which terrestrial organisms use the acoustic realm is fundamentally important and shapes behavior, populations, and communities, but how background acoustics, or noise, influence the patterns and processes in ecology is still relatively understudied. In this review, we summarize how background acoustics have traditionally been studied from the signaling perspective, discuss what is known from a receiver's perspective, and explore what is known about population- and community-level responses to noise. We suggest that there are major gaps linking animal physiology and behavior to fitness; that there is a limited understanding of variation in hearing within and across species, especially in the context of real-world acoustic conditions; and that many puzzling responses to noise could be clarified with a community-level lens that considers indirect effects. Failing to consider variation in acoustic conditions, and the many ways organisms use and interact via this environmental dimension, risks a limited understanding of natural systems. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 54 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7988,"journal":{"name":"Annual Review of Ecology, Evolution, and Systematics","volume":"1 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89049609","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}