Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa

Background

Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A5*1 (expresser allele); CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago.

Results

We estimate that ~43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A5*3 as ~76,400 years and CYP3A5*6 as ~218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann’s Rho= −0.465, p=0.004] and 50,000 years ago [Spearmann’s Rho= −0.379, p=0.02].

Conclusions

Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation.

Modeling recent human evolution in mice by expression of a selected EDAR variant

An adaptive variant of the human Ectodysplasin receptor, EDARV370A, is one of the strongest candidates of recent positive selection from genome-wide scans. We have modeled EDAR370A in mice and characterized its phenotype and evolutionary origins in humans. Our computational analysis suggests the allele arose in central China approximately 30,000 years ago. Although EDAR370A has been associated with increased scalp hair thickness and changed tooth morphology in humans, its direct biological significance and potential adaptive role remain unclear. We generated a knockin mouse model and find that, as in humans, hair thickness is increased in EDAR370A mice. We identify new biological targets affected by the mutation, including mammary and eccrine glands. Building on these results, we find that EDAR370A is associated with an increased number of active eccrine glands in the Han Chinese. This interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.

Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers

Data from developing Brangus heifers (3/8 Brahman-Bos indicus × 5/8 Angus-Bos taurus; n ≈ 802 from 67 sires) registered with International Brangus Breeders Association were analyzed to detect QTL associated with growth traits and ultrasound measures of carcass traits. Genotypes were from BovineSNP50 (Infinium BeadChip, Illumina, San Diego, CA; 53,692 SNP). Phenotypes included BW collected at birth and ∼205 and 365 d of age, and yearling ultrasound assessment of LM area, percent intramuscular fat, and depth of rib fat. Simultaneous association of SNP windows with phenotype were undertaken with Bayes C analyses, using GenSel software. The SNP windows were ≈ 5 SNP in length. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.999 having no effect on phenotype. Bootstrap analyses were used to obtain significance values for the SNP windows with the greatest contribution to observed variation. The SNP windows with P < 0.01 were considered as QTL associated with a trait in which case their location was queried from dbSNP and the presence of a previously reported QTL in that location was checked in CattleQTLdb. For 9 traits, QTL were mapped to 139 regions on 25 chromosomes. Forty-one of these QTL were already described in CattleQTLdb, so 98 are new additions. The SNP windows on chromosomes 1, 3, and 6 were associated with multiple traits (i.e., 205- and 365- d BW, and ADG from birth to 205 and 365 d of age). Several chromosomes harbored regions associated with multiple traits; however, the SNP that comprised the window often varied among traits (i.e., chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 20, 21, 22, 24, 28, and 29). Results from whole genome association of SNP with growth and ultrasound carcass traits in developing Brangus heifers confirmed several published QTL and detected several new QTL.

Neuropsychiatric symptoms are common in immunocompetent adult patients with Toxoplasma gondii acute lymphadenitis

BACKGROUND

Chronic toxoplasmosis has been shown to be strongly associated with a range of neuropsychiatric effects including schizophrenia and suicide. However there have not been any prospective, community-based studies of the neuropsychiatric effects of acute toxoplasmosis in adult immunocompetent patients.

METHODS

Adult patients with a positive serum IgM anti-Toxoplasma gondii test result, in the context of an acute illness with lymphadenopathy, were invited to complete a questionnaire seeking information relating to the nature, severity, and duration of symptoms in the months following the diagnosis of acute toxoplasmosis.

RESULTS

Laboratory testing identified a total of 187 adults who had a positive serum IgM anti-T. gondii test result between 1 January and 30 November 2011. Consent to contact 108/187 (58%) patients was provided by their family doctor; 37 (34%) of these 108 patients completed and returned the questionnaire. Questionnaires from the 31/108 (29%) patients who reported swollen lymph nodes during their illness were included in the study. Fatigue (90%), headache (74%), difficulty concentrating (52%), and muscle aches (52%) were the most commonly reported symptoms. These symptoms commonly persisted for at least 4 weeks. Twenty-seven of 31 (87%) subjects reported a moderate or severe reduction in their overall physical and mental health during the first 2 months of illness.

