Runs of homozygosity implicate autozygosity as a schizophrenia risk factor

Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Here, we use runs of homozygosity in genome-wide SNP data to estimate the proportion of the autosome that exists in autozygous tracts in 9,388 cases with schizophrenia and 12,456 controls. We estimate that the odds of schizophrenia increase by ~17% for every 1% increase in genome-wide autozygosity. This association is not due to one or a few regions, but results from many autozygous segments spread throughout the genome, and is consistent with a role for multiple recessive or partially recessive alleles in the etiology of schizophrenia. Such a bias towards recessivity suggests that alleles that increase the risk of schizophrenia have been selected against over evolutionary time.     

Runs of homozygosity have utility in mammalian conservation and evolutionary studies

Runs of homozygosity (ROHs) arise due the transmission from parents to offspring of segments that are either identical by decent (IBD) or identical by state (IBS). The former is due to consanguineous matings whereas the latter is due to demographic processes. ROHs reduce individual nucleotide diversity (θ) as a function of homozygosity, and thus ROH distributions and θ are expected to vary among species because inbreeding levels, recombination rates, and demographic histories vary widely. To help interpret genetic diversity within and among species, we utilized genome sequence data from 78 mammalian species to compare θ and ROH burden (i.e., number and length of ROHs in the genome) among groups of mammals to assess genomic signatures of inbreeding. We compared θ and ROHs: (i) among threatened and non-threatened mammals to determine the significance of contemporary conservation status; (ii) among carnivorous and non-carnivorous mammals to determine the relevance of trophic effects; (iii) relative to body size because mutation rates generally vary with body mass; and (iv) across mammals from different latitudes to test for gradients in genomic diversity (e.g., due to effects of historic climatic regimes). Our results illustrate the considerable variance in genomic diversity across mammals, and that trophic level, body mass, and latitude have significant effects on θ and ROH burden. However, conservation status was not a reliable indicator of genomic diversity. We argue that genetic or genomic diversity should be an explicit component of conservation status, as such diversity is critical to the long-term sustainability of populations, and anticipate that ROHs will become more commonly used to estimate inbreeding in wild animals.     

Runs of homozygosity and distribution of functional variants in the cattle genome

Background

Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches of homozygous genomic regions. For cattle, a large proportion of these runs of homozygosity (ROH) are likely the result of inbreeding due to the accumulation of elite alleles from long-term selective breeding programs. In the present study, ROH were characterized in four cattle breeds with whole genome sequence data and the distribution of predicted functional variants was detected in ROH regions and across different ROH length classes.

Results

On average, 19.5 % of the genome was located in ROH across four cattle breeds. There were an average of 715.5 ROH per genome with an average size of ~750 kbp, ranging from 10 (minimum size considered) to 49,290 kbp. There was a significant correlation between shared short ROH regions and regions putatively under selection (p < 0.001). By investigating the relationship between ROH and the predicted deleterious and non-deleterious variants, we gained insight into the distribution of functional variation in inbred (ROH) regions. Predicted deleterious variants were more enriched in ROH regions than predicted non-deleterious variants, which is consistent with observations in the human genome. We also found that increased enrichment of deleterious variants was significantly higher in short (<100 kbp) and medium (0.1 to 3 Mbp) ROH regions compared with long (>3 Mbp) ROH regions (P < 0.001), which is different than what has been observed in the human genome.

Conclusions

This study illustrates the distribution of ROH and functional variants within ROH in cattle populations. These patterns are different from those in the human genome but consistent with the natural history of cattle populations, which is confirmed by the significant correlation between shared short ROH regions and regions putatively under selection. These findings contribute to understanding the effects of inbreeding and probably selection in shaping the distribution of functional variants in the cattle genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1715-x) contains supplementary material, which is available to authorized users.     

