Rare DNA variants in the brain-derived neurotrophic factor gene increase risk for attention-deficit hyperactivity disorder: a next-generation sequencing study

Attention-deficit hyperactivity disorder (ADHD) is a prevalent and highly heritable disorder of childhood with negative lifetime outcomes. Although candidate gene and genome-wide association studies have identified promising common variant signals, these explain only a fraction of the heritability of ADHD. The observation that rare structural variants confer substantial risk to psychiatric disorders suggests that rare variants might explain a portion of the missing heritability for ADHD. Here we believe we performed the first large-scale next-generation targeted sequencing study of ADHD in 152 child and adolescent cases and 188 controls across an a priori set of 117 genes. A multi-marker gene-level analysis of rare (<1% frequency) single-nucleotide variants (SNVs) revealed that the gene encoding brain-derived neurotrophic factor (BDNF) was associated with ADHD at Bonferroni corrected levels. Sanger sequencing confirmed the existence of all novel rare BDNF variants. Our results implicate BDNF as a genetic risk factor for ADHD, potentially by virtue of its critical role in neurodevelopment and synaptic plasticity.

Association of AKAP6 and MIR2113 with cognitive performance in a population-based sample of older adults

Genetic factors make a substantial contribution to inter-individual variability in cognitive function. A recent meta-analysis of genome-wide association studies identified two loci, AKAP6 and MIR2113, that are associated with general cognitive function. Here, we extend this previous research by investigating the association of MIR2113 and AKAP6 with baseline and longitudinal non-linear change across a broad spectrum of cognitive domains in a community-based cohort of older adults without dementia. Two single nucleotide polymorphisms (SNPs), MIR211-rs10457441 and AKAP6-rs17522122 were genotyped in 1570 non-demented older Australians of European ancestry, who were examined up to 4 times over 12 years. Linear mixed effects models were used to examine the association between AKAP6 and MIR2113 with cognitive performance in episodic memory, working memory, vocabulary, perceptual speed and reaction time at baseline and with linear and quadratic rates of change. AKAP6-rs17522122*T was associated with worse baseline performance in episodic memory, working memory, vocabulary and perceptual speed, but it was not associated with cognitive change in any domain. MIR2113-rs10457441*T was associated with accelerated decline in episodic memory. No other associations with baseline cognitive performance or with linear or quadratic rate or cognitive changes were observed for this SNP. These results confirm the previous finding that AKAP6 is associated with performance across multiple cognitive domains at baseline but not with cognitive decline, while MIR2113 primarily affects the rate at which memory declines over time.

APOE*E2 allele delays age of onset in PSEN1 E280A Alzheimer's disease

Alzheimer's disease (AD) age of onset (ADAOO) varies greatly between individuals, with unique causal mutations suggesting the role of modifying genetic and environmental interactions. We analyzed ~50 000 common and rare functional genomic variants from 71 individuals of the 'Paisa' pedigree, the world's largest pedigree segregating a severe form of early-onset AD, who were affected carriers of the fully penetrant E280A mutation in the presenilin-1 (PSEN1) gene. Affected carriers with ages at the extremes of the ADAOO distribution (30s-70s age range), and linear mixed-effects models were used to build single-locus regression models outlining the ADAOO. We identified the rs7412 (APOE*E2 allele) as a whole exome-wide ADAOO modifier that delays ADAOO by ~12 years (β=11.74, 95% confidence interval (CI): 8.07-15.41, P=6.31 × 10(-8), PFDR=2.48 × 10(-3)). Subsequently, to evaluate comprehensively the APOE (apolipoprotein E) haplotype variants (E1/E2/E3/E4), the markers rs7412 and rs429358 were genotyped in 93 AD affected carriers of the E280A mutation. We found that the APOE*E2 allele, and not APOE*E4, modifies ADAOO in carriers of the E280A mutation (β=8.24, 95% CI: 4.45-12.01, P=3.84 × 10(-5)). Exploratory linear mixed-effects multilocus analysis suggested that other functional variants harbored in genes involved in cell proliferation, protein degradation, apoptotic and immune dysregulation processes (i.e., GPR20, TRIM22, FCRL5, AOAH, PINLYP, IFI16, RC3H1 and DFNA5) might interact with the APOE*E2 allele. Interestingly, suggestive evidence as an ADAOO modifier was found for one of these variants (GPR20) in a set of patients with sporadic AD from the Paisa genetic isolate. This is the first study demonstrating that the APOE*E2 allele modifies the natural history of AD typified by the age of onset in E280A mutation carriers. To the best of our knowledge, this is the largest analyzed sample of patients with a unique mutation sharing uniform environment. Formal replication of our results in other populations and in other forms of AD will be crucial for prediction, follow-up and presumably developing new therapeutic strategies for patients either at risk or affected by AD.

