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Fig. 5 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 5. Species tree and species delimitation in the Cryptopone gilva complex.The species tree was inferred using SNP data and the Bayesian program SNAPP, with the resulting tree set displayed using DensiTree.The SNAPP densitree shows at least four clearly differentiated species-level lineages. Species delimitation using the programs BPP, SODA, and bPTP, recovered between 4 and 17 species.The results for the UCE samples only are mapped onto the SNAPP densitree result. The connected red bars represent single species that were not monophyletic in the SNAPP phylogeny. The colored boxes and blue species names represent the final species delimitation and taxonomy.

Fig. 3. Relationships among samples within the C in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 3. Relationships among samples within the C. gilva complex based on analysis of 2,199 UCE loci and the SWSC-EN partitioning scheme. Four main clades were recovered and these were delimited as species using an integrative approach. Support values are UFB/SH-aLRT with maximum supports (100/100) not shown.The photo inset is of C. guatemalensis (CASENT0646802; Credit: John Longino).The same tree with support values is available in Supp Fig. 2 (online only).

Fig. 15 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 15. Holotype of Wadeura holmgrenita (CASENT0637779), lateral and dorsal views. Scale is the same for both images.

Fig. 19–26 in Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera:

Fig. 19–26. Pseudomyrmex elongatulus group: distribution maps. 19, P. apache; 20, P. arcanus (circles), P. fasciatus (triangles); 21, P. championi; 22, P. capillatus (triangles), P. cognatus (circles); 23, P. elongatulus (circles), probable introduced populations (stars); 24, P. comitator (square), P. ereptor (triangle), P. exoratus (circles); 25, P. salvini; 26, P. nimbus (circles), P. veracruzensis (triangle).

opencc-zeroDec 2023View details →

dryad32/100

Phylogenetic relationships and divergence dating of Mantodea using mitochondrial phylogenomics

Mantodea is a predatory insect group, its members occupying a diverse array of widely distributed habitats. Praying mantis species utilize hunting strategies including remarkable mimicry and unique camouflage for hiding from natural enemies while catching their prey. The emergence of a "cyclopean ear" in mantises is thought to be a morphological innovation of the group, and an "arms race" with echolocating bats is one of the hypotheses put forward to account for the emergence of the mantis ear from a coevolutionary perspective. However, this hypothesis has not been rigorously tested because of a lack of robust higher‐level phylogeny and a detailed chronogram of Mantodea. Previous phylogenetic studies found an incongruence between traditional classification and molecular phylogenetics due to the convergent evolution of various ecomorphic strategies of the lineage. Here, we performed a comprehensive phylogenetic analysis of Mantodea based on data from 61 mitogenomes. Our analyses showed that the monophyly of Acanthopidae, Haaniidae, Nanomantidae, Miomantidae and Mantidea was supported. The newly updated Gonypetidae were paraphyletic, whereas Eremiaphilidae, Deroplatyidae and Toxoderidae were polyphyletic. Our molecular dating analyses inferred that Spinomantodea originated at ca. 149 Ma (Late Jurassic), whereas the origin of hearing mantises (Cernomantodea) was inferred as Early Cretaceous (119 Ma, 95% CI: 110–129 Ma). The molecular dating results indicated that the hearing organ in mantises did not arise in response to bat predation. Our study provides a robust framework for further evolutionary comparative studies of mantises.

opencc-zeroJan 2024View details →

Supplementary material 2 from: Du W, Wang Y, Xie D, Li E, Bai Y, Shang C, Zhang Z (2024) Phylogenomics reveal Populus gonggaensis as a hybrid between P. lasiocarpa and P. cathayana (Salicaceae). PhytoKeys 237: 161-177. https://doi.org/10.3897/phytokeys.237.103012

Species tree of 57 samples of the genus Populus constructed by IQ-TREE, based on high-quality SNPs data with an outgroup of P. euphratica, using the sliding window method

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-4.0Jul 2024View details →

Data from: A densely sampled nuclear phylogenomic analysis of the coryphoid palms (Arecaceae − Coryphoideae)

