Ditte Marie Christiansen, Johan Ehrlén, Kristoffer Hylander
As the climate is changing, species respond by changing their distributions and abundances. The effects of climate are not only direct, but also occur via changes in biotic interactions, such as competition. Yet, the role of competition in mediating the effects of climate is still largely unclear. To examine how climate influences species performance, directly and via competition with other species, we transplanted two moss species differing in climate niches, alone and together at 59 sites along a climate gradient. Growth was monitored over three growing seasons. In the absence of competition, both species performed better under warmer conditions. Yet, when transplanted together, a warmer climate had negative effects on the northern moss, while the effects remained positive for the southern species. The negative effect of a cold climate on the southern species was larger when both species were transplanted together. Over three growing seasons, the southern species almost outcompeted the northern in warmer climates. Our results illustrate how competitive interactions can modify, and even reverse, the direct effects of climate on organism performance. A broader implication of our results is that species interactions can have important effects on how environmental and climate change influence performance and abundance.
{"title":"Competitive interactions modify the direct effects of climate","authors":"Ditte Marie Christiansen, Johan Ehrlén, Kristoffer Hylander","doi":"10.1111/ecog.07322","DOIUrl":"https://doi.org/10.1111/ecog.07322","url":null,"abstract":"As the climate is changing, species respond by changing their distributions and abundances. The effects of climate are not only direct, but also occur via changes in biotic interactions, such as competition. Yet, the role of competition in mediating the effects of climate is still largely unclear. To examine how climate influences species performance, directly and via competition with other species, we transplanted two moss species differing in climate niches, alone and together at 59 sites along a climate gradient. Growth was monitored over three growing seasons. In the absence of competition, both species performed better under warmer conditions. Yet, when transplanted together, a warmer climate had negative effects on the northern moss, while the effects remained positive for the southern species. The negative effect of a cold climate on the southern species was larger when both species were transplanted together. Over three growing seasons, the southern species almost outcompeted the northern in warmer climates. Our results illustrate how competitive interactions can modify, and even reverse, the direct effects of climate on organism performance. A broader implication of our results is that species interactions can have important effects on how environmental and climate change influence performance and abundance.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"176 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142672926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Martin Philippe-Lesaffre, Corey J. A. Bradshaw, Irene Castañeda, John Llewelyn, Christopher R. Dickman, Christopher A. Lepczyk, Jean Fantle-Lepczyk, Clara Marino, Franck Courchamp, Elsa Bonnaud
Co-evolutionary relationships associated with biogeographical context mediate the response of native prey to introduced predators, but this effect has not yet been demonstrated for domestic cats. We investigated the main factors influencing the vulnerability of prey species to domestic cat Felis catus predation across Australia, Europe and North America, where domestic cats are introduced. In addition to prey data from empirical records, we used machine-learning models to compensate for unobserved prey in the diet of cats. We found continent-specific patterns of predation: birds were more frequently depredated by cats in Europe and North America, while mammals were favoured in Australia. Bird prey traits were consistent across continents, but those of mammalian prey diverged, notably in Australia. Differences between prey and non-prey species included mass, distribution, and reproductive traits, except in Australian mammals where there was no evidence for a relationship between mass and the probability of being prey. Many Australian mammal prey also have a high extinction risk, emphasizing their vulnerability compared to European and North American counterparts. Our findings highlight the role of eco-evolutionary context in assessing predation impacts and also demonstrate the potential for machine learning to identify at-risk species, thereby aiding global conservation efforts to reduce the negative impacts of introduced predators.
