TL;DR: A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches was applied to estimate the divergence ages between the major clades of ruminants, confirming the traditional view that separates Tragulina and Pecora.
Abstract: The ruminants constitute the largest group of ungulates, with >190 species, and its distribution is widespread throughout all continents except Australia and Antarctica. Six families are traditionally recognized within the suborder Ruminantia: Antilocapridae (pronghorns), Bovidae (cattle, sheep, and antelopes), Cervidae (deer), Giraffidae (giraffes and okapis), Moschidae (musk deer), and Tragulidae (chevrotains). The interrelationships of the families have been an area of controversy among morphology, palaeontology, and molecular studies, and almost all possible evolutionary scenarios have been proposed in the literature. We analyzed a large DNA data set (5,322 nucleotides) for 23 species including both mito- chondrial (cytochrome b, 12S ribosomal RNA (rRNA), and 16S rRNA) and nuclear (•-casein, cytochrome P-450, lactoferrin, andfi-lactalbumin) markers. Our results show that the family Tragulidae occupies a basal position with respect to all other ruminant families, confirming the traditional view that separates Tragulina and Pecora. Within the pecorans, Antilocapridae and Giraffidae emerge first, and the families Bovidae, Moschidae, and Cervidae are allied, with the unexpected placement of Moschus close to bovids rather than to cervids. We used these molecular results to assess the homoplastic evolution of morphological characters within the Ruminantia. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches was applied to estimate the divergence ages between the major clades of ruminants. The evolutionary radiation of Pecora occurred at the Early/Late Oligocene transition, and Pecoran families diversified and dispersed rapidly during the Early and Middle Miocene. We propose a biogeographic scenario to explain the extraordinary expansion of this group during the Cenozoic era. (Bayesian relaxed clock; Bovidae; molecules; morphology; Moschidae; phylogeny; Ruminantia.)
TL;DR: The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Giraffidae are more primitive.
Abstract: A total of 7,806 nucleotide positions derived from one mitochondrial and eight nuclear DNA segments were used to provide a robust phylogeny for members of the order Artiodactyla. Twenty-four artiodactyl and twocetaceanspecieswere included, andthe horse(order Perissodactyla) was used as the outgroup. Limited rate heterogeneity was observed among the nuclear genes. The partition homogeneity tests indicated no coneicting signal among the nuclear gene fragments, so the sequence data were analyzed together and as separate loci. Analyses based on the individual nuclear DNAfragmentsandon34uniqueindelsallproducedphylogenieslargelycongruentwiththetopology from the combined data set. In sharp contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data showed high levels of homoplasy, failed to produce a robust phylogeny, and were remarkably sensitive to taxon sampling. The nuclear DNA data clearly support the paraphyletic nature of the Artiodactyla. Additionally, the family Suidae is diphyletic, and the nonruminating pigs and peccaries (Suiformes) were the most basal cetartiodactyl group. The morphologically derived Ruminantia was always monophyletic; within this group, all taxa with paired bony structures on their skulls clustered together. The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Girafedae are more primitive. (Artiodactyla; Cetacea; cytochrome b; indels; nuclear DNA; Ruminantia) The order Artiodactyla has a worldwide distribution and at present comprises three morphologically diverse suborders, the Suiformes, Tylopoda, and Ruminantia. Their evolution dates to the Paleocene (»70-80 million years ago; Waddell et al., 1999), the Suiformes (currently including swine and hippopotamus) apparently being the most primitive group in the order, based on fossil (O'Leary and Geisler, 1999) and other morphological characters (nonrumi- nating, two-/three-chambered stomach, re- tained upper incisors and canines, low crowned cusped molars, and absence of hornsorantlers;Nowak,1999).Although the suborder Tylopoda (camel and llama) shares many of these primitive features, the three- chambered digestive system of its members is based on rumination, and their molars are high crowned with crescents (Nowak, 1999). These latter dental features are considered to be synapomorphic, uniting the Tylopoda with the most derived suborder Ruminan- tia (Tragulidae-chevrotain; Antilocapridae- pronghorn; Girafedae-giraffe and okapi; Cervidae-deer, elk, and muntjac; Bovidae- cattle, sheep, and other antelope). Except for the primitive chevrotain (which is charac- terized by a three-chambered stomach, pres- 1
TL;DR: This morphological analysis of a comprehensive set of taxa and characters offers a robust solution to the origins of Hippopotamidae, which appears to be deeply nested within the otherwise extinct artiodactyl family Anthracotheriidae, most precisely within the most advanced selenodont forms.
Abstract: The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution. Here, we compare opposing hypotheses implicating several “suiform” families. This morphological analysis of a comprehensive set of taxa and characters offers a robust solution to the origins of Hippopotamidae. This family appears to be deeply nested within the otherwise extinct artiodactyl family Anthracotheriidae, most precisely within the most advanced selenodont forms. The proposed sister group of hippos is the middle to late Miocene African semiaquatic Libycosaurus. Any close relationships of hippos with suoids, particularly with Tayassuidae, are rejected. Furthermore, the clade (Hippopotamidae, Anthracotheriidae) is proposed as the sister group of the Cetacea, offering broad morphological support for a molecular phylogeny, such support being also consistent with the fossil record. Corroboration of this relationship requires an exploration of anthracothere affinities with other Paleogene artiodactyls. Among those, the position of Ruminantia is a central question, still to be solved. Further progress in this debate is likely to come from morphological studies of paleontological data, whether known or still to be discovered.