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The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these parameters in Drosophila pseudoobscura. To measure recombination rate, we genotyped 1,294 backcross hybrids at 50 markers across the largest assembled linkage group in this species. Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage. Alignment to the sequenced genome of the closely related species, Drosophila persimilis, provided nucleotide site orthology. Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale cross-over rate estimates are far stronger predictors of both diversity and interspecies difference than broad-scale estimates. The correlation of fine-scale recombination rate to diversity and interspecies difference appears to be genome-wide, evidenced by examination of an X-linked region in greater detail. Because we observe a strong correlation of cross-over rate with interspecies difference, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter in regions of low crossing over. We propose that it is not cross-overs per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gone conversion. variation | crossing over

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.

As whole-genome sequence assemblies accumulate, a challenge is to determine how these can be used to address fundamental evolutionary questions, such as inferring the process of speciation. Here, we use the sequence assemblies of Drosophila pseudoobscura and D. persimilis to test hypotheses regarding divergence with gene flow. We observe low differentiation between the two genome sequences in pericentromeric and peritelomeric regions. We interpret this result as primarily a remnant of the correlation between levels of variation and local recombination rate observed within populations. However, we also observe lower differentiation far from the fixed chromosomal inversions distinguishing these species and greater differentiation within and near these inversions. This finding is consistent with models suggesting that chromosomal inversions facilitate species divergence despite interspecies gene flow. We also document heterogeneity among the inverted regions in their degree of differentiation, suggesting temporal differences in the origin of each inverted region consistent with the inversions arising during a process of divergence with gene flow. While this study provides insights into the speciation process using two single-genome sequences, it was informed by lower throughput but more rigorous examinations of polymorphism and divergence. This reliance highlights the need for complementary genomic and population genetic approaches for tackling fundamental evolutionary questions such as speciation.

[F.sub.1] hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant autosomal interactors have been more difficult to localize precisely and/or have been shown to be of relatively smaller effect. Here, we identified and mapped at least four dominant autosomal factors contributing to hybrid male sterilily in the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana. Using these results, we tested predictions of reduced recombination models of speciation. Consistent with these models, three of the four QTL associated with hybrid male sterility occur in collinear (uninverted) regions of these genomes. Furthermore, these QTL do not contribute significantly to hybrid male sterility in crosses between the sympatric species D. persimilis and D. pseudoobscura pseudoobscura. The autosomal loci identified in this study provide the basis for introgression mapping and, ultimately, for molecular cloning of interacting genes that contribute to [F.sub.1] hybrid sterility.

There is increasing evidence that chromosomal inversions may facilitate the formation or persistence of new species by allowing genetic factors conferring species-specific adaptations or reproductive isolation to be inherited together and by reducing or eliminating introgression. However, the genomic domain of influence of the inverted regions on introgression has not been carefully studied. Here, we present a detailed study on the consequences that distance from inversion breakpoints has had on the inferred level of gene flow and divergence between Drosophila pseudoobscura and D. persimilis. We identified the locations of the inversion breakpoints distinguishing D. pseudoobscura and D. persimilis in chromosomes 2, XR, and XL. Population genetic data were collected at specific distances from the inversion breakpoints of the second chromosome and at two loci inside the XR and XL inverted regions. For loci outside the inverted regions, we found that distance from the nearest inversion breakpoint had a significant effect on several measures of divergence and gene flow between D. pseudoobscura and D. persimilis. The data fitted a logarithmic relationship, showing that the suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1-2 Mb). Further, we detected a significant reduction in nucleotide variation inside the inverted second chromosome region of D. persimilis and near one breakpoint, consistent with a scenario in which this inversion arose and was fixed in this species by natural selection.

We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation. Consideration of summary statistics rather than entire nucleotide sequences permits a compact description of the genealogy of the sample. We use importance sampling first to propose a genealogical and mutational history consistent with the observed array of summary statistics and then to correct the likelihood with the exact probability of the history determined from a system of recursions. Analysis of a subset of the data, for which recursive computation of the exact likelihood was feasible, indicated close agreement between the approximate and exact likelihoods. Our results for the complete data set also compare well with those obtained through Metropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.

Characterizing genes that are misregulated in hybrids may elucidate the genetic basis of hybrid sterility or other hybrid dysfunctions that contribute to speciation. Previously, a small segment of a male-predominant transcript that is underexpressed in adult male hybrids of Drosophila pseudoobscura and D. persimilis relative to pure species was identified in a differential display screen. Here, we obtained the full sequence of this 1330-bp transcript and determined that it is an antisense message with high sequence similarity to the D. melanogaster TRAP100 gene, part of the Mediator protein complex that regulates transcriptional initiation during development. Both the sense and the antisense messages are transcribed in D. pseudoobscura, but only the sense message (TRAP100) is transcribed in D. melanogaster complex species. Unlike the antisense message, the sense message is transcribed similarly in D. pseudoobscura males and females and in hybrids of D. pseudoobscura and D. persimilis. The high sequence similarity between distantly related species suggests that the sense message is functionally constrained within the genus. We speculate that the antisense transcript may have evolved a role in male-specific post-transcriptional regulation of TRAP100 in the D. pseudoobscura lineage and that its underexpression in sterile hybrid males may cause an overproduction of TRAP100 protein, possibly yielding deleterious effects.

We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the 'small X-effect' that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

Drosophila pseudoobscura and D. persimilis have been studied relative to backcross hybrid males and the genetics of reproductive isolation and potential for gene exchange in them. It appear gene flow between the two species via hybrid males may be possible at loci spread across much of the autosomes.

