The Nylanderia fauna of Vietnam: A morphological and phylogenomic revision (Hymenoptera: Formicidae)
Data files
Jun 15, 2026 version files 106.68 MB
-
Collection_data.xlsx
29.12 KB
-
Measurement_data.xlsx
24.03 KB
-
ML_90p.phylip
23.99 MB
-
ML_90pswsc.charsets
192.23 KB
-
ML_90pswsc.treefile
1.44 KB
-
phased_90p.phylip
58.18 MB
-
phased_90pswsc.charsets
217.39 KB
-
phased_ML_90pswsc.treefile
3.09 KB
-
phased_msc_astral.tre
2.30 KB
-
README.md
3.58 KB
-
unphased_astral_90p.phylip
23.99 MB
-
unphased_astral.charsets
54.42 KB
-
unphased_msc_astral.tre
1.05 KB
Abstract
Vietnam's diverse tropical habitats remain underexplored for ant biodiversity despite being part of the Indo-Burma biodiversity hotspot. This study presents the first detailed taxonomic revision of the ant genus Nylanderia Emery, 1906 in Vietnam, based on a combined approach using morphological characteristics and phylogenomic data. Using targeted enrichment of ultraconserved elements (UCEs) from 18 specimens and extensive morphological assessment of > 200 individuals across all castes, we delimit 11 species from Vietnam. Three species are newly described: Nylanderia camon sp. nov., N. congtroi sp. nov., and N. didactica sp. nov., and one subspecies is elevated to species rank (N. donisthorpei (Forel, 1908) stat. nov.). Our analysis reveals three new country-level records and clarifies the status of morphologically cryptic species through concordant genomic and morphological signals. All known Vietnamese Nylanderia species are diagnosed, with taxonomic accounts provided for each, including high-resolution montage images of all available castes and distribution maps. A revised illustrated key to the worker caste is also presented. This study highlights the utility of UCE-based phylogenetics for species delimitation within morphologically conservative taxa and contributes to a broader understanding of Nylanderia diversity in the Indomalayan region.
Dataset DOI: 10.5061/dryad.7d7wm388c
Description of the data and file structure
A combined morphological and phylogenomic approach was used to revise the taxonomy of the ant genus Nylanderia in Vietnam. Ultra-Conserved Elements (UCE) sequence data were generated from 18 specimens, and phylogenetic reconstruction was performed using the maximum likelihood approach with both phased and unphased data. Species trees were generated from both unphased and phased UCE datasets under the multispecies coalescent (MSC) model using ASTRAL. A detailed description of the methodology, including UCE sequence data generation and phylogenetic reconstruction, is available in the associated manuscript. The PHYLIP files and charsets used for phylogenetic reconstruction, maximum likelihood (ML) phylogeny, and species trees from both unphased and phased data, as well as collection and measurement data of specimens, are available here:
Files and variables
Files include:
Collection and measurement data:
- Collection data: An Excel sheet (Collection_data.xlsx) with locality information for specimens examined in this study.
- Measurement data: An Excel sheet (Measurement_data.xlsx) with measurements of specimens used in this study. All measurements are recorded in millimeters. The value "n/a" indicates that a measurement or collection code was not available. PrW (Propodeal Width) measurements were not taken for queen and male specimens, as wings typically obscure the view of the propodeum in these castes. A complete metadata sheet describing all variables and units is provided in the Excel file.
Ultraconserved Element (UCE) data matrices:
- Maximum likelihood phylogeny (ML) using unphased data: PHYLIP (ML_90p.phylip) and charsets (ML_90pswsc.charsets) used for reconstructing phylogeny with the ML approach, using a 90 % complete matrix retaining 1,818 loci for 33 taxa. Site entropy information from Sliding-Window Site Characteristics (SWSC-EN) was used to inform the partition scheme for the 90 % complete matrix.
- ML phylogeny using phased UCE data: PHYLIP (phased_90p.phylip) and charsets (phased_90pswsc.charsets) used for generating phylogeny with the ML approach of the allelic-phased 90 % complete matrix, retaining 2,051 loci for 66 taxa (33 × 2 alleles).
- Multispecies coalescent (MSC) phylogeny using ASTRAL: PHYLIP (unphased_astral_90p.phylip) and charsets (unphased_astral.charsets) were used for generating the species tree under the MSC model from unphased UCE data without SWSC-EN. A species tree was also generated from the phased dataset with SWSC-EN using phased_90p.phylip and phased_90pswsc.charsets.
Four tree files generated from the above data matrices:
- ML phylogeny generated using IQ-TREE 2 from a 90 % complete, unphased, SWSC-partitioned UCE matrix (ML_90pswsc.treefile).
- ML phylogeny generated using IQ-TREE 2 from a 90 % complete, allelic-phased, SWSC-partitioned UCE matrix (phased_ML_90pswsc.treefile).
- MSC phylogeny generated using the unphased UCE matrix (unphased_msc_astral.tre).
- MSC phylogeny generated using the phased UCE matrix (phased_msc_astral.tre).
Access information
Sequence data
Raw UCE sequence data newly generated in this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra; BioProject ID: PRJNA1347443)