Data from: Pleistocene sea-level fluctuation shapes archipelago-wide population structure in the critically endangered Lord Howe Island cockroach Panesthia lata
Data files
May 12, 2026 version files 48.02 MB
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Adams.etal.SNP_data.csv
47.89 MB
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Figure3_raw.tre
1.19 KB
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Figure4_raw.tre
63.40 KB
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FigureS6_raw.tre
62.73 KB
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FigureS8_raw.tre
2.24 KB
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README.md
3.95 KB
Abstract
The Lord Howe Island Group (LHIG) is one of Australia’s most renowned archipelagos. Although several studies have investigated the biogeography and genetic diversity of species on Lord Howe Island (LHI) itself, the evolutionary distinctiveness of populations across LHI’s satellite islets remains poorly understood. In this study, we explored the genetic structure and health of the critically endangered, endemic cockroach Panesthia lata across four islands of the LHIG, using a panel of nuclear single-nucleotide polymorphisms and complete mitochondrial genomes. Our analyses reveal that the lineage on the permanently isolated islet Ball’s Pyramid is highly divergent from the remaining populations, while those on the episodically connected LHI, Roach Island, and Blackburn Island may have diverged as recently as the end of the last interglacial period. These results offer the first evidence that Pleistocene sea level lowstands allowed for historical faunal connectivity across the LHIG. Further, while P. lata was believed to have been locally extirpated by rodents on LHI; we discovered a surviving, relict population, albeit with high pairwise kinship indicative of a strong population bottleneck. We also detect relatively high levels of kinship in the other populations, suggesting potential inbreeding that could necessitate ongoing management. Finally, the combination of shallow genetic structure and low diversity suggests that genetic rescue from another island may be a viable strategy to conserve the LHI population of P. lata, as well as other species that have been similarly impacted by rodents.
Dataset DOI: 10.5061/dryad.bk3j9kdrm
Description of the data and file structure
These data were collected for the manuscript "Pleistocene sea-level fluctuation shapes archipelago-wide population structure in the critically endangered Lord Howe Island cockroach Panesthia lata".
Files and variables
File: Figure3_raw.tre
Description: Raw maximum-likelihood phylogeny of P. lata estimated from mitochondrial genomes.
File: Figure4_raw.tre
Description: Raw Bayesian time-calibrated phylogeny of P. lata estimated from mitochondrial genomes, depicting our maximum age estimate.
File: Adams.etal.SNP_data.csv
Description: Raw nuclear SNP data generated by DArTseq
- AlleleID: Unique identifier for the sequence in which the SNP marker occurs
- CloneID: Unique identifier for the sequence in which the SNP marker occurs
- AlleleSequenceRef: The sequence of the reference allele
- AlleleSequenceSnp: The sequence of the SNP allele
- TrimmedSequenceRef: The sequence of the reference allele, but with removed adapters
- TrimmedSequenceSnp: The sequence of the SNP allele, but with removed adapters
- Chrom_Panesthia_cribata_v2: Contig(s) with the best alignmenmarker/tag/ tag to Panesthia cribrata reference genome
- ChromPosTag_Panesthia_cribata_v2: Position(s) on contig(s) with the best alignment marker/tag/ tag to P. cribrata reference genome
- ChromPosSnp_Panesthia_cribata_v2: Calculated position(s) of the SNP for the best aligned marker on a contig(s) to P. cribrata reference genome
- AlnCnt_Panesthia_cribata_v2: Total count of align markers/tags
- AlnEvalue_Panesthia_cribata_v2: E value of the best alignment to P. cribrata reference genome
- Strand_Panesthia_cribata_v2: Strand of the marker alignment - Plus for forward and Minus for reverse
- SNP: Reference and alternate allele(s)
- SnpPosition: The position (zero-indexed) in the sequence tag at which the defined SNP variant base occurs
- CallRate: The proportion of samples for which the genotype call is either "1" or "0", rather than "-"
- OneRatioRef: The proportion of samples for which the genotype score is "1", in the Reference allele row
- OneRatioSnp: The proportion of samples for which the genotype score is "1", in the SNP allele row
- FreqHomRef: The proportion of samples that have a homozygous score for the Reference allele
- FreqHomSnp: The proportion of samples that have a homozygous score for the SNP allele
- FreqHets: The proportion of samples that have a score as heterozygous
- PICRef: The polymorphism information content (PIC) for the Reference allele row
- PICSnp: The polymorphism information content (PIC) for the SNP allele row
- AvgPIC: The average of the polymorphism information content (PIC) of the Reference and SNP allele rows
- AvgCountRef: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row
- AvgCountSnp: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row
- RepAvg: The proportion of technical replicate assay pairs for which the marker score is consistent
- Remaining columns: P. lata samples
File: FigureS6_raw.tre
Description: Raw Bayesian time-calibrated phylogeny of P. lata estimated from mitochondrial genomes, depicting our minimum age estimate.
File: FigureS8_raw.tre
Description: Raw maximum-likelihood phylogeny of P. lata estimated from nuclear SNPs.
Code/software
SNP data can be analysed using the dartR package in RStudio, and trees can be visualised using FigTree.
Access information
Data was derived from the following sources:
- GenBank
