An all-evidence species-level supertree for the palms (Arecaceae)

Faurby, Søren; Eiserhardt, Wolf L.; Baker, William J.; Svenning, Jens‐Christian

doi:10.1016/j.ympev.2016.03.002

Cited by 76 publications

(152 citation statements)

References 40 publications

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“…The crown nodes of each of the subfamilies differ between the SUPERSMART and earlier results, some being older and others younger than previous estimates (Supplementary Table S2 available on Dryad). We also compared our tree topology with a recently published palm phylogeny (Faurby et al 2016a), finding both similarities and differences (Supplementary Fig. S5 available on Dryad) that likely reflect differences in the underlying data and analytical steps between our studies.…”

Section: Empirical Examplesmentioning

confidence: 94%

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

et al. 2016

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Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

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Section: Empirical Examplesmentioning

confidence: 94%

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

et al. 2016

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Section: Phylogenetic and Habitat Datamentioning

confidence: 99%

“…We used the species-level phylogeny for all palms (Faurby, Eiserhardt, Baker, & Svenning, 2016) based on the taxonomy from Govaerts, Dransfield, Zona, Hodel, and Henderson (2011), which includes 2,539 species. Analyses were performed either on a set of 100 randomly sampled palm phylogenetic trees available from Faurby et al (2016) or on a maximum clade credibility (MCC) tree. The MCC tree was calculated from 1,000 phylogenies from the posterior distribution of trees available from Faurby et al (2016) using the "phangorn" package (Schliep, 2011) in the R statistical platform (R Development Core Team, 2016).…”

Section: Phylogenetic and Habitat Datamentioning

confidence: 99%

Niche conservatism drives a global discrepancy in palm species richness between seasonally dry and moist habitats

Cássia‐Silva

Freitas

Alves

et al. 2019

Global Ecol Biogeogr

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Aim Rapid global environmental change predicts increasingly seasonal climate in the tropics, causing expansion of seasonally dry habitats and leading to shifts in species distribution and potential extinction. Here, we use a macroevolutionary framework to understand the processes driving palm diversity patterns between moist and seasonally dry tropical habitats. We hypothesize that the discrepancy in species richness between habitats is explained by higher speciation rates in moist habitat and that niche conservatism prevents frequent shifts between habitats. Location Global. Time period Last 100 Ma. Major taxa studied Arecaceae. Methods We used trait‐dependent diversification models to test whether different habitats affect palm speciation rates. Furthermore, palm assemblages were divided into three regions (Africa, Australasia and Neotropics) to test for niche conservatism and evaluate phylogenetic dissimilarity. Results We found no relationship between speciation rate and habitat type. We detected phylogenetic signal for habitats at both global and continental scales, indicating that closely related species were more similar than expected by chance. Colonization of seasonally dry habitats occurred c. 60 Ma, yet most clades only diversified after c. 30 Ma. The high phylogenetic dissimilarity between habitat types at both global and continental scales was driven by high lineage turnover, at least for Africa and the Neotropics. Main conclusions We found a lack of differential speciation rates in setting the seasonally dry and moist palm‐richness discrepancy. However, over evolutionary history most palm lineages fail to colonize seasonally dry habitats owing to a tendency to retain ancestral habitat. Indeed, seasonally dry palm assemblages are the result of the diversification of particular lineages. Likewise, long‐term dry periods appear to induce shifts in taxonomic and functional diversity, and we emphasize that the expansion of dry habitats might also imply a loss of palm clades, hence a reduction in phylogenetic diversity.

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“…Following standard practice, we assumed three values of relative 121 6 extinction ε of 0.0, 0.5 and 0.9 when estimating diversification (Magallon and Sanderson 122 2001 We also repeated our diversification analysis as above with two large clades that were 125 well sampled at a species-level in separate time-calibrated phylogenies. These clades 126 included 70% of all 651 accepted Pinales (extant conifers) (Leslie et al 2012) and all 2,539 127 Arecaceae (palms) (Faurby et al 2016). We intersected risk statuses of the two clades with 128 species stem ages, giving n = 433 and 547, respectively.…”

Section: Methods 95mentioning

confidence: 99%

“…We intersected risk statuses of the two clades with 128 species stem ages, giving n = 433 and 547, respectively. For the palms, we used the 129 maximum clade credibility tree that we computed from the posterior distribution of trees that 130 was generated using topological constraints based on Govaerts taxonomy recommended in 131 Faurby et al (2016). 132…”

Section: Methods 95mentioning

confidence: 99%

Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants

Tanentzap

Igea

Johnston

et al. 2017

Preprint

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8Extinction threatens many species, yet few factors predict this risk across the plant Tree of 9 Life (ToL). Taxon age is one factor that may associate with extinction if occupancy of 10 geographic and adaptive zones varies with time. Age-dependent occupancy can also 11 influence diversification rates and thus extinction risk where new taxa have small range and 12 population sizes. Here we found that faster diversifying plant genera had more species 13 threatened by extinction across the ToL. Evolutionary age had no effect in 297 sampled 14 genera, potentially because they were older, on average, than expected. Repeating our 15 analyses in two large, well-sampled groups, we found that extinction risk decreased with 16 evolutionary age in conifer species but not palms. Range filling increased in older, non-17 threatened conifers more strongly than in threatened taxa. Our results suggest contrasting 18 modes of speciation may explain differing patterns of extinction risk across the ToL with 19 consequences for biodiversity conservation. 20

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An all-evidence species-level supertree for the palms (Arecaceae)

Cited by 76 publications

References 40 publications

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Niche conservatism drives a global discrepancy in palm species richness between seasonally dry and moist habitats

Range size dynamics can explain why evolutionarily age and diversification rate correlate with contemporary extinction risk in plants

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