The role of climate and islands in species diversification and reproductive-mode evolution of Old World tree frogs

Ellepola, Gajaba; Pie, Márcio R.; Pethiyagoda, Rohan; Howard, James L.; Meegaskumbura, Madhava

doi:10.1038/s42003-022-03292-1

Cited by 11 publications

(15 citation statements)

References 78 publications

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“…This will simplify workflows and facilitate reproducibility for researchers studying spatial biodiversity with R. Furthermore, canaper features efficient computing routines and simple yet flexible implementation of parallel computing, thereby decreasing computation time. canaper has already been used at least five studies while in development (Ellepola et al 2022, Lu et al 2022, Nitta et al 2022, Naranjo et al 2023, van Galen et al 2023). We expect canaper will become a major tool in the toolkit of the emerging field of spatial phylogenetics alongside Biodiverse.…”

Section: Discussionmentioning

confidence: 99%

canaper: Categorical analysis of neo‐ and paleo‐endemism in R

et al. 2023

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Biodiversity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of biodiversity. CANAPE (categorical analysis of neo‐ and paleo‐endemism) is one such method that can provide insight into the evolutionary processes generating biodiversity. The only currently available software implementing CANAPE is Biodiverse, which is written in Perl and can be used either through a graphical user interface (GUI) or user‐developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. Here, we present canaper, a new R package (www.r‐project.org) that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility; CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. Our case study shows that canaper produces equivalent results to Biodiverse and can complete computations on moderately sized datasets quickly (<10 min to reproduce a canonical study). canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby obviating the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing biodiversity in R.

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Section: Discussionmentioning

confidence: 99%

canaper: Categorical analysis of neo‐ and paleo‐endemism in R

et al. 2023

View full text Add to dashboard Cite

show abstract

“…This will simplify workflows and facilitate reproducibility for researchers studying spatial biodiversity with R. Furthermore, canaper features efficient computing routines and simple yet flexible implementation of parallel computing, thereby decreasing computation time. canaper has already been used at least three studies while in development (Ellepola et al, 2022;Lu et al, 2022;Nitta et al, 2022). We expect canaper will become a major tool in the toolkit of the emerging field of spatial phylogenetics alongside Biodiverse.…”

Section: Discussionmentioning

confidence: 99%

canaper: Categorical analysis of neo- and paleo-endemism in R

Nitta

Laffan

Mishler

et al. 2022

Preprint

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Biodiversity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of biodiversity. CANAPE (categorical analysis of neo- and paleo-endemism) is one such method that can provide insight into the evolutionary processes generating biodiversity. The only currently available software implementing CANAPE is Biodiverse, which is written in Perl and can be used either through a graphical user interface (GUI) or user-developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. Here, we present canaper, a new R package that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility; CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. Our case study shows that canaper produces equivalent results to Biodiverse and can complete computations on moderately sized datasets quickly (< 10 min to reproduce a canonical study). canaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby averting the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing biodiversity in R.

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“…Understanding the drivers of species diversity and its distribution pattern is among the fundamental goals in ecology and evolution (Chazot et al ., 2021; Jin et al ., 2021). Many researchers have made significant progress in understanding such drivers on alpine flora (Ding et al ., 2020), bamboos (Guo et al ., 2020), birches (Yang et al ., 2022), oaks (Zhou et al ., 2022), pines (Jin et al ., 2021) and rosids (Ellepola et al ., 2022) in plants; and butterflies (Chazot et al ., 2021), birds (Aves) (Prum et al ., 2015) and frogs (Ellepola et al ., 2022) in animals. Their investigations revealed significant influences of Cenozoic climatic and geological events, such as the fluctuations of global temperature and aridity, mountains uplifting, on species diversification.…”

Section: Introductionmentioning

confidence: 99%

The rapid diversification of Boletales is linked to Early Eocene and Mid-Miocene Climatic Optima

Wu,

Halling

et al. 2023

Preprint

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Investigating the mechanisms that underpin the diversity and distribution patterns of species is fundamental in ecology and evolution. However, the study of fungi, particularly the ectomycorrhizal group, has been relatively constrained in this field. We conducted a high-resolution phylogenomic analysis of Boletales, an ecologically and economically significant group of fungi, covering 83 genera across 15 families. We subsequently investigated its evolutionary history using sequences at four genes obtained from 984 species across 121 genera within 15 families. The findings unveiled that Boletales likely originated in Early Jurassic and underwent two remarkable episodes of rapid diversification, commencing in early Eocene (~54 Mya) and early Miocene (~17 Mya) epochs. The notable surges were predominantly driven by ectomycorrhizal clades, with a specific emphasis on East Asia and North America. These expansions were strongly correlated with the warm-humid paleoclimates during the Early Eocene Climatic Optimum and Mid-Miocene Climatic Optimum, as well as the rapid expansion of Fagales and Pinaceae hosts. This study provides novel insights into the spatiotemporal evolution of fungi, highlighting the synergistic impact of abiotic factors, such as warm and humid paleoclimates, and the biotic factor of rapid diversification of host plants on the fungal diversification.

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The role of climate and islands in species diversification and reproductive-mode evolution of Old World tree frogs

Cited by 11 publications

References 78 publications

canaper: Categorical analysis of neo‐ and paleo‐endemism in R

canaper: Categorical analysis of neo‐ and paleo‐endemism in R

canaper: Categorical analysis of neo- and paleo-endemism in R

The rapid diversification of Boletales is linked to Early Eocene and Mid-Miocene Climatic Optima

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