* Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
Asa Zoological Park, Hiroshima, Japan
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Abstract |
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Key Words: Afrotheria genome monophyletic phylogenetic taxon SINE
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Introduction |
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Emergence of new SINEs during evolution is not well understood. Apparently, SINEs are specific to order, family, genus, or, sometimes, even to species (Kido et al. 1991; Takasaki et al. 1994; Shedlock and Okada 2000). This suggests that SINEs were newly created sporadically in a common ancestor of some lineages during evolution. For example, Alus were created in a common ancestor of primates and are thus only present in primate genomes (Schmid 1996; Batzer and Deininger 2002). CHR-1 and CHR-2 SINEs were created in a common ancestor of cetaceans, hippopotamuses, and ruminants and are thus present only in these genomes (Shimamura et al. 1997; Shimamura et al. 1999). Horizontal transfer of SINEs (Hamada et al. 1997), as well as that of LINEs (Kordis and Gubensek 1998), is believed to be very rare, so the distribution of SINEs among animals generally reflects their phylogenetic relationships. To date, more than 40 families of SINEs have been characterized, and no example was reported in which the same family of SINEs was sporadically distributed among different species, except for SmaI SINEs in salmonid species (Hamada et al. 1997). Therefore, the sporadic distribution of SINEs is informative for phylogenetic inference (Serdobova and Kramerov 1998; Shimamura et al. 1999; Nikaido et al. 2001).
The possibility that afrotherian animals were related was first recognized by de Jong, Zweers, and Goodman (1981), who proposed that elephant, hyrax, aardvark, and elephant shrew form a monophyletic group by determining alpha Acrystallin protein sequences of several mammalian species. Following this study, several groups independently confirmed this hypothesis by molecular analyses (e.g., de Jong, Leunissen, and Wistow 1993; Madsen et al. 1997; Springer et al. 1997; Madsen et al. 2001; Murphy et al. 2001a, 2001b). Currently, animals such as sea cow, tenrec, and golden mole are also recognized as afrotherians, and the superorder Afrotheria is now accepted as one of the biggest assembly among the placental mammals (e.g., Hedges 2001). Accordingly, placental mammals are now divided into four large groups, namely Xenarthra (edentatans), Afrotheria, Laurasiatheria (carnivores, cetartiodactyls, chiropterans, eulipothyphlans, perissodactyls, and pholidotans), and Euarchonta (primates, dermopterans, and scandentians) plus Glires (rodents and lagomorphans) (e.g., Waddell, Okada, and Hasegawa 1999; Cao et al. 2000; Scally et al. 2001). This assembly contradicts the hypothesis suggested by morphological classifications, which failed to define the precise position of aardvarks and elephant shrews among the mammalian taxa (Novacek 1992). Based on the molecular data, it is currently proposed that Afrotheria includes species belonging to six orders, namely Hyracoidea, Sirenia, Proboscidea, Tubulidentata, Macroscelidea, and Insectiv-ora, some of which had been distantly classified previously. In particular, the monophyly of the order Insectivora was denied by the afrotherian status and it was divided into two groups, Eulipotyphla (hedgehog, mole, and sorex) and Afrosoricida (tenrec and golden mole) (Stanhope et al. 1998b). From an evolutionary point of view, the major contribution of establishing afrotherian membership is not only to recognize a novel clade, but also to connect phylogeny with plate tectonics (Hedges 2001). Although Africa is now connected to Eurasia, it was isolated from the other continents between 105 and 40 MYBP (Hedges 2001). This caused reproductive isolation that presumably gave rise to Afrotherian species. Although from a molecular point of view the afrotherian unity appears robust, its morphological synapomorphy has not been discovered, and it is now being explored extensively (e.g., Whidden 2002). Therefore, from both morphological and molecular perspectives, it is important for us to identify additional evidence that unifies the afrotherians into one clade (van Dijk et al. 2001).
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Materials and Methods |
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We isolated genomic DNAs from the following species according to the procedure described by Blin and Stafford (1976): Cape hyrax (Procavia capensis), dugong (Dugong dugong), African elephant (Loxodonta africana), lesser hedgehog tenrec (Echinops telfairi), Cape golden mole (Chrysochloris asiatica), aardvark (Orycteropus afer), elephant shrew (Elephantulus sp.), common long-nosed armadillo (Dasypus novemcinctus), spotted hyena (Crocuta crocuta), Ryukyu flying fox (Pteropus dasymallus), horseshoe bat (Rhinolophus pumilus), cow (Bos taurus), hippopotamus (Hippopotamus amphibius), bottlenosed dolphin (Tursiops truncatus), house mouse (Mus musculus), and human (Homo sapiens).
The nucleotide sequence reported in this paper has been submitted to GenBank and has been assigned accession numbers AB095814 to AB095844
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Results and Discussions |
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In analyzing the PCR products generated using primers F3 and R1, we detected two bands with slightly different mobilities (fig. 2, panel c). We sequenced these bands, and the sequence alignment revealed that the upper band was the AfroSINE we had already characterized, whereas the shorter band contains a small 25-bp deletion at the 3' end (see fig. 1A). This deletion type is found in all afrotherian species. An alignment of the consensus sequences of each subfamily of AfroSINEs from all afrotherian species is shown in figure 3. In this alignment, both the sequences isolated by screening the genomic library and those of the PCR products are included. Consensus sequences were deduced from at least more than three sequences for each subfamily. The diagnostic deletions shared among subfamilies in the alignment are obvious, but no distinct diagnostic nucleotide changes were found in these sequences.
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As described, monophyly of species belonging to Afrotheria and Paenungulata, respectively, has already been established by DNA sequence comparison. However, the interrelationships among these species have not been resolved. For example, phylogenetic relationships among Paenungulata (hyraxes, sea cows, and elephants), Afrosoricida (tenrecs and golden moles), Tubulidentata (aardvarks), and Macroscelidea (elephant shrews) are now in controversy (Madsen et al. 2001; Murphy et al. 2001a, 2001b). An intrarelationship of paenungulates is also still unresolved (Amrine and Springer 1999; Madsen et al. 2001; Murphy et al. 2001a, 2001b), which concerns the issue of tethytherian monophyly or paraphyly. The latter issue is very important in that rejection of tethytherian monopyhly challenges the traditional hypothesis that connects Sirenia and Proboscidea. If this is the case, the phylogenetic position of extinct Desmostylia (tethytheria relatives, see Shoshani 1998) will become much more uncertain (e.g., Porter, Goodman, and Stanhope 1996; Ozawa, Hayashi, and Mikhelson 1997; Springer et al. 1997; Stanhope et al. 1998a). Recently, this problem was extensively discussed by Amrine and Springer (1999). The AfroSINEs characterized in this study might be very useful as phylogenetic markers to resolve the phylogenetic relationships of afrotherians. In particular, insertion analyses of members of the HSP subfamily may be instrumental in settling the long-standing dispute regarding tethytherian phylogeny.
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Acknowledgements |
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Footnotes |
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