Data from: Early colonization of New Caledonia by ultrasonic crickets from New Guinea (Orthoptera: Gryllidae: Eneopterinae): Historical biogeography and description of a new genus
Data files
Apr 28, 2025 version files 3.18 MB
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areas_adjacency.txt
769 B
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areas_allowed.txt
772 B
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BEAST_Eneopterinae.xml
372.20 KB
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Dated_tree.newick
5.69 KB
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dispersal_multipliers.txt
1.54 KB
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Distribution.data
3.23 KB
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Eneopterinae_biogeobears_script.R
44.30 KB
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File_S1.BioGeoBEARS_results.pdf
2.04 MB
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IQTREE2_Eneopterinae_partitions.nexus
479 B
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IQTREE2_Eneopterinae.fasta
328.10 KB
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IQTREE2_Eneopterinae.tre
5.35 KB
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MRBAYES_Eneopterinae.nexus
333.66 KB
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MRBAYES_Eneopterinae.tre
40.76 KB
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README.md
4.54 KB
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timeperiods.txt
16 B
Abstract
New Caledonian crickets of the tribe Lebinthini are renowned for their high endemicity and their use of high-frequency calling songs. While previous studies have found them to originate from New Guinea around 30 Ma, recent discoveries of new lineages of Lebinthini in New Caledonia and in Australia questioned this result. Here, we describe Kanakinthus koniambo Le Flanchec & Robillard gen. et sp.nov., a new genus and species endemic to New Caledonia. We also describe three new species of the endemic genus Agnothecous: A. anonymous Le Flanchec, Vendanger & Robillard sp.nov., A. borendyi Le Flanchec, Vendanger & Robillard sp.nov. and A. kwakwe Le Flanchec, Vendanger & Robillard sp.nov. We include these new taxa and the Australian Lebinthini in a molecular phylogeny of the subfamily Eneopterinae, estimate their divergence times and reconstruct their historical biogeography. Our results confirm the monophyly of the clade endemic to New Caledonia and its origin from a single colonization event from New Guinea, around 30 Ma, shortly after the archipelago completely re-emerged in its current configuration, 34 Ma. We also infer an independent colonization of Australia by the genus Julverninthus from New Guinea, around 25 Ma.
Dataset DOI: 10.5061/dryad.wwpzgmstk
Description of the data and file structure
Scripts, datasets, and results of the phylogenetic and biogeographic analyses
These are the raw results of our biogeographic analyses (File_S1.BioGeoBEARS_results.pdf), the R sript we used (Eneopterinae_biogeobears_script.R), the dated Eneopterinae phylogeny (Dated_tree.newick), the geographic distribution of species (Distribution.data), the time periods (time_periods.txt), the area-adjacency matrix (areas_adjacency.txt), the areas allowed matrix (areas_allowed.txt), the dispersal multipliers matrix (dispersal_multipliers.txt), the sequences we used for our phylogenetic analyses (IQTREE2_Eneopterinae.fasta), the partitions we used (IQTREE2_Eneopterinae_partitions.nexus), the raw maximum likelihood tree (IQTREE2_Eneopterinae.tre), the MrBayes script (MrBayes_Eneopterinae.nexus), the raw bayesian inference tree (MRBAYES_Eneopterinae.tre), and the BEAST script (BEAST_Eneopterinae.xml).
Descriptions
File_S1.BioGeoBEARS_results.pdf
Reconstructions of the historical biogeography of Eneopterinae, for each of the six models implemented in BioGeoBEARS: DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE and BAYAREALIKE+J.
Letters correspond to the eight biogeographic areas we included: New Caledonia, excluding the Loyalty islands (A); Australia (B); New Guinea (C); Indomalaya (D); Palearctic (E); sub-Saharan Africa (F); Neotropics (G) and Southwest Pacific, including the Loyalty islands (H).
Eneopterinae_biogeobears_script.R
The R script we used to carry out historical biogeography analyses with BioGeoBEARS, with sections for each of the six implemented models.
Dated_tree.newick
Dated phylogeny of Eneopterinae, obtained with BEAST. Format is directly compatible with the R script provided here.
Distribution.data
For each species included in the dated phylogeny, presence (1) or absence (0) in each of the eight biogeographic areas included in our historical biogeography analyses.
time_periods.txt
The time intervals we defined for historical biogeography analyses. Unit is millions of years ago (Ma).
areas_adjacency.txt
Area-adjacency matrix, in which we specified which combinations of two areas are allowed in each time slice. We allowed states consisting of two areas only when the areas are either connected by land or separated by shallow water. 1 is allowed, 0 is not.
areas_allowed.txt
Areas allowed matrix, specifying that NC was drowned in the 75–60 Ma time slice and should therefore not be authorized in the analyses.
dispersal_multipliers.txt
Dispersal multiplier matrix for each time slice, with the following dispersal probabilities: 1.0 for areas connected by land, 0.75 for areas separated by shallow water and 0.01 for long-distance-dispersal (LDD).
IQTREE2_Eneopterinae.fasta
Concatenated sequences from eight molecular markers, five mitochondrial markers (COX1, COX2, Cytb, 12S, 16S) and three nuclear markers (18S, 28S, H3), for 85 eneopterine species and 1 outgroup species.
IQTREE2_Eneopterinae_partitions.nexus
Partition file we included in the IQTREE2 analysis, from which ModelFinder found the best partition scheme and the best-fit model for each partition.
IQTREE2_Eneopterinae.tre
Raw output tree from the IQTREE2 maximum likelihood analysis. Branch support was assessed using 1000 Shimodaira-Hasegawa approximate likelihood ratio test (SH-aLRT) replicates and 1000 non-parametric Ultrafast Bootstrap (UFBoot) replicates.
MRBAYES_Eneopterinae.nexus
The script we used for our bayesian inference analysis using MrBayes.
MRBAYES_Eneopterinae.tre
Raw output tree from the MrBayes bayesian inference analysis. Branch support is provided by clade posterior probabilities (PP).
BEAST_Eneopterinae.xml
The script we used for our molecular dating analyses using BEAST.
Code/software
Archives contain .txt and sheet files and R scripts runnable using the package biogeobears.
Phylogenetic data files and scripts can all be opened usign .txt; tre file correspond to phylogenetic trees that can be opened using the software FigTree.
Software versions :
- MrBayes v.3.2.7
- IQTREE2 v.2.2.2.6
- BEAST v.1.10.4
- R v.4.3.0
- BioGeoBEARS v.1.1.3