| 1. |
- Andersson, Jan O, et al.
(författare)
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Genome degradation is an ongoing process in Rickettsia
- 1999
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Ingår i: Molecular biology and evolution. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038 .- 1537-1719. ; 16:9, s. 1178-1191
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- To study reductive evolutionary processes in bacterial genomes, we examine sequences in the Rickettsia genomes which are unconstrained by selection and evolve as pseudogenes, one of which is the metK gene, which codes for AdoMet synthetase. Here, we sequenced the metK gene and three surrounding genes in eight different species of the genus Rickettsia. The metK gene was found to contain a high incidence of deletions in six lineages, while the three genes in its surroundings were functionally conserved in all eight lineages. A more drastic example of gene degradation was identified in the metK downstream region, which contained an open reading frame in Rickettsia felis. Remnants of this open reading frame could be reconstructed in five additional species by eliminating sites of frameshift mutations and termination codons. A detailed examination of the two reconstructed genes revealed that deletions strongly predominate over insertions and that there is a strong transition bias for point mutations which is coupled to an excess of GC-to-AT substitutions. Since the molecular evolution of these inactive genes should reflect the rates and patterns of neutral mutations, our results strongly suggest that there is a high spontaneous rate of deletions as well as a strong mutation bias toward AT pairs in the Rickettsia genomes. This may explain the low genomic G + C content (29%), the small genome size (1.1 Mb), and the high noncoding content (24%), as well as the presence of several pseudogenes in the Rickettsia prowazekii genome.
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| 2. |
- Andersson, SGE, et al.
(författare)
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Molecular phylogeny and rearrangement of rRNA genes in Rickettsia species
- 1999
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Ingår i: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 16:7, s. 987-995
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- It has previously been observed that Rickettsia prowazekii has an unusual arrangement of the rRNA genes. In this species, the three rRNA genes, 16S (rrs), 23S (rrl), and 5S (rrf), are not linked in the typical arrangements for bacteria. Rather, the 16S rR
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| 3. |
- Brynnel, EU, et al.
(författare)
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Evolutionary rates for tuf genes in endosymbionts of aphids
- 1998
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Ingår i: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 15:5, s. 574-582
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The gene encoding elongation factor Tu (tuf) in aphid endosymbionts (genus Buchnera) evolves at rates of 1.3 X 10(-10) to 2.5 X 10(-10) nonsynonymous substitutions and 3.9 X 10(-9) to 8.0 X 10(-9) synonymous substitutions per position per year. These rate
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| 4. |
- Greenwood, AD, et al.
(författare)
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Nuclear DNA sequences from late Pleistocene megafauna
- 1999
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Ingår i: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 16:11, s. 1466-1473
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We report the retrieval and characterization of multi- and single-copy nuclear DNA sequences from Alaskan and Siberian mammoths (Mammuthus primigenius). In addition, a nuclear copy of a mitochondrial gene was recovered. Furthermore, a 13,000-year-old grou
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| 5. |
- Hastad, O, et al.
(författare)
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Nucleotide substitution models and estimation of phylogeny
- 1998
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Ingår i: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 15:11, s. 1381-1389
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The nucleotide substitution matrix inferred from avian data sets using cytochrome b differs considerably from the models commonly used in phylogenetic analyses. To analyze the possible effects of this particular pattern of change in phylogeny estimation w
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| 6. |
- Pamilo, P, et al.
(författare)
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Evolution of the Sry genes
- 1997
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Ingår i: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 14:1, s. 49-55
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Existing DNA sequence data on the Sry gene, the mammalian sex-determining locus in the Y chromosome, were analyzed for primates, rodents, and bovids. In all three taxonomic groups, the terminal sequences evolved faster than the HMG (high mobility group) b
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| 7. |
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| 8. |
- Wittzell, Håkan, et al.
(författare)
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Concerted evolution of two Mhc class II B loci in pheasants and domestic chickens
- 1999
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Ingår i: Molecular biology and evolution. - 0737-4038. ; 16:4, s. 479-490
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Tidskriftsartikel (refereegranskat)abstract
- The major histocompatibility complex (Mhc) of the ring-necked pheasant contains two polymorphic Mhc class II B genes. We show here, by screening of a cDNA library and RT-PCR from RNA, that both of these loci, Phco-DAB1 and Phco-DAB2, normally are transcribed in the spleen. They differ mainly in the 3' untranslated (UT) region, with the transcript lengths, not including the poly(A) tails, being 1,100 nt for DAB1 and 955 nt for DAB2. These two loci are orthologous to the B-LBI and B-LBII loci of the domestic chicken, respectively. DAB1 and DAB2 therefore seem to have evolved from a duplication before the split of the evolutionary lineages leading to the pheasant and the domestic chicken ca. 20 MYA. This is the first report of an orthologous relationship between avian Mhc genes. Yet, the third exons of DAB1 and DAB2 were identical in all available sequences and differed at 10 positions from the exon 3 sequences of B-LBI/B-LBII. The species-specific exon 3 suggests that DAB1 and DAB2 are subject to concerted evolution, i.e., interlocus genetic exchange. The exon 2 sequences show characteristic polymorphism, with hypervariable segments occurring in different combinations in different alleles. Given the divergence in the 3'UT region, the finding of the same exon 2 sequence at both the DAB1 and the DAB2 loci in one of the pheasant haplotypes also suggests that interlocus genetic exchange does occur. Accordingly, the exon 2 sequences tended to cluster irrespective of locus in the phylogenetic analyses. Genetic exchange simultaneously involving both exon 2 and exon 3 may be facilitated by the short length of the intervening intron (<100 bp) in pheasants and domestic chickens compared with, e.g., humans (about 3 kb).
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| 9. |
- Xu, Xiufeng, et al.
(författare)
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The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla and Artiodactyla (plus Cetacea)
- 1996
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Ingår i: Molecular biology and evolution. - 0737-4038. ; 13:9, s. 1167-1173
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Tidskriftsartikel (refereegranskat)abstract
- The sequence (16,829 nt) of the complete mitochondrial genome of the greater Indian rhinoceros, Rhinoceros unicornis, was determined. Like other perissodactyls studied (horse and donkey) the rhinoceros demonstrates length variation (heteroplasmy) associated with different numbers of repetitive motifs in the control region. The 16,829-nt variety of the molecule includes 36 identical control region motifs. The evolution of individual peptide-coding genes was examined by comparison with a distantly related perissodactyl, the horse, and the relationships among the orders Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) were examined on the basis of concatenated sequences of 12 mitochondrial peptide-coding genes. The phylogenetic analyses grouped Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) into a superordinal clade and within this clade a sister group relationship was recognized between Carnivora and Perissodactyla to the exclusion of Artiodactyla (+ Cetacea). On the basis of the molecular difference between the rhinoceros and the horse and by applying as a reference the Artiodactyl/Cetacean divergence set at 60 million years ago (MYA), the evolutionary divergence between the families Rhinocerotidae and Equidae was dated to approximate to 50 MYA.
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