Phylogenetic markers and models of evolution.

<p>* one individual of <i>H</i>. <i>cyaenoviridis</i> has one long indel</p><p>Phylogenetic markers used in the current study and models of evolution applied in Bayesian analyses of the full (128 specimens) and reduced dataset (38 specimens).</p

A. Combined Bayesian half-compatible consensus tree of <i>Horismenus</i> based on mitochondrial and nuclear DNA regions.

<p>The species of parasitoid wasps defined by the Bayesian Poisson tree process coupled with the evolutionary placement algorithm and node supports are represented. Bayesian posterior probabilities and bootstrap support values are displayed below branches. Please see text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136063#pone.0136063.t001" target="_blank">Table 1</a> for abbreviations. <b>B</b>. Barplot of the nucleotide diversities of each species. This analysis does not include information provided by the gaps and species that are not represented have a nucleotide diversity of zero.</p

Tritrophic relationships.

<p><i>Phaseolus species</i>: Depicted at the top of the figure are three wild bean species sorted into categories based on the other beans found in their immediate environment. <i>Phaseolus lunatus</i> with a red background is found on the far left with its sympatric partner, <i>P</i>. <i>vulgaris</i> in green. To their right, <i>P</i>. <i>vulgaris</i> (again in green) is depicted alone as it is found at median altitudes to be in allopatry. This is followed by <i>P</i>. <i>vulgaris</i> (in green) and <i>P</i>. <i>coccineus</i> (in blue) found in sympatry and finally <i>P</i>. <i>coccineus</i> (in blue) alone to represent where it is found in allopatry. <i>Altitude range</i>: Directly beneath these is an altitude measure on the y-axis. The bars indicate the range of altitudes within which each of the above categories was collected. <i>Bruchine species</i>: Beneath this are the most common bruchine beetle speces that attack each one of the <i>Phaseolus</i> categories. <i>Horismenus profile</i>: Photos on the left identify the three species of described <i>Horismenus</i> wasp found emerging from bean seeds. Blue bars indicate emergence from the first field season (2006–7) and pink bars indicate emergence from the second field season (2007–8). Numbers below in gray are the number of emerging wasps from that category for that season. The pink and blue bars are the proportions of each wasp species to emerge from that category in each season and will all add to 1.</p

Locations sampled in Central Mexico.

<p>Locations sampled in Central Mexico with their geographical coordinates. Locations where sampled for bean species (<i>Phaseolus vulgaris</i>, <i>P</i>.<i>coccineus</i> and P. <i>lunatus</i>) and <i>Horismenus</i> parasitoid emergence. Table shows site code for each location, state, bean species present at each location (symp(vc) = sympatric populations of <i>P</i>. <i>vulgaris</i> and <i>P</i>. <i>coccineus</i>; symp(vl) = sympatric populations of <i>P</i>. <i>vulgaris</i> and <i>P</i>. <i>lunatus</i>; allop(c) = allopatric populations of <i>P</i>. <i>coccineus</i>; allop(v) = allopatric populations of <i>P</i>. <i>vulgaris</i> and allop (cult,v) = allopatric population of cultivated <i>P</i>. <i>vulgaris</i>), bean species from which parasitoids emerged, geographical coordinates (altitude, latitude and longitude) and parasitoid species emerging from the beans (B = <i>Horismenus butcheri</i> 1, 2 or 3; D = <i>H</i>. <i>depressus</i>2 and M = <i>H</i>. <i>missourensis</i> 2, or 3.</p

Supplementary Figure 4: Parsimony-based strict consensus of the matK data matrix for the Pleurostylia analysis. Jackknife values ≥ 50% are shown above each branch.

Parsimony-based strict consensus of the matK data matrix for the Pleurostylia analysis. Jackknife values ≥ 50% are shown above each branch

Occurrence of dispersal events through time for Hyacinthaceae inferred by Lagrange.

<p>The lineage through time plot (shown in red and based on the PL-dated consensus tree) is displayed with an estimation of climatic oscillations in blue (estimated from the variation of O₁₈ concentration through time <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039377#pone.0039377-Zachos1" target="_blank">[54]</a>).</p

Posterior probability distributions for the speciation and extinction parameters.

<p>Speciation and extinction shown within a given region (sA and xA, respectively) and the remainder of the distributional range of Hyacinthaceae (sB and xB, respectively) for each area estimated by the GeoSSE analyses for the Hyacinthaceae dataset (see text for more details).</p

Biogeographical scenario of Hyacinthaceae inferred by the Lagrange analysis.

<p>Results are shown for before (A) and after (B) the Mid-Miocene Climate Optimum (16 Ma). Arrows depict dispersal events, whereas circles represent extinction events as estimated by the DEC model. See Fig. 1 for the abbreviations of biogeographical areas.</p

Area definition used to infer the biogeographical scenario of Hyacinthaceae.

<p>Species richness for each area is indicated. The numbers of species per area are based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039377#pone.0039377.s005" target="_blank">Tables S1</a>. B, Madagascar; C, sub-Saharan Africa; D, Cape of South Africa; E, Mediterranean Basin; F, Northern Europe; G, Middle East; H, Asia. Area A corresponds to America and is not represented in this figure.</p

Data_Sheet_1_Biogeography and Ecological Diversification of a Mayfly Clade in New Guinea.PDF

Understanding processes that have driven the extraordinary high level of biodiversity in the tropics is a long-standing question in biology. Here we try to assess whether the large lineage richness found in a New Guinean clade of mayflies (Ephemeroptera), namely the Thraulus group (Leptophlebiidae) could be associated with the recent orogenic processes, by applying a combination of phylogenetic, biogeographic and ecological shift analyses. New Guinean representatives of the Thraulus group appear monophyletic, with the possible exception of a weakly-supported early-diverging clade from the Sunda Islands. Dating analyses suggest an Eocene origin of the Thraulus group, predating by several million years current knowledge on the origin of other New Guinean aquatic organisms. Biogeographic inferences indicate that 27 of the 28 inferred dispersals (96.4%) occurred during the Eocene, Oligocene and Miocene, while only one dispersal (3.6%) took place during the Pliocene-Pleistocene. This result contrasts with the higher number of altitudinal shifts (15 of 22; 68.2%) inferred during the Pliocene-Pleistocene. Our study illustrates the role played by—potentially ecological—diversification along the elevation gradient in a time period concomitant with the establishment of high-altitude ecological niches, i.e., during orogenesis of the central New Guinean mountain range. This process might have taken over the previous main mode of diversification at work, characterized by dispersal and vicariance, by driving lineage divergence of New Guinean Leptophlebiidae across a wide array of habitats along the elevation gradient. Additional studies on organisms spanning the same elevation range as Thraulus mayflies in the tropics are needed to evaluate the potential role of the ecological opportunity or taxon cycles hypotheses in partly explaining the latitudinal diversity gradient.</p