| 其他摘要 | The study of evolutionary relationships among organisms is vital in evolutionary biology and receiving unprecedented attention in recent times. U.S.A and some European countries have initiated "The Tree of Life (TOL)" program which is going to have far-reaching impact on biological development. Aiming at this international focus, we attempt to conduct phylogenetic analyses of mammalian order Carnivora, an intriguing animal group with evolutionarily theoretic significance and conservation values. Besides popular mitochondrial (mt) genes, unlinked nuclear genes are also utilized as the source of characters in our study. The carnivore phylogeny was inferred from combined analyses of multiple mt and nuclear gene sequences. In addition, we unexpectedly observed SENEs insertion in an intronic region from some carnivoran species. Considering that this intronic region may be a hot spot for the insertions of SINEs, we also extended SINEs analyses of the same intron by including additional taxa from other placental orders of mammals beyond the Carnivora. Extant carnivores include 11 families and 280 species. In general, they are divided into two superfamilies: Caniformia (Ursidae, Canidae, Procyonidae, Mustelidae, Otariidae, Odobenidae and Phocidae) and Feliformia (Viverridae, Felidae, Hyaenidae and Herpestidae). The Caniformia is rather heterogeneous and morphologically diverse, and hence has had many controversial issues surrounding its phylogeny. We sequenced four nuclear and one protein-coding mt genes (4417bp in total) from 16 species within Caniformia to investigate interfamilial relationships and the placements of the two pandas. Phylogenetic results showed that nuclear and mt genes are phylogenetically complementary for the higher-level analyses, resulting in a well-supported tree topology for most branches when they were combined. The preferred hypothesis provides evidence in favor of the red panda as the closest taxon to the sister-grouping of Procyonidae and Mustelidae, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae, and Canidae, the most basal lineage in the Caniformia. The giant panda was the earliest diverging member of Ursidae, Although the placements of pinnipeds and Ursidae were strongly supported in ML and Bayesian analyses of combined nuclear and mt genes, it was not in MP analysis. Therefore, the resolution of trichotomy among pinnipeds, Ursidae and the clade containing Procyonidae, Mustelidae and the red panda may be the emphases in future carnivore higher-level phylogeny. Not only interfamilial, but also intrafamilial relationships within Carnivora are subjects of debate, especially in case of Ursidae and Felidae. Because they represent typical examples of rapid evolutionary radiation and recent speciation events, so attempts to clarify relationships among the species within the two families have encountered challenge. We are among the first to employ two nuclear DNA data, together with previously published five mt data in both separate and combined analyses (about 4kb in total) to gain new insight into the phylogeny of Ursidae (8 bear species). Our study not only corroborated prior hypotheses, positioning the giant panda and spectacled bear most basaily and grouping the brown and polar bear together but also supported the close relatedness of Asiatic and American black bears. Notably, nuclear analyses suggested a novel sister-taxa association between sloth bear and sun bear with strong support, in contrast to those from the mt and combined analyses recognizing the sloth bear as the earliest diverging species among the ursine species. Thus, the precise positions of the sun and sloth bears in bear phylogeny still required confirmation by analyzing additional character information* In addition* we also discussed possible reasons for conflicting signals between nuclear and mt genes. The cat species of Felidae is generally assigned into the pantherine, domestic cat, and ocelot lineages. The pantherine lineage consists of five big cats of genus Panther a and a great many midsized cats species. As it is the most recently evolved and largest felid group in Felidae, the pantherine lineage has demonstrated greatest confusion in its phylogeny. We are the first to explore the potential of three nuclear genes in phylogenetic study of 14 cat species, mainly pantherine cats. Moreover, two complete protein-coding mt genes newly sequenced by us and four previously reported mtgenes were also added to our analyses. Evolutionary patterns of different genes and their values for resolution of low level feline questions were also discussed. Analyses of 9 genes from pantherine cats in a variety of combinations produced several valuable conclusions. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within the genus revealed a novel branching pattern. In addition, close association of the clouded leopard to Panthera, the phylogenetic redefinition of pallas cat within the domestic cat group, and the relatedness of puma and cheetah were all important finding in the resulting phytogenies. Our study demonstrate that nuclear DNA accumulated low sequence divergence in the event of tracking the evolutionary history for such a young lineage and consequently had limited phylogenetic contributions. They are expected to give better resolution at higher-level phylogeny of carnivores. An analysis of the nuclear p~fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of SINE insertion events. MIRs are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage -specific SINEs are also found to have independently inserted into this intron in Camivora, Artiodactyla and Lagomorpha. In Carnivora, the unique amplification pattern of CAN SINE provides important evidence for the "pan-carnivore" hypothesis. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs5 suggesting that the MIR element is a hot spot for successive insertions of other SINEs. Our study indicated that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. In the thesis, we also elaborately describe some tree reconstruction methods that were widely used in modem phylogenetics* and expatiate on enormous superiority and potential of a new synthesized discipline as a result of the genomic era coming, that is "Phylogenomics", to the reconstruction of "the Tree of Life". |
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