Sex and age specificity of susceptibility genes modulating survival at old age

OBJECTIVE: We aimed to investigate the influence of the genetic variability of candidate genes on survival at old age in good health. METHODS: First, on the basis of a synthetic survival curve constructed using historic mortality data taken from the Italian population from 1890 onward, we defined three age classes ranging from 18 to 106 years. Second, we assembled a multinomial logistic regression model to evaluate the effect of dichotomous variables (genotypes) on the probability to be assigned to a specific category (age class). Third, we applied the regression model to a cross-sectional dataset (10 genes; 972 subjects selected for healthy status) categorized according to age and sex. RESULTS: We found that genetic factors influence survival at advanced age in good health in a sex- and age-specific way. Furthermore, we found that genetic variability plays a stronger role in males than in females and that, in both genders, its impact is especially important at very old ages. CONCLUSIONS: The analyses presented here underline the age-specific effect of the gene network in modulating survival at advanced age in good health.     

HLA and beta-myosin heavy chain do not influence susceptibility to Chagas disease cardiomyopathy

An inflammatory dilated cardiomyopathy occurs in 30% of Chagas' disease patients, chronically infected by Trypanosoma cruzi, while the remaining infected individuals are asymptomatic. Studies have indicated a role for genetic factors in the susceptibility to Chagas' disease cardiomyopathy. In an attempt to identify the genetic factors influencing the development and outcome of Chagas' cardiomyopathy, we compared the frequencies of alleles from two candidate gene loci, class II HLA and a microsatellite marker for the human cardiac beta-myosin heavy chain gene in different clinical groups. Patients were grouped as asymptomatic or with severe or mild cardiomyopathy. The results indicate that the HLA and myosin microsatellite allele profiles in all cardiomyopathy and in asymptomatic groups are similar. In conclusion, these results establish that polymorphism of HLA-DR and -DQ molecules, as well as beta-cardiac myosin, do not influence the susceptibility to different clinical forms of Chagas' disease or the progression to severe Chagas' cardiomyopathy. On the other hand, male sex was identified as a risk factor for progression to the more severe forms of cardiomyopathy (relative risk = 8.75).     

To age or not to age

According to the antagonistic pleiotropy theory of ageing, natural selection has favoured genes conferring short-term benefits to the organism at the cost of deterioration in later life. The 'disposable soma' theory expresses this as a life-history strategy in which somatic maintenance is below the level required to prevent ageing, thus enabling higher immediate fertility. It has been argued that a non-ageing strategy will always be bettered by a low but non-zero rate of ageing, because the costs of such ageing will be felt only in the distant future when they are of negligible importance. Here, we examine this argument critically. We find that a non-ageing strategy will be locally optimal if, in the presence of ageing, the onset of deterioration is sufficiently rapid or early. Conversely, ageing will be optimal if deterioration is sufficiently slow or late. As the temporal profile of ageing changes from one of steady deterioration to one involving a sudden loss of vitality after a period of little or no decline, the conditions for a non-ageing strategy to be locally optimal become progressively more stringent. But for all forms of profile considered, conditions can be found for which a strategy involving no ageing is locally optimal.     

Why brown-headed cowbirds do not influence red-winged blackbird parent behaviour

Brown-headed cowbirds, Molothrus ater, frequently parasitize red-winged blackbirds,Agelaius phoeniceus . The presence of a brood parasite, unrelated to both host nestlings and parents, has provoked speculation regarding within-brood food allocation and parental provisioning. This study is the first to compare directly the effect of brood parasitism on host parent and offspring behaviour in younger and older broods. We videotaped 28 unparasitized red-winged blackbird broods and compared them to 22 parasitized broods. Red-winged blackbird nestling begging appears largely unaffected by cowbird parasitism. The presence of the cowbird in the nest affected neither the latency nor duration of host nestling begging, but stimulated more frequent begging by red-winged blackbird nestlings following food distribution. Begging by cowbirds was unique in two ways: (1) cowbirds maintained a consistent begging effort throughout the nestling period (but did not receive a consistent food share); and (2) cowbirds begged longer and more frequently following the allocation of food. Persistent begging by the cowbird following the allocation of food has implications for the division of parental care, if by doing so the brood parasite is able to provoke the foster parent to increase provisioning, at the expense of brooding. We found no evidence for the adjustment of parental care. Neither the foraging rates nor the lengths of the parental feeding visits differed markedly between parasitized and unparasitized broods. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

Commercial agrochemical applications in vineyards do not influence ant communities

