| 1. |
- Andersson, Jan O, et al.
(author)
-
Genome degradation is an ongoing process in Rickettsia
- 1999
-
In: Molecular biology and evolution. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038 .- 1537-1719. ; 16:9, s. 1178-1191
-
Journal article (other academic/artistic)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.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Webster, Matthew T., et al.
(author)
-
Compositional evolution of the human and chimpanzee genomes
- 2003
-
In: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 20:2, s. 278-286
-
Journal article (other academic/artistic)abstract
- We have examined the compositional evolution of noncoding DNA in the primate genome by comparison of lineage-specific substitutions observed in 1.8 Mb of genomic alignments of human, chimpanzee, and baboon with 6542 human single-nucleotide polymorphisms (SNPs) rooted using chimpanzee sequence. The pattern of compositional evolution, measured in terms of the numbers of GC→AT and AT→GC changes, differs significantly between fixed and polymorphic sites, and indicates that there is a bias toward fixation of AT→GC mutations, which could result from weak directional selection or biased gene conversion in favor of high GC content. Comparison of the frequency distributions of a subset of the SNPs revealed no significant difference between GC→AT and AT→GC polymorphisms, although AT→GC polymorphisms in regions of high GC segregate at slightly higher frequencies on average than GC→AT polymorphisms, which is consistent with a fixation bias favoring high GC in these regions. However, the substitution data suggest that this fixation bias is relatively weak, because the compositional structure of the human and chimpanzee genomes is becoming homogenized, with regions of high GC decreasing in GC content and regions of low GC increasing in GC content. The rate and pattern of nucleotide substitution in 333 Alu repeats within the human-chimpanzee-baboon alignments are not significantly affected by the GC content of the region in which they are inserted, providing further evidence that, since the time of the human-chimpanzee ancestor, there has been little or no regional variation in mutation bias.
|
|
| 5. |
- Andersson, SGE, et al.
(author)
-
Molecular phylogeny and rearrangement of rRNA genes in Rickettsia species
- 1999
-
In: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 16:7, s. 987-995
-
Journal article (other academic/artistic)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
|
|
| 6. |
- Brynnel, EU, et al.
(author)
-
Evolutionary rates for tuf genes in endosymbionts of aphids
- 1998
-
In: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 15:5, s. 574-582
-
Journal article (other academic/artistic)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
|
|
| 7. |
- Greenwood, AD, et al.
(author)
-
Nuclear DNA sequences from late Pleistocene megafauna
- 1999
-
In: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 16:11, s. 1466-1473
-
Journal article (other academic/artistic)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
|
|
| 8. |
- Hastad, O, et al.
(author)
-
Nucleotide substitution models and estimation of phylogeny
- 1998
-
In: MOLECULAR BIOLOGY AND EVOLUTION. - : SOC MOLECULAR BIOLOGY EVOLUTION. - 0737-4038. ; 15:11, s. 1381-1389
-
Journal article (other academic/artistic)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
|
|
| 9. |
|
|
| 10. |
|
|
