Ancestral haplotype reconstruction in endogamous populations using identity-by-descent.

In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies and track disease inheritance patterns. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between identifying a source for each IBD segment and assembling IBD segments placed within each ancestral individual. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs. We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to North America from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 12 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 224 ancestral individuals per chromosome. For these ancestral individuals, on average we reconstruct 79% of their haplotypes. We also identify a region on chromosome 16 that is difficult to reconstruct-we find that this region harbors a short Amish-specific copy number variation and the gene HYDIN. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families.

Diel rhythm of volatile emissions of males and females of the peach fruit fly Bactrocera zonata.

Fruit flies in the genus Bactrocera are among the most destructive insect pests of fruits and vegetables throughout the world. A number of studies have identified volatiles from fruit flies, but few reports have demonstrated behavioral effects or sensitivities of fly antennae to these compounds. We applied a recently developed method of automated headspace analysis using SPME (Solid Phase Microextraction) fibers and GC-MS (gas chromatography mass spectrometry), termed SSGA, to reveal volatiles specific to each sex of B. zonata that are emitted in a diel periodicity. The volatiles released primarily at dusk were identified by GC-MS and chemical syntheses as several spiroacetals, pyrazines, and ethyl esters. Solvent extraction of male rectal glands or airborne collections from each sex, followed by GC-MS, showed that certain of the volatiles increase or decrease in quantity sex-specifically with age of the flies. Electroantennographic (EAG) analysis of dose-response indicates differences in sensitivities of male and female antenna to the various volatiles. Our study provides a comprehensive analysis of the volatile chemicals produced and released by B. zonata and their antennal responses. The possible pheromone and semiochemical roles of the various volatiles released by each sex and the difficulties of establishing behavioral functions are discussed.

Correction: The population genetics of human disease: The case of recessive, lethal mutations.

[This corrects the article DOI: 10.1371/journal.pgen.1006915.].

A population genetic interpretation of GWAS findings for human quantitative traits.

Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes-notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space. We solve the model for the phenotypic distribution and allelic dynamics at steady state and derive robust, closed-form solutions for summary statistics of the genetic architecture. Our results provide a simple interpretation for missing heritability and why it varies among traits. They predict that the distribution of variances contributed by loci identified in GWASs is well approximated by a simple functional form that depends on a single parameter: the expected contribution to genetic variance of a strongly selected site affecting the trait. We test this prediction against the results of GWASs for height and body mass index (BMI) and find that it fits the data well, allowing us to make inferences about the degree of pleiotropy and mutational target size for these traits. Our findings help to explain why the GWAS for height explains more of the heritable variance than the similarly sized GWAS for BMI and to predict the increase in explained heritability with study sample size. Considering the demographic history of European populations, in which these GWASs were performed, we further find that most of the associations they identified likely involve mutations that arose shortly before or during the Out-of-Africa bottleneck at sites with selection coefficients around s = 10-3.

The population genetics of human disease: The case of recessive, lethal mutations.

Do the frequencies of disease mutations in human populations reflect a simple balance between mutation and purifying selection? What other factors shape the prevalence of disease mutations? To begin to answer these questions, we focused on one of the simplest cases: recessive mutations that alone cause lethal diseases or complete sterility. To this end, we generated a hand-curated set of 417 Mendelian mutations in 32 genes reported to cause a recessive, lethal Mendelian disease. We then considered analytic models of mutation-selection balance in infinite and finite populations of constant sizes and simulations of purifying selection in a more realistic demographic setting, and tested how well these models fit allele frequencies estimated from 33,370 individuals of European ancestry. In doing so, we distinguished between CpG transitions, which occur at a substantially elevated rate, and three other mutation types. Intriguingly, the observed frequency for CpG transitions is slightly higher than expectation but close, whereas the frequencies observed for the three other mutation types are an order of magnitude higher than expected, with a bigger deviation from expectation seen for less mutable types. This discrepancy is even larger when subtle fitness effects in heterozygotes or lethal compound heterozygotes are taken into account. In principle, higher than expected frequencies of disease mutations could be due to widespread errors in reporting causal variants, compensation by other mutations, or balancing selection. It is unclear why these factors would have a greater impact on disease mutations that occur at lower rates, however. We argue instead that the unexpectedly high frequency of disease mutations and the relationship to the mutation rate likely reflect an ascertainment bias: of all the mutations that cause recessive lethal diseases, those that by chance have reached higher frequencies are more likely to have been identified and thus to have been included in this study. Beyond the specific application, this study highlights the parameters likely to be important in shaping the frequencies of Mendelian disease alleles.

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.

Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.

Symbiotic bacteria enable olive flies (Bactrocera oleae) to exploit intractable sources of nitrogen.

Insects are often associated with symbiotic micro-organisms, which allow them to utilize nutritionally marginal diets. Adult fruit flies (Diptera: Tephritidae) associate with extracellular bacteria (Enterobacteriaceae) that inhabit their digestive tract. These flies obtain nutrients by foraging for plant exudates, honeydew and bird droppings scattered on leaves and fruit­a nutritional niche which offers ample amounts of carbohydrates, but low quantities of available nitrogen. We identified the bacteria resident in the gut of the olive fly (Bactrocera oleae)­a worldwide pest of olives and examined their contribution to nitrogen metabolism in the adult insect. By suppressing bacteria in the gut and monitoring female fecundity, we demonstrate that bacteria contribute essential amino acids and metabolize urea into an available nitrogen source for the fly, thus significantly elevating egg production. In an ecological context, bacteria were found to be beneficial to females subsisting on bird droppings, but not on honeydew­two natural food sources. We suggest that a main gut bacterium (Candidatus Erwinia dacicola) forms an inseparable, essential part of this fly's nutritional ecology. The evolution of this symbiosis has allowed adult flies to utilize food substrates which are low or imbalanced in assimilable nitrogen and thereby to overcome the nitrogen limitations of their natural diet.

The deleterious mutation load is insensitive to recent population history.

Human populations have undergone major changes in population size in the past 100,000 years, including recent rapid growth. How these demographic events have affected the burden of deleterious mutations in individuals and the frequencies of disease mutations in populations remains unclear. We use population genetic models to show that recent human demography has probably had little impact on the average burden of deleterious mutations. This prediction is supported by two exome sequence data sets showing that individuals of west African and European ancestry carry very similar burdens of damaging mutations. We further show that for many diseases, rare alleles are unlikely to contribute a large fraction of the heritable variation, and therefore the impact of recent growth is likely to be modest. However, for those diseases that have a direct impact on fitness, strongly deleterious rare mutations probably do have an important role, and recent growth will have increased their impact.

Emergence of stability in a stochastically driven pendulum: beyond the Kapitsa pendulum.

We consider a prototypical nonlinear system which can be stabilized by multiplicative noise: an underdamped nonlinear pendulum with a stochastically vibrating pivot. A numerical solution of the pertinent Fokker-Planck equation shows that the upper equilibrium point of the pendulum can become stable even when the noise is white, and the "Kapitsa pendulum" effect is not at work. The stabilization occurs in a strong-noise regime where WKB approximation does not hold.

Gut bacterial communities in the Mediterranean fruit fly (Ceratitis capitata) and their impact on host longevity.

Fruit flies (Diptera: Tephritidae) harbor stable bacterial communities in their digestive system, composed mainly of members of the Enterobacteriaceae. However, the Enterobacteriaceae are not the sole community in this habitat. We examined the hypothesis that Pseudomonas spp. form a cryptic community in the gut of Ceratitis capitata, the Mediterranean fruit fly ('medfly'). Suicide polymerase restriction PCR (SuPER PCR), a novel culture-independent technique, revealed that Pseudomonas spp. form minor, common and stable communities within the medfly's gut. These include P. aeruginosa, a known pathogen of arthropods. Experimental inoculations with high levels of P. aeruginosa reduced the medfly's longevity while inoculations with members of the Enterobacteriaceae extended the fly's life. Accordingly, we suggest that in addition to their possible contribution to the fly's nitrogen and carbon metabolism, development and copulatory success (as shown in previous studies), the Enterobacteriaceae community within the medfly's gut may also have an indirect contribution to host fitness by preventing the establishment or proliferation of pathogenic bacteria.

Bringing back the fruit into fruit fly-bacteria interactions.

Female Mediterranean fruit flies (Ceratitis capitata) oviposit in fruits, within which the larvae develop. This development is associated with rapid deterioration of the fruit, and frequently with invasion by secondary pests. Most research on the associations between medflies and microorganisms has focused on the bacteria inhabiting the digestive system of the adult fly, while the role of the fruit in mediating, amplifying or regulating the fruit fly microflora has been largely neglected. In this study, we examine the hypothesis that the host fruit plays a role in perpetuating the fly-associated bacterial community. Using direct and cultured-based approaches, we show that this community is composed in its very large majority of diazotrophic and pectinolytic Enterobacteriaceae. Our data suggest that this fly-associated enterobacterial community is vertically transmitted from the female parent to its offspring. During oviposition, bacteria are transferred to the fruit, establish and proliferate within it, causing its decay. These results show that the host fruit is indeed a central partner in the fruit fly-bacterial interaction as these transmitted bacteria are amplified by the fruit, and subsequently maintained throughout the fly's life. This enterobacterial community may contribute to the fly's nitrogen and carbon metabolism, affecting its development and ultimately, fitness.

