The preservation and postglacial history of ice age Holartic beetles, as inferred from museum and ancient DNA
Bibliographic record
Abstract
Degraded DNA can be recovered from specimens that are preserved in museums and the natural environment. Data generated from such DNA have provided valuable evidence for the assessment of a suite of biologically important questions. However, research of this nature is limited for invertebrate taxa, despite their diversity and ecological necessity. Using DNA data from dry-stored museum and permafrost- preserved ancient specimens, this thesis greatly extends the study of degraded DNA from invertebrates. The thesis focuses on two arctic ground beetle species (Amara alpina, Pterostichus brevicornisi, which are abundant in museum collections and permafrost deposits. A lack of data that characterises the preservation and potential of degraded beetle DNA, and thereby assessment of future possibilities for this emerging field, provided the impetus for the first three results chapters. Using two different sequencing approaches, the preservation of DNA in museum and ancient specimens was investigated. In addition, the taxonomic utility of DNA extracted from these specimens was assessed. These chapters demonstrate that DNA could be routinely recovered from museum specimens. DNA from ancient specimens could be recovered . from A. alpina but not P. brevicornis. In most cases therefore, degraded DNA from these beetles could be used to address further questions. The final two results chapters focus on the response of ~he two study species to a past period of climatically driven change, using DNA data from museum and ancient specimens. In these chapters, the mode of postglacial colonisation of Canada at the end of the last ice age was investigated. It was found that existing models of this process were broadly, but not wholly, correct. This may have implications for models of how beetles will respond to future climatic change. Although some challenges lie ahead, this thesis demonstrates the potential for museum and ancient permafrost-preserved beetle specimens in future, DNA-based, large-scale investigations.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
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".