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      Spatial phylogenetics of the native woody plant species in Hainan, China

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          Abstract

          To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.

          Abstract

          Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated four major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests, natural secondary growth forest at the margins of Hainan, and the nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves).

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

            RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
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              Global patterns and determinants of vascular plant diversity.

              Plants, with an estimated 300,000 species, provide crucial primary production and ecosystem structure. To date, our quantitative understanding of diversity gradients of megadiverse clades such as plants has been hampered by the paucity of distribution data. Here, we investigate the global-scale species-richness pattern of vascular plants and examine its environmental and potential historical determinants. Across 1,032 geographic regions worldwide, potential evapotranspiration, the number of wet days per year, and measurements of topographical and habitat heterogeneity emerge as core predictors of species richness. After accounting for environmental effects, the residual differences across the major floristic kingdoms are minor, with the exception of the uniquely diverse Cape Region, highlighting the important role of historical contingencies. Notably, the South African Cape region contains more than twice as many species as expected by the global environmental model, confirming its uniquely evolved flora. A combined multipredictor model explains approximately 70% of the global variation in species richness and fully accounts for the enigmatic latitudinal gradient in species richness. The models illustrate the geographic interplay of different environmental predictors of species richness. Our findings highlight that different hypotheses about the causes of diversity gradients are not mutually exclusive, but likely act synergistically with water-energy dynamics playing a dominant role. The presented geostatistical approach is likely to prove instrumental for identifying richness patterns of the many other taxa without single-species distribution data that still escape our understanding.
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                Author and article information

                Contributors
                wanghuafeng2012@foxmail.com
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                01 February 2021
                March 2021
                : 11
                : 5 ( doiID: 10.1002/ece3.v11.5 )
                : 2100-2109
                Affiliations
                [ 1 ] Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources College of Tropical Crops Hainan University Haikou China
                [ 2 ] Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Science Guangzhou China
                [ 3 ] Department for Environment and Water State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide SA Australia
                [ 4 ] Departamento de Silvicultura y Conservación de la Naturaleza Facultad de Ciencias Forestales y Conservación de la Naturaleza Universidad de Chile Santiago Chile
                Author notes
                [*] [* ] Correspondence

                Hua‐Feng Wang, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China.

                Email: wanghuafeng2012@ 123456foxmail.com

                Author information
                https://orcid.org/0000-0003-3215-1201
                https://orcid.org/0000-0003-3331-2898
                Article
                ECE37180
                10.1002/ece3.7180
                7920777
                36acfe8d-5325-4730-b0af-ebbd41aacd39
                © 2021 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
                : 17 August 2020
                : 05 December 2020
                : 18 December 2020
                Page count
                Figures: 6, Tables: 0, Pages: 10, Words: 6667
                Funding
                Funded by: Hainan University , open-funder-registry 10.13039/501100005693;
                Award ID: kyqd(zr)1633
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                March 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.9 mode:remove_FC converted:01.03.2021

                Evolutionary Biology
                community assembly,hotspots,island,phylogenetic diversity
                Evolutionary Biology
                community assembly, hotspots, island, phylogenetic diversity

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