Verrucous carcinoma of the scalp.

Verrucous carcinoma is a distinctive form of low-grade squamous cell carcinoma. It typically involves the oral cavity, larynx, esophagus, and skin. Cutaneous lesions typically arise in the genitocrural area and plantar surface of the foot, with rare case reports of verrucous carcinoma arising elsewhere on the body. Human papillomaviruses, predominately types 6 and 11, have been associated with some case reports. We present a case of verrucous carcinoma arising on the scalp with negative human papillomavirus testing in a relatively young patient.

Enterobacteria-mediated nitrogen fixation in natural populations of the fruit fly Ceratitis capitata.

Nitrogen, although abundant in the atmosphere, is paradoxically a limited resource for multicellular organisms. In the Animalia, biological nitrogen fixation has solely been demonstrated in termites. We found that all individuals of field-collected Mediterranean fruit flies (Ceratitis capitata) harbour large diazotrophic enterobacterial populations that express dinitrogen reductase in the gut. Moreover, nitrogen fixation was demonstrated in isolated guts and in live flies and may significantly contribute to the fly's nitrogen intake. The presence of similar bacterial consortia in additional insect orders suggests that nitrogen fixation occurs in vast pools of terrestrial insects. On such a large scale, this phenomenon may have a considerable impact on the nitrogen cycle.

Histochemical and histofluorescence tracing of chelatable zinc in the developing mouse.

Zinc is an essential element in mammalian development. However, little is known about concentrations of zinc in specific regions/organs in the embryo. We have employed selenite autometallography (AMG) and TSQ histofluoroscence to detect histochemically reactive (chelatable) zinc in whole midsagittal embryos and sections from neonatal mice. Chelatable zinc exhibited a broad distribution, being particularly localized to rapidly proliferating tissues, such as skin and gastrointestinal epithelium. Zinc was also observed in various types of tissues such as bone and liver. In the perinatal central nervous system, zinc was present almost exclusively in choroid plexus. The two methods used demonstrated generally similar distributions with some exceptions, e.g., in liver and blood. The ubiquity of zinc in the embryo, particularly in rapidly proliferating tissues, suggests a widespread role in fetal physiology.

Clioquinol effects on tissue chelatable zinc in mice.

Recent evidence for the involvement of zinc in the formation of beta-amyloid plaques in the brain in Alzheimer's disease has led to the establishment of new therapeutic strategies for the degenerative disorder based on metal chelation. The present experiment was conducted on a membrane-permeable zinc chelator, clioquinol (CQ), that has shown potential in initial studies on a mouse model of Alzheimer's disease [1]. The degree of chelatable zinc in mice treated with CQ, delivered by two different routes, was measured using complementary protocols for identifying chelatable zinc: 6-methoxy-8-quinolyl- p-toluenesulfonamide (TSQ) histofluorescence, and selenite autometalography. Mice injected intraperitoneally with CQ showed a dramatic reduction in chelatable zinc in brain, testis, and pancreas. In contrast, mice given CQ orally showed no significant change in levels of chelatable zinc in these tissues. This suggests that CQ administered orally to patients with Alzheimer's disease should not significantly perturb chelatable zinc levels in key organs and may be used over long periods without adverse endocrinological and reproductive effects related to zinc deficiency. In contrast, CQ injected intraperitoneally may be used not only as a tool for investigating chelatable zinc pools but also in a clinical context. For example, injected CQ could be employed in situations requiring the rapid buffering of excessive chelatable zinc following ischemic episodes or brain trauma. Thus, our findings indicate that CQ has considerable potential as a versatile scientific and clinical tool used for selective modulation of zinc pools.

Regulation of sexual receptivity of female Mediterranean fruit flies: old hypotheses revisited and a new synthesis proposed.

The objective of this study was to examine the relative contributions of copula duration and sperm transfer to the inhibition of sexual receptivity of female Mediterranean fruit flies (Ceratitis capitata, Diptera: Tephritidae). Females choosing to remate had significantly fewer sperm in their spermathecae than females who chose not to remate. Duration of a female's first copulation did not affect her subsequent receptivity. Furthermore, on the first day following copulation significantly more females whose first mate was sterile and from a laboratory strain (sterile males transfer fewer sperm than wild males) chose to copulate than did females whose mate was fertile and recently derived from wild stock. Finally, we offer a synthesis of the available information on remating in this species, and suggest that while females are facultatively polyandrous, copula duration, sperm transfer and male accessory gland secretions act in succession to inhibit female receptivity.

