Estimation of the molecular clock rate in lineages of the Drosophila virilis species group

Abstract Background Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. Results We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. Conclusions A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.

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Discordant Rates of Chromosome Evolution in the Drosophila virilis Species Group

Genetics ◽

10.1093/genetics/147.1.223 ◽

1997 ◽

Vol 147 (1) ◽

pp. 223-230 ◽

Cited By ~ 1

Author(s):

Jorge Vieira ◽

Cristina P Vieira ◽

Daniel L Hartl ◽

Elena R Lozovskaya

Keyword(s):

Polytene Chromosome ◽

Genomic Dna ◽

Chromosome Evolution ◽

Species Group ◽

Drosophila Virilis ◽

Chromosome 1 ◽

Chromosome 3 ◽

Bacteriophage P1 ◽

Minimum Number ◽

Chromosome Maps

Abstract In Drosophila, the availability of polytene chromosome maps and of sets of probes covering most regions of the chromosomes allows a direct comparison of the organization of the genome in different species. In this work, we report the localization, in Drosophila virilis, D. montana, and D. novamexicana, of >100 bacteriophage P1 clones containing ~65 kilobase inserts of genomic DNA from D. virilis. Each clone hybridizes with a single euchromatic site in either chromosome 1 or chromosome 3 in D. virilis. From these data, it is possible to estimate the minimum number of inversions required to transform the map positions of the probes in one species into the map positions of the same probes in a related species. The data indicate that, in the D. virilis species group, the X chromosome has up to four times the number of inversions as are observed in chromosome 3. The first photographic polytene chromosome maps for D. montana and D. novamexicana are also presented.

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Molecular Phylogeny of the Drosophila virilis Species Group (Diptera: Drosophilidae) Inferred from Mitochondrial 12S and 16S Ribosomal RNA Genes

Annals of the Entomological Society of America ◽

10.1603/0013-8746(2002)095[0156:mpotdv]2.0.co;2 ◽

2002 ◽

Vol 95 (2) ◽

pp. 156-161 ◽

Cited By ~ 51

Author(s):

Greg S. Spicer ◽

C. D. Bell

Keyword(s):

Molecular Phylogeny ◽

Ribosomal Rna ◽

Species Group ◽

Ribosomal Rna Genes ◽

Drosophila Virilis ◽

16S Ribosomal Rna ◽

Rna Genes

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Molecular phylogeny and genome evolution in the Drosophila virilis species group: duplications of the alcohol dehydrogenase gene

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025551 ◽

1996 ◽

Vol 13 (1) ◽

pp. 132-149 ◽

Cited By ~ 50

Author(s):

D. I. Nurminsky ◽

E. N. Moriyama ◽

E. R. Lozovskaya ◽

D. L. Hartl

Keyword(s):

Molecular Phylogeny ◽

Alcohol Dehydrogenase ◽

Genome Evolution ◽

Species Group ◽

Drosophila Virilis ◽

Dehydrogenase Gene

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The genetic basis of a species-specific character in the Drosophila virilis species group.

Genetics ◽

10.1093/genetics/128.2.331 ◽

1991 ◽

Vol 128 (2) ◽

pp. 331-337 ◽

Cited By ~ 2

Author(s):

G S Spicer

Keyword(s):

Genetic Basis ◽

Sex Chromosome ◽

Species Group ◽

Drosophila Virilis ◽

Interspecific Crosses ◽

Chromosome 2 ◽

Specific Character ◽

Number Of Factors ◽

Species Specific ◽

Dorsal Stripe

Abstract The genetic basis of the species-specific dorsal abdominal stripe of Drosophila novamexicana was examined. The dorsal stripe is present in D. novamexicana and absent in all other members of the Drosophila virilis species group. Interspecific crosses between D. novamexicana and genetically marked D. virilis revealed that all four of the autosomes (except the tiny dot chromosome, which was not marked) and the sex chromosomes (the X and Y chromosome effects could not be disentangled) showed a significant effect on the width of the dorsal stripe. All the autosomes act approximately additively; only minor interactions were detected among them. No significant maternal effects were found. This means that a minimum of five loci are involved in the character difference between the two species, and this is the maximum number that this technique could discern. These results suggest that, based on the number of factors involved in the character difference, the inheritance of this character should be considered polygenic, but because chromosome 2 (the largest chromosome in the species) contributed over half of the variance toward the character difference, it is best to consider the inheritance oligogenic based on effect. The implications of these findings are discussed in light of the importance of macromutation in speciation and the sex chromosome theory of speciation.

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