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Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers - PubMed

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Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers

Barbara Turner et al. Mol Phylogenet Evol. 2013 Dec.

Abstract

To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK-matK and trnS-trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9 million years ago. The oldest species are around 7 million years old and the youngest ones probably much less than 1 million years.

Keywords: Endemism; Genome size; Island flora; Low-copy nuclear markers; Molecular dating.

Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

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Figures

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Graphical abstract
Supplementary Figure 1
Supplementary Figure 1

Dated phylogeny of Ericales based on the a joint matrix the data set of Bell et al. (2010) together with our plastid sequences. Taxa from families other than Ebenaceae are collapsed to family level, taxa other than Diospyros are collapsed to generic level. Multiple accessions of a species are collapsed to species level. The NC clade III part of the tree is mostly collapsed due to lack of support of respective nodes. Nodes which were calibrated with fossils are marked with a black dot. Yellow bars represent the 95% highest posterior density interval. New Caledonian taxa are coloured, red represents clade III NC.

Fig. 1
Fig. 1

Examples of Diospyros species from New Caledonia (A–N) and Map of New Caledonia with collection points (O). A: D. vieillardii; B: D. umbrosa; C: D. flavocarpa, D: D. labillardierei; E: D. pancheri, F: D. veillonii; G: D. minimifolia; H: D. pustulata; I: D. cherrieri; J: D. parviflora; K: D.perplexa; L: D. yaouhensis; M: D. revolutissima; N: D. glans; O: Map of New Caledonia with sampling localities. Photographs taken by: C. Chambrey (I), V. Hequet (F, K, L), J. Munzinger (A, B, C, E, G, H, J, M, N) and B. Turner (D).

Fig. 2
Fig. 2

Schematic diagram of exon 7–exon 11 of ncpGS with primer positions and length of exons and introns. Numbers in parentheses give 5′ end of primers.

Fig. 3
Fig. 3

Schematic diagram of exon 1 of phyA with primer positions and length of exon. Numbers in parentheses give 5′ end of primers.

Fig. 4
Fig. 4

One of 210 equally parsimonius trees of the plastid data set. Clades are named according to Duangjai et al. (2009). Bold branches have more than 70% support in all three analysis. New Caledonian taxa are coloured, red represents clade III NC.

Fig. 5
Fig. 5

Maximum parsimony trees inferred from the nuclear data sets, branch length scaled to same value on both trees. Bold branches have more than 70% support in all three analysis. New Caledonian taxa are coloured, red represents clade III NC. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 6
Fig. 6

Baysian maximum clade credibility tree inferred from the combined data set. Bold branches have more than 70% support in all three analysis, nodes with at least one support value ⩾70% are indicated with blue dots (BPP/BMP/BML). New Caledonian taxa are coloured, red represents clade III NC. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 7
Fig. 7

Chronogram based on the combined data set. Ages are given (in million years) for nodes with more than 0.85 BPP. Nodes which were calibrated are marked with a black dot. Yellow bars represent the 95% highest posterior density interval. New Caledonian taxa are coloured, red represents clade III NC.

Fig. 8
Fig. 8

Boxplot of genome size differences between taxa from clade III and those from clades VII–XI.

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