Insights into the evolutionary process from patterns of DNA sequence variability

Current Opinion in Genetics and Development

Volumn 7, Issue 6, 1997, Pages 835-840

  Aquadro, Charles F ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; DNA SEQUENCE; DROSOPHILA; GENE MUTATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; HUMAN; HUMAN CELL; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PRIORITY JOURNAL; REVIEW;

EID: 0031460177     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(97)80048-2     Document Type: Article

References (63)

1. Begun DJ, Aquadro CF. Levels of naturally occurring DNa polymorphism correlate with recombination rates in D. melanogaster. Nature. 356:1992;519-520.
2. Aquadro CF, Begun DJ, Kindahl EC. Selection, recombination, and DNA polymorphism in Drosophila. Golding B. Non-neutral Evolution: Theories and Molecular Data. 1994;46-55 Chapman and Hall, London.
3. Pritchard JK, Schaeffer SW. Polymorphism and divergence at a Drosophila pseudogene locus. Genetics. 147:1997;199-208.
4. Aguadé M, Langley CH. Polymorphism and divergence in regions of low recombination in Drosophila. Golding B. Non-neutral Evolution: Theories and Molecular Data. 1994;67-76 Chapman and Hall, London.
5. Stephan W. Effects of genetic recombination and population subdivision on nucleotide sequence variation in Drosophila ananassae. Golding B. Non-neutral Evolution: Theories and Molecular Data. 1994;57-66 Chapman and Hall, London.
6. Nachman MW, Churchill G. Heterogeneity in rates of recombination across the mouse genome. of special interest Genetics. 142:1996;537-548 See annotation [7].
7. Nachman MW. Patterns of DNA variability at X-linked loci in Mus domesticus. of special interest Genetics. 147:1997;1303-1316 These two papers [6, 7] document the heterogeneity in rates of recombination across the mouse genome and provide evidence that levels of DNA variation are positively correlated with recombination. This result significantly extends the generality of the correlation seen in Drosophila.
8. Hamblin MT, Aquadro CF. High nucleotide sequence variation in a region of low recombination in Drosophila simulans is consistent with the background selection model. of special interest Mol Biol Evol. 13:1996;1133-1140 The importance of knowledge of differences in rates of recombination in different species is demonstrated in this study of DNA sequence variation in D. simulans, a sibling species of D. melanogaster that has a higher average rate of recombination.
9. Moriyama EN, Powell JR. Intraspecific nuclear DNA variation in Drosophila. of special interest Mol Biol Evol. 13:1996;261-277 The authors provide a thorough summary of within-species estimates of synonymous, non-synonymous, and non-coding nucleotide variation for all available nuclear DNA sequences for D. melanogaster, D. simulans and D. pseudoobscura. Tests of departure from neutrality show that about half of the loci depart from the expectations of strict neutrality. Hypotheses to explain general patterns of variation within and between species are reviewed.
10. Wang R-L, Hey J. The speciation history of Drosophila pseudoobscura and close relatives: inferences from DNA sequence variation at the period locus. Genetics. 144:1996;1113-1126.
11. Wells RS. Nucleotide variation at the Gpdh locus in the genus Drosophila. Genetics. 143:1996;375-384.
12. True JR, Mercer JM, Laurie CC. Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics. 142:1996;507-523.
13. Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 134:1993;1289-1303.
14. Keightley PD. Nature of deleterious mutation load in Drosophila. Genetics. 144:1996;1993-1999.
15. Fernandez J, Lopez-Fanjul C. Spontaneous mutational variances and covariances for fitness related traits in Drosophila melanogaster. Genetics. 143:1996;829-837.
16. Keightley PD, Caballero A. Genomic mutation rates for lifetime reproductive output with lifespan in Caenorhabditis elegans. Proc Natl Acad Sci USA. 94:1997;3823-3827.
17. Hudson RR, Kaplan NL. Deleterious background selection with recombination. Genetics. 141:1995;1605-1617.
18. Charlesworth B. Background selection and patterns of genetic diversity in Drosophila melanogaster. of outstanding interest Genet Res. 68:1996;131-149 A thoughtful and detailed exploration of the ability of background selection to explain the positive correlation between DNA variation and rates of recombination across the Drosophila genome. The author incorporates detailed genetic map data as well as the observed distribution of transposable elements which tend to be clustered in regions of low recombination and contribute to the mutational load (and thus background selection) in these regions.
19. Hamblin MT, Aquadro CF. Contrasting patterns of nucleotide sequence variation at the glucose dehydrogenase (Gld) locus in different populations of Drosophila melanogaster. Genetics. 145:1997;1053-1062.
