Genomes and Genes
Affiliation: University of California
- Patterns of intron sequence evolution in Drosophila are dependent upon length and GC contentPenelope R Haddrill
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
Genome Biol 6:R67. 2005..No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns...
- Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genomePeter Andolfatto
Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
Genome Res 17:1755-62. 2007....
- Adaptive evolution of non-coding DNA in DrosophilaPeter Andolfatto
Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
Nature 437:1149-52. 2005..These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster...
- An approximate bayesian estimator suggests strong, recurrent selective sweeps in DrosophilaJeffrey D Jensen
Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, United States of America
PLoS Genet 4:e1000198. 2008..It will thus be of great interest to apply this method to emerging whole-genome polymorphism data sets in many taxa...
- Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly speciesAndrea S Putnam
Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA
Evolution 61:912-27. 2007..Our approach can be used to test alternative models of speciation and can potentially assign chronological order to the appearance of factors contributing to reproductive isolation between species...
- Selection, recombination and demographic history in Drosophila mirandaDoris Bachtrog
Division of Biological Sciences, University of California, San Diego, California 92093, USA
Genetics 174:2045-59. 2006..These departures from neutral equilibrium expectations are discussed in the context of nonequilibrium models of demography and selection...
- Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species groupDoris Bachtrog
Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California 92093, USA
Evolution 60:292-302. 2006..Although natural selection is usually thought of as accentuating divergence between species, our results imply that it can also act as a homogenizing force...
- X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolutionKevin Thornton
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Genome Res 16:498-504. 2006..The lack of a detectable faster-X effect in these species suggests either that beneficial amino acids are not partially recessive on average, or that adaptive evolution does not often use newly arising amino acid mutations...
- Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populationsPenelope R Haddrill
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
Genome Res 15:790-9. 2005..Demographic departures from equilibrium expectations in both ancestral and derived populations thus represent a serious challenge to detecting positive selection in genome-wide scans using current methodologies...
- Patterns of evolutionary constraints in intronic and intergenic DNA of DrosophilaDaniel L Halligan
University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK
Genome Res 14:273-9. 2004....
- Inference of population structure under a Dirichlet process modelJohn P Huelsenbeck
Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Genetics 175:1787-802. 2007..We develop the notion of the mean population partition, which is the partition of individuals to populations that minimizes the squared partition distance to the partitions sampled by the MCMC algorithm...
- Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogasterPeter Andolfatto
Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
Genetics 165:1289-305. 2003..e., toward an excess of LD) in this Zimbabwean population. Our results also have implications for the dynamics of weakly selected mutations in regions of reduced crossing over...
- No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucusPeter Andolfatto
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh Scotland, EH9 3JT United Kingdom
Evolution 57:305-16. 2003..This finding suggests that genetic exchanges between maternal and paternal mitochondrial DNAs may have contributed to the lack of association we observe between phenotype and genotype...
- The evolution of gene regulation underlies a morphological difference between two Drosophila sister speciesSangyun Jeong
Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
Cell 132:783-93. 2008..We submit that there is sufficient empirical evidence to support the general prediction that functional evolutionary changes at pleiotropic loci will most often involve mutations in their discrete, modular cis-regulatory elements...
- Positive and negative selection on noncoding DNA in Drosophila simulansPenelope R Haddrill
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Mol Biol Evol 25:1825-34. 2008..simulans lineage difficult to reconcile with demographic explanations...
- Testing models of selection and demography in Drosophila simulansJeffrey D Wall
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 162:203-16. 2002..autosome variability levels, they suggest that demography alone may account for patterns of linkage disequilibrium and the frequency spectrum of segregating mutations in this population of D. simulans...