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Also apparent is the considerable degree of rate variation among placental lineages (Figure 1).
Several taxa are clearly accelerated relative to the others, such as the caviomorph rodents (e.g., 90% in all three methods.
Moreover, it is possible that the bootstrap support for the basal relationships among the four major clades of placentals was actually decreased by inclusion of the marsupial outgroup, due to its unstable placement (Swofford et al. In this article we reexamine the phylogeny, dating, and biogeography of early placental mammals using three approaches: (1) a comparison of the bootstrap support for basal eutherian nodes in extensive rooted versus unrooted phylogenetic analyses of nearly 10,000 aligned nucleotides examined in 64 placental mammal species; (2) a maximum-likelihood-based rate constancy test (quartet dating), which allows for rate heterogeneity among lineages, aiming to specifically test whether the supraordinal divergences within Eutheria preceded the K-T boundary; and (3) an estimation of the dates and 95% confidence intervals for the deep nodes which define the four major clades of eutherian mammals.
Using conservative fossil calibrations (which are almost certainly underestimates of true divergence times at those internal nodes) our results support the hypothesis that most, if not all, of the early supraordinal eutherian diversification did precede the K-T boundary (Hedges et al.
See Table 3 for a complete list of bootstrap values for all major eutherian groups.
† Species included in the pruned dataset for ML analyses.
Minimum divergence dates of the earliest nodes in the placental mammal phylogeny were estimated with a quartet-based maximum-likelihood method that accommodates rate variation among lineages using conservative fossil calibrations from nine different nodes in the eutherian tree.
These minimum estimates resolve the earliest placental mammal divergence nodes at periods between 64 and 104 million years ago, in essentially every case predating the Cretaceous-Tertiary (K-T) boundary.
Although these studies provide evidence for the placement of the root of the eutherian tree (between clade I [Afrotheria] and the other three clades), we could not exclude two alternative roots (at the base of Xenarthra or between [Afrotheria, Xenarthra] and the other two clades).
The primers used to amplify these segments are listed in Table 2. Distance analyses employed different distance corrections (Kimura two-parameter, Logdet paralinear, maximum likelihood with an HKY85 model and parameters estimated from the dataset) to examine effects on topological stability.
The use of a long, concatenated data set as opposed to several separate short segments has been suggested to improve the reliability of phylogenetic and dating estimates (Bromhan et al. The maximum-likelihood analysis was based on a pruned dataset containing 37 taxa representing all major eutherian lineages.
Our current estimate of the placement of the root (Murphy et al. 2001) is shown by a black circle, and the tree is presented here with this arrangement for clarity.
Eutherian orders are identified on the right (boldface type) and the four principal clades of placental mammals are indicated by roman numerals (I–IV)." path-from-xml="hred-92-02-15-f01.gif" /Unrooted maximum parsimony (MP) phylogeny of placental mammals (TL = 25,106, CI = 0.346, RI = 0.479).
Our analyses provided consistently high bootstrap support for the four major phylogenetic clades of placental mammals identified by Madsen et al. (2001), as well as for the branch separating Afrotheria Xenarthra from all other placentals.