Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow.

Speciation, the evolution of reproductive isolation among populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting gene flow locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in factors such as background selection and selective sweeps, recombination and mutation rate variation, and heterogeneous gene density. Extracting the effects of gene flow, divergent selection and reproductive isolation from such modifying factors presents a major challenge to speciation genomics. We argue one of the principal aims of the field is to identify the barrier loci involved in limiting gene flow. We first summarize the expected signatures of selection at barrier loci, at the genomic regions linked to them and across the entire genome. We then discuss the modifying factors that complicate the interpretation of the observed genomic landscape. Finally, we end with a road map for future speciation research: a proposal for how to account for these modifying factors and to progress towards understanding the nature of barrier loci. Despite the difficulties of interpreting empirical data, we argue that the availability of promising technical and analytical methods will shed further light on the important roles that gene flow and divergent selection have in shaping the genomic landscape of speciation.

Mapping of within-species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura.

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system.

Recombination rate variation in closely related species.

Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species.

Over the past decade, many studies documented high genetic divergence between closely related species in genomic regions experiencing restricted recombination in hybrids, such as within chromosomal rearrangements or areas adjacent to centromeres. Such regions have been called 'islands of speciation' because of their presumed role in maintaining the integrity of species despite gene flow elsewhere in the genome. Here, we review alternative explanations for such patterns. Segregation of ancestral variation or artifacts of nucleotide diversity within species can readily lead to higher F(ST) in regions of restricted recombination than other parts of the genome, even in the complete absence of interspecies gene flow, and thereby cause investigators to erroneously conclude that islands of speciation exist. We conclude by discussing strengths and weaknesses of various means for testing the role of restricted recombination in maintaining species.

Oral health status among Kenyans in a rural arid setting: dental caries experience and knowledge on its causes.

OBJECTIVE: To determine the dental caries experience and knowledge on the causes and preventive measures for dental diseases. DESIGN: A community based cross-sectional descriptive study. SETTING: Elwak sub-district hospital, North Eastern Province, Kenya. SUBJECTS: One hundred and forty one adults who presented themselves during a dental check up at a sub-district hospital and gave written consent. MAIN OUTCOME MEASURES: Dental caries status and knowledge on its causes and preventive measures. The importance of outreach programmes in obtaining information as well as helping to alleviate the pain and suffering caused by dental diseases among communities living in remote areas is also revealed. RESULTS: Of the one hundred and forty one individuals, who were included in the study, 63.1% were women and 36.9% were men. Their ages ranged between 18 and over 65 years. 41.1% were in the 18-24-year age bracket. Regarding the oral health knowledge, 43% did not know any causes of dental diseases while 36%, 17% and 12% knew that diet, "dirt" on teeth and bacteria were possible causes, respectively. Fifty percent did not know any preventive measures for dental diseases while the rest indicated abstention from the consumption of sugary foods; and only 0.8% mentioned use of fluoridated toothpaste as a preventive measure for dental caries. 56.7% of the subjects were caries free. The mean DMFT for all ages was 3.4. Of those with caries 72.1% were women. CONCLUSION: There is a low level of oral health awareness and a moderately high level of dental caries experience in this community with women apparently carrying the biggest burden of dental caries.

Oral health status among kenyans in a rural arid setting: dental caries experience and knowledge on its causes

Objective: To determine the dental caries experience and knowledge on the causes and preventive measures for dental diseases. Design: A community based cross-sectional descriptive study.Setting: Elwak sub-district hospital; North Eastern Province; Kenya. Subjects: One hundred and forty one adults who presented themselves during a dental check up at a sub-district hospital and gave written consent. Main outcome measures: Dental caries status and knowledge on its causes and preventive measures. The importance of outreach programmes in obtaining information as well as helping to alleviate the pain and suffering caused by dental diseases among communities living in remote areas is also revealed. Results: Of the one hundred and forty one individuals; who were included in the study; 63.1

Molecular evolution of X-linked accessory gland proteins in Drosophila pseudoobscura.

