Zitteliana B 32 (2014) 5 Current taxonomy and diversity of crown ruminants above the species level Colin Groves School of Archaeology & Anthropology, Australian National University Zitteliana B 32, 5 – 14 Canberra, ACT 0200 Australia München, 31.12.2014 E-mail: [email protected] Manuscript received 17.01.2014; revision accepted 20.10.2014 ISSN 1612 - 4138 Abstract Linnaeus gave us the idea of systematics, with each taxon of lower rank nested inside one of higher rank; Darwin showed that these taxa are the result of evolution; Hennig demonstrated that, if they are to mean anything, all taxa must represent monophyla. He also pro- posed that, to bring objectivity into the system, each taxonomic rank should be characterised by a particular time depth, but this is not easy to bring about: genera such as Drosophila and Eucalyptus have a time-depth comparable to whole orders among mammals! Within restricted groups of organisms, however, time-depths do tend to vary within limits: we will not do too much violence to current usage if we insist that a modern mammal (including ruminant) genus must have a time-depth of about 5 million years, i.e. going back at least to the Miocene-Pliocene boundary, and a modern family must have a time-depth of about 25 million years, i.e. going back to the Oligocene- Miocene boundary. Molecular studies show that living ruminants present examples where the „traditional“ classification (in the main laid down in the mid- 20th-century, and all too often still accepted as standard even today) violates Hennigian principles. Among Bovidae, the genera Bos, Tragelaphus, Gazella and Hemitragus are paraphyletic, and so, among Cervidae, are the genera Cervus and Mazama. I will discuss what we can do about these, and will then present, with commentary, a classification of living ruminants. Key words: Morphology, molecules, cladistics, genus, Bos, Tragelaphus, Gazella, Hemitragus, Cervus, Mazama. 1. Introduction: analysing the phylogeny 1.1 Cladistic analysis Ever since the Hennigian revolution of the 1960s Cladistic analysis has numerous disadvantages. (Hennig 1966), it has been recognised that taxonomy Homoplasy is widespread, and there is frequently no above the species level must reflect phylogeny, but logical means of deciding between alternative phylo- the reconstruction of a phylogeny is still often fraught genetic trees. It lacks a calibrated time component: with problems and controversies. different characters can be expected to change at We study both extant and fossil organisms, using different rates. Frequently, it is difficult to decide some methods which are available for both, others what characters actually are: do we risk atomisation which are available only for extant organisms. In the of functional units, or do we combine potential char- case of fossils, normally only methods applicable to acters into what we deem functional sets? We often phenotypic traits are available; the rapid advance do not know how (or whether) characters are corre- of ancient DNA techniques, however, is beginning lated. We are ignorant of their genetic basis. Finally, to open up new horizons. Extant organisms may be cladistic analysis assumes a branching phylogeny; it studied by methods applicable to a variety of pheno- cannot detect reticulation, although it can of course, typic traits (morphology, behaviour, some molecular) in cases of rampant homoplasy, generate hypothes- or by methods applicable to some genotypic traits es that hybridisation might have taken place. (today, almost entirely nuclear acids, both DNA and Nonetheless, the method does have its own con- RNA). Methodologically, we can use cladistic analy- siderable advantages. The characters used in cla- sis, morphometrics and the molecular clock. Each of distic analysis include any kind, but, with caution, these methods and data sources has its own advan- morphometrics; only DNA sequences themselves tages and disadvantages, some of them are pointed should be excluded from analyses of phenotypes. out here in more detail: (I am aware that DNA and phenotypic characters, Zitteliana B 32 (2014) 6 generally morphological, are sometimes included in rates of evolution cannot be assumed to be con- the same dataset, under the heading of Total Evi- stant: local and more global clocks often run at very dence Analysis, but they are quite different types different rates. Molecular data, like non-molecular, is of characters, and should normally be kept sepa- subject to homoplasy (Broughton et al. 2000). And rate – at any rate, caution should always be applied. there is still some risk of over-reliance on mtDNA as For a discussion of Total Evidence, see for example opposed to nuclear sequences. Eernisse & Kluge 1993; Gatesy et al., 1999; Gatesy, Looking at molecular data, we can often find as 2002). Cladistic analysis is of course all that is availa- few phylogenetically informative characters as in ble to the palaeontologist, yet an advantage which non-molecular data. Genetic data are in this sense is often overlooked in the case of living organisms is not