Bibliographic record
Abstract
In this thesis I provide among the first detailed studies of orangutan host/parasite co-evolution by bridging the disciplines of molecular virology/parasitology and biological anthropology. I used the tools of both disciplines to study the evolution of three infectious agents: simian foamy virus (SFV), simian T-lymphotropic virus 1 (STLV-1), and the protozoan parasite, Plasmodium, in orangutans Genus Pongo. Key to my thesis is the importance placed on the use of accurate calibration dates informed by archaeological and fossil data. Using this approach, I examine the evolutionary history of these infectious agents, including an estimation of the ages of divergence. The results suggest that SFV is the oldest of these infectious agents in orangutans, dating to >4 million years ago. My results challenge a previous hypothesis surrounding the appearance of a unique cladistic pattern for orangutan SFV based on the Mount Toba supervolcanic eruption at ~73 kya. The results of the present research suggest that the events leading to the development of this clade pattern is ~1.6 million years old, which rules out the Toba supereruption. My results also showed that there is a statistically significant level of host-virus coevolution in orangutans. My thesis research indicates the Plasmodium parasites in orangutans are much younger than previously thought. Finally, I estimate the origins of PTLV-1 in orangutans to between 7-343.7 kya. Overall, my thesis shows that the Pleistocene was an important period for the evolution of these infectious agents in orangutans and that it is at least possible that some of this evolution occurred on the Indochinese mainland before orangutans reached the islands of Sumatra and Borneo.
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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 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 teacher head, 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".