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Wyświetlanie 1-10 z 14
Tytuł:
Quantifying macro‐evolutionary patterns of trait mean and variance with phylogenetic location-scale models
Autorzy:
Mizuno, Ayumi
Williams, Coralie
Nakagawa, Shinichi
Yang, Yefeng
Drobniak, Szymon
Lagisz, Malgorzata
Opis:
1. Understanding how both the mean (location) and variance (scale) of traits differ among species and lineages is fundamental to unveiling macroevolutionary patterns. Yet, traditional phylogenetic comparative methods primarily focus on modelling mean trait values, often overlooking variability and heteroscedasticity that can provide critical insights into evolutionary dynamics. 2. Here, we introduce phylogenetic location-scale models (PLSMs), a novel framework that jointly analyses the evolution of trait means and variances. This dual approach captures heteroscedasticity and evolutionary changes in trait variability, allowing for the detection of clades with differing variances and revealing patterns of adaptation, diversification, and evolutionary constraints. 3. Extending PLSMs to a multivariate context enables simultaneous analysis of multiple traits and their covariances, facilitating the testing of hypotheses about evolutionary trade-offs, pleiotropy and phenotypic integration. By modelling covariances between phylogenetic effects in both the location and scale parts, we can discern whether changes in one trait's mean or variance are associated with changes in another's, thereby offering deeper insights into the mechanisms driving trait co-evolution and co-divergence or ‘contra-divergence’. 4. We also describe how an extended version of PLSMs incorporating within-species variability can enhance our understanding of trait convergence and divergence arising from ecological and environmental factors. 5. Our framework provides a powerful tool for exploring macroevolutionary patterns and can be used to reassess previously published comparative data, offering new insights into the mechanisms driving the diversity of life.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
Location‐scale meta‐analysis and meta‐regression as a tool to capture large‐scale changes in biological and methodological heterogeneity : a spotlight on heteroscedasticity
Autorzy:
Mizuno, Ayumi
Morrison, Kyle
Williams, Coralie
Ricolfi, Lorenzo
Nakagawa, Shinichi
Yang, Yefeng
Drobniak, Szymon
Lagisz, Malgorzata
Opis:
Heterogeneity is a defining feature of ecological and evolutionary meta-analyses. While conventional meta-analysis and meta-regression methods acknowledge heterogeneity in effect sizes, they typically assume this heterogeneity is constant across studies and levels of moderators (i.e., homoscedasticity). This assumption could mask potentially informative patterns in the data. Here, we introduce and develop a location-scale meta-analysis and meta-regression framework that models both the mean (location) and variance (scale) of effect sizes. Such a framework explicitly accommodates heteroscedasticity (differences in variance), thereby revealing when and why heterogeneity itself changes. This capability, we argue, is crucial for understanding responses to global environmental change, where complex, context-dependent processes may shape both the average magnitude and the variability of biological responses. For example, differences in study design, measurement protocols, environmental factors, or even evolutionary history can lead to systematic shifts in variance. By incorporating hierarchical (multilevel) structures and phylogenetic relationships, location-scale models can disentangle the contributions from different levels to both location and scale parts. We further attempt to extend the concepts of relative heterogeneity and publication bias into the scale part of meta-regression. With these methodological advances, we can identify patterns and processes that remain obscured under the constant variance assumption, thereby enhancing the biological interpretability and practical relevance of meta-analytic results. Notably, almost all published ecological and evolutionary meta-analytic data can be re-analysed using our proposed analytic framework to gain new insights. Altogether, location-scale meta-analysis and meta-regression provide a rich and holistic lens through which to view and interpret the intricate tapestry woven with ecological and evolutionary data. The proposed approach, thus, ultimately leads to more informed and context-specific conclusions about environmental changes and their impacts.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
orchaRd 2.0 : an R package for visualising meta-analyses with orchard plots
Autorzy:
Noble, Daniel W. A.
Pottier, Patrice
O'Dea, Rose E.
