In traditional phylogenies, the age of clades was not taken into account. However, modern techniques allow divergence times to be assessed with reasonable accuracy, although they may still differ among authors.
Divergence-time estimates are based on molecular dating techniques, which in turn depend on reliable fossil calibrations, i.e. reliably dated and correctly placed fossils. To some extent they also depend on the selection of fossils and the maximum age constraint set by investigators.
Time-calibrated (dated) phylogenies, in which branch lengths are proportional to time, are usually referred to as chronograms or less often as timetrees. I prefer the latter term because of its euphony.
The availability of reliably dated phylogenies offers the opportunity for clades to be categorised and ranked according to their absolute ages. To establish age-based classifications, temporal frames have to be defined for each category, This approach, first proposed by Willi Hennig (1966), has been termed "temporal banding" by Avise & John (1999). The younger limit of the temporal bands, which is of particular relevance, is referred to as cutoff age, cutoff line, cutoff point, or cutoff. I will use the term „cutoff“ because it’s the shortest.
The greatest challenge for applying temporal banding to timetrees lies in answering the question to which groups of organisms the same temporal bands shall be applied. While I agree with Kraichach et al. (2017) that „with different groups of organisms having different evolutionary histories and timelines, trying to find one universal cut-off for each taxonomic rank might not be productive“, Naomi (2014) did propose an integrated framework of biological taxonomy for animals, plants, and fungi.
In the following, I will apply the approach of temporal banding to the clade Aves that has been ranked as a “classis” since Linnaeus (1758), thus literally providing a CLASSification. In Wikipedia (as of May 2021), a list of 107 animal classes is given, e.g. Amphibia, Aves, Gastropoda, Insecta, and Mammalia.
To provide temporal information to clades above class level, either timeclips (Avise & Mitchell, 2007), or plain age information (Zachos, 2011) could be used. The combination of temporal banding and timeclipping ensures relative nomenclatural stability within classes as well as temporal comparability among classes.
Before applying temporal banding to the avian timetree of Kuhl et al. (2021), I have to define a continuous series of temporal bands, each of which is associated with a particular Linnaean rank:
Definition of temporal bands and corresponding ranks that are going to be applied for the temporal banding of the avian timetree of Kuhl et al. (2021).
Temporal bands for avian categorical ranks were determined by initially setting the cutoff for avian orders at 55 Ma. The remaining cutoffs were then aligned at 10 Ma intervals for higher, and progressively shorter time intervals for lower categorical ranks in order to roughly conform to the previous results of Holt & Jønsson (2014). In their pioneering study these authors cut phylogenies at ages that returned the same number of clades as found in the original rankings, resulting in cutoffs at 65 Ma for orders, at 37 Ma for families, and at 11 Ma for genera.
Interestingly, many clade ages recognised by both Avise & Johns (1999, table 2) and Naomi (2014, table 2), who based their temporal bands on geological episodes, are pretty close to the average clade ages established by Holt & Jønsson (2014).
Holt & Jønsson (2014), who based their temporal banding on the timetree of Jetz er al. (2012), also were the first to convincingly demonstrate that the intrinsic classification of Passeriformes is not at all compatible with other avian orders. For example, they lumped 14 out of 15 families of Passeroidea into a single family.
Futuristic family-level timetree of extant Aves based on Kuhl et al. (2021), to which temporal banding has been applied here. A number of clades that are traditionally considered families have been downgraded to subfamily or tribal rank, or even below (red, orange and yellow family names, respectively). In Passeriformes, the situation is particularly challenging, as more than one hundred traditional families will have to be merged to only seven families. On the other hand, only few traditional families will have to be split, e.g. Cuculidae, Falconidae, and probably Scolopacidae.