In Drosophila melanogaster and Drosophila simulans, positive Darwinian selection drives high rates of evolution of male reproductive genes, and accessory gland proteins (Acps) in particular. Here, we tested whether 13 X-linked male-specific genes, 4 Acps and 9 non-Acps, are under selective forces in the Drosophila pseudoobscura species group, much as those in the D. melanogaster group. We observed a statistically significant correlation in relative rates of nonsynonymous evolution between the two species groups tested. One Acp examined had a higher rate of nonsynonymous substitution than predicted by a neutral model in both species groups, suggesting its divergence was driven by positive Darwinian selection. To further test for the signature of selection, we examined polymorphism of three Acps within D. pseudoobscura. From this test, no Acp individually bore the signature of positive selection, but the 3 Acps together possessed an excess of nonsynonymous differences between species, relative to polymorphism within species. We conclude that faster evolution of Acps in the D. pseudoobscura group appears to be driven by positive selection, as previously suggested in the D. melanogaster group.

The effect of intracalyceal distribution on the clearance of renal stones of > or = 20 mm in children after extracorporeal lithotripsy.

OBJECTIVES: To determine the effect of the intracalyceal distribution of renal stones on clearance rates after treating paediatric nephrolithiasis with extracorporeal shock wave lithotripsy (ESWL). PATIENTS AND METHODS: We assessed a retrospective case series of children (aged < or = 14 years) undergoing lithotripsy on an MPL 9000 (Dornier GmbH, Germany) echo-guided lithotripter. Patients were identified using an international coding and indexing system and ESWL registry. In all, 125 children were treated during 1990-2003, but 21 had stones of > or = 20 mm. Stone clearance was assessed at 1 and 3 months, the stone-free state being defined as no radiological evidence of stone or fragments of < or = 3 mm. Failed treatments were analysed to identify any correlation with stone site. RESULTS: The overall stone-free rate was 81%; in four children the treatment failed (all girls) and subsequently they required ancillary procedures. Nineteen patients (90%) received up to three sessions of ESWL; two required four or more sessions. Of the four children in whom treatment failed, two had JJ stents; the stones were in the lower pole calyx in two, and the renal pelvis and lower pole calyx in two. The mean stone size in those where treatment failed was 25 mm, vs 21 mm in the stone-free group. The complication rate was 19%, but only one child required admission to hospital. CONCLUSIONS: ESWL is very effective for renal stones in children, with minimal morbidity. Lower pole and partial staghorn stones with a major component in the lower pole calyx should preferably be treated by a percutaneous approach.

Population genetics of a polyploid: is there hybridization between lineages of Hyla versicolor?

Several studies have demonstrated that polyploid species can form recurrently from their progenitors, but few studies have evaluated gene flow between the resultant polyploid lineages. Here we examine the possibility of hybridization between lineages of the tetraploid common gray treefrog (Hyla versicolor). We utilize a polymerase chain reaction (PCR) cloning approach to estimate the genotypes of tetraploid individuals and measure genetic differentiation between (1) sympatric populations of two lineages and (2) allopatric populations of a single lineage. We find that allele frequencies in sympatric populations of two lineages do not differ, suggesting that frogs of these two lineages hybridize in areas where they co-occur.

Strong founder effect in Drosophila pseudoobscura colonizing New Zealand from North America.

The North American native species Drosophila pseudoobscura was first identified in New Zealand in the last few decades. Here, we have studied the genetic consequences of its spread across the Pacific Ocean. Using 10 microsatellites that are highly variable in North American populations, we found that the New Zealand population has substantially fewer alleles, a much lower average heterozygosity, and significantly different allele frequencies at these loci. We have discussed the relative sensitivity of these parameters for detecting the founding event. X-linked loci were more strongly differentiated between continents than autosomal loci, as reflected by larger changes in allele frequencies and greater reductions in numbers of alleles and average heterozygosity. The severity of the genetic diversity loss supports a scenario of a few D. pseudoobscura females being introduced to New Zealand from North America.

Chromosomal inversions and the reproductive isolation of species.

Recent genetic studies have suggested that many genes contribute to differences between closely related species that prevent gene exchange, particularly hybrid male sterility and female species preferences. We have examined the genetic basis of hybrid sterility and female species preferences in Drosophila pseudoobscura and Drosophila persimilis, two occasionally hybridizing North American species. Contrary to findings in other species groups, very few regions of the genome were associated with these characters, and these regions are associated also with fixed arrangement differences (inversions) between these species. From our results, we propose a preliminary genic model whereby inversions may contribute to the speciation process, thereby explaining the abundance of arrangement differences between closely related species that co-occur geographically. We suggest that inversions create linkage groups that cause sterility to persist between hybridizing taxa. The maintenance of this sterility allows the species to persist in the face of gene flow longer than without such inversions, and natural selection will have a greater opportunity to decrease the frequency of interspecies matings.

