Computational protocol: An elusive Neotropical giant, Hondurantemnachespiritoi gen. n. & sp. n. (Antemninae, Mantidae): a new lineage of mantises exhibiting an ontogenetic change in cryptic strategy

Similar protocols

Protocol publication

[…] We took high resolution photos with a Passport Storm© system (Visionary Digital™, 2012), which included a Stackshot z-stepper, a Canon 5D SLR, macro lenses (50mm, 100mm and MP-E 65mm), three Speedlight 580EX II flash units with initial image processing done on Adobe Lightroom 3.6. Z-stepper was controlled using Zerene stacker 1.04, and images stacked with P-Max protocol. Photos were edited using Adobe Photoshop CC to correct for background noise and to add scale bars. We created illustrations with Adobe Illustrator CC based on high-resolution photos of the structures. We constructed plates with Adobe Illustrator CC. [...] We conducted phylogenetic analyses to test the position of our new taxon using molecular data. The ingroup sample included taxa within Antemninae, Stagmatopterinae, Stagmomantinae, and Vatinae (Table ), which provided coverage across the four major lineages of Neotropical Mantidae. Representative outgroup taxa were included to test the position of our new taxon relative to Acanthopoidea () and African and Asian taxa recovered in close relation to our ingroup (). Representatives of Chaeteessidae and Mantoididae were included to root the phylogeny based on their consistent recovery as the two earliest branches of Mantodea (, , ). We assembled a molecular dataset from previously published works (, , ) and newly generated sequence data (see Table for GenBank accession numbers). The molecular dataset included four genes: the mitochondrial cytochrome oxidase I (COI) and NADH dehydrogenase subunit 4 (ND4) and the nuclear Histone subunits 2 and 3 (H2A and H3). Lab protocols for extraction, amplification, and sequencing followed published procedures (, , ). New sequence data was imported, verified, and aligned along with published data using Geneious alignment on Geneious v7.1.4. The resulting alignment included 3512 characters. We determined the best fit models for each gene using the Akaike Information Criterion implemented in MEGA v.7 (): GTR+Ɣ+I for COI, T92+Ɣ for ND4, HKY+Ɣ for H2A and T92+I for H3. We conducted four independent mixed model Bayesian inference (BI) using MrBayes ver. 3.2.5 (, ). For all BI, each run was started from a random tree. All sampled generations (every 1000) prior to stationarity were discarded (burn-in). The trees sampled from the stationary distribution were summarized as a 50% majority rule consensus tree to find posterior probabilities (PP) (, ). We also performed partitioned maximum likelihood (ML) analysis using RAxML v8 (). Nucleotide substitution parameters were estimated independently from each data partition. One thousand nonparametric bootstrap (BS) pseudoreplicates were performed under a GTR model with CAT approximation of Gamma-distributed among-site rate heterogeneity. Every fifth BS tree was used as a starting tree for more thorough optimization of the real data under GTR+Gamma. FigTree v1.4.2 () was used to visualize topologies and produce figures for both ML and Bayesian analyses. […]

Pipeline specifications

Software tools Adobe Illustrator, Geneious, MEGA-V, MrBayes, RAxML, FigTree
Applications Miscellaneous, Phylogenetics, GWAS
Organisms Mantis religiosa