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      A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences

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          Abstract

          Pennantia , which comprises four species distributed in Australasia, was the subject of a monographic taxonomic treatment based on morphological characters in 2002. When this genus has been included in molecular phylogenies, it has usually been represented by a single species, P. corymbosa J.R.Forst. & G.Forst., or occasionally also by P. cunninghamii Miers. This study presents the first dated phylogenetic analysis encompassing all species of the genus Pennantia and using chloroplast DNA. The nuclear ribosomal 18S–26S repeat region is also investigated, using a chimeric reference sequence against which reads not mapping to the chloroplast genome were aligned. This mapping of off-target reads proved valuable in exploiting otherwise discarded data, but with rather variable success. The trees based on chloroplast DNA and the nuclear markers are congruent but the relationships among the members of the latter are less strongly supported overall, certainly due to the presence of ambiguous characters in the alignment resulting from low coverage. The dated chloroplast DNA phylogeny suggests that Pennantia has diversified within the last 20 My, with the lineages represented by P. baylisiana (W.R.B.Oliv.) G.T.S.Baylis, P. endlicheri Reissek and P. corymbosa diversifying within the last 9 My. The analyses presented here also confirm previous molecular work based on the nuclear internal transcribed spacer region showing that P. baylisiana and P. endlicheri , which were sometimes considered synonyms, are not sister taxa and therefore support their recognition as distinct species.

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          We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees--i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.
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            Preservation of Plant Samples for DNA Restriction Endonuclease Analysis

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                Author and article information

                Contributors
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2020
                07 August 2020
                : 155
                : 15-32
                Affiliations
                [1 ] The University of Waikato – School of Science, Private Bag 3105, Hamilton 3240, New Zealand The University of Waikato Hamilton New Zealand
                Author notes
                Corresponding author: Kévin J. L. Maurin ( kjlm1@ 123456students.waikato.ac.nz )

                Academic editor: James W. Byng

                Article
                53460
                10.3897/phytokeys.155.53460
                7428460
                Kévin J. L. Maurin

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Funding
                Funded by: University of Waikato 100010061 http://doi.org/10.13039/100010061
                Categories
                Research Article
                Apiales
                Icacinaceae
                Phylogeny
                Cenozoic
                Australasia
                Australia
                New Zealand

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