Tree of life reveals clock-like speciation and diversification - PubMed (original) (raw)

Tree of life reveals clock-like speciation and diversification

S Blair Hedges et al. Mol Biol Evol. 2015 Apr.

Abstract

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

Keywords: biodiversity; diversification; speciation; timetree; tree of life.

© The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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Figures

F<sc>ig</sc>. 1.

Fig. 1.

(2 columns) A timetree of 50,632 species synthesized from times of divergence published in 2,274 studies. Evolutionary history is compressed into a narrow strip and then arranged in a spiral with one end in the middle and the other on the outside. Therefore, time progresses across the width of the strip at all places, rather than along the spiral. Time is shown in billions of years on a log scale and indicated throughout by bands of gray. Major taxonomic groups are labeled and the different color ranges correspond to the main taxonomic divisions of our tree.

F<sc>ig</sc>. 2.

Fig. 2.

(1 column) A timeline from the perspective of humans, showing divergences with other groups of organisms. In each case, mean ± standard error (among studies) is shown, with number of studies in parentheses. Also shown are the times for the origin of life, eukaryotes, and last universal common ancestor (Hedges and Kumar 2009).

F<sc>ig</sc>. 3.

Fig. 3.

(1 column) Temporal relationships of Linnaean ranks of eukaryotes, showing mode and 95% confidence intervals. Prokaryotes are not shown because of large differences in scale (

supplementary Materials and Methods

,

Supplementary Material

online).

F<sc>ig</sc>. 4.

Fig. 4.

(1 column) Patterns of lineage diversification. (a) Cumulative lineages-through-time (LTT) curve for eukaryotes (50,455 sp.), in black, showing the number of lineages through time (unsmoothed, dashed; smoothed, solid) and variance (red, 500 replicates). (b) Same LTT curve (black line), but compared with a simulated constant-expansion LTT curve (λ (speciation rate) = 0.073 and μ (extinction rate) = 0.070) shown as ± 99% confidence intervals (red). (c) Diversification rate plot of same data showing only significant changes in rate as determined in maximum-likelihood tests; variance (red, 500 replicates) shown as ± 99% intervals.

F<sc>ig</sc>. 5.

Fig. 5.

(1 column) Diversification analyses of major Linnaean clades in the timetree of life. (a–b) Results of coalescent analyses testing models of diversification. Of 48 tetrapod clades, 37 showed significant model selected and they were used in these analyses. (a) Effect of clade size (number of described species). (b) Effect of clade age. (c) Diagram illustrating difference between stem and crown age for two clades. (d–e) Relationship of stem branch and crown age in mammals (d; _r_2 = 0.07) and birds (e; _r_2 = 0.04).

F<sc>ig</sc>. 6.

Fig. 6.

(2 columns) Estimation of time-to-speciation. (a) Analytical design showing expected results. Intervals between stem age and crown age of seven species contain time-to-speciation (dashed line represents the modal time-to-speciation). Divergences among populations, and corresponding histogram, are in red. (b) Colored histograms of observed time-to-speciation, showing modes (vertical lines) and confidence intervals (bars) in vertebrates (N = 213, 2.1 Ma, 1.74–2.55 Ma), arthropods (N = 85, 2.2 Ma, 1.57–3.07 Ma), and plants (N = 55, 2.7 Ma, 2.37–3.63 Ma). Black curves to the right are histograms of population divergences.

F<sc>ig</sc>. 7.

Fig. 7.

(1 column) Summary model of speciation. (a) Biogeographic history showing the contact and isolation of areas occupied by the two populations. (b) Phylogenetic lineages showing times of independence (two lineages) and times of interbreeding (one lineage). (c) Genic incompatibilities between the two populations, showing how they accrue at a time-dependent rate during geographic isolation, reset to zero during contact (interbreeding), increase to the S-value (the number of GIs that will cause speciation, the point of no return), and continue increasing beyond the S-value despite later contact of the newly formed species. (d) Hypothetical phylogeny, with numbered species, illustrating parameters of speciation in (a–c) to splits and branches in a tree.

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