Nucleotide diversity of the fragment of cytocrhome oxidase gene subunit 1 of mitochondrial DNA in (<i>Oncorhynchus Nerka</i>) populations
Bibliographic record
Abstract
Purpose: to analyze the nucleotide diversity of the cytochrome oxidase gene fragment of the 1 mt DNA subunit in the Asian and American populations of sockeye salmon. Materials and methods. The material for analysis is nucleotide sequences obtained by the author for the sockeye salmon population of the Ola River, and for a number of Asian and American sockeye salmon populations, located in the Gene Bank (www.ncbi.nlm.nih.gov). 139 sequences were analyzed, the unifies number of nucleotide was 640. The statistical parameters are as follows: ps – the proportion of polymorphic sites, θ - the proportion of polymorphic sites taking into account the number of sites (i) p s /a 1 = 1\ 1\i = 1\ 1 + ½ + 1/3 + … + 1/i, π T – nucleotide diversity, π s – average nucleotide diversity within a population, δ ST – interpopulation nucleotide diversity. N ST – coefficient of nucleotide differentiation, N ST = δ ST / π T . The dendrogram is built using the values of the so-called p-distances, using the UPGMA clustering method. Results. The nucleotide diversity of sockeye salmon from the Ola River (πT = 0,00505 (s=0,000080)) turned out to be slightly higher than in American populations (π T = 0,00403) (s=0,000002)). The coefficient of nucleotide differentiation N ST and the number of polymorphic sites in Asian populations are higher than in American populations. Due to this, a higher level of nucleotide diversity was found in Asian sockeye salmon populations (π T = 0,00504 (s=0,000004)) than in North American ones. The nucleotide sequences of all individuals are divided into 2 groups. Individuals of these groups do not have territorial attachment, i.e. noted in both Asian and American populations. It is most likely that these groups formed as a result of Late Pleistocene climate fluctuations and the associated presence of two refugia on the Asian coast – the rivers of the northern coast of the Sea of Okhotsk and the rivers of the Kamchatka Peninsula, the second salmon, it is also assumed that two refugia will exist during the period of climate cooling, one in the area of the Alaska Peninsula, the second in the area of Vancouver Island. Almost all large populations of sockeye salmon are influenced by fishing and, in many cases, artificial farming. To reliably distinguish hatchery fish from sockeye salmon produced in natural spawning grounds, the characteristic nucleotide sequence of the mtDNA cytochrome oxidase gene can be used.
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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) | 0.000 | 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".