20. Wayne M, Kreitman M. Reduced variation at concertina, a heterochromatic locus in Drosophila. Genet Res. 68:1996;101-108.
21. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics. 140:1995;783-796.
22. Simonsen KL, Churchill GA, Aquadro CF. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics. 141:1995;413-429.
23. Kirby DA, Stephan W. Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics. 144:1996;635-645.
24. Gillespie JH. Alternatives to the neutral theory. Golding B. Non-neutral Evolution: Theories and Molecular Data. 1994;1-17 Chapman and Hall, London.
25. Bauer VL, Aquadro CF. Rates of DNA sequence evolution are not sex-biased in Drosophila melanogaster and D. simulans. Mol Biol Evol. 1997;. in press.
26. Slatkin M. Hitchhiking and associative overdominance at a microsatellite locus. Mol Biol Evol. 12:1995;473-480.
27. -6) than has been reported for humans, mice and other mammals. The lower rate is hypothesized to be associated, perhaps causally, with the small average size of these tandem repeats in Drosophila.
28. England PR, Briscoe DA, Frankham R. Microsatellite polymorphisms in a wild population of Drosophila melanogaster. Genet Res. 67:1996;285-290.
29. Michalakis Y, Veuille M. Length variation of CAG-CAA trinucleotide repeats in natural populations of Drosophila melanogaster and its relation to the recombination rate. of special interest Genetics. 143:1996;1713-1725 These authors examine trinucleotide repeat microsatellite variation in several European and African populations of D. melanogaster and find no correlation between variation and recombination rate. They interpret their result as reflecting the impact of selective sweeps caused by fixations of linked advantageous mutations.
30. Schloetterer C, Vogl C, Tautz D. Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. of outstanding interest Genetics. 146:1997;309-320 Microsatellite variation is surveyed in several natural population samples from the world-wide distribution of D. melanogaster. The particularly striking result is the finding that numerous loci have dramatically reduced variation in only one or two localities, despite high levels of variation for these same loci in other populations. These results appear to reflect a high frequency of local adaptive fixation linked to these microsatellites, perhaps associated with movement of the species out of Africa into new habitats.
31. Schug MD, Wetterstrand KA, Gaudette MS, Lim RH, Hutter CM, Aquadro CF. The distribution and frequency of microsatellite loci in Drosophila melanogaster. Mol Ecol. 1997;. in press.
32. Fu YX. Estimating the age of the common ancestor of a DNA sample using the number of segregating sites. Genetics. 144:1996;829-838.
33. Fu YX, Li WH. Estimating the age of the common ancestor of a sample of DNA sequences. Mol Biol Evol. 14:1997;195-199.
34. Tavare S, Balding DJ, Griffiths RC, Donnelly P. Inferring coalescence times from DNA sequence data. Genetics. 145:1997;505-518.
35. Harding RM, Fullerton SM, Griffiths RC, Bond J, Cox MJ, Schneider JA, Moulin DS, Clegg JB. Archaic African and Asian lineages in the genetic ancestry of modern humans. of outstanding interest Am J Hum Genet. 60:1997;772-789 The authors present and analyze 349 copies of a 3 kb region including the β-globin gene of humans sampled from Africa, Asia and Europe. Using a new method, they estimate the coalescent time for this gene to be on the order of 800,000 years and that the effective population size of humans has been -10,000 over this period. They also show that selection acting at this locus in malarial regions has been recent and has not substantially affected the distribution of DNA variation from that expected under neutrality.
36. Kreitman M, Akashi H. Molecular evidence for natural selection. Annu Rev Ecol Syst. 26:1995;403-422.
37. McDonald JH. Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol Biol Evol. 13:1996;253-260.
38. Fu YX. New statistical tests of neutrality for DNA samples from a population. Genetics. 143:1996;557-570.
39. Templeton AR. Contingency tests of neutrality using intra-interspecific gene trees: The rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics. 144:1996;1263-1270.
40. Kelly JK. A test of neutrality based on interlocus associations. Genetics. 146:1997;1197-1206.
41. Endo T, Ikeo K, Gojobori T. Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 13:1996;685-690.
42. Hudson RR, Saez AG, Ayala FJ. DNA variation at the Sod locus of Drosophila melanogaster: an unfolding story of natural selection. Proc Natl Acad Sci USA. 94:1997;7725-7729.
43. Begun DJ, Aquadro CF. Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of Drosophila: selection and geographic differentiation. Genetics. 136:1994;155-171.