CONCLUSIONS

Acute toxoplasmosis in immunocompetent adults commonly causes moderately severe neuropsychiatric symptoms that might result from replication of the organism in the central nervous system with consequent effects on brain function. Patients should be advised that such symptoms are common and reassured that they usually resolve completely within a few months.

Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

The flickering genes of the last mammoths

Woolly mammoths, Mammuthus primigenius, are arguably the most iconic of the extinct Pleistocene megafauna, and an abundance of large permafrost-embedded bone and ivory material (Fig. 1) means they were also among the first to yield credible DNA sequences (Hagelberg et al. 1994; Hoss et al. 1994). Despite mammoth remains being numerous throughout northern Eurasia and North America, both the earliest and most recent fossils are found in northeast Siberia, with the last known population being confined to Wrangel Island in the Arctic Ocean from around 10,000 years ago until their extinction around 4,000 years ago. The extent to which these Holocene mammoths were descended from the Pleistocene populations of Wrangel Island and the demographic nature of their terminal decline have, until now, remained something of a mystery. In this issue of Molecular Ecology, Nyström et al. (2012) report the first use of autosomal variation to track the decline of the last mammoths and, in doing so, take a significant step towards resolving these questions. The authors genotyped four microsatellite loci in 59 Pleistocene and Holocene mammoths from Wrangel Island and Chukotka in mainland northeastern Siberia and showed that while the Pleistocene-to-Holocene transition is associated with a significant reduction in genetic diversity, subsequent levels of variation remain constant until extinction. Such a pattern is somewhat surprising as it indicates that while the last mammoths were confined to only a few Arctic islands, their final extinction on Wrangel Island was not a gradual process resulting from loss of genetic diversity/inbreeding. Instead, it seems they maintained a viable effective population size of around 500 until near their presumably rapid extinction. While the ultimate agent of mammoth extinction remains unknown, the work of Nyström et al. (2012). suggests that we should be looking for something sudden, like a rapid change in climate/ecology or perhaps the arrival of humans.

Reconstruction of the perineum following extralevator abdominoperineal excision for carcinoma of the lower rectum: a systematic review

AIM

An improvement in oncological outcome has been reported following an extralevator approach to abdominoperineal excision (ELAPE) for low rectal carcinoma. A larger perineal defect following ELAPE and the impact of neoadjuvant radiotherapy are sources of considerable morbidity for patients. We report an evidence-based systematic review of published data on the outcome of perineal reconstruction following ELAPE for low rectal carcinoma, comparing the use of tissue flap and biological mesh techniques.

METHOD

A literature search was performed of electronic databases including the Medline, Embase and Scopus databases (1995-2011). Studies describing outcomes relating to the perineum following ELAPE were included for review.

RESULTS

Eleven small cohort studies reported the outcome relating to the perineum following ELAPE. Pooled-analysis of 255 combined patients undergoing flap repair and 85 undergoing biological mesh repair showed no significant difference in the rates of perineal wound complications or perineal hernia formation.

CONCLUSION

There is little information on the optimal technique of perineal wound closure following ELAPE. With the limited data available, there was no significant difference in complication rates between biological mesh and flap repair. There is a need for high-quality prospective trials to compare methods of reconstruction to determine the long-term results, quality of life and function.

The genetic history of Europeans

The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.

