DNA loss and evolution of genome size in Drosophila

  title={DNA loss and evolution of genome size in Drosophila},
  author={Dmitri A. Petrov},
Mutation is often said to be random. Although it must be true that mutation is ignorant about the adaptive needs of the organism and thus is random relative to them as a rule, mutation is not truly random in other respects. Nucleotide substitutions, deletions, insertions, inversions, duplications and other types of mutation occur at different rates and are effected by different mechanisms. Moreover the rates of different mutations vary from organism to organism. Differences in mutational biases… 
Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
By multiplying u by an estimate of the fraction of mutations that are deleterious in natural populations of Drosophila, it is estimated that U is 1.2 per diploid genome, which suggests that selection against deleteriously mutations may have a key role in explaining patterns of genetic variation in the genome, and help to maintain recombination and sexual reproduction.
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
This work sequenced eight genomes produced by a mutation-accumulation experiment in Drosophila melanogaster to estimate genome-wide rates of large deletions and tandem duplications and reveals that point mutation and small indel rates vary significantly between the two different genetic backgrounds examined.
Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster
The first rigorous test of substitution rate heterogeneity in the Drosophila melanogaster genome is presented using almost 1500 nonfunctional fragments of the transposable element DNAREP1_DM and suggests that substitutional patterns in heterochromatic and euchromatic sequences are different.
Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection
Insertions and deletions (collectively indels) obviously have a major impact on genome evolution. However, before large-scale data on indel polymorphism became available, it was difficult to estimate
Rates and Fitness Consequences of New Mutations in Humans
It is argued that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations.
The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.
Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.
Mutational equilibrium model of genome size evolution.
  • D. Petrov
  • Biology
    Theoretical population biology
  • 2002
A mutational equilibrium model of genome size evolution is described, which suggests that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions.
Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
It is proposed that heterozygosity for an indel is mutagenic to surrounding sequences, and yeast genome-wide polymorphism data is used to estimate the increase in mutation rate, suggesting that indel-associated substitution is a general mutational mechanism.
Rapid sequence turnover at an intergenic locus in Drosophila.
No evidence suggesting that the size of this locus has been maintained over evolutionary time is found, consistent with the model of a dynamic equilibrium between persistent DNA loss through small deletions and more sporadic DNA gain through less frequent but longer insertions.


Pseudogene evolution and natural selection for a compact genome.
The implications of selection for genome size relative to small (1-400 bp) deletions, in light of empirical evidence pertaining to the size distribution of deletions observed in Drosophila and mammalian pseudogenes, are examined.
High intrinsic rate of DNA loss in Drosophila
Phylogenetic analysis of a non-LTR element, Helena, demonstrates that copies lose DNA at an unusually high rate, suggesting that lack of pseudogenes in Drosophila is the product of rampant deletion of DNA in unconstrained regions, and has important implications for the study of genome evolution in general and the 'C-value paradox' in particular.
The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.
The study of the proposed dynamic model, taking into account interference among selected sites, might shed light on many aspects of the comparative biology of genome sizes including the C value paradox.
Genome size as a mutation-selection-drift process.
New data presented here rule out the possibility that the transposition process itself is highly mutagenic, hence the observed linear relation between number of deletions and number of nucleotide substitutions is most easily explained by the hypothesis that both types of changes accumulate in unconstrained sequences over time.
Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
A revised estimate of the pattern of point mutation is obtained by considering more pseudogene sequences and indicates that mutation occurs nonrandomly among the four nucleotides, with a high proportion of transitional mutations.
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.
The results strongly suggest that the high rate of DNA loss is a general feature of Drosophila and not a peculiar property of a particular stretch of DNA in a particular species group.
Pseudogene evolution in Drosophila suggests a high rate of DNA loss.
This approach relied on using maximum parsimony to separate the evolution of individual DOA insertions of Helena from the Evolution of active lineages, which allowed us to demonstrate a lack of purifying selection acting on individualDOA elements (Petrov, Lozovskaya, and Hartl 1996; Petrov andHartl 1997, 1998).
Evidence for DNA loss as a determinant of genome size.
The indel spectrum in Laupala crickets, which have a genome size 11 times larger than that of Drosophila, is examined to test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms.
Genomic gigantism: DNA loss is slow in mountain grasshoppers.
The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila.