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Tree of life reveals clock-like speciation and diversification.

Hedges SB, Marin J, Suleski M, Paymer M, Kumar S - Mol. Biol. Evol. (2015)

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Center for Biodiversity, Temple University Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University sbh@temple.edu.

No MeSH data available.


(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.
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msv037-F6: (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.

Mentions: The rate of formation of new species is the primary input into the diversification of life over time. This process starts as two or more lineages split from an existing species at a node in the tree. To learn more about the timing of speciation, we assembled a separate data set of studies containing timetrees that included populations and species of eukaryotes (supplementary Materials and Methods, Supplementary Material online). Considering a standard model of speciation based on geographic isolation, in the absence of gene flow (Sousa and Hey 2013), we estimated the time required for speciation to occur. For a given species, the time-to-speciation (TTS), after isolation, must fall between the crown and the stem age of the species (fig. 6a). All lineages younger than the crown age of a species lead to populations that are still capable of interbreeding and, therefore, must be younger than the TTS. On the other hand, the stem age is the time when a species joins its closest relative and, therefore, it must be older than the TTS. A sampling omission of either a population or species could lower the crown age estimate or raise the stem age estimate, but the resulting interval would still contain the TTS. Although coalescence of alleles may lead to overestimates of time (Nei and Kumar 2000), those times were interpreted as population and species splits, not allelic splits, in the published studies reporting them. Also, calibrations can ameliorate the effect of allelic coalescence because they are usually based on population and species divergences, not coalescence events. We conducted a simulation to test this approach (supplementary Materials and Methods, Supplementary Material online) finding that the true TTS is estimated precisely with a mode because of skewness of the statistical distribution and it is robust to undersampling of lineages, either younger (populations) or older (species). We also found that the true TTS was not affected by the addition of 10% noise (intervals that do not include the TTS) and only weakly affected (2.5%) by adding a large amount (50%) of noise.Fig. 6.


Tree of life reveals clock-like speciation and diversification.

Hedges SB, Marin J, Suleski M, Paymer M, Kumar S - Mol. Biol. Evol. (2015)

(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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379413&req=5

msv037-F6: (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.
Mentions: The rate of formation of new species is the primary input into the diversification of life over time. This process starts as two or more lineages split from an existing species at a node in the tree. To learn more about the timing of speciation, we assembled a separate data set of studies containing timetrees that included populations and species of eukaryotes (supplementary Materials and Methods, Supplementary Material online). Considering a standard model of speciation based on geographic isolation, in the absence of gene flow (Sousa and Hey 2013), we estimated the time required for speciation to occur. For a given species, the time-to-speciation (TTS), after isolation, must fall between the crown and the stem age of the species (fig. 6a). All lineages younger than the crown age of a species lead to populations that are still capable of interbreeding and, therefore, must be younger than the TTS. On the other hand, the stem age is the time when a species joins its closest relative and, therefore, it must be older than the TTS. A sampling omission of either a population or species could lower the crown age estimate or raise the stem age estimate, but the resulting interval would still contain the TTS. Although coalescence of alleles may lead to overestimates of time (Nei and Kumar 2000), those times were interpreted as population and species splits, not allelic splits, in the published studies reporting them. Also, calibrations can ameliorate the effect of allelic coalescence because they are usually based on population and species divergences, not coalescence events. We conducted a simulation to test this approach (supplementary Materials and Methods, Supplementary Material online) finding that the true TTS is estimated precisely with a mode because of skewness of the statistical distribution and it is robust to undersampling of lineages, either younger (populations) or older (species). We also found that the true TTS was not affected by the addition of 10% noise (intervals that do not include the TTS) and only weakly affected (2.5%) by adding a large amount (50%) of noise.Fig. 6.

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Center for Biodiversity, Temple University Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University sbh@temple.edu.

No MeSH data available.