Evaluation of gut bacterial populations using an electronic e-nose and field asymmetric ion mobility spectrometry: further insights into 'fermentonomics'

The fermentation of undigested foods in the large bowel, by its resident bacteria, results in the production of several chemicals including volatile gases. Perturbance in gut bacteria is known to influence colonic and metabolic health, but to determine this requires prolonged culture (often unsuccessful) or expensive genomic sequencing. Clearly this is not practical for daily clinical practice. Previously, we have reported our insights into fermentonomics through the detection of volatile organic compounds (VOCs) in patients with gastrointestinal and metabolic diseases, using the electronic nose. In this paper we report on the changes in the fermentone produced by patients undergoing complete versus partial bowel cleansing. Using urine samples, preliminary results from 23 individuals receiving bowel cleansing indicate the ability of the electronic nose to distinguish between the partial and complete procedures. Moreover in a subset of individuals, we have been able to track evolving bacterial recolonization over time using the e-nose and field asymmetric ion mobility spectrometry (FAIMS). Such an approach has practical application in tracking bacterial dysbiosis following perturbation.

Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors

Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.

Effects of intravenous zoledronate on bone turnover and bone density persist for at least five years in HIV-infected men

CONTEXT

In HIV-infected men, the antiresorptive effects of zoledronate persist for at least 2 yr after the second annual dose.

OBJECTIVE

Our objective was to determine the duration of action of zoledronate in men.

DESIGN AND SETTING

This was 4-yr extension of a 2-yr, double-blind, randomized, placebo-controlled trial at an academic research center.

PARTICIPANTS

Participants included 43 HIV-infected men with bone mineral density (BMD) T score below -0.5, 35 of whom entered the extension study.

INTERVENTION

Intervention was annual administration of 4 mg iv zoledronate or placebo at baseline and 1 yr and no intervention subsequently.

MAIN OUTCOME MEASURES

We evaluated changes in the bone turnover markers, serum osteocalcin and serum C-telopeptide (CTx), and changes in BMD at the lumbar spine, total hip, and total body.

RESULTS

There was no time × treatment interaction between 1 and 5 yr after the second zoledronate dose for osteocalcin or CTx (P > 0.4) or any BMD site (P > 0.7). Between 1 and 5 yr after the second dose, on average, osteocalcin was 41% lower (95% confidence interval = 19-62%; P < 0.001), CTx 52% lower (33-71%; P < 0.001), lumbar spine BMD 3.7% greater (0.3-7.0%; P = 0.03), total hip BMD 2.3% greater (0.3-4.3%; P = 0.02), and total body BMD 2.5% greater (0.8-4.1%; P = 0.004) in the zoledronate group than the placebo group. Five years after the second dose, the between-groups differences were 38% (13-62%) for osteocalcin, 49% (20-77%) for CTx, 3.5% (0.7-6.7%) for lumbar spine BMD, 3.4% (1.4-5.4%) for total hip BMD, and 1.6% (0.2-3.1%) for total body BMD.

CONCLUSION

The effects of two annual 4-mg doses of zoledronate in men persist for at least 5 yr after the second dose. Larger trials assessing the antifracture efficacy of less frequent dosing of zoledronate are justified.

Stable bone mineral density over 6 years in HIV-infected men treated with highly active antiretroviral therapy (HAART)

OBJECTIVE

Most longitudinal studies of bone mineral density (BMD) in HIV-infected cohorts have been of short duration, typically 1-2 years. Some studies, especially of cohorts treated with highly active antiretroviral therapy (HAART), report short-term stable or increasing BMD, but other studies, often in cohorts initiating HAART, report short-term losses in BMD. We assessed BMD changes over the medium term in HIV-infected men already established on HAART at baseline.

DESIGN

Six-year, prospective, longitudinal study.

SUBJECTS

Forty-four HIV-infected men treated with HAART and 37 uninfected, healthy controls.

MEASUREMENTS

Participants had measurements of BMD at baseline, 2 and 6 years.

RESULTS

In the HIV-infected men at baseline, the mean age was 49 years, the mean duration of infection was 8 years, and the mean duration of HAART was 50 months. Over 6 years of follow-up, there was a greater increase in lumbar spine BMD (5·3%, 95% CI 3·8-6·5%) in the HIV-infected men compared with controls (0·3%, 95% CI -1·0 to 1·6%), P < 0·001. There was no difference between the groups in the change in BMD over time at the total hip (HIV group: -0·6%, 95% CI -1·7 to 0·4%, controls -1·0%, 95% CI -2·2 to 0%, P = 0·8) or at the total body (HIV group, 0·3%, 95% CI -0·3 to 1·0%; controls, 0·5%, 95% CI -0·2 to 1·1%, P = 0·15). Lean mass increased in the HIV group, but not in the controls.