{"title":"Differential predation patterns of free-ranging cats among continents","authors":"Martin Philippe-Lesaffre, Corey J. A. Bradshaw, Irene Castañeda, John Llewelyn, Christopher R. Dickman, Christopher A. Lepczyk, Jean Fantle-Lepczyk, Clara Marino, Franck Courchamp, Elsa Bonnaud","doi":"10.1111/ecog.07169","DOIUrl":"https://doi.org/10.1111/ecog.07169","url":null,"abstract":"Co-evolutionary relationships associated with biogeographical context mediate the response of native prey to introduced predators, but this effect has not yet been demonstrated for domestic cats. We investigated the main factors influencing the vulnerability of prey species to domestic cat <i>Felis catus</i> predation across Australia, Europe and North America, where domestic cats are introduced. In addition to prey data from empirical records, we used machine-learning models to compensate for unobserved prey in the diet of cats. We found continent-specific patterns of predation: birds were more frequently depredated by cats in Europe and North America, while mammals were favoured in Australia. Bird prey traits were consistent across continents, but those of mammalian prey diverged, notably in Australia. Differences between prey and non-prey species included mass, distribution, and reproductive traits, except in Australian mammals where there was no evidence for a relationship between mass and the probability of being prey. Many Australian mammal prey also have a high extinction risk, emphasizing their vulnerability compared to European and North American counterparts. Our findings highlight the role of eco-evolutionary context in assessing predation impacts and also demonstrate the potential for machine learning to identify at-risk species, thereby aiding global conservation efforts to reduce the negative impacts of introduced predators.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"26 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142672925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Billur Bektaş, Chelsea Chisholm, Dagmar Egelkraut, Joshua Lynn, Sebastián Block, Thomas Deola, Fanny Dommanget, Brian J. Enquist, Deborah E. Goldberg, Sylvia Haider, Aud H. Halbritter, Yongtao He, Renaud Jaunatre, Anke Jentsch, Kari Klanderud, Paul Kardol, Susanne Lachmuth, Gregory Loucougaray, Tamara Münkemüller, Georg Niedrist, Hanna Nomoto, Lorah Seltzer, Joachim Paul Töpper, Lisa J. Rew, Tim Seipel, Manzoor A. Shah, Richard James Telford, Tom W.N. Walker, Shiping Wang, David A. Wardle, Peter Wolff, Yan Yang, Vigdis Vandvik, Jake M. Alexander
Global warming is changing plant communities due to the arrival of new species from warmer regions and declining abundance of cold-adapted species. However, experimentally testing predictions about trajectories and rates of community change is challenging because we normally lack an expectation for future community composition, and most warming experiments fail to incorporate colonization by novel species. To address these issues, we analyzed data from 44 whole-community transplant experiments along 22 elevational gradients across the Northern Hemisphere. In these experiments, high-elevation communities were transplanted to lower elevations to simulate warming, while also removing dispersal barriers for lower-elevation species to establish. We quantified the extent and pace at which warmed high-elevation communities shifted towards the taxonomic composition of lower elevation communities. High-elevation plant communities converged towards the composition of low-elevation communities, with higher rates under stronger experimental warming. Strong community shifts occurred in the first year after transplantation then slowed over time, such that communities remained distinct from both origin and destination control by the end of the experimental periods (3-9 years). Changes were driven to a similar extent by both new species colonization and abundance shifts of high-elevation species, but with substantial variation across experiments that could be partly explained by the magnitude and duration of experimental warming, plot size and functional traits. Our macroecological approach reveals that while warmed high-elevation communities increasingly resemble communities at lower elevations today, the slow pace of taxonomic shifts implies considerable colonization and extinction lags, where a novel taxonomic composition of both low- and high-elevation species could coexist for long periods of time. The important contribution of the colonizing species to community change also indicates that once dispersal barriers are overcome, warmed high-elevation communities are vulnerable to encroachment from lower elevation species.
