DOI: 10.5061/dryad.6hdr7sr86
title: ‘Picking up signals’ in male genital morphospace and integrating phylogenomics to delimit Neotropical Nylanderia Emery species (Hymenoptera: Formicidae)

description: Genital morphology, a cornerstone in taxonomy that predates
 Linnaeus's Systema Naturae, is vital for species delimitation.
 However, the widely accepted paradigm that genitalia are taxonomically
 informative lacks robust testing between closely related species, and
 supporting evidence is often limited to taxonomic literature in which
 genitalia are assumed a priori to be species-specific. The cosmopolitan
 ant genus Nylanderia Emery includes 125 described species, with most in
 the Neotropics still undescribed. Workers are often morphologically
 cryptic, and males are rare in collections but required for morphological
 delimitation. Using Ultraconserved Elements (UCEs) from 236 samples
 including 50 Neotropical Nylanderia species, we reconstructed phylogeny as
 a framework to compare genitalia (gonopods) of males collected alongside
 workers. We used geometric morphometrics on images of slide mounted
 genitalia from 14 morphospecies and nano-CT scans of Nylanderia fulva
 (Mayr) and Nylanderia pubens (Forel) genital capsules and interpreted
 results considering phylogeny under maximum likelihood and the
 multispecies coalescent. We found strong morphological and molecular
 support for two distantly related American clades, identifiable by gonopod
 shape, with significant differences observed among most species. Three
 previously reported COI clades of N. fulva were not supported as
 monophyletic, nor were their gonopods significantly different. However, N.
 pubens was supported as distinct by all phylogenetic and 3DGM results. Our
 findings emphasize the importance of male genitalia for delimiting species
 boundaries and revising Neotropical Nylanderia. Given their importance,
 particularly in morphologically cryptic taxa, we recommend a greater focus
 on linking male and worker phenotypes, which can be facilitated through
 comprehensive nest series collection.
description: # ‘Picking up signals’ in male genital morphospace and integrating
 phylogenomics to delimit Neotropical *Nylanderia* Emery species
 (Hymenoptera: Formicidae)
 [https://doi.org/10.5061/dryad.6hdr7sr86](https://doi.org/10.5061/dryad.6hdr7sr86) ## Description of the data and file structure The dataset for this study includes molecular and morphological data collected from Neotropical species in the ant genus *Nylanderia *Emery. The molecular dataset includes ultraconserved element (UCE) sequences from 53 species across 236 specimens, including three samples that were used as outgroups. The morphological dataset is comprised of: (1) two-dimensional landmark data for male genitalia (gonopods) from 83 specimens representing 16 species; and (2) three-dimensional models and landmark data for gonopods from 38 specimens representing lineages specifically within the* Nylanderia fulva* (Mayr) complex of species. Further information on bioinformatics, phylogenetic reconstruction, dissection, nano-CT scanning, and geometric morphometric analysis can be found in the associated manuscript, along with details on the sampling methods and the criteria used for species delimitation. Files include: * Three Ultraconserved Element (UCE) data matrices: * **NT-90p (NT-90p.phy, NT90p.charsets):** A 90% complete matrix retaining 1,555 loci for 234 taxa selected to represent American *Nylanderia* species * **clade1-phased (clade1-phased.phy, clade1-phased.charsets):** An allelic phased 90% complete matrix retaining 2,220 loci for 100 taxa selected to represent *Nylanderia* 'American clade I' * **clade2-phased (clade2-phased.phy, clade2-phased.charsets):** An allelic phased 90% complete matrix retaining 1,830 loci selected for 133 to represent *Nylanderia* 'American clade II' * Three tree files generated using the above three data matrices: * **NT-90p (ML-swsc-90p.tre):** Maximum Likelihood phylogeny generated using IQ-TREE 2 on a SWSC-EN partitioning scheme * **clade1-phased (clade1-90p-astral.tre):** Multispecies Coalescent phylogeny generated using ASTRAL-III * **clade2-phased (clade2-90p-astral.tre):** Multispecies Coalescent phylogeny generated using ASTRAL-III * Files used for two-dimensional geometric morphometric (2DGM) analysis of male *Nylanderia* gonopods (n = 83): * **2DGM Landmarking Scheme** (2DGMgonopods.tps) * **2DGM Classifiers File (2DGMclassifiers.csv)** providing species identities from each specimen with two columns for: (1) specimen identification (**'ID'**), referring directly to unique identifiers given to each specimen in the landmarking scheme file; (2) and species identity (**'Species'**) * **R Script** **(2DGMgonopods.R)** to perform 2DGM analysis using the 'geomorph' package * Files used for three-dimensional geometric morphometric (3DGM) analysis of male gonopods (n = 38) from the *Nylanderia fulva* complex: * **3D Models (.stl and .ply format)** of each specimen * **3DGM Landmarking Files (.nts format)** for each specimen * **3DGM Classifiers File  (3DGMspecimens.csv)** providing species identities to each specimen with two columns for: (1) specimen identification (**'specimen_id'**), referring directly to unique identifiers given to each specimen; and (2) species identity (**'species_id'**) * **R Script** **(3DGMgonopods.R)** to perform 3DGM analysis using the 'geomorph' package ## Sharing/Access information Sequence data used to generate the data matrix are deposited in the National Center for Biotechnology Sequence Read Archive ([http://www.ncbi.nlm.nih.gov/sra](http://www.ncbi.nlm.nih.gov/sra); PRJNA1105377, PRJNA728185, PRJNA553590).