CONCLUSIONS

There was no evidence of accelerated bone loss over 6 years in middle-aged, HIV-infected men treated with HAART. For such patients, routine monitoring of BMD is not necessary over the short/medium term.

Modern taurine cattle descended from small number of near-eastern founders

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.

Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia: Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island

Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the island's endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the island's biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the island's geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniola's geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).

Physiology and Endocrinology Symposium: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females

The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promise. Several SNP from the BovineSNP50 assay have tentatively been associated with reproductive traits including age at puberty, antral follicle count, and pregnancy observed on different sets of heifers. However, sample sizes are too small and SNP density is too sparse to definitively determine genomic regions harboring causal variants affecting reproductive success. Additionally, associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear to be globally applicable to cattle of different breeds. Discrepancies may be a result of different QTL segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns such that the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Several approaches can be used independently or in combination to improve detection of genomic factors affecting heifer puberty and fertility. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies can also be used to effectively increase sample size. High-density genotyping with heifers pooled by pregnancy status or early and late puberty can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Example analyses are provided to demonstrate how integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays might enhance knowledge of genomic mechanisms affecting puberty and fertility, enabling reliable DNA tests to guide heifer selection decisions.

The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

50,000 years of genetic uniformity in the critically endangered Iberian lynx

Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long-term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50,000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long-term viability, and so should not preclude conservation efforts.

Herders of Indian and European cattle share their predominant allele for lactase persistence

Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region--part of an enhancer--approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subcontinent. Here, we present the results of the first comprehensive survey of the LCT enhancer region in south Asia. Having genotyped 2,284 DNA samples from across the Indian subcontinent, we find that the previously described west Eurasian -13910 C>T mutation accounts for nearly all the genetic variation we observed in the 400- to 700-bp LCT regulatory region that we sequenced. Geography is a significant predictor of -13910*T allele frequency, and consistent with other genomic loci, its distribution in India follows a general northwest to southeast declining pattern, although frequencies among certain neighboring populations vary substantially. We confirm that the mutation is identical by descent to the European allele and is associated with the same>1 Mb extended haplotype in both populations.

Ancient hybridization and an Irish origin for the modern polar bear matriline

BACKGROUND

Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.

RESULTS

We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.

CONCLUSIONS

The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.

Evolution of lactase persistence: an example of human niche construction

Niche construction is the process by which organisms construct important components of their local environment in ways that introduce novel selection pressures. Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (-13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East. Current estimates for the age of lactase persistence-associated alleles bracket those for the origins of animal domestication and the culturally transmitted practice of dairying. We report new data on the distribution of -13910*T and summarize genetic studies on the diversity of lactase persistence worldwide. We review relevant archaeological data and describe three simulation studies that have shed light on the evolution of this trait in Europe. These studies illustrate how genetic and archaeological information can be integrated to bring new insights to the origins and spread of lactase persistence. Finally, we discuss possible improvements to these models.

Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand

AIM

To estimate the burden of skin and soft tissue infection caused by Staphylococcus aureus (S. aureus), and to determine the effects of ethnicity and age on the rate of skin and soft tissue due to MRSA in the Auckland community.

MATERIALS AND METHODS

We reviewed the culture and susceptibility results of all wound swabs processed by Auckland's only community microbiology laboratory in 2007. Demographic data for a random sample of 1000 people who had a wound swab collected and for all people from whom a methicillin-resistant S. aureus (MRSA) strain was isolated were obtained and compared to demographic data for the total population of Auckland.