{"title":"Colonization and extinction lags drive non-linear responses to warming in mountain plant communities across the Northern Hemisphere","authors":"Billur Bektaş, Chelsea Chisholm, Dagmar Egelkraut, Joshua Lynn, Sebastián Block, Thomas Deola, Fanny Dommanget, Brian J. Enquist, Deborah E. Goldberg, Sylvia Haider, Aud H. Halbritter, Yongtao He, Renaud Jaunatre, Anke Jentsch, Kari Klanderud, Paul Kardol, Susanne Lachmuth, Gregory Loucougaray, Tamara Münkemüller, Georg Niedrist, Hanna Nomoto, Lorah Seltzer, Joachim Paul Töpper, Lisa J. Rew, Tim Seipel, Manzoor A. Shah, Richard James Telford, Tom W.N. Walker, Shiping Wang, David A. Wardle, Peter Wolff, Yan Yang, Vigdis Vandvik, Jake M. Alexander","doi":"10.1111/ecog.07378","DOIUrl":"https://doi.org/10.1111/ecog.07378","url":null,"abstract":"Global warming is changing plant communities due to the arrival of new species from warmer regions and declining abundance of cold-adapted species. However, experimentally testing predictions about trajectories and rates of community change is challenging because we normally lack an expectation for future community composition, and most warming experiments fail to incorporate colonization by novel species. To address these issues, we analyzed data from 44 whole-community transplant experiments along 22 elevational gradients across the Northern Hemisphere. In these experiments, high-elevation communities were transplanted to lower elevations to simulate warming, while also removing dispersal barriers for lower-elevation species to establish. We quantified the extent and pace at which warmed high-elevation communities shifted towards the taxonomic composition of lower elevation communities. High-elevation plant communities converged towards the composition of low-elevation communities, with higher rates under stronger experimental warming. Strong community shifts occurred in the first year after transplantation then slowed over time, such that communities remained distinct from both origin and destination control by the end of the experimental periods (3-9 years). Changes were driven to a similar extent by both new species colonization and abundance shifts of high-elevation species, but with substantial variation across experiments that could be partly explained by the magnitude and duration of experimental warming, plot size and functional traits. Our macroecological approach reveals that while warmed high-elevation communities increasingly resemble communities at lower elevations today, the slow pace of taxonomic shifts implies considerable colonization and extinction lags, where a novel taxonomic composition of both low- and high-elevation species could coexist for long periods of time. The important contribution of the colonizing species to community change also indicates that once dispersal barriers are overcome, warmed high-elevation communities are vulnerable to encroachment from lower elevation species.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"19 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142672924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacob Socolar, Batbayar Galtbalt, Alison Johnston, Frank A. La Sorte, Orin J. Robinson, Kenneth V. Rosenberg, Adriaan M. Dokter
Avian population sizes fluctuate and change over vast spatial scales, but the mechanistic underpinnings remain poorly understood. A key question is whether spatial and annual variation in avian population dynamics is driven primarily by variation in breeding season recruitment or by variation in overwinter survival. We present a method using large-scale volunteer-collected data from project eBird to develop species-specific indices of net population change as proxies for survival and recruitment, based on twice-annual, rangewide snapshots of relative abundance in spring and fall. We demonstrate the use of these indices by examining spatially explicit annual variation in survival and recruitment in two well-surveyed nonmigratory North American species, Carolina wren Thryothorus ludovicianus and northern cardinal Cardinalis cardinalis. We show that, while interannual variation in both survival and recruitment is slight for northern cardinal, eBird abundance data reveal strong and geographically coherent signals of interannual variation in the overwinter survival of Carolina wren. As predicted, variation in wintertime survival dominates overall interannual population fluctuations of wrens and is correlated with winter temperature and snowfall in the northeastern United States, but not the southern United States. This study demonstrates the potential of participatory science (also known as citizen science) datasets like eBird for inferring variation in demographic rates and introduces a new complementary approach towards illuminating the macrodemography of North American birds at comprehensive continental extents.
