Ficus plastid genome alignment

MAFFT alignment of 59 near-complete Ficus plastid genomes and 6 Castilleae plastid genomes as outgroup produced by high throughput sequencing

Bayesian majority-rule consensus tree reconstructed from near-complete plastome sequences for 59 species of Ficus and outgroup.

Bayesian majority-rule consensus tree depicted in Figure 1 and described in publication

Panel plot of fig size (log transformed) against leaf area (log transformed) by fig placement type.

<p>The y-axis represents the residuals after controlling for phylogenetic auto-correlation (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038432#s4" target="_blank">Methods</a>). Dark grey and light grey points represent species with “red” and “green” mature figs, respectively. Relative to axial figs, cauliflorus type (ii) (est = 8.468±3.2355, t = 2.617, <i>p</i> = 0.01147) and geocarpic (est = 4.237±1.5943, t = 2.658, <i>p</i> = 0.01033) figs were significantly larger, figs on species with larger leaves were significantly larger (est = 0.998±0.1843, t = 5.418, <i>p</i> = 0.000001), and there was a significant negative interaction between fig placement and leaf area for cauliflorous type (i) (est = –1.665±0.5972, t = –2.789, <i>p</i> = 0.00729) and geocarpic (est = −0.816±0.2978, t = –2.739, <i>p</i> = 0.00832) species (<i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038432#pone.0038432.s004" target="_blank">Table S3</a></i>).</p

Model results of the analysis of fig colour.

<p>Colour was treated as a binomial response (green = 0, red = 1). We controlled for phylogenetic auto-correlation using Moran’s eigenvectors as covariates (not shown for clarity). Variables included in the analysis were fig placement, breeding system (monoecious, dioecious) and biogeographic region as factors, and fig size (log transformed), plant maximum height (square-root transformed), and maximum leaf area (log transformed) as variates. The optimal model retained just plant max. height and fig placement (Deviance explained = 27.8, Residual deviance = 53.6 on 56 d.f). The factor levels for fig placement are compared with axial figs.</p

Diversity of functional traits in <i>Ficus</i> subgenus <i>Sycomorus</i>.

<p>a) <i>F. variegata</i> reaches up to 40 m high and is often one of the largest trees in secondary forests (man in photograph ∼ 1.5 m tall (face covered to protect identity)). The cauliflorous figs, borne from small nodes, can just be made out on the trunk. b) <i>F. squamosa</i>, rheophytic (river side) shrub up to 1.5 m high with axial figs (inset). c) <i>F. pseudopalma</i> (inset to scale, the man, who is ∼2 m tall, is holding up a dead leaf) has the second largest leaves in the subgenus and is one of only two monopodial (unbranched) species <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038432#pone.0038432-Corner2" target="_blank">[15]</a>. d) <i>F. hispida</i> has cauliflorous figs borne on woody branchlets (cauliflorus type (i)). e) <i>F. cereicarpa</i> is a cauliflorous species with very large figs (∼10 cm diameter). This is a male tree, which bears figs around the base of the tree, as is typical of several other species. Older figs, whose wasps have already emerged, can be seen rotting behind and under bunches of newer figs. f) <i>F. ribes</i> has small cauliflorous figs borne on rope-like stolons (cauliflorus type (ii)). <i>F. semicordata</i>: g) a female tree bearing figs at the base of the trunk and h) male figs buried in the soil. For the latter, the leaf litter and soil were scrapped away to reveal the figs. i) Male fig of <i>F. variegata</i> with non-pollinating wasps (<i>Sycophaga</i> sp.) ovipositing through the wall. The brown dots on other figs in the background are bruises resulting from earlier ovipositor insertions. Cauliflorous figs, like this, are often heavily attacked by non-pollinating wasps, which can significantly reduce pollinator production and thus pollen dispersal.</p

A New Classification of <i>Ficus</i> Subsection <i>Urostigma</i> (Moraceae) Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS), Morphology and Leaf Anatomy

<div><p><i>Ficus</i> subsection <i>Urostigma</i> as currently circumscribed contains 27 species, distributed in Africa, Asia, Australia and the Pacific, and is of key importance to understand the origin and evolution of <i>Ficus</i> and the fig-wasp mutualism. The species of subsection <i>Urostigma</i> are very variable in morphological characters and exhibit a wide range of often partly overlapping distributions, which makes identification often difficult. The systematic classification within and between this subsection and others is problematic, e.g., it is still unclear where to classify <i>F</i>. <i>amplissima</i> and <i>F</i>. <i>rumphii</i>. To clarify the circumscription of subsection <i>Urostigma</i>, a phylogenetic reconstruction based on four nuclear DNA markers (ITS, ETS, G3pdh, and ncpGS) combined with morphology and leaf anatomy is conducted. The phylogenetic tree based on the combined datasets shows that <i>F</i>. <i>madagascariensis</i>, a Madagascan species, is sister to the remainder of subsect. <i>Urostigma</i>. <i>Ficus amplissima</i> and <i>F</i>. <i>rumphii</i>, formerly constituting sect. <i>Leucogyne</i>, appear to be imbedded in subsect. <i>Conosycea</i>. The result of the phylogenetic analysis necessitates nomenclatural adjustments. A new classification of <i>Ficus</i> subsection <i>Urostigma</i> is presented along with the morphological and leaf anatomical apomorphies typical for the clades. Two new species are described ─ one in subsect. <i>Urostigma</i>, the other in <i>Conosycea</i>. One variety is raised to species level.</p></div

Total evidence MCC tree fromBayesian analysis of four DNA markers, morphology and leaf anatomy.

<p>Posterior probabilities (PP) above and bootstrap supports (BS) below the branches.</p

Maximum Clade Credibility (MCC) tree from Bayesian analysis of four combined DNA markers (ITS, ETS, G3pdh, and ncpGS) with posterior probabilities (PP) above and bootstrap supports (BS) below the branches.

<p>Maximum Clade Credibility (MCC) tree from Bayesian analysis of four combined DNA markers (ITS, ETS, G3pdh, and ncpGS) with posterior probabilities (PP) above and bootstrap supports (BS) below the branches.</p

<i>Ficus pseudocaulocarpa</i> Chantaras.

<p>A: Twig with leaves and figs. B: Fig. C: Fig in longitudinal section. D: Staminate flower. E and F: Pistillate flowers.-Drawing: Pajaree Inthachup, 2014.</p

PCR programsadjusted from [1,2,3] as used for each molecular marker.

<p>PCR programsadjusted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128289#pone.0128289.ref001" target="_blank">1</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128289#pone.0128289.ref002" target="_blank">2</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128289#pone.0128289.ref003" target="_blank">3</a>] as used for each molecular marker.</p