Detecting shifts in diversity limits from molecular phylogenies: what can we know?

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how...

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Bibliographic Details
Published in:Proceedings of the Royal Society. B, Biological sciences Biological sciences, 2011-11, Vol.278 (1722), p.3294-3302
Main Authors: McInnes, Lynsey, Orme, C. David L, Purvis, A
Format: Article
Language:English
Subjects:
Angiosperms
Animals
Biodiversity
Diversification Pulses
Diversity Dependence
Evolution
Extinction
Extinction, Biological
Fossils
Genetic Speciation
Magnoliophyta
Magnoliopsida
Mammals
Mass extinction events
Materials
Models, Biological
Phylogeny
Speciation
Species diversity
Species extinction
Species Specificity
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Summary:Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a—probably untenable—model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification ‘rules’ and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.
ISSN:0962-8452
1471-2954
1471-2945
DOI:10.1098/rspb.2011.0241