Data from: Wrisberg, O, Petoe, P, de Lima Ferreira, P, Bacon, CD, Barfod, AS, Bellot, S, Cano, Á, Couvreur, TLP, Dransfield, J, Henderson, A, Stauffer, F, Baker, WJ, Eiserhardt, WL (in review) A densely sampled nuclear phylogenomic analysis of the coryphoid palms (Arecaceae − Coryphoideae) This repository is meant to provide the most important data outputs produced by the Pipeline created for this project. The analysis pipeline is located on github (https://github.com/pebgroup/coryphoideae_species_tree). Raw data can be found on the NCBI Sequence Read Archive.  The data folder is divided into the following subfolders: 01_unaligned_sequences_per_specimen This folder contains the unaligned sequences for each specimen. The sequences are named after the specimen number. 02_unaligned_sequences_per_gene This folder contains the unaligned sequences for each gene. The sequences are named after the gene name. 03_aligned_sequences_per_gene This folder contains the sequences aligned by MAFFT for each gene. The sequences are named after the gene name. 04_gene_trees This folder contains the gene trees for each gene. The trees are named after the gene name. The subfolder subset_single_copy_gene_trees contains copies of the gene trees for the single copy genes. 05_species_trees This folder contains the species trees. The subfolder all_genes contains the species trees based on all genes, while the subfolder single_copy_genes contains only the species trees based on the single copy genes. 06_supporting_information This folder contains a list which contains the associations between tip names and specimen numbers and a list of the single-copy genes.

Fig. 7 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 7. Simplified phylogeny of the seven tribes of Ichneumoninae according to the new classification proposed in this study. The genera Pseudalomya and Groenlabus Jussila are treated as incertae sedis within Ichneumoninae.

Fig. 6 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 6. Ancestral state reconstruction for oxypygous (blue) vs. amblypygous (red; including also 'semi-amblypygous') metasoma based on stochastic character mapping. The diagram corresponds to a density tree with the consensus of 10 000 simulated histories, with each iteration based on the relative probabilities for each state at each node, as estimated from a likelihood-based algorithm. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 5 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 5. Phylogeny of Ichneumonini as recovered with the matrix with 50% completeness partitioned by PartitionFinder. Numbers correspond to bootstrap support; nodes with no numbers indicate 100% clade support. [Colour figure can be viewed at wileyonlinelibrary.com].

opencc-zeroOct 2021View details →

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Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of diversification and colonization of Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by noise and non-phylogenetic signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to be a major cause of noise, whereas, for exons, non-phylogenetic signal may be caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

Fig. 8 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 8. Morphological diversity in mandible width and orientation, clypeus outline and malar space length. These character systems were historically used to define supra-generic groups, but our results indicate that these trait were subject to multiple events of convertent evolution. (A) Alomya semiflava; (B) Platylabus berndi; (C) Ichneumon heterocampae; (D) Phaeogenes ophthalmicus; (E) Compsophorus seyrigi; (F) Charitojoppa crassipina; (G) Ischnojoppa seyrigi; (H) Neotypus nobilator; (I) Trogomorpha trogiformis; (J) Goedartia alboguttata; (K) Pseudomaraces birmanica; (L) Ceratojoppa cornuta; (M) Oedicephalus striatus; (N) Joppa linearis; (O) Tetragonochora sp. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 4 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 4. Phylogeny of Ichneumoninae as recovered with the matrix with 50% completeness partitioned by PartitionFinder. Numbers correspond to bootstrap support; nodes with no numbers indicate 100% clade support. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 2 in Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) reveals pervasive morphological convergence and the shortcomings of previous classifications

Fig. 2. Metasomal apex in Ichneumoninae, shown in lateral (A–C) and ventrolateral (D–F) views. A, D, Aoplus confirmatus, an oxypygous species. B, E, Eutanyacra suturalis, an amblypygous species. (C, F) Thyrateles lugubrator, a 'semi-amblypygous' species. [Colour figure can be viewed at wileyonlinelibrary.com].