{"title":"Seasonal macro-demography of North American bird populations revealed through participatory science","authors":"Jacob Socolar, Batbayar Galtbalt, Alison Johnston, Frank A. La Sorte, Orin J. Robinson, Kenneth V. Rosenberg, Adriaan M. Dokter","doi":"10.1111/ecog.07349","DOIUrl":"https://doi.org/10.1111/ecog.07349","url":null,"abstract":"Avian population sizes fluctuate and change over vast spatial scales, but the mechanistic underpinnings remain poorly understood. A key question is whether spatial and annual variation in avian population dynamics is driven primarily by variation in breeding season recruitment or by variation in overwinter survival. We present a method using large-scale volunteer-collected data from project eBird to develop species-specific indices of net population change as proxies for survival and recruitment, based on twice-annual, rangewide snapshots of relative abundance in spring and fall. We demonstrate the use of these indices by examining spatially explicit annual variation in survival and recruitment in two well-surveyed nonmigratory North American species, Carolina wren <i>Thryothorus ludovicianus</i> and northern cardinal <i>Cardinalis cardinali</i>s. We show that, while interannual variation in both survival and recruitment is slight for northern cardinal, eBird abundance data reveal strong and geographically coherent signals of interannual variation in the overwinter survival of Carolina wren. As predicted, variation in wintertime survival dominates overall interannual population fluctuations of wrens and is correlated with winter temperature and snowfall in the northeastern United States, but not the southern United States. This study demonstrates the potential of participatory science (also known as citizen science) datasets like eBird for inferring variation in demographic rates and introduces a new complementary approach towards illuminating the macrodemography of North American birds at comprehensive continental extents.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"80 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shubhi Sharma, Kevin Winner, Jussi Mäkinen, Walter Jetz
The study of species' environmental niches underpins numerous questions in ecology and evolution and has increasing relevance in a rapidly changing world. Environmental niches, characterized by observations of organisms, inform about a species' specialization in multivariate environment space and help assess their exposure and sensitivity to changing conditions. Environmental niches are also the central concept behind species distribution models (SDMs), which quantify and predict the geographic variation in environmental suitability. Despite the clear role of past evolutionary processes in shaping contemporary biodiversity distribution, the assessment of multivariate or n-dimensional (where n is the number of environmental axes) niches in a phylogenetic framework has remained limited and constrained by restrictive assumptions. This hampers important existing and emerging applications, such as assessments of niche conservatism, estimates of species' adaptive potential under changing climates, and prediction of niches in less-studied parts of the tree of life. Here, we introduce a framework that extends SDMs to estimate n-dimensional environmental niches jointly with underlying evolutionary processes. Specifically, we fit the relationship between niche similarity and phylogenetic distance as a latent Gaussian process across all species in a clade. We demonstrate mathematically how the parameters of the Gaussian process can be linked to existing traditional evolutionary models. Simulations indicate that the approach successfully recovers niche and evolutionary parameters. Applied to two clades of hummingbirds, the presented joint framework uncovers the relationships among species' niches in phylogenetic space and supports the quantification and hypothesis testing of niche evolution. A key advantage of the presented framework is its joint estimation of the evolutionary process alongside niches directly from species observations with uncertainty propagated to evolutionary model parameters. The proposed approach has the potential to increase the robustness of inference about niche evolution and improve understanding of how the processes of niche formation and evolution interact.
物种环境生态位研究是生态学和进化论众多问题的基础，在瞬息万变的世界中具有越来越重要的意义。环境生态位通过对生物体的观察来描述，可以了解物种在多元环境空间中的特化情况，并有助于评估物种对不断变化的环境条件的暴露程度和敏感性。环境龛位也是物种分布模型（SDM）背后的核心概念，该模型量化并预测环境适宜性的地理差异。尽管过去的进化过程在塑造当代生物多样性分布方面发挥了明显的作用，但在系统发育框架下对多变量或 n 维（n 为环境轴的数量）生态位的评估仍然受到限制，并受到一些限制性假设的制约。这阻碍了现有的和新出现的重要应用，如评估生态位保守性、估计物种在不断变化的气候条件下的适应潜力以及预测生命树中研究较少的部分的生态位。在这里，我们介绍了一个框架，该框架扩展了 SDMs，可与潜在的进化过程共同估算 n 维环境生态位。具体来说，我们将生态位相似性与系统发育距离之间的关系拟合为一个支系中所有物种的潜在高斯过程。我们用数学方法演示了如何将高斯过程的参数与现有的传统进化模型联系起来。模拟表明，该方法成功地恢复了生态位和进化参数。应用于蜂鸟的两个支系，所提出的联合框架揭示了系统发育空间中物种生态位之间的关系，并支持生态位进化的量化和假设检验。所提出的框架的一个主要优势是，它可以直接从物种观测结果中联合估计生态位的进化过程，并将不确定性传播到进化模型参数中。所提出的方法有可能提高生态位演化推断的稳健性，并加深对生态位形成和演化过程如何相互作用的理解。
