Genetic consequences of plate tectonics: cytonuclear discordance in phrynosomatid lizards of Baja California, Mexico
Bibliographic record
Abstract
The peninsula of Baja California of northwestern Mexico has a complex geological history. Since the early Miocene, intense plate tectonic activity, volcanism, and sea level changes have combined to form a diverse landscape. The geological history has had profound effects on the regional biota. I evaluated the genetics of three common phrynosomatid lizards in relation to data from geology, paleontology, and stratigraphy to provide a better understanding of the historical biogeography of this region. I also addressed the evolutionary significance of temporary population fragmentation and the genetic interactions of reunited populations. Using sequence data from three mitochondrial genes (ca 2,000 bp), I reconstructed the genealogical histories of the zebra-tailed lizard (Callisaurus draconoides) and the black-tailed brush lizard (Urosaurus nigricaudus) based on samples spanning the entire peninsula and insular populations from the Gulf of California. The genealogies revealed several deep divergences (up to 11% sequence divergence in cytochrome b), supporting the existence of temporary seaways across the mid-peninsular, Isthmus of La Paz, and Cape regions, and extensive inundation of the peninsula in the vicinity of Loreto. My results also suggest a significantly deeper time frame for the historical biogeography of Baja California than currently postulated. This includes evidence of a mid-peninsular seaway of late Miocene age (ca 7 million years ago). This event is also a more parsimonious explanation for the geographically congruent mitochondrial DNA (mtDNA) breaks of numerous species than the effects of climate on genetics, such as the cyclic pattern of Quaternary glaciation events. The deep divergences in mtDNA strongly contrast with variation in allozyme loci, which suggests limited population differentiation consistent with gene flow along the peninsula. This cytonuclear discordance stems from the different modes of inheritance of mtDNA and nuclear DNA (maternal versus biparental inheritance) and lack of recombination in mitochondria. Accordingly, mtDNA differentiation is a poor proxy for biparental population differentiation. Cytonuclear discordance is particularly strong in old secondary contact zones in the black-tailed brush lizard and the side-blotched lizard (Uta stansburiana). These contact zones show very little geographical overlap of divergent mtDNA lineages, suggesting some form of selection against mtDNA dispersal across contact zones.
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 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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| 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".