Abstract.---Over the past ten years, the phylogenetic relationships among higher level artiodactyl taxa have been examined with multiple data sets. Many of these data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic and that Cetacea (whales) represents a highly derived "artiodactyl" subgroup. In this report, phylogenetic relationships between Cetacea and artiodactyls are tested with a combination of 15 published data sets plus new DNA sequence data from two nuclear loci, interphotoreceptor retinoid binding protein (IRBP) and von Willebrand factor (vWF). The addition of the IRBP and vWF character sets disrupts none of the relationships supported by recent cladistic analyses of the other 15 data sets. Simultaneous analyses support three critical clades: (Cetacea + Hippopotamidae), (Cetacea + Hippopotamidae + Ruminantia), and (Cetacea + Hippopotamidae + Ruminantia + Suina). Perturbations of the combined matrix show that the above clades are stable to a variety of disturbances. A chronicle of phylogenetic results over the past three years suggests that cladistic relationships between Cetacea and artiodactyls have been stable to increased taxonomic sampling and to the addition of over 1,400 informative characters from 15 data sets.
[Artiodactyla, Cetacea, stability, cladogram]

Abstract.---Recent molecular studies are inconsistent with ungulate phylogenetic trees that are based on morphological traits. These inconsistencies especially relate to the position of cetaceans and perissodactyls. Evaluation of the close phylogenetic ties between artiodactyls and cetaceans has been hampered by the absence of tarsal bones of primitive cetaceans, as artiodactyls are often diagnosed on the basis of their tarsus. We here describe newly discovered tarsal bones that are the oldest cetacean tarsals known. We present a character analysis for primitive ungulate tarsals and evaluate their impact on the ungulate phylogenetic tree. Tarsal data are consistent with some molecular studies in suggesting that the extant sistergroup of Cetacea is Artiodactyla or that Cetacea should be included within the latter order. Tarsal data do not support Cete (Mesonychia plus Cetacea) and are consistent with the exclusion of perissodactyls from paenungulates as suggested by some molecular studies.
[Cetacea, Mesonychia, Artiodactyla, Ungulata, Locomotion]

Abstract.---We look at the higher-order phylogeny of mammals, analyzing in detail the complete mtDNA sequences of over 40 species. We test the support for several proposed super-ordinal relationships. To this end, we apply a number of recently programmed methods and approaches, plus better established methods. New pairwise tests show that there is highly significant evidence that amino acid frequencies are changing among nearly all the genomes studied when unvaried sites are ignored. LogDet amino acid distances, with modifications to take into account invariant sites, are combined with bootstrapping and the Neighbor Joining algorithm to account for these violations of standard models. To weight the slower evolving sites, we exclude the more rapidly evolving sites from the data using "site stripping". This leads to changing optimal trees with nearly all methods. The bootstrap support for many hypotheses varies widely between methods, and few hypotheses can claim unanimous support from these data. Rather, we uncover good evidence that many of the earlier branching patterns in the placental subtree could be incorrect, and this includes the placement of the root. The tRNA genes, for example, favour a split between the group hedgehog, rodents and Primates versus all other sequenced placentals. Such a grouping is not ruled out by the amino acid sequence data. A grouping of all rodents plus rabbit, the old Glires hypothesis, is also feasible with stripped amino acid data, while rodent monophyly is also common. The elephant sequence allows confident rejection of the older taxon Ferungulata (Simpson 1945). In its place, the new taxa Scrotifera and Fereuungulata is defined. A new likelihood ratio test is used to detect differences between the optimal tree for tRNA versus that for amino acids. While not clearly significant as made, there are indications the test is tending towards significance with more general models of evolution. Individual placement tests suggest alternative positions for hedgehog, and the elephant. There are striking congruence arguments to support elephant and armadillo together, suggesting a superordinal group composed of Xenarthra and African endemic mammals, which in turn may be near the root of the placental subtree. Thus, the analyses while casting doubt on some recent conclusions, are also unveiling some interesting new possibilities.
[mammal phylogeny; LogDeterminant; mitochondrial DNA genomes; amino acid composition; invariant sites; statistical tests; tRNA; Proboscidea]

Abstract.---The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequence and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests that were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., >95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla (Artiodactyla and Cetacea) and Paenungulata (Hyracoidea, Proboscidea, and Sirenia). In turn, some reasonable to strong evidence (>85%) was obtained for Hyracoidea with Sirenia, Dermoptera with Scandentia, Glires (Lagomorpha with Rodentia), and Afrotheria (Amblysomus, Macroscelidea, Paenungulata, and Tubulidentata). Otherwise, no other interordinal clades were supported at these reasonable to strong levels. This overall lack of resolution for eutherian interordinal clusters agrees with other studies that further progress will continue to be slow and difficult. Further resolution will require the integration of more recently published data, the continued sampling of taxa and characters, and the use of more powerful methods of data analysis.
[Congruence; eutherian mammals; gene sequences; morphology; phylogeny.]

