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      Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

      research-article
      1 ,
      Ecology and Evolution
      John Wiley and Sons Inc.
      base substitution rate, BEAST v1.10.4, environmental changes, fossil calibration, mammals

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          Abstract

          A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. ( Palaeontologia Electronica, 2015, 1–106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K–Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non‐avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO 2 concentration, inducing global cooling, and initiating Quaternary glacial–interglacial cycles, thereby causing significant climatic changes.

          Abstract

          A robust minimum age tree shows post K–Pg Placentalia radiation, and subsequent extensive radiation connected to exponentially increased base substitution (mutation) rate including generation of Homo sapiens. This Neogene radiation may have been triggered by expansion of C4 grasses that decreased atmospheric CO 2, resulting in global cooling and initiation of Quaternary glacial–interglacial cycles.

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          Most cited references153

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          MEGA11: Molecular Evolutionary Genetics Analysis Version 11

          The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor , and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net .
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            PAML 4: phylogenetic analysis by maximum likelihood.

            PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
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              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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                Author and article information

                Contributors
                kawaoso@icloud.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                19 December 2023
                December 2023
                : 13
                : 12 ( doiID: 10.1002/ece3.v13.12 )
                : e10827
                Affiliations
                [ 1 ] Faculty of Science, Institute of Geology and Paleontology Tohoku University Sendai Japan
                Author notes
                [*] [* ] Correspondence

                Soichi Osozawa, KawaOso Molecular Bio‐Geology Institute, Sendai 982‐0807, Japan.

                Email: kawaoso@ 123456icloud.com

                Author information
                https://orcid.org/0000-0001-5554-1320
                Article
                ECE310827 ECE-2023-07-01178.R1
                10.1002/ece3.10827
                10728886
                38116126
                8390bb4b-3845-412c-b3a2-27e572ccd655
                © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 09 October 2023
                : 11 May 2023
                : 28 November 2023
                Page count
                Figures: 5, Tables: 2, Pages: 23, Words: 17980
                Funding
                Funded by: Japan Society for the Promotion of Science , doi 10.13039/501100001691;
                Award ID: 20540441
                Categories
                Global Ecology
                Research Article
                Research Articles
                Custom metadata
                2.0
                December 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.6 mode:remove_FC converted:19.12.2023

                Evolutionary Biology
                base substitution rate,beast v1.10.4,environmental changes,fossil calibration,mammals

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