Rutkowska, Joanna
Nakagawa, Shinichi
Yang, Yefeng
Lagisz, Malgorzata
Senior, Alistair M.
Opis:
1. Although meta-analysis has become an essential tool in ecology and evolution, reporting of meta-analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and individual effect sizes. 2. Here, we have added significant enhancements by integrating many new functionalities into orchaRd 2.0. This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators. 3. orchaRd 2.0 has additional functions which calculate key statistics from multilevel meta-analytic models such as $I^{2}$ and $R^{2}$. Importantly, orchaRd 2.0 contributes to better reporting by complying with PRISMA-EcoEvo (preferred reporting items for systematic reviews and meta-analyses in ecology and evolution). Taken together, orchaRd 2.0 can improve the presentation of meta-analytic results and facilitate the exploration of previously neglected patterns. 4. In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for example, by citations in a figure legend, acknowledging the use of relevant packages.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
Harnessing meta-analyses’ insights in ecology and evolution research
Autorzy:
Mizuno, Ayumi
Pollo, Pietro
Morrison, Kyle
Tam, Jesse
Williams, Coralie
Martinig, April Robin
Ricolfi, Lorenzo
Nakagawa, Shinichi
Pottier, Patrice
Yang, Yefeng
Drobniak, Szymon
Lagisz, Malgorzata
Opis:
Meta-analyses are powerful tools to synthesize the literature in several fields of study, including ecology and evolution. However, it remains uncertain whether ecologists and evolutionary biologists fully comprehend meta-analyses’ findings or effectively apply them when citing these studies in their own research. Here, we first discuss key meta-analytical concepts and provide a guide to researchers in ecology and evolution on how to harness meta-analyses’ insights. For instance, we clarify the meaning of effect sizes and heterogeneity to improve understanding of meta-analyses’ quantitative findings. In addition, we analysed articles published in 2023 in ecology and evolution to investigate how frequently and in what context meta-analyses were cited. We found that approximately 21% of articles cited at least one meta-analysis, and that the relative number of citations of meta-analyses (0.62% of all citations analysed) was greater than the publication frequency of meta-analytical articles (0.44% of all articles). Most importantly, we found that while the direction of mean effect sizes from cited meta-analyses was often mentioned, the magnitude of effect sizes and the limitations of the data analysed were frequently overlooked. These findings underscore the need for improved citation practices of meta-analyses in ecological and evolutionary research, which our recommendations seek to promote.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
AmphiTherm : a comprehensive database of amphibian thermal tolerance and preference
Autorzy:
Drobniak, Szymon
Pottier, Patrice
Lin, Hsien-Yung
Nakagawa, Shinichi
Claunch, Natalie
Varon, Sarah
Valdebenito, José O.
Rivera-Villanueva, A. Nayelli
Yang, Yefeng
Oh, Rachel R. Y.
Longo, Ana V.
Pollo, Pietro
Burke, Samantha
Amano, Tatsuya
Opis:
Thermal traits are crucial to our understanding of the ecology and physiology of ectothermic animals. While rising global temperatures have increasingly pushed research towards the study of upper thermal limits, lower thermal limits and thermal preferences are essential for defining the thermal niche of ectotherms. Through a systematic review of the literature in seven languages, we expanded an existing database of amphibian heat tolerance by adding 1,009 estimates of cold tolerance and 816 estimates of thermal preference across 375 species. AmphiTherm is a comprehensive and reproducible database that contains 4,899 thermal trait estimates from a diverse sample of 659 species (~7.5% of all described amphibians) spanning 38 families. Despite its broad geographic coverage, we report evident gaps across amphibian biodiversity hotspots in Africa, most regions of Asia, central South America, and Western Australia. By providing a more holistic understanding of amphibian thermal tolerance and preferences, AmphiTherm is a valuable resource for advancing research in evolutionary biology, ecophysiology, and biogeography of amphibians, offering insights that are increasingly needed in changing climates.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Wyświetlanie 1-10 z 14

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