Postnatal regulation of ZnT-1 expression in the mouse brain.

We have characterized the postnatal development of ZnT-1, a putative zinc transporter, in the mouse brain with respect to chelatable zinc in four distinct brain areas: cerebral cortex, hippocampus, olfactory bulb and cerebellum. At birth, both zinc and ZnT-1 immunoreactivity were nearly undetectable. Beginning at the end of the first postnatal week, ZnT-1 expression increased significantly in all areas examined except the cerebellum, which contains virtually no synaptic zinc. Moreover, neurons immunoreactive for ZnT-1 were typically present in areas rich in synaptic zinc, which increased in parallel with ZnT-1. In the cerebellum, in contrast, Purkinje cells exhibited robust immunoreactivity for ZnT-1 only in the second postnatal week. While the parallel development of zinc and ZnT-1 in forebrain regions supports a direct role for synaptic zinc in regulating ZnT-1 expression, ZnT-1 in cerebellar Purkinje cells could indicate that expression of this zinc transporter may also be regulated by a non-synaptic pool of zinc or by other mechanism(s). The striking developmental regulation of ZnT-1 expression together with synaptic zinc indicates that ZnT-1 may play a key role in protecting developing neurons against potentially toxic zinc.

Perimeter trapping strategy to reduce Mediterranean fruit fly (Diptera: Tephritidae) damage on different host species in Israel.

To evaluate the perimeter trapping strategy as a control method, field tests were conducted in three different host species of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), in Israel. Dry traps baited with a three component food-based synthetic attractant that were hung in the peripheral rows of a plum, a pear, and a persimmon orchard, caught female C. capitata (up to 20.1, 1.4, and 4.1 female C. capitata per trap per day, respectively). Fruit damage, estimated at harvest, indicated a negligible percentage for the plum orchard (< 1%), 3% for the persimmon orchard (compared with 9% at an untreated neighboring plot), and no damaged fruit in the pear orchard. Finally, dissections of female C. capitata caught in dry traps on different host plant species indicate that a high percentage (range, 84-100%) contained mature eggs. The attraction of mature females to the dry traps might explain the successful results. Future research, to determine precisely how many traps should be placed and how frequently they should be serviced, is necessary before applying this strategy on a commercial basis.

Postcopulatory sexual selection in Mediterranean fruit flies: advantages for large and protein-fed males.

Previous laboratory studies of Mediterranean fruit flies, Ceratitis capitata (medflies), have identified large size and protein feeding as positive influences on the ability of males to secure copulations. In this study, we investigated whether large and protein-fed males experience additional advantages in terms of amount and distribution of sperm stored by mates. We also examined relationships between copula duration and sperm storage. Mates of large and protein-fed males were more likely to store sperm and to store more sperm than mates of small and protein-deprived males. Probability of sperm storage was associated with copula duration; all copulations lasting less than 100 min failed whereas 98% lasting longer than 100 min succeeded. Copulations involving sperm storage were longer if males were small or protein deprived or if the female was large, although there was no evidence of a relationship between copula duration and total sperm storage. Evidence from related studies suggests that variation in latency until sperm transfer, caused by size and diet, is a likely explanation for varying copula duration. Sperm tended to be stored asymmetrically between the female's two spermathecae, consistent with a mating system in which females maintain isolated populations of sperm from different males and later select between them. Storage was less asymmetric when large numbers of sperm were stored but there was little evidence that male size or diet affected this asymmetry. It is uncertain whether postcopulatory advantages of large and protein-fed male medflies arise from female preferences or male dominance through coercion or force. Copyright 1999 The Association for the Study of Animal Behaviour.

Nutritional correlates of reproductive success of male Mediterranean fruit flies (Diptera: Tephritidae)

We examined the hypothesis that adult diet affects the reproductive success of male Mediterranean fruit flies. In particular we determined whether protein-fed males copulated more frequently than protein-deprived males. Furthermore, we determined whether the nutritional status of their first sexual partner affects the renewal of female receptivity. Males fed no protein copulated at a significantly lower rate than did males fed protein. In both diet groups, size was significantly associated with copulatory success. Protein-deprived males transferred significantly more sperm to their mates than did protein-fed males. However, significantly more females mated to protein-deprived males re-mated on the following day. We conclude that male diet is a significant factor in determining male reproductive success. Male diet affects the ability to gain copulations with virgin females, and the receptivity of these females to further copulations.