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Figure 2 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters

Figure 2. Allele size distribution of Euglossa viridissima- like males from the Yucatán peninsula, Mexico, at the microsatellite locus ann02. Overall, bidentate males (grey bars) had significantly smaller allele sizes than tridentate individuals (black bars), and there was little overlap in allele size. The seven individuals indicated as red circles were also tridentate, but had been clustered with bidentate males in the analysis of perfume similarity (see Fig. 1), lacking HNDB. These seven individuals had the third (central) mandibular tooth significantly displaced towards the tip of the mandible (nearer to the distal tooth, see Fig. 3B), unlike in other tridentate males. Their ann02 allele size suggests that they in fact belong to the bidentate lineage. See text for further explanation.

Figure 4 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters

Figure 4. Results of a PCA of 15 morphological variables measured in male Euglossa viridissima and Euglossa dilemma sp. nov. Components 1 and 3, which showed significant differences between the species, are used for this two-dimensional representation. Note that E. dilemma shows slightly less variability and is essentially nested within E. viridissima morphospace. Centroids of distributions are shown.

Figure 3. A in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters

Figure 3. A, Euglossa viridissima-like males attracted to a bait dish at Xmatkuil, Yucatán, Mexico. B, mandibular morphology of males of tridentate Euglossa dilemma sp. nov., and tridentate and bidentate males of E. viridissima. The position of the central mandibular tooth in tridentate individuals is expressed as the ratio of the distance between the distal and the central tooth to the distance between the central and the basal tooth. Means and standard deviations are given.

Figure 1 in Characterization of the orchid bee Euglossa viridissima (Apidae: Euglossini) and a novel cryptic sibling species, by morphological, chemical, and genetic characters

Figure 1. Differences in the chemical composition of tibial perfumes between tridentate (black circles) and bidentate (grey circles) Euglossa viridissima-like males as revealed by a multidimensional scaling (MDS) analysis. Only tridentate males contained HNDB. Tridentate males without HNDB are highlighted (red symbols).

FIGURE 1. Cephalanthera yintiaolingensis. A in Cephalanthera yintiaolingensis (Orchidaceae, Epidendroidee, Neottieae), a new mycoheterotrophic orchid from Northeast Chongqing, China

FIGURE 1. Cephalanthera yintiaolingensis. A) Habitat; B) Habit; C) front view of a flower; D) anatomy of a flower; E) side view of lip and column; F) dorsal view of colume; G) side view of column; H) ventral view of column. A, B and C photographed by Feng Chen, others photographed by Chi Xiong.

FIGURE 2 in Epidendrum scandens: an unusual new orchid species endemic to the Cordillera de Talamanca in Costa Rica

FIGURE 2. Distribution of Epidendrum scandens based on the only specimens currently known of this species.

FIGURE 1 in Epidendrum scandens: an unusual new orchid species endemic to the Cordillera de Talamanca in Costa Rica

FIGURE 1. Lankester Composite Dissection Plate of Epidendrum scandens. A. Habit. B. Inflorescence with flower in 3/4 view. C. Inflorescence with flowers in frontal view. D. Perianth dissected. E. Ovary, column and lip in lateral view and longitudinal section. F. Ovary and column in ventral (left) and lateral (right) views. Photographs by A.P. Karremans, LCDP by G. Rojas-Alvarado based on the type.

FIGURE 3 in Epidendrum scandens: an unusual new orchid species endemic to the Cordillera de Talamanca in Costa Rica

FIGURE 3. Epidendrum scandens in situ. A. Plants growing over the understory plants and soil organic matter (Chinchilla et al. 5284). B. Closeup of the scandent growth of the stems (Karremans & Contreras Fernández 9012). Photographs by I. Chinchilla (A) and A.P. Karremans (B).

opennotspecifiedDec 2023View details →

FIGURE 3 in Serendipita officinale sp. nov. (Serendipitaceae): a new species of orchid mycorrhizal fungus

FIGURE 3. Phylogenetic tree based on LSU sequences of Serendipita and related Sebacinaceae species. Ceratosebacina calosporawas included as an outgroup. The numbers at each branch represented Bayesian posterior probabilities (left) (≥ 0.5 are shown) and bootstrap support calculated from 1000 replicates (right) (≥ 50% are shown). Note that the name Serendipita vermifera is given to a wide range of different Serendipita samples. in the literature. See Table S1 for a complete description of GenBank accessions used in the analysis.

opennotspecifiedDec 2023View details →

FIGURE 1 in Serendipita officinale sp. nov. (Serendipitaceae): a new species of orchid mycorrhizal fungus

FIGURE 1. Morphological features of Serendipita officinalesp. nov. a, b: Colonies on PDA after 14 and 30 days; c: aerial mycelium; d: Transmission electron micrograph showing monilioid hyphae with a septate (arrows); e: DAPI-stained hyphae (n = nuclei; S = septa); f & g: Micrograph and scanning electron micrograph of hyphae on the agar surface showing typical hyphal coils; h: Branched monilioid cell chains under microscope; i: Monilioid hyphae under scanning electron micrograph; j: Scanning electron micrograph showing chlamydospores in the roots of Dendrobium officinale; k: Micrograph showing chlamydospores in the roots of Dendrobium flexicaule. l: Transmission electron micrograph of the dolipore septum with a flat and imperforate parenthesome (arrow) as typical for members of the Sebacinales.

opennotspecifiedDec 2023View details →

FIGURE 2 in Serendipita officinale sp. nov. (Serendipitaceae): a new species of orchid mycorrhizal fungus

FIGURE 2. Phylogenetic tree based on ITS sequences of Serendipita and related Sebacinaceae species. Tremiscus helvelloides was included as an outgroup. The numbers at each branch represented Bayesian posterior probabilities (left) (≥ 0.5 are shown) and bootstrap support calculated from 1000 replicates (right) (≥ 50% are shown). Note that the name Serendipita sp. is given to a wide range of different Serendipita spp. in the literature. See Table S1 for a complete description of GenBank accessions used in the analysis.

