Elzbieta Sliwerska

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

Examining Y The evolution of human populations has long been studied with unique sequences from the nonrecombining, male-specific Y chromosome (see the Perspective by Cann). Poznik et al. (p. 562) examined 9.9 Mb of the Y chromosome from 69 men from nine globally divergent populations—identifying population and individual specific sequence variants that elucidate the evolution of the Y chromosome. Sequencing of maternally inherited mitochondrial DNA allowed comparison between the relative rates of evolution, which suggested that the coalescence, or origin, of the human Y chromosome and mitochondria both occurred approximately 120 thousand years ago. Francalacci et al. (p. 565) investigated the sequence divergence of 1204 Y chromosomes that were sampled within the isolated and genetically informative Sardinian population. The sequence analyses, along with archaeological records, were used to calibrate and increase the resolution of the human phylogenetic tree. Global diversity in the Y chromosome and mitochondrial DNA coalesce at approximately the same times in humans. [Also see Perspective by Cann] The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (TMRCA) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome TMRCA to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages.

Association Between Val66Met Brain-Derived Neurotrophic Factor (BDNF) Gene Polymorphism and Post-Treatment Relapse in Alcohol Dependence

BACKGROUND The purpose of this study was to examine relationships between genetic markers of central serotonin (5-HT) and dopamine function, and risk for post-treatment relapse, in a sample of alcohol-dependent patients. METHODS The study included 154 patients from addiction treatment programs in Poland, who met DSM-IV criteria for alcohol dependence. After assessing demographics, severity of alcohol use, suicidality, impulsivity, depression, hopelessness, and severity of alcohol use at baseline, patients were followed for approximately 1 year to evaluate treatment outcomes. Genetic polymorphisms in several genes (TPH2, SLC6A4, HTR1A, HTR2A, COMT, and BDNF) were tested as predictors of relapse (defined as any drinking during follow-up) while controlling for baseline measures. RESULTS Of 154 eligible patients, 123 (80%) completed follow-up and 48% (n = 59) of these individuals relapsed. Patients with the Val allele in the Val66Met BDNF polymorphism and the Met allele in the Val158Met COMT polymorphism were more likely to relapse. Only the BDNF Val/Val genotype predicted post-treatment relapse [odds ratio (OR) = 2.62; p = 0.019], and time to relapse (OR = 2.57; p = 0.002), after adjusting for baseline measures and other significant genetic markers. When the analysis was restricted to patients with a family history of alcohol dependence (n = 73), the associations between the BDNF Val/Val genotype and relapse (OR = 5.76, p = 0.0045) and time to relapse (hazard ratio = 4.93, p = 0.001) were even stronger. CONCLUSIONS The Val66Met BDNF gene polymorphism was associated with a higher risk and earlier occurrence of relapse among patients treated for alcohol dependence. The study suggests a relationship between genetic markers and treatment outcomes in alcohol dependence. Because a large number of statistical tests were conducted for this study and the literature on genetics and relapse is so novel, the results should be considered as hypothesis generating and need to be replicated in independent studies.

Increased activity of Diaphanous homolog 3 (DIAPH3)/diaphanous causes hearing defects in humans with auditory neuropathy and in Drosophila

Auditory neuropathy is a rare form of deafness characterized by an absent or abnormal auditory brainstem response with preservation of outer hair cell function. We have identified Diaphanous homolog 3 (DIAPH3) as the gene responsible for autosomal dominant nonsyndromic auditory neuropathy (AUNA1), which we previously mapped to chromosome 13q21-q24. Genotyping of additional family members narrowed the interval to an 11-Mb, 3.28-cM gene-poor region containing only four genes, including DIAPH3. DNA sequencing of DIAPH3 revealed a c.-172G > A, g. 48G > A mutation in a highly conserved region of the 5′ UTR. The c.-172G > A mutation occurs within a GC box sequence element and was not found in 379 controls. Using genome-wide expression arrays and quantitative RT-PCR, we demonstrate a 2- to 3-fold overexpression of DIAPH3 mRNA in lymphoblastoid cell lines from affected individuals. Likewise, a significant increase (≈1.5-fold) in DIAPH3 protein was found by quantitative immunoblotting of lysates from lymphoblastoid cell lines derived from affected individuals in comparison with controls. In addition, the c.-172G > A mutation is sufficient to drive overexpression of a luciferase reporter. Finally, the expression of a constitutively active form of diaphanous protein in the auditory organ of Drosophila melanogaster recapitulates the phenotype of impaired response to sound. To date, only two genes, the otoferlin gene OTOF and the pejvakin gene PJVK, are known to underlie nonsyndromic auditory neuropathy. Genetic testing for DIAPH3 may be useful for individuals with recessive as well as dominant inheritance of nonsyndromic auditory neuropathy.

Microbial interactions lead to rapid micro-scale successions on model marine particles.

In the ocean, organic particles harbour diverse bacterial communities, which collectively digest and recycle essential nutrients. Traits like motility and exo-enzyme production allow individual taxa to colonize and exploit particle resources, but it remains unclear how community dynamics emerge from these individual traits. Here we track the taxon and trait dynamics of bacteria attached to model marine particles and demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. Motile, particle-degrading taxa are selected for during early successional stages. However, this selective pressure is later relaxed when secondary consumers invade, which are unable to use the particle resource but, instead, rely on carbon from primary degraders. This creates a trophic chain that shifts community metabolism away from the particle substrate. These results suggest that primary successions may shape particle-attached bacterial communities in the ocean and that rapid community-wide metabolic shifts could limit rates of marine particle degradation.

