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      A new time tree reveals Earth history’s imprint on the evolution of modern birds

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          Abstract

          Estimates of the timing of evolution of modern birds reveals the influence of paleogeography and paleoclimate on diversification.

          Abstract

          Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth’s dynamics.

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          Most cited references58

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          Trends, rhythms, and aberrations in global climate 65 Ma to present.

          Since 65 million years ago (Ma), Earth's climate has undergone a significant and complex evolution, the finer details of which are now coming to light through investigations of deep-sea sediment cores. This evolution includes gradual trends of warming and cooling driven by tectonic processes on time scales of 10(5) to 10(7) years, rhythmic or periodic cycles driven by orbital processes with 10(4)- to 10(6)-year cyclicity, and rare rapid aberrant shifts and extreme climate transients with durations of 10(3) to 10(5) years. Here, recent progress in defining the evolution of global climate over the Cenozoic Era is reviewed. We focus primarily on the periodic and anomalous components of variability over the early portion of this era, as constrained by the latest generation of deep-sea isotope records. We also consider how this improved perspective has led to the recognition of previously unforeseen mechanisms for altering climate.
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            Speciation in amazonian forest birds.

            J Haffer (1969)
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              Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

              We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                December 2015
                11 December 2015
                : 1
                : 11
                : e1501005
                Affiliations
                Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
                Author notes
                [* ]Corresponding author. E-mail: sclaramunt@ 123456amnh.org (S.C.); jlc@ 123456amnh.org (J.C.)
                Article
                1501005
                10.1126/sciadv.1501005
                4730849
                26824065
                f7a575df-947a-4256-87a1-b2894b2ed004
                Copyright © 2015, The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 29 July 2015
                : 02 November 2015
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: ID0EOABG4147
                Award ID: 1241066
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000076, Directorate for Biological Sciences;
                Award ID: ID0EYFBG4148
                Award ID: 1146423
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100005835, American Museum of Natural History;
                Award ID: ID0ECLBG4149
                Award Recipient :
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Evolutionary Ecology
                Custom metadata
                Meann Ramirez

                avian evolution,global biogeography,divergence times,diversification rates,k-pg mass extinction

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