Abstract.---We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid binding protein (IRBP), von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora, Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set, we recognized nine mitochondrial partitions (stems and loops, respectively, for 12S rRNA, tRNA valine, 16S rRNA; first, second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony, minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99-100% bootstrap support for Afrotheria and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also high bootstrap support (89-100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic analyses. Mitochondrial-gene trees associate cow and horse together, whereas nuclear-gene trees associate cow and hedgehog and these two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.
[Afrotheria; base composition; Eutheria; Paenungulata; phylogeny reconstruction]

Abstract.---We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
[amino acid composition, K/T boundary, CSR Logdeterminant, mammalian evolution, mitochondrial DNA genomes, rodent monophyly]

Abstract.---Shared insertions or deletions (indels) in protein-coding DNA can be strong indicators of the monophyly of a taxon. A three-amino acid deletion had previously been noted in the eye lens protein (A-crystallin of two species of sloths and two species of anteaters, which represent the Pilosa, one of the two infraorders of Xenarthra (Edentata). This deletion has not been observed in 55 species from 16 other eutherian orders, nor in two species of marsupials and 34 non-mammalian vertebrates, from birds to shark. At the genomic level, we have now detected this deletion in two species of armadillos of the second xenarthran infraorder, Cingulata, as well as in an additional species of anteater. Phylogenetic trees were constructed from a 145-bp sequence of the (A-crystallin gene of 39 tetrapod species, supporting xenarthran monophyly with values from 86 to 90%. To quantify the additional support for xenarthran monophyly, as given by the three-residue deletion, we computed the probabilities for the occurrence of this deletion per evolutionary time unit for alternative hypothetical tree topologies. In the obtained estimates, the six trees in which the xenarthran subgroups are unresolved or paraphyletic give an increasingly lower likelihood than the two trees which assume xenarthran monophyly. For the monophyletic trees, the probability that the deletion observed in the xenarthrans is due to a single event is >0.99. Thus, this deletion in (A-crystallin gives strong molecular support for the monophyly of this old and diverse order.
[Edentata; indels; molecular phylogeny; Xenarthra.]

Abstract.---Paleontologists long have argued that the most important evolutionary radiation of mammals occurred during the early Cenozoic, if not that all eutherians originated from a single common post-Cretaceous ancestor. Nonetheless, several recent molecular analyses claim to show that because several interordinal splits occurred during the Cretaceous, a major therian radiation was then underway. This claim conflicts with statistical evidence from the well-sampled latest Cretaceous and Cenozoic North American fossil record. Paleofaunal data confirm that the there were fewer mammalian species during the latest Cretaceous than during any interval of the Cenozoic, and that a massive diversification took place during the early Paleocene, immediately after a mass extinction. Measurement data show that Cretaceous mammals were on average small and occupied a narrow range of body sizes; after the Cretaceous-Tertiary mass extinction, there was a rapid and permanent shift in the mean. The fact that there was an early Cenozoic mammalian radiation is entirely compatible with the existence of a few Cretaceous splits among modern mammal lineages.

Abstract.---Using the set of all published vertebrate mtDNA protein sequences as of May 1998, plus unpublished examples for elephant and birds, we examine divergence times in Placentalia and Aves. Using a parsimony based test, a subset of slower evolutionary rate placental sequences that do not appear to violate the clock assumption are identified. Analysing just these sequences decreases support for Marsupionta and the carnivore + perissodactyl group, but increases support for armadillo diverging earlier than rabbit (which may represent the whole Glires group). A major theme of the paper is to use more comprehensive divergence time standard error estimates. Using the well studied horse/rhino split estimated to be 55 million years before present (mybp), the splitting time within carnivores is confidently shown to be older than 50 million years. Some of our estimates of divergence times within placentals are relatively old at up to 169 million years, but within 2 standard errors of other published estimates. The whale/cow split at 65 mybp may be older than commonly assumed. All the sampled splits between fereuungulates (the clade of carnivores, cetartiodactyls, perissodactyls, and pholidotes) seem to be distinctly before the KT boundary. Combined with analyses suggesting a close relationship between elephants (representing Afrotheria) and armadillos (Xenarthra), our timing of this splitting is coincident with the opening of the South Atlantic, a major vicariant event. Recalibrating with this event (at 100 mybp), we obtain younger estimates for the earliest splits among placentals. Divergence times within birds are also assessed using previously unpublished sequences. We fail to reject a clock for all taxa available. Unfortunately, available deep bird calibration points are questionable, so, a new calibration based on the age of the Anseriform stem lineage is estimated. The divergence time of rhea and ostrich may be much more recent than commonly assumed, while that of passerines may be older. Our major concern is the rooting point of the bird subtree, as the nearest outgroup (alligator) is very distant.
[molecular divergence times, bird phylogeny, mammal order phylogeny, mitochondrial genomes, sequencing errors]

