Scripts from: Whole-genome resequencing reveals complex effects of geographical–palaeoclimatic interactions on diversification of moustache toads in East Asia
Bibliographic record
Abstract
Geographical features and paleoclimatic fluctuations are two classical evolutionary forces for shaping genetic diversification within species. However, fine-grain analysis of mechanisms through population demographic processes remains limited. Taking advantage of two recently published reference genomes, we re-sequenced the genomes and examined the evolutionary history of the Moustache toads, a group endemic to East Asia where complex topography and fluctuating paleoclimate are known to have profound impacts on organisms. Moustache toads likely originated from southeast Yunnan of China and diversified towards the northwest of Yunnan, as well as central and eastern China. We further focused on three widespread Moustache toad species (Leptobrachium ailaonicum, L. boringii, and L. liui), assessed current population structure, and explored evolutionary processes using demographic modelling and species distribution modelling within each species. We find that mountains and river valleys in East Asia not only function as geographic barriers but also provide dispersal corridors and facilitate continuous migration or post-glacial secondary contact among Moustache toad populations. Furthermore, periodic oscillations of effective population size accompanying fluctuations of historical temperature, and the evident population contraction at the Last Glacial Maximum support a widespread impact of Pleistocene climatic changes on species diversification in East Asia. This impact is moderate for species in the southwestern mountains but is severe in the eastern lowland regions of continental East Asia, which is supported by a mild decrease of effective population size for populations of L. ailaonicum and L. boringii but a drastic population decline for L. liui. Our findings provide molecular mechanisms underlying genetic diversification among Moustache toads and highlight the power of genomic data and demographic modelling for examining complex population-level processes and understanding how geographic and paleoclimatic factors interactively shape current intraspecific diversity.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.036 | 0.016 |
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".