The divergence of Drosophila pseudoobscura from its close relatives, D. persimilis and D. pseudoobscura bogotana, was examined using the pattern of DNA sequence variation in a common set of 50 inbred lines at 11 loci from diverse locations in the genome. Drosophila pseudoobscura and D. persimilis show a marked excess of low-frequency variation across loci, consistent with a model of recent population expansion in both species. The different loci vary considerably, both in polymorphism levels and in the levels of polymorphisms that are shared by different species pairs. A major question we address is whether these patterns of shared variation are best explained by gene flow or by persistence since common ancestry. A new test of gene flow, based on patterns of linkage disequilibrium, is developed. The results from these, and other tests, support a model in which D. pseudoobscura and D. persimilis have exchanged genes at some loci. However, the pattern of variation suggests that most gene flow, although occurring after speciation began, was not recent. There is less evidence of gene flow between D. pseudoobscura and D. p. bogotana. The results are compared with recent work on the genomic locations of genes that contribute to reproductive isolation between D. pseudoobscura and D. persimilis. We show that there is a good correspondence between the genomic regions associated with reproductive isolation and the regions that show little or no evidence of gene flow.

Lake Malawi contains a f lock of >500 species of cichlid fish that have evolved from a common ancestor within the last million years. The rapid diversification of this group has been attributed to morphological adaptation and to sexual selection, but the relative timing and importance of these mechanisms is not known. A phylogeny of the group would help identify the role each mechanism has played in the evolution of the f lock. Previous attempts to reconstruct the relationships among these taxa using molecular methods have been frustrated by the persistence of ancestral polymorphisms within species. Here we describe results from a DNA fingerprinting technique that overcomes this problem by examining thousands of polymorphisms distributed across the genome. The resulting dendrogram averages the evolutionary history of thousands of genes and should accurately ref lect the evolutionary history of these species. Our tree resolves relationships among closely related Lake Malawi cichlids and provides insights into the pattern of speciation in this group. We demonstrate that adaptive divergence in trophic morphology played an important role during the early history of the lake. Subsequent species diversity has arisen with little change in trophic morphology, which suggests that other forces are responsible for the continued speciation of these fishes.Lake Malawi and its fish fauna have attracted the attention of ecological, behavioral, and evolutionary biologists for over a century (1). Lake Malawi cichlids exhibit spectacular diversity in trophic morphology, including specialist algal scrapers, planktivores, insectivores, piscivores, paedophages, snail crushers, and fin biters. As rich as they are in trophic diversity, these fishes are even more striking in their array of color patterns (2). Their complex mating behavior, polyandrous mating systems (3), and tendency to breed in leks also are intriguing to behaviorists.Both adaptive and nonadaptive processes likely have played a role in the explosive radiation of East African cichlids, but the importance of each mechanism has been the focus of considerable debate (4). On one hand, it has been suggested that morphological adaptation, particularly of the feeding apparatus, is a ''key innovation'' for rapid evolutionary change (5). An opposing hypothesis suggests that adaptive morphological change is not the primary cause of speciation but occurs after the establishment of genetic isolation by other means (6, 7). These authors argue that sexual selection is the force that creates reproductive isolation, allowing subsequent morphological differentiation. The competing hypotheses could be evaluated if a robust phylogeny of these taxa was available. If morphological adaptation is critical to speciation, then we expect that even closely related species will show significant divergence in trophic morphology. If sexual selection is responsible for speciation, then we expect that sister taxa will frequently differ in color pattern but not morphology.Most attempts to dete...

BackgroundWhen a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis.ResultsPopulations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and population fitness overall; however, AFLP markers performed poorly at detecting modest but consequential losses of genetic diversity. High diversity lines in the stressful environment showed some evidence of relative improvement as the experiment progressed while the low diversity lines did not.ConclusionsThe combined effects of reduced average fitness and increased variability contributed to increased extinction rates for very low diversity populations. More modest losses of genetic diversity resulted in measurable decreases in population fitness; AFLP markers did not always detect these losses. However when AFLP markers indicated lost genetic diversity, these losses were associated with reduced population fitness.