{"title":"Measuring the evolution of n-dimensional environmental niches","authors":"Shubhi Sharma, Kevin Winner, Jussi Mäkinen, Walter Jetz","doi":"10.1111/ecog.07285","DOIUrl":"https://doi.org/10.1111/ecog.07285","url":null,"abstract":"The study of species' environmental niches underpins numerous questions in ecology and evolution and has increasing relevance in a rapidly changing world. Environmental niches, characterized by observations of organisms, inform about a species' specialization in multivariate environment space and help assess their exposure and sensitivity to changing conditions. Environmental niches are also the central concept behind species distribution models (SDMs), which quantify and predict the geographic variation in environmental suitability. Despite the clear role of past evolutionary processes in shaping contemporary biodiversity distribution, the assessment of multivariate or <i>n</i>-dimensional (where <i>n</i> is the number of environmental axes) niches in a phylogenetic framework has remained limited and constrained by restrictive assumptions. This hampers important existing and emerging applications, such as assessments of niche conservatism, estimates of species' adaptive potential under changing climates, and prediction of niches in less-studied parts of the tree of life. Here, we introduce a framework that extends SDMs to estimate <i>n</i>-dimensional environmental niches jointly with underlying evolutionary processes. Specifically, we fit the relationship between niche similarity and phylogenetic distance as a latent Gaussian process across all species in a clade. We demonstrate mathematically how the parameters of the Gaussian process can be linked to existing traditional evolutionary models. Simulations indicate that the approach successfully recovers niche and evolutionary parameters. Applied to two clades of hummingbirds, the presented joint framework uncovers the relationships among species' niches in phylogenetic space and supports the quantification and hypothesis testing of niche evolution. A key advantage of the presented framework is its joint estimation of the evolutionary process alongside niches directly from species observations with uncertainty propagated to evolutionary model parameters. The proposed approach has the potential to increase the robustness of inference about niche evolution and improve understanding of how the processes of niche formation and evolution interact.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"112 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142672957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jamie M. Kass, Adam B. Smith, Dan L. Warren, Sergio Vignali, Sylvain Schmitt, Matthew E. Aiello-Lammens, Eduardo Arlé, Ana Márcia Barbosa, Olivier Broennimann, Marlon E. Cobos, Maya Guéguen, Antoine Guisan, Cory Merow, Babak Naimi, Michael P. Nobis, Ian Ondo, Luis Osorio-Olvera, Hannah L. Owens, Gonzalo E. Pinilla-Buitrago, Andrea Sánchez-Tapia, Wilfried Thuiller, Roozbeh Valavi, Santiago José Elías Velazco, Alexander Zizka, Damaris Zurell
The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.
生物多样性数据的在线可用性不断提高，生态建模技术不断进步，导致开源建模工具激增。特别是，用于物种分布建模的 R 软件包不断增多，但却没有指导如何将它们结合起来使用，导致研究人员高度忠实于一个或几个软件包。在此，我们将对种类繁多的物种分布模型（SDM）软件进行评估，并重点介绍这些软件包如何在建模工作流程的每个步骤中协同工作，以实现分析的多样化和扩展性。我们还介绍了新的 R 软件包 "sdmverse"，它可以对软件包的元数据进行编目，根据方法功能对软件包进行聚类，并可视化它们之间的关系。为了展示软件使用的多元化如何有助于改进 SDM 工作流程，我们提供了三份内容广泛、记录完整的分析报告，其中使用了多个软件包的建模和可视化工具，然后根据最新的方法标准对这些教程进行评分。最后，我们指出了当前工具在功能上的差距，并强调了在开发 SDM 软件方面面临的突出挑战。
{"title":"Achieving higher standards in species distribution modeling by leveraging the diversity of available software","authors":"Jamie M. Kass, Adam B. Smith, Dan L. Warren, Sergio Vignali, Sylvain Schmitt, Matthew E. Aiello-Lammens, Eduardo Arlé, Ana Márcia Barbosa, Olivier Broennimann, Marlon E. Cobos, Maya Guéguen, Antoine Guisan, Cory Merow, Babak Naimi, Michael P. Nobis, Ian Ondo, Luis Osorio-Olvera, Hannah L. Owens, Gonzalo E. Pinilla-Buitrago, Andrea Sánchez-Tapia, Wilfried Thuiller, Roozbeh Valavi, Santiago José Elías Velazco, Alexander Zizka, Damaris Zurell","doi":"10.1111/ecog.07346","DOIUrl":"https://doi.org/10.1111/ecog.07346","url":null,"abstract":"The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"5 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Niels Preuk, Daniel Romero-Mujalli, Damaris Zurell, Manuel Steinbauer, and Juergen Kreyling
Ecological niche models (ENMs) are an essential modelling technique in biodiversity prediction and conservation and are frequently used to forecast species responses to global changes. Classic species-level models may show limitations as they assume species homogeneity, neglecting intraspecific variation. Composite ENMs allow the integration of intraspecific variation by combining intraspecific-level ENMs, capturing individual environmental responses over the species' geographic range. While recent studies suggest that accounting for intraspecific variation improves model predictions, we currently lack methods to test the significance of the improvement. Here, we propose a null model approach that randomises observed intraspecific structures as an appropriate baseline for comparison. We illustrate this approach by comparing predictive performance of a species-level ENM to composite ENMs for European beech Fagus sylvatica. To investigate the influence of spatial lineage structure, we tested all models against the same withheld