RESULTS

S. aureus was isolated from 23853/47047 (51%) wound swab cultures performed in 2007; the estimated annual incidence of S. aureus isolation from a wound swab was 1847/100,000 people; and the estimated annual incidence of MRSA isolation from a wound swab was 145/100,000 people. Maori and Pacific people had higher rates of non-multiresistant MRSA infection compared with New Zealand European and Asian people; elderly New Zealand European people had much higher rates of multiresistant MRSA infections compared with people from other ethnic groups.

CONCLUSION

S. aureus is a very common cause of disease in the community and the incidence of infection with MRSA subtypes varies with ethnicity.

Nasal carriage of Staphylococcus aureus in healthy Aucklanders

BACKGROUND

Studies have reported higher rates of diseases caused by Staphylococcus aureus (S. aureus) amongst Maori and Pacific people, compared with people of other ethnicities.

AIM

We aimed to estimate the prevalence of nasal carriage and to explore demographic differences between S. aureus carriers and non-carriers in Auckland, New Zealand.

MATERIALS AND METHODS

Nasal swab specimens were obtained from healthy population volunteers, who did not have recent healthcare contact. Each participant completed a short questionnaire.

RESULTS

78/424 (18%; 95%CI, 15-22) S. aureus carriers were identified. Female participants were less likely to be S. aureus carriers than males; but there were no differences in the ages or ethnic groups between S. aureus carriers and non-carriers. Socioeconomic deprivation, recent non-hospital healthcare contact and past history of S. aureus infection were not associated with S. aureus carriage.

CONCLUSION

Ethnic variation in the prevalence of S. aureus nasal carriage does not contribute to an increased risk of disease caused by S. aureus.

Prevalence of clinically relevant UGT1A alleles and haplotypes in African populations

Variation of a short (TA)(n) repeat sequence (rs8175347) covering the TATA box of UGT1A1 (UDP-glucuronosyltransferase1A1) is associated with hyperbilirubinaemia (Gilbert's syndrome) and adverse drug reactions, and is used for dosage advice for irinotecan. Several reports indicate that the low-activity (risk) alleles ((TA)(7) and (TA)(8) )) are very frequent in Africans but the patterns of association with other variants in the UGT1A gene complex that may modulate these responses are not well known. rs8175347 and two other clinically relevant UGT1A variants (rs11692021 and rs10929302) were assayed in 2616 people from Europe and Africa. Low-activity (TA)(n) alleles frequencies were highest in equatorial Africa, (TA)(7,) being the most common in Cameroon, Ghana, southern Sudan, and in Ethiopian Anuak. Haplotypic diversity was also greatest in equatorial Africa, but in Ethiopia was very variable across ethnic groups. Resequencing of the promoter of a sample subset revealed no novel variations, but rs34547608 and rs887829 were typed and shown to be tightly associated with (TA)(n) . Our results illustrate the need for investigation of the effect of UGT1A variants other than (TA)(n) on the risk of irinotecan toxicity, as well as hyperbilirubinaemia due to hemolytic anaemia or human immunodeficiency virus protease inhibitors, so that appropriate pharmacogenetic advice can be given.

Coping processes and health-related quality of life in Parkinson's disease

OBJECTIVE

This study investigated the predictive value of various coping processes for the psychological and disease specific aspects of health-related quality of life (HRQoL) in Parkinson's disease (PD).

METHOD

Cross-sectional study of 85 participants with PD using the Ways of Coping Questionnaire (WCQ), Depression, Anxiety, and Stress Scale (DASS-21), quality of life (PDQ-39), and socio-demographic and clinical variables.

RESULTS

Greater use of planful problem solving coping was found to be significantly associated with better HRQoL in relation to cognitive impairment, communication and bodily discomfort. In addition to greater disease duration, greater use of escape-avoidance coping processes were identified as significant predictors of poorer HRQoL outcomes in the domains of mood and emotional well-being.

CONCLUSION

Psychological interventions such as mindfulness training, aimed at reducing the use of escape-avoidance copying, may help to improve HRQoL in PD.