Phylogeny and Classification

Phylogenetic inferences ideally should be based on all available evidence, but practical considerations restrict most analyses. The majority of studies have been based on either morphological traits or molecular sequences, and usually on only a subset of those data partitions. For example, analyses of fossil taxa are necessarily limited to the anatomy of the hard parts, because soft anatomy and molecular data are not available. In addition, the outcome of phylogenetic analysis may vary depending on such factors as the choice of taxa, outgroups, and characters, the description and scoring of those characters, weighting of characters, and methods used. Consequently there are many reasons not to accept phylogenetic hypotheses uncritically

Recent attempts to combine morphological and molecular data, optimistically called "total evidence" analysis, suffer from our ignorance of how to analyze such disparate characters meaningfully. How do individual base-pairs in a gene sequence compare with specific anatomical features, and should they be equally weighted in phylogenetic analyses? Total evidence analyses commonly treat individual base-pairs (sometimes even noninformative base-pairs) as equivalent to anatomical characters. Because a single gene segment may consist of hundreds of base-pairs, this practice almost always results in the molecular characters far outnumbering anatomical characters and potentially biasing the outcome.

Another approach to combining data partitions is called "supertree" analysis. This method constructs a phylogeny based on multiple "source trees" drawn from individual phy-logenetic analyses of morphological or molecular data (e.g., Sanderson et al., 1998; Liu et al., 2001). It is not clear, how ever, that this approach is superior to the individual analyses on which it is based. Some of the weaknesses of this approach were summarized by Springer and de Jong (2001).

Phylogenetic analyses typically use such methods as parsimony for morphological data sets and maximum likelihood or Bayesian analysis for molecular data sets. Which method is more likely to yield the most accurate tree is debatable, but it is probable that evolution does not always proceed parsimoniously. The results of these analyses are presented in cladograms that depict hypothetical relationships in branching patterns. The best resolved patterns are dichotomous; unresolved relationships are shown as multiple branches from the same point or node (polytomies).

This text focuses on the morphological evidence for mammalian relationships, although mention is made of contrasting phylogenetic arrangements suggested by molecular analyses. Most chapters include both classifications and cladograms. Although both are based on relationships, their goals are somewhat different. Cladograms place taxa in phylogenetic context by depicting hypotheses of relationship; consequently they are inherently more mutable. A classification provides a systematic framework and should therefore retain stability to the extent possible while remaining "consistent with the relationships used as its basis" (Simpson, 1961: 110; see also Mayr, 1969). Most classifications adopted in individual chapters loosely follow the classification of McKenna and Bell (1997, 2002). Minor modifications, such as changes in rank, are present throughout the book; but where significant departures from that classification are made, they are noted in the text or tables. For ease of reference, families and genera known from the Paleocene or Eocene are shown in boldface in the tables accompanying Chapter 5 and beyond. The cladograms presented reflect either individual conclusions or a consensus of recent studies, and they do not always precisely mirror the classifications.

The taxonomy employed in this volume represents a compromise between cladistic and traditional classifications, while attempting to present a consensus view of interrelationships. Such a compromise is necessary in order to use taxonomic ranks that reflect relationship and indicate roughly equivalent groupings, and at the same time avoid the nomenclatural problems inherent in a nested hierarchy (McKenna and Bell, 1997). The standard Linnaean categories, as modified by McKenna and Bell (1997), remain useful and are employed here, although unranked taxa between named ranks are necessary in a few cases (e.g., Catarrhini and Platyrrhini in the classification of Primates). As pointed out by McKenna and Bell (1997), among others, taxa of the same rank (apart from species) are not commensurate. For example, it is not possible to establish that a family in one order is an equivalent unit to families in other orders (or in the same order, for that matter). Nor are the orders themselves equivalent. Nevertheless, the taxonomic hierarchy does provide a useful relative measure of affinity within groups and of the distance between them.

As recognized in this volume, higher taxa are primarily stem-based. A stem-based taxon consists of all taxa that

Phylogenetic Tree Elephantidae

Fig. 1.3. Stem-based versus crown-group definition of taxa, illustrated by the Proboscidea. A crown-group definition limits Proboscidea to node B, equivalent to the extant family Elephantidae. Using a stem-based definition, Proboscidea includes all taxa more closely related to living elephants than to Sirenia or Desmostylia or Embrithopoda, as indicated here at node A. This stem-based definition is adopted in the most recent study of primitive proboscideans (Gheerbrant, Sudre, et al., 2005) and is followed here. See Chapter 13 for details of the proboscidean and tethythere radiations.

