Phylogenetic relationships of shorebirds (Aves: Charadriiformes): Evidence from sequences of nuclear and mitochondrial genes
Bibliographic record
Abstract
The shorebirds (Aves: Charadriiformes) are a large and diverse group of non-passerine birds, whose phylogenetic relationships have been difficult to recover because previous studies have used characters that are limited in their resolution power. Here, I examine the utility of DNA sequences from both the mitochondrial and nuclear genomes to infer phylogeny at the family and generic levels in shorebirds. Both types of sequence data recover three subordinal clades of shorebirds: Scolopaci (sandpipers and allies), Lari (gulls and alcids) and Charadrii (plovers and oystercatchers), and highly-supported, congruent topologies. The Charadrii is found to be sister to a (Scolopaci + Lari) clade, which is different than all previous hypotheses of shorebird phylogeny based on morphological and biochemical data. Patterns of evolution in a 3 kb nuclear exon (RAG-1) reveal a homogeneous nucleotide composition and rate of substitution among lineages, making this gene useful for resolving and estimating the timing of deep divergences in this clade. The 14 mitochondrial genes examined are variable in rate, and therefore are useful to construct phylogeny at many different taxonomic levels. However, complex models of substitution are required to accurately estimate distances among taxa that are divergent. This approach confirms the historically recognized division of Paleognath and Neognath birds, when shorebird mitochondrial DNA is analyzed with other published avian mitochondria) genomes. The mitochondrial gene order of shorebirds was also found to be variable around the control region, and is associated with a tandom duplication of these sequences. In addition to contributions to avian systematics, the mitochondrial genomes of shorebirds will also advance understanding of patterns of evolution at the genomic level.
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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 | 0.000 | 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) | 0.001 | 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".