data to allow comparison across models based on five common performance metrics. We found that the species-level ENM expressed higher overall performance (i.e. AUC, TSS, and Boyce index) and specificity (ability to predict absences), while the composite ENMs achieved higher sensitivity (ability to predict presences). In line with this, the composite ENMs also showed increased sensitivity and decreased specificity compared to the null models that randomised lineage structure. We showed that the assessment of model performance strongly varies based on the used measures, emphasising a careful investigation of multiple measures for evaluation. The application of null models allowed us to disentangle the effect of observed patterns of intraspecific variation in ENMs. Further, we highlight the validation and use of well-founded subgroups for modelling. Although intraspecific variation improves the prediction of occurrences of European beech, it did not fully outcompete the classic species-level model and should be used with care and rather to improve understanding and to supplement, not replace, species-level models.
{"title":"Randomising spatial patterns supports the integration of intraspecific variation in ecological niche models","authors":"Niels Preuk, Daniel Romero-Mujalli, Damaris Zurell, Manuel Steinbauer, and Juergen Kreyling","doi":"10.1111/ecog.07289","DOIUrl":"https://doi.org/10.1111/ecog.07289","url":null,"abstract":"Ecological niche models (ENMs) are an essential modelling technique in biodiversity prediction and conservation and are frequently used to forecast species responses to global changes. Classic species-level models may show limitations as they assume species homogeneity, neglecting intraspecific variation. Composite ENMs allow the integration of intraspecific variation by combining intraspecific-level ENMs, capturing individual environmental responses over the species' geographic range. While recent studies suggest that accounting for intraspecific variation improves model predictions, we currently lack methods to test the significance of the improvement. Here, we propose a null model approach that randomises observed intraspecific structures as an appropriate baseline for comparison. We illustrate this approach by comparing predictive performance of a species-level ENM to composite ENMs for European beech <i>Fagus sylvatica</i>. To investigate the influence of spatial lineage structure, we tested all models against the same withheld data to allow comparison across models based on five common performance metrics. We found that the species-level ENM expressed higher overall performance (i.e. AUC, TSS, and Boyce index) and specificity (ability to predict absences), while the composite ENMs achieved higher sensitivity (ability to predict presences). In line with this, the composite ENMs also showed increased sensitivity and decreased specificity compared to the null models that randomised lineage structure. We showed that the assessment of model performance strongly varies based on the used measures, emphasising a careful investigation of multiple measures for evaluation. The application of null models allowed us to disentangle the effect of observed patterns of intraspecific variation in ENMs. Further, we highlight the validation and use of well-founded subgroups for modelling. Although intraspecific variation improves the prediction of occurrences of European beech, it did not fully outcompete the classic species-level model and should be used with care and rather to improve understanding and to supplement, not replace, species-level models.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"43 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142599929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gengping Zhu, Luis Osorio-Olvera, Vera Pfeiffer, Javier Gutierrez Illan, Lisa G. Neven, David W. Crowder
Ecological niche models are often used to predict the distribution of invasive species before or after they have been detected in new regions. Such models should also be used to guide surveys to promote the early detection and eradication of invasive species. Here we propose a practical framework that seamlessly uses ecological niche models to develop sampling routes that promote detection of invasive species. Our framework uses habitat suitability predictions and occurrence data on incursion populations to generate potential survey sites, which are then prioritized for sampling based on their size and suitability. The generated survey route is then displayed on an open street map platform. Our framework was developed into the ‘enmRoute' R package and a user‐friendly website to facilitate its application, and we validated our framework with a case study. We show that integrating ecological niche models with human transport routes promotes identification of survey sites that are predicted to collect more individuals and have a greater potential for species detection than traditional sampling approaches. Our framework may help industries, invasion biologists, and regulators develop economical and efficient survey programs for invasive pest monitoring that make eradication programs more attainable.
