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      Cradles and museums of generic plant diversity across tropical Africa

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          Summary

          • Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth.

          • Regions containing nonrandom concentrations of young (neo‐) and old (paleo‐) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time‐calibrated mega‐phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs).

          • At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo‐ and paleo‐endemism. By contrast, the Guineo‐Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%).

          • We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large‐scale taxonomically verified distribution datasets and mega‐phylogenies lead to an improved understanding of tropical plant biodiversity evolution.

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          Preserving the evolutionary potential of floras in biodiversity hotspots.

          One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.
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            The age and diversification of the angiosperms re-revisited.

            • It has been 8 years since the last comprehensive analysis of divergence times across the angiosperms. Given recent methodological improvements in estimating divergence times, refined understanding of relationships among major angiosperm lineages, and the immense interest in using large angiosperm phylogenies to investigate questions in ecology and comparative biology, new estimates of the ages of the major clades are badly needed. Improved estimations of divergence times will concomitantly improve our understanding of both the evolutionary history of the angiosperms and the patterns and processes that have led to this highly diverse clade. • We simultaneously estimated the age of the angiosperms and the divergence times of key angiosperm lineages, using 36 calibration points for 567 taxa and a "relaxed clock" methodology that does not assume any correlation between rates, thus allowing for lineage-specific rate heterogeneity. • Based on the analysis for which we set fossils to fit lognormal priors, we obtained an estimated age of the angiosperms of 167-199 Ma and the following age estimates for major angiosperm clades: Mesangiospermae (139-156 Ma); Gunneridae (109-139 Ma); Rosidae (108-121 Ma); Asteridae (101-119 Ma). • With the exception of the age of the angiosperms themselves, these age estimates are generally younger than other recent molecular estimates and very close to dates inferred from the fossil record. We also provide dates for all major angiosperm clades (including 45 orders and 335 families [208 stem group age only, 127 both stem and crown group ages], sensu APG III). Our analyses provide a new comprehensive source of reference dates for major angiosperm clades that we hope will be of broad utility.
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              treePL: divergence time estimation using penalized likelihood for large phylogenies.

              Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST. Source code, example files, binaries and documentation for treePL are available at https://github.com/blackrim/treePL.
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                Author and article information

                Contributors
                leo-paul.dagallier@ird.fr
                Journal
                New Phytol
                New Phytol
                10.1111/(ISSN)1469-8137
                NPH
                The New Phytologist
                John Wiley and Sons Inc. (Hoboken )
                0028-646X
                1469-8137
                02 December 2019
                March 2020
                : 225
                : 5 ( doiID: 10.1111/nph.v225.5 )
                : 2196-2213
                Affiliations
                [ 1 ] DIADE, IRD University of Montpellier 911 Avenue Agropolis 34394 Montpellier France
                [ 2 ] Meise Botanic Garden Nieuwelaan 38 BE‐1860 Meise Belgium
                [ 3 ] AMAP, IRD, CIRAD, CNRS, INRA University of Montpellier Bd de la Lironde 34398 Montpellier France
                [ 4 ] Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) Department of Bioscience Aarhus University Ny Munkegade 114 DK‐8000 Aarhus C Denmark
                [ 5 ] Section for Ecoinformatics and Biodiversity Department of Bioscience Aarhus University Ny Munkegade 114 DK‐8000 Aarhus C Denmark
                [ 6 ] Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR UK
                [ 7 ] Herbarium et Bibliothèque de Botanique Africaine Université Libre de Bruxelles Boulevard du Triomphe B‐1050 Bruxelles Belgium
                [ 8 ] Africa & Madagascar Department Missouri Botanical Garden St Louis MO 631109 USA
                [ 9 ] Laboratoire de Botanique systématique et d'Écologie Département des Sciences Biologiques École Normale Supérieure Université de Yaoundé I BP 047 Yaoundé Cameroon
                [ 10 ] Naturalis Biodiversity Center Darwinweg 2 2333 CR Leiden the Netherlands
                [ 11 ] Evolutionary Biology and Ecology Faculté des Sciences Université Libre de Bruxelles Av. F.D. Roosevelt 50 1050 Brussels Belgium
                Author notes
                [*] [* ] Author for correspondence:

                Léo‐Paul M. J. Dagallier

                Tel: + 33 4 67 41 64 74

                Email: leo-paul.dagallier@ 123456ird.fr

                [*]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-3270-1544
                https://orcid.org/0000-0003-0603-7587
                https://orcid.org/0000-0002-9498-413X
                https://orcid.org/0000-0002-0200-1547
                https://orcid.org/0000-0003-1966-7553
                https://orcid.org/0000-0001-9798-5616
                https://orcid.org/0000-0002-3415-0862
                https://orcid.org/0000-0002-6997-5813
                https://orcid.org/0000-0002-6801-2484
                https://orcid.org/0000-0002-4310-3603
                https://orcid.org/0000-0003-0566-372X
                https://orcid.org/0000-0003-2052-1527
                https://orcid.org/0000-0002-8509-6587
                Article
                NPH16293 2019-30550
                10.1111/nph.16293
                7027791
                31665816
                36453169-3c7f-4f49-800b-cb1fdbb0add9
                © 2019 The Authors. New Phytologist © 2019 New Phytologist Trust

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 04 July 2019
                : 20 October 2019
                Page count
                Figures: 9, Tables: 1, Pages: 18, Words: 12216
                Funding
                Funded by: French Foundation for Research on Biodiversity , open-funder-registry 10.13039/501100003137;
                Funded by: Agence Nationale de la Recherche , open-funder-registry 10.13039/501100001665;
                Award ID: ANR‐15‐CE02‐0002‐01
                Funded by: VILLUM FONDEN , open-funder-registry 10.13039/100008398;
                Award ID: 16549
                Funded by: Independent Research Fund Denmark|Natural Sciences
                Award ID: 6108‐00078B
                Funded by: Belgian Fund for Scientific Research
                Categories
                Full Paper
                Research
                Full Papers
                Custom metadata
                2.0
                March 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.5 mode:remove_FC converted:18.02.2020

                Plant science & Botany
                angiosperms,canape,east africa,endemism,mountains,phylogenetic diversity,protected areas

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