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      Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life

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          Abstract

          Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

          Author Summary

          Species richness varies by many orders of magnitude across the evolutionary "tree of life." Some groups, like beetles and flowering plants, contain nearly incomprehensible species diversity, but the overwhelming majority of groups contain far fewer species. Many processes presumably contribute to this variation in diversity, but the most general explanatory variable is the evolutionary age of each group: older groups will simply have had more time for diversity to accumulate than younger groups. We tested whether evolutionary age explains differences in species richness by compiling diversity and age estimates for nearly 1,400 groups of multicellular organisms. Surprisingly, we find no evidence that old groups have more species than young groups. This result appears to hold across the entire tree of life, for taxa as diverse as ferns, fungi, and flies. We demonstrate that this pattern is highly unlikely under simple but widely used evolutionary models that allow diversity to increase through time without bounds. Paleontologists have long contended that diversity-dependent processes have regulated species richness through time, and our results suggest that such processes have left a footprint on the living biota that can even be seen without data from the fossil record.

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          Most cited references34

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          Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.

          The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced "living fossils." In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.
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            A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation.

            Beetles represent almost one-fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre-Cretaceous origin of more than 100 present-day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.
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              Ecological opportunity and the origin of adaptive radiations.

              Ecological opportunity--through entry into a new environment, the origin of a key innovation or extinction of antagonists--is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                plosbiol
                PLoS Biology
                Public Library of Science (San Francisco, USA )
                1544-9173
                1545-7885
                August 2012
                August 2012
                28 August 2012
                : 10
                : 8
                : e1001381
                Affiliations
                [1 ]Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
                [2 ]Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
                [3 ]Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
                University College London, United Kingdom
                Author notes

                The authors have declared that no competing interests exist.

                The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: DLR GJS MEA. Performed the experiments: DLR GJS MEA. Analyzed the data: DLR GJS MEA. Contributed reagents/materials/analysis tools: DLR GJS MEA. Wrote the paper: DLR GJS MEA.

                Article
                PBIOLOGY-D-11-04389
                10.1371/journal.pbio.1001381
                3433737
                22969411
                7c14f021-18f4-4fe1-9b40-dbe60ad02f86
                Copyright @ 2012

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 28 October 2011
                : 12 July 2012
                Page count
                Pages: 11
                Funding
                This research was supported by NSF-DEB-081-4277, by NSF-DEB-091-8748, and by the Miller Institute for Basic Research in Science at the University of California. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Evolutionary Systematics
                Phylogenetics

                Life sciences
                Life sciences

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