{"title":"Enhancing monitoring to promote early detection and eradication of invasive species","authors":"Gengping Zhu, Luis Osorio-Olvera, Vera Pfeiffer, Javier Gutierrez Illan, Lisa G. Neven, David W. Crowder","doi":"10.1111/ecog.07105","DOIUrl":"https://doi.org/10.1111/ecog.07105","url":null,"abstract":"Ecological niche models are often used to predict the distribution of invasive species before or after they have been detected in new regions. Such models should also be used to guide surveys to promote the early detection and eradication of invasive species. Here we propose a practical framework that seamlessly uses ecological niche models to develop sampling routes that promote detection of invasive species. Our framework uses habitat suitability predictions and occurrence data on incursion populations to generate potential survey sites, which are then prioritized for sampling based on their size and suitability. The generated survey route is then displayed on an open street map platform. Our framework was developed into the ‘<jats:italic>enmRoute</jats:italic>' R package and a user‐friendly website to facilitate its application, and we validated our framework with a case study. We show that integrating ecological niche models with human transport routes promotes identification of survey sites that are predicted to collect more individuals and have a greater potential for species detection than traditional sampling approaches. Our framework may help industries, invasion biologists, and regulators develop economical and efficient survey programs for invasive pest monitoring that make eradication programs more attainable.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"30 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142599123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Remington J. Moll, Austin M. Green, Maximilian L. Allen, Roland Kays
Variation in animal abundance is shaped by scale-dependent habitat, competition, and anthropogenic influences. Coyotes Canis latrans have dramatically increased in abundance while expanding their range over the past 100 years. Management goals typically seek to lower coyote populations to reduce their threats to humans, pets, livestock and sensitive prey. Despite their outsized ecological and social roles in the Americas, the factors affecting coyote abundance across their range remain unclear. We fit Royle–Nichols abundance models at two spatial scales in a Bayesian hierarchical framework to three years of data from 4587 camera trap sites arranged in 254 arrays across the contiguous USA to assess how habitat, large carnivores, anthropogenic development and hunting regulations affect coyote abundance. Coyote abundance was highest in southwestern USA and lowest in the northeast. Abundance responded to some factors as expected, including positive (soft mast, agriculture, grass/shrub habitat, urban–natural edge) and negative (latitude and forest cover) relationships. Colonization date had a negative relationship, suggesting coyote populations have not reached carrying capacity in recently colonized regions. Several relationships were scale-dependent, including urban development, which was negative at local (100-m) scales but positive at larger (5-km) scales. Large carnivore effects were habitat-dependent, with sometimes opposing relationships manifesting across variation in forest cover and urban development. Coyote abundance was higher where human hunting was permitted, and this relationship was strongest at local scales. These results, including a national map of coyote abundance, update ecological understanding of coyotes and can inform coyote management at local and landscape scales. These findings expand results from local studies suggesting that directly hunting coyotes does not decrease their abundance and may actually increase it. Ongoing large carnivore recoveries globally will likely affect subordinate carnivore abundance, but not in universally negative ways, and our work demonstrates how such effects can be habitat and scale dependent.
