Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly: Additional Data
Bibliographic record
Abstract
This repository is intended to accompany the final report to the US Fish and Wildlife Service, entitled: Conservation Genetics and Genomics of the Narrowly Endemic Island Marble Butterfly The purpose of this study was to collect and analyze non-invasive DNA specimens from the endangered island marble butterfly (Euchloe ausonides insulanus) to assess population structure, identify adaptive potential, facilitate captive propagation, and support translocation planning. We used DNA extracted from meconium, exuviae, and natural mortalities to generate and test thirteen new microsatellite markers for use in population structure and kinship analyses. We also used DNA from natural mortalities to determine whether non-invasively collected samples could be used to generate enough single nucleotide polymorphisms (SNPs) to perform fine-scale genomic analyses. Whole mitochondrial genomes were assembled, annotated, and used to infer a phylogeny with museum specimens of insulanus collected ~100 years ago from Vancouver Island and other members of the E. ausonides species complex. The results indicated that insulanus suffers from low heterozygosity, a small effective population size (Ne), and low allelic diversity. There was evidence of high levels of inbreeding in some individuals, but inbreeding was uneven across the population. There was no population structure or partitioning by host plant detected. The mitogenomes of extant insulanus were all identical and there was a loss of allelic diversity in modern samples compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management decisions and genetic monitoring. Included in this repository are: Sample metadata for all samples used, including which analysis they were used in (microsatellite, mitogenome, and/or ddRAD), and the BioSample and SRA accessions for sequenced samples desposited with NCBI GenBank under BioProject PRJNA1156227 (IMB_metadata.csv) The VCF file of SNPs produced from ddRAD NovaSeq sequencing (novaseq_IMB_20_depth_Q30_50_missing.vcf) The microsatellite loci used for population genetic analyses (IMB_microsatellite_loci.csv)
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.022 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".