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      Diversification of Neoaves: integration of molecular sequence data and fossils

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          Abstract

          Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

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          Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

          M. Sanderson (2002)
          Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
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            Phylogeny and diversification of the largest avian radiation.

            F. Barker, A Cibois, P. Schikler … (2004)
            The order Passeriformes ("perching birds") comprises extant species diversity comparable to that of living mammals. For over a decade, a single phylogenetic hypothesis based on DNA-DNA hybridization has provided the primary framework for numerous comparative analyses of passerine ecological and behavioral evolution and for tests of the causal factors accounting for rapid radiations within the group. We report here a strongly supported phylogenetic tree based on two single-copy nuclear gene sequences for the most complete sampling of passerine families to date. This tree is incongruent with that derived from DNA-DNA hybridization, with half of the nodes from the latter in conflict and over a third of the conflicts significant as assessed under maximum likelihood. Our historical framework suggests multiple waves of passerine dispersal from Australasia into Eurasia, Africa, and the New World, commencing as early as the Eocene, essentially reversing the classical scenario of oscine biogeography. The revised history implied by these data will require reassessment of comparative analyses of passerine diversification and adaptation.
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              Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.

              Dan Graur, William Martin (2004)
              For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred approximately 4 billion years ago. Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by definition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made to look deceptively precise. For example, on the basis of just 15 genes, the arthropod-nematode divergence event was 'calculated' to have occurred 1167+/-83 million years ago (i.e. within a 95% confidence interval of approximately 350 million years). Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger ( approximately 14.2 billion years).
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                Author and article information

                Journal
                Title: Biology Letters
                Abbreviated Title: Biol. Lett.
                Publisher: The Royal Society
                ISSN (Print): 1744-9561
                ISSN (Electronic): 1744-957X
                Publication date Created: August 08 2006
                Publication date Created: December 22 2006
                Publication date (Electronic): August 09 2006
                Publication date (Print): December 22 2006
                Volume: 2
                Issue: 4
                Pages: 543-547
                Affiliations
                [1 ]Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural HistoryPO Box 50007, 10405 Stockholm, Sweden
                [2 ]Department of Systematic Botany, Evolutionary Biology Centre, University of UppsalaNorbyvägen 18D, 752 36 Uppsala, Sweden
                [3 ]Department of Mathematics, University of Stockholm106 91 Stockholm, Sweden
                [4 ]Institute of Zoology, University of Wroclaw21 Sienkiewicz Street, 50335 Wroclaw, Poland
                [5 ]DST/NRF Centre of Excellence at the Percy Fitzpatrick Institute, Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag XI, Maiteland 7602, South Africa
                [6 ]Department of Zoology, University of Stockholm106 91 Stockholm, Sweden
                [7 ]International Commission on Missing PersonsAlipašina 45 A, 71000 Sarajevo, Bosnia
                [8 ]Forschungsinstitut Senckenberg, Sektion für OrnithologieSenckenberganlage 25, 60325 Frankfurt am Main, Germany
                Article
                DOI: 10.1098/rsbl.2006.0523
                PMC ID: 1834003
                PubMed ID: 17148284
                SO-VID: ffb91dea-af2b-4d88-85ec-b46cb92d8865
                Copyright © © 2006
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