(Chrono-) CLASSification

With respect to conveying useful comparative information, current biological classifications are seriously flawed because they fail to (i) standardize criteria for taxonomic ranking and (ii) equilibrate assignments of taxonomic rank across disparate kinds of organisms. In principle, these problems could be rectified by adopting a universal taxonomic yardstick based on absolute dates of the nodes in evolutionary trees.” (John C. Avise & Glenn C. Johns 1999, p. 7358)


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. 

Timetrees offer the opportunity for clades to be categorised and ranked according to their absolute ages. To establish age-based classifications, temporal threshold values have to be defined for each categorical rank. For supraspecific ranks, this approach was first proposed by Willi Hennig (1966) and has been repeatedly advocated since, e.g. by Avise & Johns (1999), Holt & Jonsson (2014), Naomi (2014), and Jønsson et al (2016). 

The greatest challenge for applying temporal thresholds to timtrees is to decide to which groups of organisms the same temporal thresholds shall be applied. Naomi (2014), for example, proposed a broad taxonomic framework covering all animals, plants and fungi. However, 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".

In the following, I propose temporal threshold values (cutoffs) that are specifically tailored to Aves, a clade that has been ranked as a "classis" since Linnaeus (1758). The proposed cutoffs for class Aves were determined by initially setting the cutoff for orders at 55 Ma. The remaining cutoffs were then aligned at 10 Ma intervals to roughly conform to the results of Holt & Jønsson (2014). In their pioneering study, these authors cut phylogenies of class Aves at ages that returned the same number of clades as found in original ranks, resulting in cutoffs at 65 Ma for avian orders, at 37 Ma for avian families, and 11.4 Ma for avian genera.

The approach of restricting rank-defining cutoffs to individual taxonomic classes will subsequently be referred to as "CLASSification", with emphasis on the first syllable.

Proposal of temporal threshold values (cutoffs) to define individual categorial ranks for class Aves. 

Once cutoffs are agreed upon, ranks can be assigned to clades in timetrees: 

Exemplary species-level timetree to which temporal thresholds are applied to assign categorial ranks to clades. In contrast to other cutoffs, the generic cutoff should be applied rather flexible to allow preservation of well-established genera as long as they arose between 8 Ma and 12 Ma.

Rank-assigned timetrees can serve as templates for creating age-based CLASSifications. The process of creating CLASSifications from rank-assigned timetrees will be referred to as "treescription". There are several ways how to display treescribed CLASSifications. For didactive reasons, I first present an arrangement that closely mirrors the underlying timetree: 

CLASSification (horizontally arranged), derived from the rank-assigned timetree presented above. 

Typically, however, CLASSifications are represented as linear lists: 

CLASSification (arranged in coloured indented linear sequence), derived from the rank-assigned timetree presented above. 

To provide temporal information to clades above class rank, either timeclips (Avise & Mitchell, 2007), or plain age information (Zachos et al., 2011) could be used. The use of both temporal thresholds and timeclipping provides relative nomenclatural stability within classes, as well as temporal comparability among classes.

 

Comment

How many categorial ranks are needed?

Personally, I prefer to rely on the categorial ranks that are considered in the ICZN-Code, because the traditional ranking system represents a well-balanced trade-off between phylogenetic resolution on the one hand and taxonomic manageability on the other. Ranked clades are recognised by standardised endings (-oidea, -idae, -inae, -ini, -ina). 

 

Alternative cutoffs for birds

Temporal threshold values (cutoffs) 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 accordingly. For example, 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. Comparably young family ages are also found in Charadriiformes, Procellariiformes, and Piciformes. For most avian orders, however, shifting temporal cutoffs towards younger ages would lead to profound taxonomic changes. Such young family ages would not conform to previous suggestions of family-rank ages in zoology (Avise & Johns, 1999; Holt & Jønsson, 2014: Naomi, 2014).

 

Alternative recognition of class Reptilia

In their higher-level classification of all extant living organisms, Ruggiero et al. (2015) treated Aves (as well as Crocodylomorpha, Rhynchocephalia, Squamata, and Testudinata) as a subclass of class Reptilia. This is a feasible alternative approach that would, however, lead to major rearrangements to conventional avian classifications.

 

References/Literature

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)


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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)


Cai T, Wu G, Sun L, Zhang Y, Peng Z, Guo Y, Liu X, Pan T, Chang J, Sun Z, and Zhang B (2021), Biogeography and diversification of Old World buntings (Aves: Emberizidae): radiation in open habitats, J. Avian Biol., e:02672. (pdf) 


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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)

 

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