The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.
Several subfamilies of the salmonid Hpa I short interspersed element (SINE) family were isolated from salmonid genomes and were sequenced. For each genomic locus that represented the subfamily, amplification by PCR of the orthologous loci in the 12 fish aflowed us to determine the order of branching of the Pacific salmonid species. The deduced phylogeny suggests three evolutionary lines, namely, a line of chum salmon, pink salmon, and kokanee; a line of coho salmon and chinook salmon; and a line ofsteelhead trout. Our data also support a change in the phylogenetic ament of steelhead trout from Salmo to Oncorhynchus. We present here an extensive phylogenetic tree constructed from an analysis of differential insertion of SINEs, and we propose that SINE insertion analysis is one of the best available methods for clarifying the order of divergence of closely related species.A retroposon is defined as a nucleotide sequence, present initially as a cellular RNA transcript, that has been reincorporated into the genome, presumably via a cDNA intermediate. Retroposons constitute roughly 10% of the human genome and are similarly abundant in other mammalian genomes (1, 2). As a result, the remarkable fluidity of eukaryotic genomes reflects the contributions of retroposition (2) as well as mechanisms operating at the DNA level such as mutation and recombination (1-4). Retroposons can be unique to one species, a few species, a genus, or in some cases a family. Retroposition is therefore a specialized form of gene duplication, which is believed to be of major importance in the creation of genetic diversity during evolution (5).Nonviral retroposons are classified into three main groups: processed retropseudogenes, LINEs (long interspersed elements), and SINEs (short interspersed elements) (6). Except for the rodent type 1 and human Alu families (7,8), all of the SINE families examined to date have been shown to be derived from tRNAs (9)(10)(11)(12)(13)(14). In contrast to DNA transposable elements, which are often capable of being excised precisely, SINEs appear to be inserted irreversibly and should therefore provide an ideal evolutionary and phylogenetic marker (4).The Pacific salmon and trout (Oncorhynchus) not in other species (16). These results suggest that these SINEs were amplified specifically within certain salmonid lineages during evolution.Our data prompted us to attempt to construct a phylogenetic tree for the salmonid species by using SINE insertions as irreversible events that would serve as informative markers of evolution. In this report, we present a characterization of the four subfamilies of the Hpa I family.t These subfamilies were amplified in the four different ancestral species within the genus Oncorhynchus. Such characterization provides a highly reliable order of branching of the various species of Oncorhynchus. MATERIALS AND METHODSExperiments were performed by using standard techniques (18)(19)(20)(21).The fish species examined in this study and their geographic sources are listed in Table ...
Three families of tRNA-derived repeated retroposons in the genomes of salmonid species have been isolated and characterized. These three families differ in sequence, but all are derived from a tRNALYS or from a tRNA species structurally related to tRNALyS. The salmon Sma I family is present in the genomes of two species of the genus Oncorhynchus but not in other species, including five other species of the same genus. The charr Fok I family is present only in four species and subspecies of the genus Salvelinus. The third family, the salmonid Hpa I family, appears to be present in all salmonid species but is not present in species that are not members of the Salmonidae. Thus, the genome of protoSalmonidae was originally shaped by amplification and dispersion of the salmonid Hpa I family and then reshaped by amplification of the Sma I and Fok I families in the more recently evolved species of salmon and charr, respectively. We speculate that amplification and dispersion of retroposons may have played a role in salmonid speciation.Gene duplication is believed to be of major importance in creating genetic diversity (1). The genes for immunoglobulins, histocompatibility complexes, and globins are examples of this gene duplication. This mechanism operates at the DNA level and probably has as old a history as DNA genomes themselves. Another mechanism for maintaining the fluidity of eukaryotic genomes is that recently characterized retroposition, in which information in nonviral cellular RNA can flow back into the genome via cDNA intermediates (2,3). Retroposition creates additional sequence combinations through dispersal of genetic information and can shape and reshape eukaryotic genomes in many different ways (3,4). The precise mechanism of retroposition is at present speculative. Recently, Weiner and Meizels (5) presented an interesting hypothesis concerning the mechanism of generation of duplex DNA at the beginning of the DNA world, proposing that duplex DNA genomes may have been derived from earlier DNA genomes that replicated like retroviruses through an RNA intermediate. This suggests that the mechanism of retroposition might be closely linked to that of replication of retroviruses (6).The highly repetitive sequences that are interspersed throughout eukaryotic genomes have been classified into two categories based on size: long interspersed repetitive elements (LINEs), which include Li sequences, and short interspersed repetitive elements (SINEs), such as the primate Alu and rodent type 1 or 2 Alu families (7). Previously, highly repetitive and transcribable sequences have been found in the genome of the chum salmon (Oncorhynchus keta) (8,9). Like all SINE families examined so far (10-14) other than Alu (15, 16), this Sma I family [formerly the salmon polymerase (Pol) III/SINE family] has been shown to be derived from a tRNA; moreover the Sma I family has several of the characteristic features of retroposons and appears to be the youngest SINE family characterized to date.The genus Oncorhynchus has many s...
The specific features of the plasticity of adult stem cells are largely unknown. Recently, we demonstrated the hepatic differentiation of human adipose tissue-derived mesenchymal stem cells (AT-MSCs). To identify the genes responsible for hepatic differentiation, we examined the gene expression profiles of AT-MSC-derived hepatocytes (AT-MSC-Hepa) using several microarray methods. The resulting sets of differentially expressed genes (1639 clones) were comprehensively analyzed to identify the pathways expressed in AT-MSC-Hepa. Clustering analysis revealed a striking similarity of gene clusters between AT-MSC-Hepa and the whole liver, indicating that AT-MSC-Hepa were similar to liver with regard to gene expression. Further analysis showed that enriched categories of genes and signaling pathways such as complementary activation and the blood clotting cascade in the AT-MSC-Hepa were relevant to liver-specific functions. Notably, decreases in Twist and Snail expression indicated that mesenchymal-to-epithelial transition occurred in the differentiation of AT-MSCs into hepatocytes. Our data show a similarity between AT-MSC-Hepa and the liver, suggesting that AT-MSCs are modulated by their environmental conditions, and that AT-MSC-Hepa may be useful in basic studies of liver function as well as in the development of stem cell-based therapy.
Partial regions of the mRNA encoding a major part of translation elongation factor 1 alpha (EF-1 alpha) from a mitochondrion-lacking protozoan, Glugea plecoglossi, that belongs to microsporidians, were amplified by polymerase chain reaction (PCR) and their primary structures were analyzed. The deduced amino acid sequence was highly divergent from typical EF-1 alpha's of eukaryotes, although it clearly showed a eukaryotic feature when aligned with homologs of the three primary kingdoms. Maximum likelihood (ML) analyses on the basis of six different stochastic models of amino acid substitutions and a maximum parsimony (MP) analysis consistently suggest that among eukaryotic species being analyzed, G. plecoglossi is likely to represent the earliest offshoot of eukaryotes. Microsporidians might be the extremely ancient eukaryotes which have diverged before an occurrence of mitochondrial symbiosis.
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