https://doi.org/10.5061/dryad.18931zd45

Summary

This dataset is comprised of Ultra-conserved element (UCE) sequence data, supplemental metadata about each specimen used, and morphometric measurements used to infer physical traits that exhibit ant-mimetic characteristics.

Ultra-conserved elements are short regions of a genome that retain highly similar structure across even distantly-related taxonomic groups. The "centre" of these elements is the most conserved, with increasing variation in the UCE as you move away from the centre. Because of this characteristic, UCEs produce an excellent phylogenetic signal at both deep and shallow nodes of a phylogeny. We used UCEs to construct both Maximum Likelihood and Bayesian inferences of phylogeny for two separate spider clades.

Description of the data and file structure

Ultra-conserved element (UCE) final alignments

Each taxonomic group (Corinnidae, Salticidae) has its own separate UCE dataset. Each dataset comprises 3 formats: BEAST (.xml), FASTA (.fasta), and NEXUS (.nex). There is no difference between the FASTA and NEXUS alignments apart from the format; the Maximum Likelihood analyses used the FASTA alignments, but the NEXUS format are also included to facilitate data compatibility. The BEAST alignments are a slightly modified set of the previous alignments in XML format, which includes priors and other model parameters used to compute Bayesian phylogenetic inferences.

Corinnidae.fasta
Corinnidae.nex
Corinnidae.xml
Salticidae.fasta
Salticidae.nex
Salticidae.xml

FASTA Format

The data for each individual spans two lines within the file. The first line is always prefixed by a ">" and lists the individual's identifier, usually the taxon name. The next line contains the full concatenated DNA sequence. Each UCE locus was aligned separately prior to concatenation. DNA nucleotides are represented by "A", "T", "C", and "G", with gaps coded as "-".

NEXUS Format

The NEXUS format is more versatile than FASTA, as it separates data into separate "blocks", which can have various attributes and contributions depending on the program reading/writing the data. The data file starts with "#NEXUS"; each block is defined by the "begin" operator, followed by a description of the block type and closed with a semicolon, e.g., "begin taxa;". The data section follows, with an extra line at the end containing only a semicolon to designate the end of the section. The block is completed with "end;". Our data files include two blocks: a taxa block and a characters block. The taxa block contains the name of each taxon in the dataset, and the character block contains the DNA alignments for each specimen. DNA nucleotides are represented by "A", "T", "C", and "G", with missing data coded as "?", and with gaps coded as "-".

BEAST Format

The BEAST format is even more versatile than the NEXUS format, with a similar structure of separate "blocks" to represent different data types or to encode model parameters. Unlike FASTA and NEXUS, it is not meant to be edited manually; rather, data in the file is manipulated using BEAUTi, a graphical interface used to prepare data to be run using BEAST. The same format is used with BEAST and BEAST 2 (and their respective versions of BEAUTi), but XML files produced in one version often have compatibility problems with the other version. Our files are compatible with BEAST 2.

Supplemental information files

Appendix_2__Dataset_S1_-_sample_information.xlsx

This is a Microsoft Excel spreadsheet that lists various metadata associated with each specimen used in this study. There are two tabs, one for Corinnidae, and one for Salticidae. The types of metadata are:

Sample name / Unique I.D.
Author
Sex
Identified by
Voucher Institution
Voucher Collection Identifier / Reg #
CAT # / Tissue.ID Preparation SRA #
Higher Taxon
FAMILY
SUBFAMILY
Country
State Prov Region
County
Specific Locality
Decimal lat
Decimal long
Collection Date
Preservative
DNA extraction method
Approximate total extracted DNA (ng)
Reads Pass QC
Contigs
UCE loci (50% from PHYLUCE; after QC)
Notes
Name used in early phylogenetic work and comparative analyses

Appendix_3__Dataset_S2_-_biometric_measurements.xlsx

This is a Microsoft Excel spreadsheet that lists biometric/morphometric measurements for each each specimen used in this study. There are four tabs: Castianeirinae trait indices, Castianeirinae raw measurements, Myrmarachnini trait indices, and Myrmarachnini raw measurements. The trait indices are:

Sample name / Unique I.D.
Thin_legs
Elong_ceph.
Elong_abdomen
Elong_pedicel
Ill_by_colour
Lat_ceph._const
Dor_ceph._const
Lat_abdominal_const
Dor_abdominal_const
Mimic_accuracy
Level of mimetic accuracy
Extrapolated data (values in red colour font) #Castianeirinae only

The raw measurements are:

Sample name / Unique I.D.
Leg III Femur: width
Leg III Femur: length
Leg III Femur: ratio (width/length)
1 - Leg III Femur ratio
Cephalothorax: width
Cephalothorax: length
Cephalothorax: ratio (width/length)
1 - Cephalothorax ratio
Abdomen: width
Abdomen: length
Abdomen: ratio (width/length)
1 - Abdomen ratio
Pedicel: length
Body length
Pedicel length/body length
Note on illusion by colouration
Illusion by colouration score
Constriction height
Cephalothorax height
Constriction height/Cephalothorax height: ratio
1 - Constriction height/Cephalothorax height: ratio
Constriction width
Cephalothorax width
Constriction width/Cephalothorax width: ratio
1 - Constriction width/Cephalothorax width: ratio
Constriction height
Abdomen height
Constriction height/Abdomen height: ratio
1 - Constriction height/Abdomen height: ratio
Constriction width
Abdomen width
Constriction width/Abdomen width: ratio
1 - Constriction width/Abdomen width: ratio
Mimic Accuracy