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.

Crinkle-Cut Coronary Arteries in a Patient With Granulomatosis With Polyangiitis.

Granulomatosis with polyangiitis (GPA) is a rare type of small to medium vessel necrotizing vasculitis that usually affects vessels of the upper or lower airways and kidneys. Cardiac involvement in GPA is often subclinical and if clinically significant has been rarely reported, even less so as an initial presentation. We describe the case of a 44-year-old man who presented with what appeared to be inferior ST-segment elevation myocardial infarction and was found to have small vessel vasculitis of the coronary arteries with associated myocarditis as a presenting manifestation of GPA, which was ultimately treated with steroids, rituximab, and avacopan.

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.

Speciation by reinforcement: a model derived from studies of Drosophila.

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.

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.

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.

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.

Genetic variation in the spread of Drosophila subobscura from a nonequilibrium population.

Drosophila subobscura was first identified in North America in the early 1980s, and a newer D. subobscura population in Utah appears to have been established more than 10 years later. In this study, we use nuclear microsatellite allele frequencies, mitochondrial restriction fragment length polymorphism (RFLP) allele frequencies, and computer simulations to investigate possible scenarios of how this species has spread across North America. Our method develops a 95% confidence interval for the maximum and minimum number of founders that could have colonized the new population given various scenarios for spread. Unlike many other methods, it may be applied to nonequilibrium source populations given certain conditions. We find that observed allele frequency differences between newer and older D. subobscura populations are consistent with very few inseminated females being transported east from the coast in a single step or with larger numbers of colonizers invading after several intermediate steps. They are not consistent with a large, panmictic population of D. subobscura colonizing Utah in a single step.

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.

High frequency of microsatellites in Drosophila pseudoobscura.

Using 30,000 bp of anonymous sequence data, we note that dinucleotide repeat arrays appear to be much more common in Drosophila pseudoobscura than in D. melanogaster or D. simulans. Repeat arrays bearing five or more units are situated on average once every 3000 bp in D. pseudoobscura, and repeat arrays bearing ten or more units are situated on average once every 7500 bp. We did not detect an association between microsatellite presence and GC-content of flanking regions.

A report of the first 20 cases using a simple external fixator.

The results of treatment using a locally-designed external fixator in 20 patients are presented. Open fractures were the main indications for external fixation. Pin tract infection occurred in 8 patients. Only 2 patients had unstable fixation which required removal of the device. One third of patients developed malunion exceeding 15 degrees and two thirds had joint stiffness after conversion to plaster cast. This external fixator is adequate in the treatment of most open fractures of the tibia. However, improved techniques of pin insertion and cast application upon removal of the external fixator may help to reduce the incidence of pin tract infections and malunion.

A simple and inexpensive external fixator.

A simple and inexpensive external fixator has been designed. It is constructed of galvanized iron pipe and mild steel bolts and nuts. It can easily be manufactured in a hospital workshop with a minimum of tools.

Reinforcement and other consequences of sympatry.

The pattern of greater species mating discrimination between sympatric taxa than between allopatric taxa has been attributed to the strengthening of mate discrimination to avoid maladaptive hybridization. This process, termed reinforcement, has been highly contentious, particularly with regard to its role in speciation. Here, I review some recent studies of reinforcement, discuss alternative explanations for the pattern of greater species discrimination in sympatric taxa, and point to some new directions that may help to clarify the evolutionary forces involved. In particular, we need more ecological work on putative cases of reinforcement, more theoretical models that give diagnostic predictions of reinforcement relative to other modes of divergence, and empirical studies to evaluate these diagnostic predictions.