Futuristic order-level timetree of extant Aves based on Kuhl et al. (2021), to which temporal banding has been applied here. The cutoffs at 55 Ma and 65 Ma were chosen to define oders and superorders, respectively. As a result, several traditional orders had to be split (blue and green order names), while only two traditional orders, flamingos (Phoenicopteriformes) and grebes (Podicipediformes), had to be merged (red order name). It would have been possible to set the superordinal cutoff at 65,5 Ma to retain loons (Gaviiformes) in traditional Aequornithes. However, I found it tempting to set cutoffs in steps of 10 Ma. The new taxonomy distinguishes 43 orders and 10 superorders. Note that crown-group ages derived from Kuhl et al. (2021, suppl.) are indicated by blue lines, whereas crown-group ages derived from other sources are indicated by green lines.
How to create an age-based CLASSification?
The broader temporal banding approach as a means of deriving age-based CLASSifications from timetrees encompasses the following consecutive steps:
Step 1: Select a class.
Step 2: Create or select a timetree.
Step 3: Determine "Temporal Error Scores" (sensu Holt & Jønsson, 2014) for orders, families, and genera.
Step 4: Define temporal bands of equal age (e.g. 10 Ma, 20 Ma, 50 Ma), taking into account the results of the previous step.
Step 5: Apply "Cutoff Collapsing" to each temporal band (see Note: "CLASSification") to transcribe the revised timetree into a formal CLASSification.
While steps 1-4 have been executed above, step 5 will be implemented in the Note “CLASSification.
Alternative temporal banding of CLASS Aves
Temporal bands are inherently arbitrary and only depend on conventions that taxonomists agree upon. Thus countless alternatives are possible. For example, some scientists might want to retain the current classification of Passeriformes and adjust other avian orders instead. In this case, temporal bands would have to be arranged quite differently.
Jønsson et al. (2016) assigned family rank at 21.5 Ma, Cai et al. (2019) at 18 Ma, and Cai et al. (2021) at 15 Ma. Comparable young family ages are also found in Charadriiformes, Procellariiformes, and Piciformes. For most avian orders, however, shifting temporal bands towards younger ages would lead to profound changes of current Linnaean ranks.
These very young family ages would not conform to any previous suggestion (Avise & Johns, 1999; Holt & Jønsson, 2014; Naomi, 2014).
Alternative recognition of CLASS Reptilia
In their higher-level classification of all living organisms, Ruggiero et al. (2015) treated Aves (as well as Crocodylomorpha, Rhynchocephalia, Squamata, and Testudinata) as a subclass of the CLASS Reptilia. This is a feasible alternative approach. However, it would lead to major rearrangements to conventional avian classifications.
Avise JC, and Johns GC (1999), Proposal for a standardized temporal scheme of biological classification for extant species, Proc. Natl. Acad. Sci. USA 96, 7358-63. (pdf)
Avise JC, and Mitchell D (2007), Time to standardize taxonomies, Syst. Biol. 56, 130-133. (pdf)
Avise JC, and Liu JX (2011), On the temporal inconsistencies of Linnean taxonomic ranks, Biol. J. Linn. Soc. 102, 707-714. (pdf)
Cai T, Cibois A, Alström P, Moyle RG, Kennedy JD, Shao S, Zhang R, Irestedt M, Ericson PGP, Gelang M, Qu Y, Lei F, and Fjeldså (2019), Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes), Mol. Phylogenet. Evol. 130, 346-356. (open manuscript)
Divakar PK, Crespo A, Kraichak E, Leavitt SD, Singh G, Schmitt I, and Lumbsch HT (2017), Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi, Fungal Divers. 84, 101-117. (abstract)
Dubois A (2008), Phylogenetic hypotheses, taxa and nomina in zoology, Zootaxa 1950, 51-86. (pdf)
