(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), Jønsson et al. (2016), and Fjeldså et al. (2020). The latter author, however, did apply a loose, not a strict cutoff to delimit passerine families, knowing that confidence intervals of nodes are often wide (Sangster et al. 2022). 

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. This traditional ranking system represents a well-balanced trade-off between phylogenetic resolution on the one hand and taxonomic manageability on the other. In addition, ranked clades are recognised by standardised endings (-oidea, -idae, -inae, -ini, -ina). 

 

Alternative cutoffs for birds

Temporal threshold values (cutoffs) are inherently arbitrary and depend on conventions that taxonomists must 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)


Avise JC, and Liu JX (2011), On the temporal inconsistencies of Linnean taxonomic ranks, Biol. J. Linn. Soc. 102, 707-714. (pdf)


Barker FK, Burns KJ, Klicka J, Lanyon SM, and Lovette Zizka (2015), New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies, Auk 132, 333-338. (free 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)


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) 


Cracraft J (1981), Toward a phylogenetic classification of the recent birds of the world (class Aves), Auk 98, 681-714. (pdf)


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)

 

Fjeldså J, Christidis L, Ericson PGP, Stervander M, Ohlson LI, and Alström P (2020), An updated classification of passerine birds, In: The largest avian radiation (Fjeldså, J, Christidis L, and Ericson PGP, eds.), pp. 45-63. Lynx Edicions, Barcelona (link). 


Garnett ST, and Christidis L (2017), Taxonomy anarchy hampers conservation, Nature 546, 25-27. (pdf)


Hennig W (1966) Phylogenetic systematics, University of Illinois Press, Chicago, IL. (link)

 

Holt BG, and Jønsson KA (2014), Reconciling hierarchical taxonomy with molecular phylogenies, Syst. Biol. 63, 1010-17(pdf) (suppl.) 


Jetz W, Thomas GH, Joy JB, Hartmann K, and Mooers AO (2012), The global diversity of birds in space and 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, e: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: 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: e0130114. (pdf)

 

Sangster G, Cibois A, and Sushma R (2022), Pteruthiidae and Erpornithidae (Aves: Corvides): two new family-group names for babbler-like outgroups of the vireos (Vireonidae), Bull. BOC 142, 239-243. (pdf)


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)