OneZoom: A Fractal Explorer for the Tree of Life

Rosindell, James; Harmon, Luke J.

doi:10.1371/journal.pbio.1001406

Cited by 81 publications

(68 citation statements)

References 11 publications

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“…Phylogeny. We constructed a species-level phylogenetic tree [www.onezoom.org/ FWifhj38wjf/Salguero-Gomez_et_al_2014.htm (65)] with branch length transformations to account for phylogenetic signal, estimated by Pagel's λ (30). See SI Appendix, section 2 for details.…”

Section: Methodsmentioning

confidence: 99%

Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide

Salguero‐Gómez

Jones

Jongejans

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

347

498

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The identification of patterns in life-history strategies across the tree of life is essential to our prediction of population persistence, extinction, and diversification. Plants exhibit a wide range of patterns of longevity, growth, and reproduction, but the general determinants of this enormous variation in life history are poorly understood. We use demographic data from 418 plant species in the wild, from annual herbs to supercentennial trees, to examine how growth form, habitat, and phylogenetic relationships structure plant life histories and to develop a framework to predict population performance. We show that 55% of the variation in plant life-history strategies is adequately characterized using two independent axes: the fast–slow continuum, including fast-growing, short-lived plant species at one end and slow-growing, long-lived species at the other, and a reproductive strategy axis, with highly reproductive, iteroparous species at one extreme and poorly reproductive, semelparous plants with frequent shrinkage at the other. Our findings remain consistent across major habitats and are minimally affected by plant growth form and phylogenetic ancestry, suggesting that the relative independence of the fast–slow and reproduction strategy axes is general in the plant kingdom. Our findings have similarities with how life-history strategies are structured in mammals, birds, and reptiles. The position of plant species populations in the 2D space produced by both axes predicts their rate of recovery from disturbances and population growth rate. This life-history framework may complement trait-based frameworks on leaf and wood economics; together these frameworks may allow prediction of responses of plants to anthropogenic disturbances and changing environments.

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Section: Methodsmentioning

confidence: 99%

Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide

Salguero‐Gómez

Jones

Jongejans

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

347

498

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“…We calculate the various indices for the species shown on a schematic phylogenetic tree for apes and humans (modified from OneZoom [61]; www.onezoom.org). Table 1 provides calculations for some basic phylogenetic measures that are applicable to whole trees or clades; here they are calculated for both the 18 species in the great ape clade and for the seven species forming the apes plus humans clade (figure 1).…”

Section: A Bewildering Array Of Methods and Indicesmentioning

confidence: 99%

Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency

Forest

Crandall

Chase

et al. 2015

Phil. Trans. R. Soc. B

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Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.

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“…The earliest diversification date (based on extant lineages) of the clade that performed the transition was used as the crown age value. The dates were derived from the OneZoom online engine [18], accessed 11 -19 September 2013. This was at the time incomplete for Squamata, so information was in this case retrieved from published papers (see the electronic supplementary material).…”

Section: Methodsmentioning

confidence: 99%

K-Pg events facilitated lineage transitions between terrestrial and aquatic ecosystems

2014

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We use dated phylogenetic trees for tetrapod vertebrates to identify lineages that shifted between terrestrial and aquatic ecosystems in terms of feeding or development, and to assess the timing of such events. Both stem and crown lineage ages indicate a peak in transition events in correspondence with the K-Pg mass extinction. This meets the prediction that changes in competitive pressure and resource availability following mass extinction events should facilitate such transitions.

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OneZoom: A Fractal Explorer for the Tree of Life

Abstract: An intuitively simple zooming interface offers a visually appealing way to explore very large phylogenetic trees with metadata.

Cited by 81 publications

References 11 publications

Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide

Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide

Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency

K-Pg events facilitated lineage transitions between terrestrial and aquatic ecosystems

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