Fig. 5 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 5. Color phenotypes and phyloheatmap of the morphological characters of E. meriana and E. atleticana, visualized using the (A) mtDNA and (B) UCE phylogenies. Circles at the end of individual names indicate the color phenotype of that individual. Names above the phyloheatmaps indicate the character that was measured. BL, Body length; HW, Head width; ID, Intertegular distance;WTII,Width of colored bands on tergum II; WTIII,Width of colored bands on tergum III. In this phyloheatmap, each column of the measured characters was standardized to have the same variance prior to analysis.The scale below indicates how much each value deviates from the mean.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.

Fig. 4 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 4. Chronogram of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated using BEAST2 and 500 UCE loci. All nodes had a posterior probability of 1. The arrow indicates the node used for calibration of the tree and acronyms correspond to geographic regions outlined in Fig. 1. CA, Central America; CR, Choco Region; AM, Amazon Forest; AF, Atlantic Forest. In the calibration point, M = mean age, and S = confidence interval.

Fig. 2 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 2. Phylogenetic relationships of the E. meriana and E. bombiformis species complexes based on (A) mitochondrial data (mtDNA; CO1 and Cytb) and (B) ultraconserved elements (UCE; 2022 loci). The mtDNA phylogeny was estimated using Bayesian inference in BEAST2, posterior probabilities on nodes were all above 0.9 except for nodes with asterisks (*). The UCE phylogeny was estimated with maximum likelihood using IQ-TREE and a concatenated 100% completeness matrix. Support values on nodes indicate ultrafast bootstrap (UFB) and SH-like (SH) approximate likelihood ratio test scores (SH-aLRT). All support values were above 95/95 except for nodes indicated with asterisks (* or **). One of the E. cingulata individuals (TA12) was pruned to improve the cophylogenetic visualization.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.

Fig. 1 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 1. Geographic distribution of the different color phenotypes in the E. meriana and E. bombiformis species complexes. (A) Colored areas in the map indicate approximate distribution for both species complexes as well as the different areas that correspond to lineages recovered in López-Uribe et al. (2014), including Central America (green), Choco region (orange), Amazon Forest (blue), and Brazilian Atlantic Forest (pink). (B) Photos of color phenotypes are shown for each species and the geographic region in which that phenotype is present. Photos of E. meriana and E. bombiformis by NashTurley, photos of E. niveofasciata and E. atleticana by Marcelo de Oliveira Gonzaga.

Fig. 3 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 3. Maximum clade credibility (MCC) species tree of the phylogenetic relationships in the E. meriana and E. bombiformis species complexes estimated under the multi-species coalescent model (MSC) using *BEAST in BEAST2.The species tree was estimated using the 50 most informative UCE loci from the 100% completeness dataset. Nodes without labels had posterior probabilities <0.5.The colors of the clades correspond to geographic regions outlined in Fig. 1. Green: Central America, Orange: Choco region, Blue: Amazon Forest, and Pink: Atlantic Forest.

Fig. 6 in Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Fig. 6. Scatterplots of first against second principal component of the morphological measurements of the (A) E. bombiformis and (B) E. meriana complexes. Insets display boxplots of the first principal component between groups outlined by geographic regions: CA, Central America (Green); CR, Choco Region (Orange); AM, Amazon Forest (Blue); AF, Atlantic Forest (Pink). The letters above boxplots represent groups that are statistically differentiated after a Tukey′s honest significant test. Colors represent individuals grouped by geographic regions.

opencc-by-4.0May 2024View details →

Code and Data for manuscript "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes"

Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation -------- This repository contains all the R code used in the manuscript: * Title: "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation" * Authors: Anais Gibert, Schatz Bertrand, Buscail Roselyn, Dominique Nguyen, Baguette Michel, Bartes Nicolas and Joris Bertrand * Year of publication: 2024 * doi: https://doi.org/10.1101/2024.03.21.586062   Synopsis of the study -------- <ul> <li> Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape. </li> <li> Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation. </li> <li> We identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor. </li> <li> This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes. </li> </ul>   Running the code -------- Here we present the data and code for carrying out the analyses, as well as the figures and tables from the article and the supplementary material. Once you have installed the necessary packages, run the commands in 'analysis_share.R'. This script uses several functions available in the '/R' directory. Figures and tables are produced in a 'manuscript/figures' and 'manuscript/tables' directory.  The `/data' directory contains the data used in the analyses (data/input or data/output), but also the resulting datasets produced by the code (data/RData/).

opennotspecifiedNov 2021View details →

FIGURE 2 in Cremastra saprophytica (Orchidaceae: Epidendroideae), a new leafless autonomously self-pollinating orchid species from Gifu Prefecture, Japan

FIGURE 2. Cremastra saprophytica (holotype). A. Habit. B. Pseudobulb with roots and a coralloid mycorrhizal rhizome; arrow points to mycorhizome. C. Flower, dorsal view. D. Lip. E. Dorsal sepals. F. Lateral sepals. H. Column (lateral, ventral and dorsal views). I. Close-up of the upper part of the lip (lateral and dorsal views). J. Close-up of the upper part of the column (lateral, ventral and dorsal views); arrow points to contact between pollinia and stigma. Scale bars: A = 10 cm; B–H = 1 cm; I–J = 5 mm.