DOI: 10.5061/dryad.nk98sf7z3
title: Fossil calibrated molecular phylogenies of Southern cave weta

description: Aim: The biota of continents and islands are commonly considered to have a
 source-sink relationship, but small islands can harbour distinctive taxa.
 The distribution of four monotypic genera within the southern subfamily
 Macropathinae on young oceanic islands indicates a role for long-distance
 dispersal and extinction. We used molecular dating to estimate the timing
 of the southern radiation and infer potential processes involved.
 Location: Subantarctic islands, South Africa, South America, Australia,
 Aotearoa/New Zealand. Taxon: Southern hemisphere camel crickets subfamily
 Macropathinae within the Orthopteran family Rhaphidophoridae (Cave
 crickets/camel crickets/cave weta/tokoriro). Methods: Phylogenetic
 relationships were inferred from whole mtDNA genomes and nuclear sequences
 (45S cassette; four histones). We used a fossil and one palaeogeographic
 event to calibrate a molecular clock analysis. Results: We confirm that
 neither the Australian nor Aotearoa/New Zealand Rhaphidophoridae fauna are
 monophyletic. The Macropathinae radiation may have begun in the late
 Jurassic but trans-oceanic dispersal is required to explain the
 distribution of some lineages within the subfamily Macropathinae. Dating
 the most recent common ancestor of seven island endemic species with their
 nearest mainland relative suggests that each existed long before land
 surface on their island home was available. Main conclusions: If our
 molecular clock analysis is a good time estimate, then our data from the
 island endemic species suggest a failure to sample mainland species (New
 Zealand, Australia, or elsewhere) due to either extinction or lack of
 investment into taxonomy and species discovery.
description: We used high-throughput sequencing of whole genomic DNA to
 assemble entire mitochondrial genomes and multi-copy nuclear markers for
 molecular phylogenetics.
description: Applications needed to access the files are: Excel and Geneious
 prime
description: # Fossil calibrated molecular phylogenies of Southern cave weta This
 README file was generated JAN-2024 by Mary Morgan-Richards. GENERAL
 INFORMATION 1\. Title of Dataset: Fossil calibrated molecular phylogenies
 of Southern cave weta 2\. Author Information ``` A. Name: Eddy J. Dowle
 Institution: University of Otago, NZ B. Name: Steven A. Trewick
 Institution: Massey University Manawatu C. Name: Mary Morgan-Richards
 Institution: Massey University Manawatu, NZ email:
 m.morgan-richards@massey.ac.nz ``` 3\. Geographic location of data
 collection: Southern Hemisphere including sub Antarctic Islands, New
 Zealand, Tasmania, Chile, South Africa SHARING/ACCESS INFORMATION 1\.
 Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0)
 Public Domain 2\. Links to publications that cite or use the data: Dowle
 EJ, Trewick SA, Morgan-Richards (2024). Fossil calibrated phylogenies of
 Southern cave wētā show dispersal and extinction confound biogeographic
 signal. Royal Society Open Science. 3\. Recommended citation for this
 dataset: Dowle EJ, Trewick SA, Morgan-Richards (2024). Data from: Fossil
 calibrated phylogenies of Southern cave wētā show dispersal and extinction
 confound biogeographic signal. Dryad Digital Repository.
 DATA & FILE OVERVIEW We
 used high-throughput sequencing of whole genomic DNA to assemble entire
 mitochondrial genomes and multi-copy nuclear markers for molecular
 phylogenetics. Our sampling of all except two endemic genera of
 Rhaphidophoridae from the New Zealand region and representatives from
 South America, South Africa and Australia allow us to determine
 evolutionary relationships among the New Zealand fauna. Explicitly, we
 tested the hypothesis that members of the genus Macropathus are not part
 of a New Zealand monophyletic clade, despite being endemic to New Zealand,
 and that the Australian taxa are not monophyletic. We also tested the
 suggestion that the New Zealand diversity arose during the Neogene. Using
 molecular calibrations from both fossils and geology (age of land surface
 of Chatham Islands) we infer time since last common ancestor of island
 endemics. If the common ancestor is older than the land surface we can
 infer failure to sample. 1\. File List: A) cave_weta_metadata.xlsx B)
 Rhaps_geneious_alignment_full_cleannames.geneious C) 32CW_13mtdCDS.fasta
 D) 31CW_histones_45_28S.fasta DATA-SPECIFIC INFORMATION FOR:
 cave_weta_metadata.xlsx 1\. table providing list of insect specimens used
 for DNA sequencing with collecting location, date and link to photograph
 2\. Number of variables: 12 3\. Number of cases/rows: 33 4\. Variable
 List: ``` \* code: unique identifier given to insect specimens in this
 study \* Species: genus and species name \* Authority: the author and date
 in which the species was described \* Sub-family: taxonomic hierarchy
 within Rhaphidophoridae \* Region: Geographic region where the specimen
 was collected \* location: narrower geographic region where specimen was
 collected \* Latitude: Geographic region where the specimen was collected
 \* Longitude: Geographic region where the specimen was collected \*
 collector: name of individual or organisation responsible for collecting
 insect specimen \* date: year in which insect specimen was collected \*
 Photograph of specimen iNaturalist: URL of website where photograph of
 insect specimen was uploaded ``` 5\. Missing data codes: None
 DATA-SPECIFIC INFORMATION FOR:
 Rhaps_geneious_alignment_full_cleannames.geneious 1\. Aligned DNA
 sequences of the whole mitochondrial genome including sequences from
 Genbank. Specimen code details are provided in file:
 cave_weta_metadata.xlsx DATA-SPECIFIC INFORMATION FOR: 32CW_13mtdCDS.fasta
 3\. Aligned DNA sequences of all protein coding genes from mitochondrial
 genomes. New data generated for 32 insect specimens using short-read
 illumina DNA sequencing DATA-SPECIFIC INFORMATION FOR:
 31CW_histones_45_28S.fasta 4\. Aligned DNA sequences of nuclear markers.
 New data generated for 31 insect specimens using short-read illumina DNA
 sequencing. DNA sequences from Histone genes H2A, H2B, H3 and H4, and the
 45S Ribosomal cassette (18S,5.8S, 28S) were concatenated