Härlin M (2005), Definitions and
phylogenetic nomenclature, Proc. Calif. Acad. Sci. 56, Suppl. 1
Hennig W (1966) Phylogenetic systematics, University of Illinois Press, Chicago, IL. (link)
Jetz W, Thomas GH, Joy JB, Hartmann K, and Mooers AO (2012), The global diversity of birds in space ant time, Nature 491, 444-448. (abstract)
Jønsson KA, Fabre PH, Kennedy JD, Holt BG, Borregaard MK, Rahbek C, and Fjeldså J (2016), A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides), Mol. Phylogenet. Evol. 94, 87-94. (abstract)
Kallal RJ, Dimitrov D, Arnedo M, Giribet G, and Hormiga G (2020), Monophyly, taxon sampling, and the nature of ranks in the classification of orb-weaving spiders (Araneae: Araneoidea), Syst. Biol. 69, 401-411. (abstract)
Kraichak E, Crespo A, Divakar PK, Leavitt SD, and Lumbsch HT (2017), A temporal banding approach for consistent taxonomic ranking above the species level, Sci. Rep. 7, 2297. (pdf)
Kuntner M, Hamilton CA, Cheng RC, Gregoric M, Lupse N, Lokovsek T, Lemmon EM, Lemmon AR, Agnarsson I, Coddington JA, and Bond JE (2019), Golden orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism, Syst. Biol. 68, 555-572. (pdf)
Laurin M (2010), The subjective nature of Linnaean categories and its impact in evolutionary biology and biodiversity studies, Contrib. Zool. 79, 131-146. (pdf)
Lücking R (2019), Stop the abuse of time! Strict temporal banding is not the future of rank-based classifications in fungi (including lichens) and other organisms, CRC Crit. Rev. Plant Sci. 38, 199-253. (abstract)
Mayr E, and Bock WJ (2002), Classifications and other ordering systems, J. Zool. Syst. Evol. Research 40, 169-194. (pdf)
Naomi SI (2014), Proposal of an integrated framework of biological taxonomy: a phylogenetic taxonomy, with the method of using names with standard endings in clade nomenclature, Bionomina 7, 1-44. (pdf)
O´Hara TD, Hugall AF, Thuy B, Stöhr S, and Martynov AS (2017) Restructuring higher taxonomy using broad scale phylogenomics: the living Ophiuroidea, Mol. Phylogenet. Evol. 107, 415-430. (abstract)
Pan T, Miao JS, Zhang HB, Yan P, Lee PS, Jiang XY, Ouyang JH, Deng YP, Zhang BW, and Wu XB (2020), Near complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data, Zool. J. Linn. Soc. 191, 1075-1089. (abstract)
Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, Cavalier-Smith T, Guiry MD, and Kirk PM (2015), A higher level classification of all living organisms, PLOS ONE 10(4): e0119248. (pdf)
Ruggiero MA, Gordon DP, Orrell TM, Bailly N, Bourgoin T, Brusca RC, Cavalier-Smith T, Guiry MD, and Kirk PM
(2015), Correction: a higher level classification of all living organisms, PLOS ONE 10(6): e0130114.
Talavera G, Lukhtanov VA, Pierce NE, and Vila R (2012), Establishing criteria for higher-level classification using molecular data: the systematics of Polyommatus blue butterflies (Lepidoptera, Lycaenidae), Cladistics 29, 166-192. (pdf)
Thomson RC, Spinks PQ, and Shaffer HB (2021), A global phylogeny of turtles reveals a burst of climate associated diversification on continental margins, PNAS 118: e2012215118. (pdf)
Vences M, Guayasamin JM, Miralles A, and de la Riva I (2013), To name or not to name: criteria to promote economy of change in Linnaean classification schemes, Zootaxa 3636, 201-244. (pdf)
Zachos FE (2011), Linnean ranks, temporal banding, and time-clipping: why not slaughter the sacred cow? Biol. J. Linn. Soc. 103, 732-734. (pdf)
Zhao RL, Zhou JL, Chen J, Margaritescu S, Sanchéz-Ramírez S, Hyde KD, Callac P, Parra LA, Li GJ, and Moncalvo JM (2016), Towards standardizing taxonomic ranks using divergence times - a case study for reconstruction of the Agaricus taxonomic system, Fungal Divers. 78, 239-292. (abstract)