PER3 Polymorphism and Insomnia Severity in Alcohol Dependence

STUDY OBJECTIVES Insomnia is common, persistent, and associated with relapse in alcohol-dependent (AD) patients. Although the underlying mechanisms are mostly unstudied, AD patients have impaired circadian rhythms and sleep drive, which may be genetically influenced. A polymorphism in the PER3 gene (PER3(4/4), PER3(4/5), PER3(5/5)) has previously been associated with circadian preference and sleep homeostasis, and the PER3(4/4)genotype has been characterized by evening preference and decreased sleep drive. The purpose of this study was to examine the influence of this polymorphism on insomnia severity in AD patients. We hypothesized that the PER3 polymorphism would be an independent predictor of insomnia severity with greatest severity observed in those with the PER3(4/4)genotype. DESIGN Cross-sectional association of patient characteristics, genotype, and insomnia severity. Significant (P < 0.05) bivariate correlates were further analyzed by hierarchical, forced entry multiple linear regression. SETTING Alcohol treatment programs in Warsaw, Poland. PATIENTS Diagnosed with alcohol dependence (n = 285), according to the Diagnostic and Statistical Manual of Mental Disorders, 4(th) edition. MEASUREMENTS AND RESULTS Drinking frequency, mental and physical health status, childhood abuse, and PER3 genotype were independent predictors of insomnia severity, as measured by a 7-item subscale of the Sleep Disorders Questionnaire, explaining 28.9% of the variance. Addition of the genotype in the final step significantly increased the amount of variance explained by 1.1% (P = 0.027). Those with the PER3(4/4)genotype had the greatest severity of insomnia symptoms. CONCLUSIONS PER3 genotype contributed unique variance in predicting insomnia severity in AD patients. These results are consistent with genetically influenced impairment in sleep regulation mechanisms in AD patients with insomnia.

Modeling Human Population Separation History Using Physically Phased Genomes

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati, and Centre de’Etude du Polymorphism Humain European populations and analyzed population size and separation history using the pairwise sequentially Markovian coalescent and multiple sequentially Markovian coalescent models. We find that statistically phased haplotypes yield a more recent split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard isolation-with-migration model. We inferred that the separation between hunter-gatherer populations and other populations happened ∼120–140 KYA, with gene flow continuing until 30–40 KYA; separation between west-African and out-of-African populations happened ∼70–80 KYA; while the separation between Maasai and out-of-African populations happened ∼50 KYA.

Population split time estimation and X to autosome effective population size differences inferred using physically phased genomes

Haplotype resolved genome sequence information is of growing interest due to its applications in both population genetics and medical genetics. Here, we assess the ability to correctly reconstruct haplotype sequences using fosmid pooled sequencing and apply the sequences to explore historical population relationships. We resolved phased haplotypes of sample NA19240, a trio child from the Yoruba HapMap collection using pools of a total of 521,783 fosmid clones. We phased 93% of heterozygous SNPs into haplotype-resolved blocks, with an N50 size of 318kb. Using trio information from HapMap, we linked adjacent blocks together to form paternal and maternal alleles, producing near-to-complete haplotypes. Comparison with 33 individual fosmids sequenced using capillary sequencing shows that our reconstructed sequence haplotypes have a sequence error rate of 0.005%. Utilizing fosmid-phased haplotypes from a Yoruba, a European and a Gujarati sample, we analyzed population history and inferred population split times. We date the initial split between Yoruba and out of African populations to 90,000-100,000 years ago with substantial gene flow occurring until nearly 50,000 years ago, and obtain congruent results with the autosomes and the X chromosome. We estimate that the initial split between European and Gujarati population occurred around 45,000 years ago and gene flow ended around 28,000 years ago. Analysis of X vs autosome inferred effective population sizes reveals distinct epochs in which the ratio of the effective number of males to females changes. We find a period of female bias during the ancestral human lineage up to 1 million years ago and a short period of male bias in Yoruba lineage from 160-400 thousand years ago. We demonstrate the construction of haplotype sequences of sufficient completeness and accuracy for population genetic analysis. As experimental and analytic methods improve, these approaches will continue to shed new light on the history of populations.Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Massai and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield an earlier split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120.0 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80.0 years ago, while the separation between Massai and out of African populations happened around 50,000 years ago.

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such as temperature and or by intrinsic ones, for example demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community composition remain poorly understood, in part because of the difficulty in identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimetre-scale biofilm granules represent true community replicates. Differences in composition are then expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genus-level resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation did not translate into any clear partitioning into discrete community types, that is, distinct compositional states, such as enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the dominant organism: genotypes of Candidatus Accumulibacter that coexisted in the metacommunity (the reactor) excluded each other within community replicates (granules). Individual granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall composition of the community, indicating a high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most probably observed at the level of recently differentiated genotypes but not at higher orders of genetic resolution.Using millimetre-scale replicate granules from an enhanced biological phosphorus removal reactor, the authors observe strain-level variability providing insights into the intrinsic drivers of microbial assembly at relevant spatial scales.