 Reference Base  The complete mitochondrial DNA sequence of the Greater In... |
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Xu, Xiufeng; Janke, A.; Arnason, U., 1996. The complete mitochondrial DNA sequence of the Greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea).. Molecular Biology and Evolution 13 (9): 1167-1173, fig. 1, tables 1-8
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World |
| Subject: |
Taxonomy - Evolution |
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Indian Rhino |
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The Phylogenetic Relationships of Carnivora, Perissodactyla, Artiodactyla, and Cetacea
Phylogenetic analyses based on single (Arnason and Johnsson 1992) and combined sequences of all (Janke et al. 1994) mtDNA protein-coding genes have grouped Carnivora and Artiodactyla (+ Cetacea) into a superordinal clade. The statistical support for this rela- tionship was detailed by Janke et al. (1994). The inclusion of a perissodactyl representative, the horse (Krettek, Gullberg, and Arnason 1995), has shown a much closer relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) than is generally recognized by classical approaches. In the present study we readdress these relationships by complementing the sampling with an additional perissodactyl, the Indian rhinoceros (family Rhinocerotidac), which is distantly related to the Equidae (horse), and a carnivore, the domestic cat (Lopez et al. 1996), of a family (Felidae) that is distantly related to the seals (family Phocidae). Thus the analysis included the following species: opossum, mouse, cow, tin whale, blue whale, domestic cat, harbor seal, grey seal, Indian rhinoceros, and horse. The phylogenetic analysis was based on the concatenated sequences of 12 peptide-coding mitochondrial genes. The NADH6 gene was not included because of the different nt composition of this gene relative to the other peptide-coding genes.
The phylogenetic analyses were performed both on nt and aa sequences applying different analytical approaches. Maximum-parsimony (MP) and neighborjoining (NJ) analyses were carried out with the PHYLIP program package (Felsenstein 1991), whereas the maximum-likelihood (ML) analyses were performed with both the PHYLIP (DNAML) and the MOLPHY (Adachi and Hasegawa 1995) program packages (PROTML and NUCML). At the nt level the analysis was based on nonsynonymous substitutions at first codon position, all substitutions at second codon position, and transversions at third codon position. First, second, first + second, and first + second + third codon positions were analyzed separately in order to examine the degree of support provided by each character set for a particular topology. Except for NJ analysis of second codon position all phylogenetic analysis (ML analysis not shown) resulted in the topology shown in figure 1. The bootstrap support for individual branches (a-g) is summarized in table 6.
The phylogenetic analyses supported a sister group relationship between Carnivora and Perissodactyla although the support for this relationship was not significant in all modes of analysis. This relationship was examined further by ML analysis of the aa sequences (PROTML with mtREV matrix). The analysis was undertaken because, relative to nt analysis, this mode of analysis is relatively insensitive to mutational and compositional effects. The three alternative hypotheses of the relationship between the carnivores and the ungulates were tested (table 7). The sister group relationship between the Carnivora and the Perissodactyla received by far the largest support also in this approach, although the traditional view of carnivores being an outgroup to ungulates (+ cetaceans) could not be rejected at the 5% level. The overall good, and in the case of the NJ analysis of aa sequences significant, support for a carnivore/ perissodactyl sister group relationship contradicts the classical view of ungulate relationships. The position of the cow was somewhat labile in the MP tree, but, consistent with previous studies (Janke et al. 1994), its grouping with the cetaceans was significantly supported by the NJ analysis. It is possible that the different support for the position of the cow, provided by different approaches, is a reflection of the somewhat slower evolutionary rate of the cow relative to the other species included in the analyses. If this is the case it suggests that NJ analysis is less sensitive to differences in evolutionary rates than is MP analysis.
Dating of the Evolutionary Divergence Between Rhinocerotidae and Equidae
Irrespective of the quality of fossil data, evolutionary separations are impossible to date precisely on the basis of the paleontological record. The reason for this is that a certain time of evolutionary separation is necessary before the development of morphological traits that can be recognized among fossil finds, even when the paleontological record is reasonably complete. The effects of incomplete paleontological records for the dating of evolutionary divergences have been addressed by Martin (1993). Although the author primarily addressed primate evolution the conclusions are of a general relevance, suggesting that paleontological finds will generally grossly underestimate the age of evolutionary divergences.
It is conceivable that radical ecological shifts will promote the development of morphological characteristics in such a way that the time between evolutionary separation and the development of these characteristics will be shorter than in cases where no drastic ecological shifts have taken place. Among the mammals the most drastic ecological shifts are probably the transitions from terrestrial to aquatic life. The divergence of the archeo- cetes from their artiodactyl relatives is not the only event of this kind, but the origin of the archeocetes is probably better documented by paleontological finds than any other similar event. The oldest archeocete fossils are 5254 million years old (Gingerich et al. 1994; Thewissen, Hussain, and Arif 1994). On the basis of the age of these fossils and analysis of the complete cytochrome b gene of more than 30 cetaceans plus several artiodactyls, it has been proposed that Cetacea and Artiodactyla separated ca 60 MYA (Arnason and Gullberg 1996).
The distances among eight species representing Perissodactyla (rhinoceros, horse), Carnivora (harbor seal. grey seal, domestic cat), Artiodactyla (cow), and Cetacea (fin whale, blue whale) plus the mouse (Rodentia) and the opossum (Marsupialia), are given in table 8. The comparison is based on the concatenated inferred protein sequence of 12 protein-coding mtDNA genes, excluding NADH6, which is encoded by a different strand relative to the other protein-coding genes. Based on an artiodactyl/cetacean separation 60 MYA, and taking into account the faster evolution of cetacean mtDNA, the values in table 8 suggest that the Rhinocerotidae and the Equidae had a last common ancestor 50 MYA (95% confidence limits 43.5-56.5 MYA).
The sequence of the cytochrome b gene of the black rhinoceros was reported by Irwin, Kocher, and Wilson (1991). The difference (aa, conservative nt) between the two rhinoceroses suggests that they diverged ca 30 MYA. This dating, however, should be considered as tentative until supported by additional data.
The presently proposed dating for the evolutionary separation between Rhinocerotidae and Equidae is consistent with the ca 50 MYA palaeontological dating (Prothero and Schoch 1989) of the evolutionary separation between the perissodactyl suborders Hippomorpha and Ceratomorpha. The Ceratomorpha includes rhinoceroses and tapirs, and a more precise molecular dating of the separation of the hippomorph Equidae and the ceratomorph Rhinocerotidae should, therefore, also include tapirid representation. The necessity of including tapir data in a comparison of this kind is exemplified by the fact that two molecular studies, one on restriction site mapping of the alphaglobin gene cluster (Flint, Ryder, and Clegg 1990) and one on aa sequence data of pancreatic polypeptide (Henry, Lance, and Conlon 1991), do not recognize tapirs and rhinoceroses as sister groups to the exclusion of the Equidae.
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