Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data
Bibliographic record
Abstract
The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK, andwingless), and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI (“barcode” region) and COI (“Pat/Jer” region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all exceptNotiokasisandArchileistobrius), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding, and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. The tribes Notiophilini, Opisthiini, Pelophilini, and Nebriini are well supported as monophyletic but relationships among these are not well resolved.Nippononebriais a distinct genus more closely related toLeistusthanNebria.Archastes,Oreonebria,Spelaeonebria, andEurynebria, previously treated as distinct genera by some authors, are all nested within a monophyletic genusNebria.WithinNebria, four major clades are recognized: (1) theOreonebriaSeries, including eight subgenera arrayed in two subgeneric complexes (theEonebriaandOreonebriaComplexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) theNebriaSeries, including ten subgenera arrayed in two subgeneric complexes, theBoreonebriaandNebriaComplexes, with the latter further subdivided into three subgeneric subcomplexes (theNebria,Epinebriola, andEunebriaSubcomplexes)); and (4) theCatonebriaSeries, including seven subgenera arrayed in two subgeneric complexes (theReductonebriaandCatonebriaComplexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (Nippononebria,VancouveriaandArchastes) are given revised status and seven are recognized as new synonymies (NebrioritesJeannel, 1941 andMarggiaHuber, 2014 =OreonebriaDaniel, 1903;PseudonebriolaLedoux & Roux, 1989 =BoreonebriaJeannel, 1937;PatrobonebriaBänninger, 1923,ParanebriaJeannel, 1937 andBarbonebriolaHuber & Schmidt, 2017 =EpinebriolaDaniel & Daniel, 1904; andAsionebriaShilenkov, 1982 =PsilonebriaAndrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species:Nebria delicataHuber & Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species:Nebria carbonariaEschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type speciesNebria sahlbergiiFischer von Waldheim, 1828),NivalonebriaKavanaughsubgen. nov.(type species:Nebria paradisiDarlington, 1931),NeaptenonebriaKavanaughsubgen. nov.(type species:Nebria ovipennisLeConte, 1878), andPalaptenonebriaKavanaughsubgen. nov.(type species:Nebria mellyiGebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particularly within subgeneraLeistusandEvanoleistus of genusLeistusand theNebriaComplex of genusNebria.
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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".