Genetics of species differences have been studied by looking at courtship songs of Drosophila pseudoobscura and D. persimilis. The genetic basis of the difference is examined in two courtship song elements, interpulse interval and intrpulse frequency using 15 molecular markers. Song differences were associated with at least two or three genomic regions. Interpulse interval is strongly associated with mating success to D. pseudoobscura females, but intrapulese frequency is associated with mating success to D. persimilis females. Implications are discussed.

This article discusses species mating discrimination between sympatric and allopatric taxa. In the former, reinforcement process prevents maladaptive hybridization. New approaches to better understand the reinforcement process using recent advances in molecular population genetics and the genetic tools are presented.

The differences between Drosophila pseudoobscura and D. persimilis in high-rate repetition song interpulse interval (IPI) and intrapulse frequency and in the amount of low-rate repetition song produced were confirmed as their courtship song elements were re-analyzed. Findings showed that X-chromosome and autosomal loci both contribute to the differences in the IPI and intrapulse frequency between the two species. None of these song parameters are used by D. pseudoobscura females in species mating discrimination, while D. persimilis does not use IPI.

A new method of estimating a lower bound of how often sympatric species interactions elevate prezygotic isolation in Drosophila is presented. The conclusion of an earlier study that prezygotic reproductive isolation in sympatric Drosophila species pairs was greater than in allopatric pairs of similar genetic divergence was affirmed, as sympatry with closely related species was found to be associated with elevated sexual isolation among Drosophila species. Such elevations were also found to be not a rare occurrence, as sympatry was found to have increased sexual isolation of Drosophila species in >21% of the phylogenies which fit the model's criteria.

Drosophila pseudoobscura and D. persimilis males fail to follow species discrimination in their courting behavior. Two experiments involving a choice and a no-choice condition indicate that males indiscriminately court with heterospecific females as quickly and readily as with conspecific females. Females alone disrupt the copulatory sequence of these Drosophila species. Species indiscrimination by males may be due to the fact that males are less likely to suffer from mis-mating than females.

Gene flow has been studied in Drosophila pseudoobscura and D. persimilis and the study is important to ongoing speciation research. Studies of interspecific gene flow cannot be done without also looking at intraspecific gene flow and genetics of reproductive isolation.

6th ed. John Alcock. Sinauer Associates, Sunderland, MA, 1998. 640 pp., illus. $54.95 (ISBN 0-87893-009-4 cloth). Few people have taken courses in animal behavior over the last twenty years without [...]

Reinforcement is an increase in premating reproductive isolation between taxa resulting from selection against hybrids. We present a model of reinforcement with a novel type of selection on female mating behavior. Previous models of reinforcement have focused on the divergence of female mating preferences between nascent species. We suggest that an increase in the level of female mating discrimination can yield reinforcement without further divergence of either male characters or female preferences. This model indicates that selection on mating discrimination is a viable mechanism for reinforcement and may allow speciation under less stringent conditions than selection on female preference. This model also incorporates empirical results from genetic studies of hybrid fitness determination in Drosophila species. We find that the details of inheritance, which include sex-linked transmission, sex-limited fertility reduction, and X-autosome epistasis, have important effects on the likelihood of reinforcement. In particular, X-autosome epistasis for hybrid fitness determination facilitates reinforcement when hybrid fertility reduction occurs in males, but hinders the process when it occurs in females. HALDANE'S rule indicates that hybrid sterility will generally evolve in males prior to females within nascent species. Thus, HALDANE's rule and X-autosome epistasis provide conditions that are surprisingly favorable for reinforcement in Drosophila.

A three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic Drosophila mojavensis was performed to study the divergence in life-history characters and correlated shifts in sexual isolation among geographically isolated populations of D. mojavensis. The regional shifts observed in life history evolution once D. mojavensis invaded mainland Mexico from Baja California by shifting host plant was genetically correlated with variation in cuticular hydrocarbon-based mate preferences.

A study examines the nature and dominance of epistasis between alleles derived from Drosophila persimilis which causes hybrid male sterility in the genetic background of its sister species Drosophila pseudoobscura, in order to assess its key role in causing hybrid incompatibilities. Results reveal that epistasis increases the dominance of individually recessive-acting QTL loci so that they play a role in hybrid male sterility.

A quantitative trait locus (QTL) analysis is performed on epicuticular hydrocarbon variation in 1650 [F.sub.2] males from crosses of Baja California and mainland Mexico populations of Drosophila mojavensis cultured on two major host cacti. Epicuticular hydrocarbon variation in Drosophila mojavensis is a multigenic trait with some epistasis, multiple QTLs have displayed pleiotropy, correlated groups of hydrocarbons and cactus substrates have determined courtship success and males have altered their hydrocarbon profiles in response to females.

The article discusses courtship and mating among Drosophila mojavensis populations in Mexico. This was investigated by examining which loci influenced the Drosophila mojavensis male mating and if females preferred to mate with males who reared on host plants like cacti.

The inversion of X-chromosome in Drosophila that distinguish D.mojavensis from D.arizonae have specific breakpoints. The localization of these breakpoints helps in genetic and evolutionary studies of Drosophila species.

Genes may acquire nonsynonymous substitutions more rapidly when X-linked than when autosomal, but evidence for 'fast-X evolution' has been elusive. Variation in functional constraints across genes may have masked the signature of fast-X evolution in some previous studies, and it is concluded paired comparisons are more powerful for examining rates of evolution of genes when X-linked over autosomal.

Ever since the modern understanding of evolution and genetics in terms of natural selection and Mendelian inheritance was formulated, generations of scientists have struggled to explain the genetic bases and [...]

For decades, evolutionary biologists strove to understand how, or even if, the process of speciation can be completed despite gene flow between the emerging species (1). Homogenization via gene flow [...]