Abstract.---Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, particularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebirds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bird lineages and the lack of characters from an extant outgroup for birds which is closely related to them by measure of time. To help resolve this question we have sequenced entire mitochondrial (mt) genomes for five birds (a rhea, a duck, a falcon, and two songbirds), one crocodilian and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences together with published sequences (18 taxa total) yield the same optimal tree topology in which a songbird (Passeriformes) is sister to all the other bird taxa. A basal position for waterfowl among the bird study taxa is rejected based on maximum likelihood analyses. However, neither the conventional view, in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in the same manner. In likelihood analyses of a subset of seven birds, alligator, and turtle (9 taxa total), we find that increasing the number of parameters in the model shifts the optimal topology from one with a songbird basal among birds to the conventional view with ratites diverging basally, and that likelihood scores for the two trees are not significantly different. Thus, although our largest set of taxa and characters support a tree with songbirds diverging basally among birds, position of this earliest divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterfowl/chicken clade and ratites, relative to songbirds and falcon. We find support for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.
[bird phylogeny, turtle phylogeny, amniote phylogeny, mitochondrial genomes, Passeriformes, ratites]

Abstract.---The discrepancy between theoretical and observed distributions of tree shapes in recent surveys of phylogeny estimates has lead to investigations of possible biological and methodological causes. I investigated whether the phylogenetic quality of characters is related to the tree shape on which they evolve. Simulated evolution revealed shape-related tendencies for characters to indicate correct cladistic relationships; these differences were measured by examining the characters directly, without deriving any phylogeny estimates. Tree stemminess indices correlated strongly with character quality when characters evolved either speciationally or phyletically. Tree balance was a significant correlate of character quality under speciational evolution, but not under phyletic evolution. These results help explain the findings of other simulation studies. It might be possible, with additional study of the behavior of evolving characters and their interaction with phylogenetic methods, to increase the accuracy of tree estimation and compensate for potential biases related to shape. These results give further reason for caution in trusting phylogeny estimates.
[Character simulation; phylogenetic accuracy; phylogenetic bias; tree balance; tree shape; tree stemminess; tree topology.]

Abstract.---The concentrated changes test (CCT) calculates the probability that changes in a binary character are distributed randomly on the branches of a cladogram. This test is used to examine hypotheses of correlated evolution, especially cases where changes in the state of one character influences changes in the state of another character. The test may be sensitive to the addition of branches lacking either trait of interest (white branches). To examine the effects of the proportion of white branches and of tree topology on the CCT probability, we conducted a simulation analysis using a series of randomly-generated 100-taxon trees, in addition to a nearly perfectly balanced (symmetrical) and a completely imbalanced (asymmetrical) 100-taxon tree. Using two models of evolution (gains only, or gains and losses), we evolved character pairs randomly onto these trees to simulate cases where (1) characters evolve independently (i.e., no correlation among the traits) and (2) all changes in the dependent character occur on branches containing the independent trait (i.e., a strong correlation among the traits). This allowed us to evaluate the sensitivity of the CCT to type I and type II errors, respectively. In our simulations, the CCT did not appear to be overly sensitive to the inclusion of white branches (low likelihood of type I error using both CCT probabilities < 0.05 and < 0.01). However the CCT was susceptible to type II error when the proportion of white branches is < 20%. The test was also sensitive to tree shape and was positively correlated to the tree imbalance statistic I (Colless). Finally, the CCT responded differently for simulations where only gains were allowed relative to those where both gains and losses were permitted. Our results indicate that the CCT is unlikely to detect correlation between characters when no such correlation exists. However, when a trait can be gained but not lost, the CCT is conservative and may fail to detect true correlations among traits (increased type II error). Determination of the sampling universe (taxa included in the comparative analysis) can strongly influenced the probability of making such type II errors. We suggest guidelines to circumvent these limitations.
[type I error; type II error; power; tree topology; tree balance; correlated evolution; character correlation; taxon sampling.]