Alignment and Tree

Alignment of DNA sequences and tree. Nexus format

Parameters of the multi-species coalescent model fit by BPP for nine subclades of <i>Canarium</i>.

<p>Parameters of the multi-species coalescent model fit by BPP for nine subclades of <i>Canarium</i>.</p

Phylogenetic inference and genetic structure analysis for 38 samples of Malagasy <i>Canarium</i>.

<p>(A) Maximum likelihood tree inferred from the min20 dataset with bootstrap support values. Accession IDs are shown alongside taxonomic identifications based on [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198882#pone.0198882.ref011" target="_blank">11</a>]. Many names are paraphyletic, as indicated by grey lines connecting labeled samples. A barplot shows the assignment of individual ancestry to eight genetic clusters. (B) A map of Madagascar with 307 georeferenced <i>Canarium</i> collections shown as grey points. Accessions included in our genomic analyses are indicated by points colored by their genetic cluster assignment. Points from the same location are offset slightly for visualization purposes.</p

Mapping of discrete traits and climatic variables onto a six species tree of Malagasy <i>Canarium</i>.

<p>(A) Suitable dry- and wet-forest habitat for <i>Canarium</i> based on remote sensing data from the Atlas of Madagascar (Royal Botanic Garden, Kew; <a href="http://www.vegmad.org" target="_blank">http://www.vegmad.org</a>). (B) Phylogeny for the six clades favored under our integrative species delimitation analyses. Colored edges on the tree show ancestral reconstructions of climatic preferences based on the first axis from outlying mean index niche separation analyses. (C) Discrete morphological traits are shown with filled circles for (1) leaf pubescence (from light to dark = glabrous, flexuous hairs evenly distributed, erect hairs in tufts, erect hairs distributed evenly); (2) fruit color (from light to dark: maturing green, maturing brown, maturing purple); and (3) stamen position (white = inserted at disk base, black = inserted outside of disc, ? = unknown). (D) Taxonomic labels associated to the six clades supported under our integrative species delimitation approach.</p

Primary concordance tree for ten clades of <i>Canarium</i>.

<p>Pie charts indicate concordance factors (CFs) for each split in the tree relative to conflicting splits from alternative trees. The CF for the clade in the tree is shown in dark grey, CFs for the two best supported conflicting clades are in light gray, and the summed CFs of all other conflicting clades are in white. An asterisk indicates significant support for a split, meaning the 95% confidence interval for its CF does not overlap with any conflicting clade. Taxonomic associations from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198882#pone.0198882.ref011" target="_blank">11</a>] and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198882#pone.0198882.ref013" target="_blank">13</a>] are indicated for each named subclade.</p

Bamboo life cycle of 27–28 y inferred from spatial congruence of mature-stage maps.

<p>(A) Congruence as a function of temporal separation. Each point represents one pair of mapped years of the 33,100 km² study area. (B) Four of the mapped years spanning one full life cycle. Overlying the 2004 map is a hachure showing highly congruent extent of mature bamboo 28 y earlier. Gray is forest with mature bamboo at time of mapping, white is forest with juvenile bamboo hidden in understory, black areas were masked due to clouds.</p

Greenness indicators and topography in the three forest types.

<p>Top graph shows green vegetation fraction (dashed trace) and non-photosynthetic vegetation fraction (solid trace) along the 50 km transect shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054852#pone-0054852-g003" target="_blank">Figure 3</a>. Contacts between forest types are at the gray vertical dashed lines. Bottom graph is the same transect across a digital elevation model, contrasting topography of the hilly eroded landscape having fertile, poorly drained clay soil supporting bamboo-dominated forest and the plateau with infertile sandy latosol that excludes bamboo.</p

Full extent of southwest Amazon bamboo-dominated forests and study locations.

<p>Bamboo extent is based on visual interpretation of two Landsat Geocover mosaics and one MODIS mosaic. Base-map is a hill-shaded Digital Elevation Model from the Shuttle Radar Topography Mission, with gray tones scaled from 0–300 m altitude. Line A-A’ is a topographic profile across the Fitzcarrald Arch, also evident as higher terrain in the inset map. Soils and spectral patterns of forest types were compared at a topographically defined edge of bamboo forest in the small white rectangle, enlarged in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054852#pone-0054852-g003" target="_blank">Figure 3</a>. Life-cycle study was conducted in the large white square. White asterisks are five sites of flowering or fruiting specimens of sarmentose <i>Guadua</i>, where Landsat images confirmed a temporal change in forest canopy spectral patterns from mature to post-reproduction life stage. Flowering specimens from west to east are: <i>Nelson 6026</i> (INPA), June 1995 (<i>Guadua sarcocarpa</i>); <i>Daly et al. 9932</i> (NY), March 1999 (<i>G. weberbaueri</i>); <i>Krukoff 5235</i> (NY), July 1933 (<i>G. sarcocarpa</i>); field observation, flowered in 1988 (<i>G. sarcocarpa</i>); <i>Daly et al. 12144</i> (NY), October 2003 (<i>G. sarcocarpa</i>).</p

Bamboo-dominated forest (cross-hatch) coincides with eutrophic haplic cambisol and luvisol soils (gray).

<p>Inset shows these two fertile soil types are uncommon elsewhere in the Brazilian Amazon. White areas in Brazil on the main map are infertile argisols on dissected surfaces, gleysols along rivers and infertile latosol on low plateaus. Soil map from IBGE and EMBRAPA.</p

Reflectance spectra of three forest types.

<p>Landsat Thematic Mapper band numbers and positions are above the graph. Each vertex is an average of 20 spatially separate samples.</p