Fossil calibrated molecular phylogenies of Southern cave weta
Data files
Jan 27, 2024 version files 894.36 KB
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31CW_histones_45_28S.fasta
201.47 KB
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32CW_13mtdCDS.fasta
359.45 KB
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cave_weta_metadata.xlsx
15.63 KB
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README.md
4.25 KB
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Rhaps_geneious_alignment_full_cleannames.geneious
313.57 KB
Abstract
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.
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. https://doi.10.5061/dryad.nk98sf7z3
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
We used high-throughput sequencing of whole genomic DNA to assemble entire mitochondrial genomes and multi-copy nuclear markers for molecular phylogenetics.
Applications needed to access the files are: Excel and Geneious prime
- Dowle, Eddy J.; Trewick, Steven A.; Morgan-Richards, Mary (2024). Fossil-calibrated phylogenies of Southern cave wētā show dispersal and extinction confound biogeographic signal. Royal Society Open Science. https://doi.org/10.1098/rsos.231118