{"title":"People or predators? Comparing habitat-dependent effects of hunting and large carnivores on the abundance of North America's top mesocarnivore","authors":"Remington J. Moll, Austin M. Green, Maximilian L. Allen, Roland Kays","doi":"10.1111/ecog.07390","DOIUrl":"https://doi.org/10.1111/ecog.07390","url":null,"abstract":"Variation in animal abundance is shaped by scale-dependent habitat, competition, and anthropogenic influences. Coyotes <i>Canis latrans</i> have dramatically increased in abundance while expanding their range over the past 100 years. Management goals typically seek to lower coyote populations to reduce their threats to humans, pets, livestock and sensitive prey. Despite their outsized ecological and social roles in the Americas, the factors affecting coyote abundance across their range remain unclear. We fit Royle–Nichols abundance models at two spatial scales in a Bayesian hierarchical framework to three years of data from 4587 camera trap sites arranged in 254 arrays across the contiguous USA to assess how habitat, large carnivores, anthropogenic development and hunting regulations affect coyote abundance. Coyote abundance was highest in southwestern USA and lowest in the northeast. Abundance responded to some factors as expected, including positive (soft mast, agriculture, grass/shrub habitat, urban–natural edge) and negative (latitude and forest cover) relationships. Colonization date had a negative relationship, suggesting coyote populations have not reached carrying capacity in recently colonized regions. Several relationships were scale-dependent, including urban development, which was negative at local (100-m) scales but positive at larger (5-km) scales. Large carnivore effects were habitat-dependent, with sometimes opposing relationships manifesting across variation in forest cover and urban development. Coyote abundance was higher where human hunting was permitted, and this relationship was strongest at local scales. These results, including a national map of coyote abundance, update ecological understanding of coyotes and can inform coyote management at local and landscape scales. These findings expand results from local studies suggesting that directly hunting coyotes does not decrease their abundance and may actually increase it. Ongoing large carnivore recoveries globally will likely affect subordinate carnivore abundance, but not in universally negative ways, and our work demonstrates how such effects can be habitat and scale dependent.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"242 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Matteo Conti, Pierfilippo Cerretti, Andrea Ferrari, Paolo Gabrieli, Francesco Paone, Carlo Polidori, Daniele Sommaggio, Gianalberto Losapio
Glaciers are retreating worldwide at an ever‐increasing rate, exposing new ice‐free areas to ecological succession. This process leads to changes in biodiversity and potentially to novel species interactions. However, we still have a limited understanding of how glacier retreat influences species interaction networks, particularly the structure and robustness of mutualistic networks. After reconstructing plant–pollinator networks along a 140‐years chronosequence on a glacier foreland, we address the effects of glacier retreat on network structure and robustness. Our results show that the prevalence of different network motifs changes over spacetime, leading to a decrease of network robustness. With glacier retreat, mutualistic networks shift from highly connected with diverse specialist interactions to loosely connected with few generalist interactions. Furthermore, despite the turnover of plant species, we find that species structural roles remain constant over spacetime while depending on species identity. Our findings suggest that glacier retreat reshuffles mutualistic networks with motifs posing low robustness, leading to increased fragility. Understanding the assembly and breaking down of species interaction networks provides novel insights into the development and stability of novel, post‐glacial ecological systems facing glacier extinction.
{"title":"Glacier retreat decreases mutualistic network robustness over spacetime","authors":"Matteo Conti, Pierfilippo Cerretti, Andrea Ferrari, Paolo Gabrieli, Francesco Paone, Carlo Polidori, Daniele Sommaggio, Gianalberto Losapio","doi":"10.1111/ecog.07558","DOIUrl":"https://doi.org/10.1111/ecog.07558","url":null,"abstract":"Glaciers are retreating worldwide at an ever‐increasing rate, exposing new ice‐free areas to ecological succession. This process leads to changes in biodiversity and potentially to novel species interactions. However, we still have a limited understanding of how glacier retreat influences species interaction networks, particularly the structure and robustness of mutualistic networks. After reconstructing plant–pollinator networks along a 140‐years chronosequence on a glacier foreland, we address the effects of glacier retreat on network structure and robustness. Our results show that the prevalence of different network motifs changes over spacetime, leading to a decrease of network robustness. With glacier retreat, mutualistic networks shift from highly connected with diverse specialist interactions to loosely connected with few generalist interactions. Furthermore, despite the turnover of plant species, we find that species structural roles remain constant over spacetime while depending on species identity. Our findings suggest that glacier retreat reshuffles mutualistic networks with motifs posing low robustness, leading to increased fragility. Understanding the assembly and breaking down of species interaction networks provides novel insights into the development and stability of novel, post‐glacial ecological systems facing glacier extinction.","PeriodicalId":51026,"journal":{"name":"Ecography","volume":"68 1","pages":""},"PeriodicalIF":5.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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