necessarily „better“ than other sorts of data. that the characters apply to the phenotype, which is the target of selection, so the resultant phylogenetic tree has the potential to inform us about the selec- 2. The potential of different data sources: tive history of the taxa involved. consilience In non-molecular data sets, it is commonplace to warn of homoplasy, although note that what is ho- The old “morphology versus molecules” debates moplastic at one node may well be informative at of the latter half of the 20th century are virtually ex- others so that, if as many characters as possible are tinct. There is no reason to expect that morpholo- used, the resulting phylogenetic tree may turn out gical characters have evolved at the same rate as to be well supported. Description of the behaviour DNA sequences; as noted above, they are subject of different characters should be part of every non- to selection, which may retard phenotypic change molecularly based cladistic analysis. or, conversely, speed it up and overlay new apo- morphies on earlier ones. Nonetheless, there are in- 1.2 Fossil record teresting cases of unexpected consilience. Affinities ofHydropotes (Chinese water-deer) have The most obvious advantage of the fossil record, long been disputed. These deer, unlike all other cer- whether analysed by cladistics or stratophenetics, vids, lack antlers: is this lack primary or seconda- is the time control it affords. First appearance data ry? If it is primary, then parsimoniously Hydropotes are essential to calibrate both cladistic and gene- would be expected to be sister to all other cervids; if tic methods of phylogeny, but these must be taken secondary, then it could be nested almost anywhere cautiously, preferably using as many calibrations as among the antlered Cervidae. Its other morphologi- possible (Bibi 2013). cal characters shed little light on its affinities. The disadvantages include the incompleteness DNA analysis, both mitochondrial and nuclear, of the record, and the incompleteness of the fossils (Randi et al. 1998, Pitra et al. 2004, Gilbert et al. themselves. Palaeontologists typically utilise cla- 2006), comes down firmly on the side of the lack of distic analysis to interpret the fossil record of the antlers being secondary: Hydropotes is sister to the group, although the stratophenetic method (ordering roe deer, Capreolus. Interestingly, characters of male fossils into a time sequence, and treating the result vocal behaviour (Cap et al. 2008) produce the same as a quasi-ancestor-descendant series) is also po- cladogram, a nice instance where behaviour con- tentially valuable. forms to the phylogeny when morphology does not. It is worthwhile drawing attention to this case be- 1.3 Genetic analysis cause the DNA result had been entirely unanticipa- ted – no morphological assessment would have pre- The advantages of basing phylogenetic re- dicted such a conclusion. constructions on genetics are manifold. We are dea- ling with the DNA itself. We have time control (the molecular clock). We are no longer restricted to blood 3. An outline taxonomy of living ruminants samples or biopsies, or even faecal samples, from living animals: laboratory protocols have improved The taxonomy of living ruminants above the spe- so much that Ancient DNA is now commonplace. In cies level adopted by Groves & Grubb (2011) is as contrast to the morphology-based cladistic method, follows: typically used to construct the phylogeny, we are no longer constrained to a model of diversification: Family Tragulidae comparison between mt- and nDNA (especially Y- Tragulus, Moschiola, Hyemoschus chromosome DNA) has the potential to detect reti- Family Moschidae culation (see below). Moschus Nonetheless, we must not be blind to some po- Family Antilocapridae tential disadvantages. The construction of molecular Antilocapra clocks depends on there being an adequate fossil Family Giraffidae record, offering multiple calibrations. Another is that Giraffa, Okapia Zitteliana B 32 (2014) 7 Family Cervidae milial” about the families, or “genus”-like about the Subfamily Capreolinae genera? Tribe Rangiferini Odocoileus, Pudu, Hippocamelus, Blastocerus, Ozotocerus, Mazama, 4. Higher taxa: what are the criteria? Rangifer Tribe Capreolini This question has rarely been asked, but as long Capreolus, Hydropotes as we claim that taxonomy is a science, we must ask Tribe Alceini it. One of the few to have asked the question in the Alces past was Mayr (1969). He suggested that we should Subfamily Cervinae take the following factors into account: Tribe Muntiacini • the distinctness of a taxon (the size of the gap Elaphodus, Muntiacus between it and its closest relatives); Tribe Cervini • its evolutionary role (the uniqueness of its adap- Dama, Axis, Rucervus, Panolia, Elaphu- tive zone); rus, Cervus • the degree of difference between one taxon and Family Bovidae others; Subfamily Bovinae • the optimal size of a taxon (how many subordinate Tribe Bovini taxa there are); Bos, Bubalus, Syncerus, Pseudoryx • and the equivalence of ranking in related taxa.