Consequences of recombination rate variation on quantitative trait locus mapping studies. Simulations based on the Drosophila melanogaster genome.

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.

The effects of recombinant human growth hormone on body composition and glucose metabolism in HIV-infected patients with fat accumulation.

GH has been proposed as a therapy for patients with HIV-associated fat accumulation, but the pharmacological doses (6 mg/d) used have been associated with impaired fasting glucose and hyperglycemia. In contrast, physiologic doses of GH ( approximately 1 mg/d) in HIV-negative men reduced visceral adiposity and eventually improved insulin sensitivity, despite initially causing insulin resistance. We conducted an open-label study to evaluate the effects of a lower pharmacologic dose of GH (3 mg/d) in eight men with HIV-associated fat accumulation. Oral glucose tolerance, insulin sensitivity, and body composition were measured at baseline, and 1 and 6 months. Six patients completed 1 month and 5, 6 months of GH therapy. IGF-I levels increased 4-fold within 1 month of GH treatment. Over 6 months, GH reduced buffalo hump size and excess visceral adipose tissue. Total body fat decreased (17.9 +/- 10.9 to 13.5 +/- 8.4 kg, P = 0.05), primarily in the trunk region. Lean body mass increased (62.9 +/- 6.4 to 68.3 +/- 9.1 kg, P = 0.03). Insulin-mediated glucose disposal, measured by a euglycemic hyperinsulinemic clamp, declined at month 1 (49.7 +/- 27.5 to 25.6 +/- 6.6 nmol/kg(LBM).min/pmol(INSULIN)/liter, P = 0.04); values improved at month 6 (49.2 +/- 22.6, P = 0.03, compared with month 1) and did not differ significantly from baseline. Similarly, the integrated response to an oral glucose load worsened at month 1 (glucose area under the curve 20.1 +/- 2.3 to 24.6 +/- 3.7 mmol.h/liter, P < 0.01), whereas values improved at month 6 (22.1 +/- 1.5, P = 0.02, compared with month 1) and did not differ significantly from baseline. One patient developed symptomatic hyperglycemia within 2 wk of GH initiation; baseline oral glucose tolerance testing revealed preexisting diabetes despite normal fasting glucose. In conclusion, GH at 3 mg/d resulted in a decrease in total body fat and an increase in lean body mass in this open-label trial. While insulin sensitivity and glucose tolerance initially worsened, they subsequently improved toward baseline. However, the dose of GH used in this trial was supraphysiologic and led to an increase in IGF-I levels up to three times the upper normal range. Because there are known adverse effects of long-term GH excess, the effectiveness of lower doses of GH should be studied. We also recommend a screening oral glucose tolerance test be performed to exclude subjects at risk for GH-induced hyperglycemia.

Metabolic effects of indinavir in healthy HIV-seronegative men.

BACKGROUND: Therapy with HIV protease inhibitors (PI) has been associated with hyperglycemia, hyperlipidemia and changes in body composition. It is unclear whether these adverse effects are drug related, involve an interaction with the host response to HIV or reflect changes in body composition. METHODS: Indinavir 800 mg twice daily was given to 10 HIV-seronegative healthy men to distinguish direct metabolic effects of a PI from those related to HIV infection. Fasting glucose and insulin, lipid and lipoprotein profiles, oral glucose tolerance (OGTT), insulin sensitivity by hyperinsulinemic euglycemic clamp, and body composition were measured prior to and after 4 weeks of indinavir therapy. RESULTS: Fasting glucose (4.9 +/- 0.1 versus 5.2 +/- 0.2 mmol/l; P = 0.05) insulin concentrations (61.7 +/- 12.2 versus 83.9 +/- 12.2 pmol/l; P < 0.05), insulin : glucose ratio (12.6 +/- 1.7 versus 15.9 +/- 1.9 pmol/mmol; P < 0.05) and insulin resistance index by homeostasis model assessment (1.9 +/- 0.3 versus 2.8 +/- 0.5;P < 0.05) all increased significantly. During OGTT, 2 h glucose (5.1 +/- 0.4 versus 6.5 +/- 0.6 mmol/l; P < 0.05) and insulin levels (223.1 +/- 48.8 versus 390.3 +/- 108.8 pmol/l;P =0.05) also increased significantly. Insulin-mediated glucose disposal decreased significantly (10.4 +/- 1.4 versus 8.6 +/- 1.2 mg/kg x min per microU/ml insulin; 95% confidence interval 0.6--.0;P < 0.01). There was no significant change in lipoprotein, triglycerides or free fatty acid levels. There was a small loss of total body fat (15.8 +/- 1.4 versus 15.2 +/- 1.4 kg;P = 0.01) by X-ray absorptiometry without significant changes in weight, waist : hip ratio, and visceral or subcutaneous adipose tissue by computed tomography. CONCLUSIONS: In the absence of HIV infection, treatment with indinavir for 4 weeks causes insulin resistance independent of increases in visceral adipose tissue or lipid and lipoprotein levels.

Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation.

Forsdyke (1999) has recently argued that differences in (G+C)%, or G+C content, may trigger new species formation. He further argues that the genic model has shortcomings that can be overcome by his "chromosomal" (hereafter, "G+C") model. We disagree on several counts. First, we do not accept that the genic model has the shortcomings suggested by Forsdyke. There is an abundance of empirical support for the contribution of individual genes, as well as of mapped chromosomal regions, to post-zygotic reproductive isolation (and Haldane's rule). Further, we argue that the G+C model suffers from the same theoretical difficulties as other speciation models based on underdominance. We also question the evidence Forsdyke uses to support his model. Finally, we describe analyses of G+C content in a well-studied model system of speciation (the Drosophila melanogaster species complex), the results of which are incompatible with the G+C model. Thus, while Forsdyke's G+C model cannot be explicitly ruled out, it is not directly supported by empirical data. In contrast, the genic model is well supported by empirical data, holds up on theoretical grounds, and does not require any assistance from the G+C model.

The genetics of reproductive isolation and the potential for gene exchange between Drosophila pseudoobscura and D. persimilis via backcross hybrid males.

Hybrid male sterility, hybrid inviability, sexual isolation, and a hybrid male courtship dysfunction reproductively isolate Drosophila pseudoobscura and D. persimilis. Previous studies of the genetic bases of these isolating mechanisms have yielded only limited information about how much and what areas of the genome are susceptible to interspecies introgression. We have examined the genetic basis of these barriers to gene exchange in several thousand backcross hybrid male progeny of these species using 14 codominant molecular genetic markers spanning the five chromosomes of these species, focusing particularly on the autosomes. Hybrid male sterility, hybrid inviability, and the hybrid male courtship dysfunction were all associated with X-autosome interactions involving primarily the inverted regions on the left arm of the X-chromosome and the center of the second chromosome. Sexual isolation from D. pseudoobscura females was primarily associated with the left arm of the X-chromosome, although both the right arm and the center of the second chromosome also contributed to it. Sexual isolation from D. persimilis females was primarily associated with the second chromosome. The absence of isolating mechanisms being associated with many autosomal regions, including some large inverted regions that separate the strains, suggests that these phenotypes may not be caused by genes spread throughout the genome. We suggest that gene flow between these species via hybrid males may be possible at loci spread across much of the autosomes.

Courtship songs of Drosophila pseudoobscura and D. persimilis. II. Genetics of species differences.

Although male courtship songs have been repeatedly implicated in sexual isolation between numerous Drosophila species, no genetic studies have evaluated the genetic basis of differences between species beyond using quantitative genetic analyses of hybrids or surveying associations of song characters to five or fewer genetic markers. Here, we dissect the genetic basis of the difference between D. pseudoobscura and D. persimilis in two courtship song elements (interpulse interval and intrapulse frequency) using 15 molecular markers. We also evaluate the association between song elements and sexual isolation in these backcross hybrid males of these species. We find that song differences between these species are associated with at least two or three genomic regions, and the species difference in interpulse interval may be oligogenic. Courtship song differences are especially strongly associated with two inversions that differentiate these species. Further, we found that interpulse interval is strongly associated with mating success to D. pseudoobscura females, while intrapulse frequency is associated with mating success to D. persimilis females. Implications of these findings are discussed.