Ants have been widely used as bioindicators for various terrestrial monitoring and assessment programs but are seldom considered in evaluation of nontarget pesticide effect. Much chemical assessment has been biased toward laboratory and bioassay testing for control of specific pest ant species. Several field studies that did explore the nontarget impacts of pesticides on ants have reported contradictory findings. To address the impact of chemical applications on ants, we tested the response of epigeal ant assemblages and community structure to three pesticide gradients (cumulative International Organization for Biological and Integrated Control toxicity rating, chlorpyrifos use rate, and sulfur use rate) in 19 vineyards. Ordination analyses using nonmetric multidimensional scaling detected community structures at species and genus levels, but the structures were not explained by any pesticide variables. There was no consistent pattern in species and genus percentage complementarities and ant assemblages along pesticide gradients. In contrast, ant community structure was influenced by the presence of shelterbelts near the sampling area. Reasons for the resilience of ants to pesticides are given and assessment at the colony level instead of workers abundance is suggested. The presence of Linepithema humile (Mayr) is emphasized.     

Radiocollars do not affect the survival or foraging behaviour of wild meerkats

The practice of radiocollaring is increasingly being used in the study of wild animal populations. However, methods of tracking and monitoring are known to affect some species negatively. On a wild population of habituated meerkats Suricata suricatta , we investigated the potential costs and consequences of carrying a radiocollar for small carnivores, focusing on detailed aspects of foraging behaviour and survival. Radiocollared individuals were no more likely to be predated than non-collared individuals in the same social group. We also found that collaring did not affect foraging efficiency, with collared individuals being equally efficient foragers (four measures) while wearing a collar compared with the pre-collaring period. To control for group-specific events, changes in foraging efficiency after collaring were compared with the behaviour of control individuals from the same group and no significant differences were found. In conclusion, we found no evidence to suggest radiocollars impact negatively on the bearer's welfare, survival or foraging ability.     

Evidence that queens do not influence nestmate recognition in Argentine ants

Summary Introduced populations of many invasive ants exhibit low levels of intraspecific aggression. Argentine ants (Linepithema humile), for example, maintain expansive supercolonies in many parts of their introduced range. Recent studies demonstrate that variation in nestmate recognition in L. humile can derive from both environmental and genetic sources. In some ants, pheromones emitted by queens also influence nestmate-recognition behavior. To test if such a phenomenon occurs in Argentine ants, we examined whether levels of intraspecific aggression vary as a function of queen presence or absence in experimental lab colonies. For each of four known supercolonies from southwestern California, we set up a pair of experimental colonies and randomly assigned replicates within each pair to treatment (queen removal) and control (no queen removal) groups. Using two different behavioral assays, we then measured aggressive behavior for ten days, removed queens from colonies in the treatment group, and continued to monitor aggression in both experimental groups for an additional 65 days. Both assays yielded qualitatively similar results: intraspecific aggression remained high throughout the experiment in both experimental groups. These results suggest that L. humile queens fail to influence levels of intraspecific aggression in introduced populations.Received 2 June 2003; revised 1 September 2003; accepted 18 September 2003.     

Pharmacokinetic genes do not influence response or tolerance to citalopram in the STAR*D sample

Background

We sought to determine whether clinical response or tolerance to the Selective Serotonin Reuptake Inhibitor (SSRI) citalopram is associated with genetic polymorphisms in potentially relevant pharmacokinetic enzymes.

Methodology

We used a two-stage case-control study design in which we split the sample of 1,953 subjects from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial into a discovery (n = 831) and validation set (n = 1,046). Fifteen polymorphisms from five (CYP2D6, ABCB1, CYP2C19, CYP3A4, and CYP3A5) pharmacokinetic genes were genotyped. We examined the associations between these polymorphisms and citalopram response and tolerance. Significant associations were validated in the second stage for those polymorphism found to be statistically significant in the first stage.

Conclusions

No genetic polymorphism in the pharmacokinetic genes examined was significantly associated with our response or tolerance phenotypes in both stages. For managing pharmacological treatment with citalopram, routine screening of the common pharmacokinetic DNA variants that we examined appears to be of limited clinical utility.