Fig. 1.3. Stem-based versus crown-group definition of taxa, illustrated by the Proboscidea. A crown-group definition limits Proboscidea to node B, equivalent to the extant family Elephantidae. Using a stem-based definition, Proboscidea includes all taxa more closely related to living elephants than to Sirenia or Desmostylia or Embrithopoda, as indicated here at node A. This stem-based definition is adopted in the most recent study of primitive proboscideans (Gheerbrant, Sudre, et al., 2005) and is followed here. See Chapter 13 for details of the proboscidean and tethythere radiations.

share a more recent common ancestor with a specified form than with another taxon (e.g., De Queiroz and Gauthier, 1992). For example, Proboscidea is considered to include all taxa more closely related to extant elephants than to sire-mans (Fig. 1.3). Therefore, using a stem-based definition, extinct moeritheriids and gomphotheres are proboscideans. This convention leaves open the possibility that other unknown stem-taxa may exist and could lie phylogenetically outside the known taxa, yet still lie closer to elephants than to any other major clade. Such was the case when the older and more primitive numidotheriids were discovered.

A node-based taxon is defined as all descendants of the most recent common ancestor of two specified taxa. In the example above, a node-based Proboscidea could be arbitrarily recognized at the common ancestor of numidotheres and other proboscideans, or of moeritheres and other proboscideans (thus excluding numidotheres). A special category of node-based taxa, which has been applied by some authors to mammalian orders, is the crown-group. A crown-group is defined as all descendants of the common ancestor of the living members of a specified taxon (Jefferies, 1979; De Queiroz and Gauthier, 1992). By such a definition, nearly all fossil groups are excluded from Proboscidea, and other well-known basal forms are excluded from higher taxa to which they have long been attributed and with which they share common ancestry and diagnostic anatomical features (Lucas, 1992; McKenna and Bell, 1997). Stem-based taxa are here considered more useful than node-based taxa for reference to the Early Cenozoic mammalian radiation.

The synoptic classification of mammals used in this book is given in Table 1.2. Mammalian relationships based on morphology are shown in Fig. 1.4, and those based on molecular data in Fig. 1.5. Although the discrepancies between morphological and molecular-based phylogenies have garnered considerable attention, it is important to note that there is substantial agreement between most morphological and molecular-based phylogenies (Archibald, 2003). This consensus underscores the significance of the discords that do exist. The two kinds of evidence have been particularly at odds with regard to two conventional orders, Lipotyphla and Artiodactyla, molecular data suggesting that neither is monophyletic. According to molecular analyses, the traditional lipotyphlan families Tenrecidae and Chrysochloridae form a monophyletic group together with Macroscelidea, Tubulidentata, Proboscidea, Sirenia, and Hyracoidea, which has been called Afrotheria. No morphological evidence supporting Afrotheria has been found. Molecular studies also indicate that the order Cetacea is nested within Artiodactyla as the sister group of hippopotamids. These debates are further discussed in the relevant chapters in this volume.

Disagreements also exist at the superordinal level, but the anatomical evidence for higher-level groupings is weak. Thus gene sequences support recognition of four main clades of placental mammals: Afrotheria, Xenarthra, Laura-siatheria (eulipotyphlans, bats, carnivores, pangolins, peris-sodactyls, artiodactyls, and whales), and Euarchontoglires (primates, tree shrews, flying lemurs, rodents, and lago-morphs), the last two of which form the clade Boreoeu-theria (e.g., Eizirik et al., 2001; Madsen et al., 2001; Murphy et al., 2001; Scally et al., 2001; Amrine-Madsen et al., 2003; Nikaido et al., 2003; Springer et al., 2003, 2005). Eizirik et al. (2001) concluded that this superordinal divergence occurred during the Late Cretaceous (about 65-104 Ma) and speculated that it was related to the separation of Africa from South America. These studies further suggest that Afrotheria was the first clade to diverge, followed by Xenarthra (usually considered the most primitive, based on morphology). However, morphological evidence suggests that most of the afrothere groups are nested within the ungulate radiation and are not closely related to tenrecs and chrysochlorids (see Chapters 13 and 15). This inconsistency implies that either the morphological or molecular data must be misleading. Methodological problems that can lead to erroneous phylogenetic conclusions in molecular analyses have been reviewed by Sanderson and Shaffer (2002) and are not further discussed here.

Notwithstanding the substantial contribution molecular systematics has made to our understanding of mammalian relationships, anatomical evidence from fossils plays the predominant role in resolving the phylogenetic positions of extinct taxa and clades for which molecular data are unavailable.

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