DOI: 10.5061/dryad.b2rbnzst2
title: Exploring the phylogeny of the Leptanillinae (Hymenoptera: Formicidae) through high-throughput sequencing and Bayesian total-evidence inference, with accommodation of systematic bias

description: Ants of the subfamily Leptanillinae (Hymenoptera: Formicidae) are minute
 and subterranean, with taxonomy impeded by the dissociation of disparate
 male and female forms. The advent of phylogenomic inference can remedy
 this dissociation while resolving leptanilline phylogeny with strong
 statistical support. However, genome-scale molecular data are vulnerable
 to systematic biases that may result in decisive statistical support for
 erroneous conclusions, and previous phylogenomic study of the
 Leptanillinae did not address this, nor attempted to resolve the
 phylogenetic positions of the several aberrant leptanilline lineages for
 which UCEs cannot be obtained. I query the phylogeny of the Leptanillinae
 from ultra-conserved elements (UCEs) using a Bayesian framework and
 mitigate the effects of several potential systematic biases by replicating
 analyses using multiple curated UCE alignments. In addition, I implemented
 Bayesian total-evidence inference from UCEs and male morphological data to
 resolve the phylogenetic positions of the monotypic former
 genus Scyphodon and three other enigmatic terminals for which
 molecular data are unavailable. The phylogeny of the Leptanillinae
 inferred herein is robust to compositional biases in phylogenomic data.
 The synonymy of Scyphodon with Leptanilla is confirmed, with the
 former being recovered within the Leptanilla havilandi species-group with
 high Bayesian posterior probability, but the phylogenetic positions of the
 remaining three morphology-only terminals were unresolved by Bayesian
 total-evidence inference due to insufficient availability phylogenetic
 information or inferential artifacts.
description: # Exploring the phylogeny of the Leptanillinae (Hymenoptera: Formicidae)
 through high-throughput sequencing and Bayesian total-evidence inference,
 with accommodation of systematic bias ## Description of data and file
 structure The phylogeny of the Leptanillinae was inferred under
 model-based statistical frameworks from 5 curated alignments of
 ultra-conserved elements (UCEs), which were generated from contigs in
 phyluce v. 1.7.1. Contigs were assembled in SPAdes. Each of these 5
 alignments was trimmed for potential misalignment using Spruceup across a
 range of 4 predetermined lognormal cutoff thresholds, resulting in 25
 alignments inclusive of those that were untrimmed in Spruceup.
 Maximum-likelihood phylogenetic inference was implemented in IQ-Tree v.
 2.2.2.5, and coalescent-based inference in ASTRAL-III, using all 25
 alignments. Bayesian phylogenetic inference was implemented in ExaBayes v.
 1.5.1 for the 5 alignments trimmed with lognormal cutoff = 0.90 in
 Spruceup. Bayesian total-evidence inference was implemented in RevBayes v.
 1.2.2 using a subsampled version of Matrix 0.90B and 65 binary male
 morphological characters. Scripts used for Bayesian inference are
 presented on Zenodo (10.5281/zenodo.16781993). --- ## Data location Raw
 sequence reads are stored in the following locations: NCBI, PRJNA629360:
 *"Systematic revision of the ant subfamily Leptanillinae
 (Hymenoptera: Formicidae) grounded in phylogenomic inference"* NCBI,
 PRJEB48742: *"Ant phylogenomics reveal a natural selection hotspot
 preceding the origin of advanced eusociality"* NCBI, PRJNA379583:
 *"Phylogenomic insights into the evolution of stinging wasps and the
 origins of ants and bees"* NCBI, PRJNA360290: *"Enriching the
 ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of
 ants and other Hymenoptera"* NCBI, PRJNA759281: *"Systematics
 and biogeography of Dorymyrmex (Hymenoptera: Formicidae)"* NCBI,
 PRJNA248919: *"Hymenopteran UCE sequences"* Hymenoptera Genome
 Database:
 *([https://hymenoptera.elsiklab.missouri.edu/](https://hymenoptera.elsiklab.missouri.edu/))* Additional data used in this study are cited in Table S1 of Romiguier et al. (2022) ([https://www.cell.com/current-biology/fulltext/S0960-9822(22)00760-6](https://www.cell.com/current-biology/fulltext/S0960-9822\(22\)00760-6)). --- ## Analytical software Programs numbered in each workflow according to order of use. ### Maximum-Likelihood Phylogenomics, concatenated ``` **1. PartitionUCE * SWSC-EN **2. IQ-Tree v. 2.2.2.5 ** ModelFinder ``` PartitionUCE was not used for by-locus partitioning. All analysis parameters for **2** (*.log*) are located in Phylogenomics\ML\by-locus or Phylogenomics\ML\within-locus. ### Two-Step Coalescent-based Inference ``` **1. IQ-Tree v. 2.1.2 **2. #### ASTRAL-III * λ = 0.5 ``` All analysis parameters for **2** (*.log*) are located in Phylogenomics\ML\SH-aLRT. ### Bayesian Phylogenomics ``` **1. PartitionUCE * SWSC-EN **2. IQ-Tree 2.2.2.5 ** ModelFinder **3. ExaBayes v. 1.5.1 ** consense * threshold = 50 * burnin value = 0.25 ``` All analysis parameters for **2** are located under Phylogenomics\ML\within-locus\ for Matrices 0.90A-C, E (*.log*); and under Phylogenomics\ML\by-locus\IQT_by-locus_0.90D.log for Matrix 0.90D. All analysis parameters for **3** are located in the configuration file EB_1e6.conf. ### Total-Evidence Bayesian Phylogenetic Inference ``` **1. IQ-Tree v. 2.2.2.2 **2. spruceup.py **3. IQ-Tree 2.1.2 **a. ModelFinder **4. genesortR **5. RevBayes v. 1.2.2 ``` All analysis parameters for **3** are located in Phylogenomics\ML\SH-aLRT\gene_trees_0.90B.log. All analysis parameters for **5** are located in TE_phylogeny_no-partitioning.rev. ***Folder list*** **For all folder contents, see respective readme.md files contained within each folder** ### anomaly_finder_output.zip #### File: readme.md ### Folder: data.zip #### File: readme.md ### Folder TE_output.zip #### File: readme.md ### Folder: Phylogenomics.zip #### Folder: Bayesian ##### File: readme.md #### Folder: ML ##### File: readme.md #### Folder: coalescent-based ##### File: readme.md