44. Eanes WF, Kirchner M, Yoon J, Biermann CH, Wang IN, McCartney MA, Verrelli BC. Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. of special interest Genetics. 144:1996;1027-1041 Evidence of species-specific differences in purifying selection at silent sites and of a burst of adaptive fixation of amino acid replacements at the G6pd locus, possibly associated with differences in species effective population sizes, is revealed by a careful analysis of DNA sequence variation within and between African, European, and North American populations of Drosophila melanogaster and D. simulans.
45. Rosato E, Peixoto AA, Gallippi A, Kyriacou CP, Costa R. Mutational mechanisms, phylogeny, and evolution of a repetitive region within a clock gene of Drosophila melanogaster. J Mol Evol. 42:1996;392-408.
46. Wayne ML, Contamine D, Kreitman M. Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila. Mol Biol Evol. 13:1996;191-199.
47. Parsch J, Tanda S, Stephan W. Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster. of special interest Proc Natl Acad Sci USA. 94:1997;928-933 A direct experimental test for compensatory interactions of nucleotide substitutions within the alcohol dehydrogenase gene transcript of D. melanogaster. Variants within evolutionarily conserved regions leading to secondary structures are shown to affect Adh activity epistatically. Such interactions are proposed as an explanation for clusters of linkage disequilibrium seen in this gene in natural populations.
48. Akashi H. Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. of outstanding interest Genetics. 144:1996;1297-1307 This analysis provides additional evidence that silent site variation is not strictly selectively neutral, and that many synonymous and non-synonymous as well as insertion/deletion variants are mildly deleterious. Reduced codon bias, along with faster rates of amino acid substitution and a trend towards larger proteins are seen along the D. melanogaster lineage compared to D. simulans, consistent with less-efficient selection associated with lower effective population size in D. melanogaster.
49. Akashi H, Schaeffer SW. Natural selection and the frequency distributions of 'silent' DNA polymorphism in Drosophila. Genetics. 146:1997;295-307.
50. Nachman MW, Brown WM, Stoneking M, Aquadro CF. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics. 142:1996;953-963.
51. Rand DM, Kann LM. Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol. 13:1996;737-748.
52. Kreitman M, Ludwig M. Tempo and mode of even-skipped stripe 2 enhancer evolution in Drosophila. Sem Cell Dev Biol. 7:1996;583-592.
53. Richter B, Long M, Lewontin RC, Nitasaka E. Nucleotide variation and conservation at the dpp locus, a gene controlling early development in Drosophila. Genetics. 145:1997;311-323.
54. Schulte PM, Gomez-Chiarri M, Powers DA. Structural and functional differences in the promoter and 5′ flanking region of Ldh-B within and between populations of the teleost Fundulus heteroclitus. Genetics. 145:1997;759-769.
55. Metz EC, Palumbi SR. Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein binding. Mol Biol Evol. 13:1996;397-406.
56. Vacquier VD, Swanson WJ, Lee Y-H. Positive Darwinian selection on two homologous fertilization proteins: what is the selective pressure driving their divergence? of special interest J Mol Evol. 44:1997;S15-S22 A summary of the evidence for, and possible explanations to account for, extremely strong positive selection for amino acid sequence divergence at two fertilization proteins in the sperm of the marine mollusk, abalone.
57. Richman AD, Uyenoyama MK, Kohn JR. Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. of special interest Science. 273:1996;1212-1216 A detailed study of DNA sequence diversity at the self-incompatibility locus in two species of flowering plants demonstrating extremely transpecific polymorphism expected with strong diversity enhancing selection. An excess of non-synonymous over synonymous substitutions is only seen, however, for evolutionarily close comparisons.
58. Ferris PJ, Pavlovic C, Fabry S, Goodenough UW. Rapid evolution of sex-related genes in Chlamydomonas. Proc Natl Acad Sci USA. 94:1997;8634-8639.
59. Tan Y, Riley MA. Nucleotide polymorphism in colicin E2 gene clusters: evidence for nonneutral evolution. Mol Biol Evol. 14:1997;666-673.
60. Messier W, Stewart CB. Episodic adaptive evolution of primate lysozymes. of outstanding interest Nature. 385:1997;151-154 The authors combine phylogenetic and population genetic approaches to demonstrate bursts of selectively driven amino acid substitutions in the evolutionary history of lysozymes in primates, followed by the more typical strong purifying selection once new functions had evolved.
61. Begun DJ. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics. 145:1997;375-382.
62. Clegg MT. Plant genetic diversity and the struggle to measure selection. J Heredity. 88:1997;1-7.
63. Nordborg M, Charlesworth B, Charlesworth D. Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc Royal Soc London Ser B Biol Sci. 263:1996;1033-1039.