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Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
TLDR
Testing the model of differential gene flow among loci by asking whether absolute divergence is also higher in the previously identified ‘islands’ finds that absolute measures of divergence are not higher in genomic islands, and simulations using the program IMa2 suggest that inferences of any gene flow may be incorrect in many comparisons. Expand
Evolution of genes and genomes on the Drosophila phylogeny
TLDR
These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Expand
CAFE: a computational tool for the study of gene family evolution
TLDR
CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss and identify which branches cause the p-value to be small for significant families. Expand
The evolution of transcriptional regulation in eukaryotes.
TLDR
The evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them are reviewed. Expand
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
TLDR
A population genetic analysis of Drosophila simulans is presented based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba, to suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophile genome. Expand
Genomic Islands of Speciation in Anopheles gambiae
TLDR
Despite appreciable levels of gene flow between the M and S forms of A. gambiae, three small regions of differentiation are isolated where genes responsible for ecological and behavioral isolation are likely to be located, and it is expected reproductive isolation to be due to changes at a small number of loci. Expand
Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.
TLDR
The results show that errors in genome annotation do lead to higher inferred rates of gene gain and loss but that CAFE 3 sufficiently accounts for these errors to provide accurate estimates of important evolutionary parameters. Expand
Genomic Variation in Natural Populations of Drosophila melanogaster
TLDR
This report of independent genome sequences of two natural populations of Drosophila melanogaster provides unique insight into forces shaping genomic polymorphism and divergence, suggesting many targets of directional selection are shared between these species. Expand
Extensive introgression in a malaria vector species complex revealed by phylogenomics
TLDR
Pervasive autosomal introgression between these human malaria vectors, including nonsister vector species, suggests that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between nonsister species. Expand
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
TLDR
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. Expand
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