No interaction between the serotonin transporter polymorphism (5-HTTLPR) and childhood adversity or recent stressful life events on symptoms of depression: results from two community surveys

In this study we investigated interactions between the 5-HTTLPR genotype and environmental risk factors (G x E) on symptoms of depression in two large Australian community samples of adolescents and young adults. We postulated that a significant interaction between the 5-HTTLPR genotype and environmental risk factors of childhood adversity or stressful life events on symptoms of depression would be observed in subjects with at least one short allele (s/l or s/s) compared with subjects with no short alleles (l/l). We did not find significant G x E interactions between the 5-HTTLPR genotype and recent stressful life events or childhood adversity on symptoms of depression in our sample populations. However, we did find adolescents aged 17-18 years homozygous for the long allele (l/l) and exposed to persistently high levels of family adversity over a 6-year period were at a greater risk of depression than subjects with the same genotype exposed to no or persistently low levels of family adversity. This interaction should be interpreted cautiously due to the small number of depressed subjects in the sample with persistently high levels of family adversity.

Memory complaints in a community sample aged 60-64 years: associations with cognitive functioning, psychiatric symptoms, medical conditions, APOE genotype, hippocampus and amygdala volumes, and white-matter hyperintensities

BACKGROUND

Previous research has found that depression is a major cause of memory complaints. However, there is evidence that memory complaints also weakly predict cognitive decline and dementia. The present study examined a range of possible determinants of memory complaints, covering psychiatric and personality factors, medical history, cognitive test performance, and biological risk factors for dementia (APOE genotype, hippocampus and amygdala volumes, and white-matter hyperintensities).

METHOD

A community survey was carried out with 2546 persons aged 60-64 years living in Canberra and Queanbeyan, Australia. Participants were asked about memory problems which interfered with daily life and whether medical help had been sought. A randomly selected subsample of 476 persons was given a brain MRI scan.

RESULTS

Participants with memory complaints were found to have poorer memory test performance, more depression and anxiety symptoms, have higher scores on personality traits involving negative affect, and to have worse physical health. Multivariate analyses showed that measures of cognitive performance did not make a unique contribution to the prediction of memory complaints above that of the other categories of predictors. Those with memory complaints did not differ on any of the biological risk factors for dementia.

CONCLUSION

In a community sample aged 60-64 years, memory complaints were most closely related to psychiatric symptoms, personality characteristics and poor physical health. There was no evidence of brain changes indicating early dementia.

Measuring environmental factors can enhance the search for disease causing genes?

The value of the concurrent measurement of environmental factors in studies aimed at the discovery of disease causing genes has been questioned on the grounds that such an approach fails to increase study power. This report discusses the issue and shows with examples from the recent literature that the examination of a gene disease association within an environmental subgroup can provide enhanced opportunities for detecting gene effects. The concurrent collection of environmental as well as genetic factors in studies of disease aetiology may enhance study informativeness and validity in several ways, including an increase in the power of the study to detect gene disease associations.

Association between chronic fatigue syndrome and the corticosteroid-binding globulin gene ALA SER224 polymorphism

Chronic fatigue syndrome (CFS) is characterized by idiopathic fatigue of greater than 6 months' duration with postexertional exacerbation and many other symptoms. A trend toward relative hypocortisolism is described in CFS. Twin and family studies indicate a substantial genetic etiologic component to CFS. Recently, severe corticosteroid-binding globulin (CBG) gene mutations have been associated with CFS in isolated kindreds. Human leukocyte elastase, an enzyme important in CBG catabolism at inflammatory sites, is reported to be elevated in CFS. We hypothesized that CBG gene polymorphisms may act as a genetic risk factor for CFS. A total of 248 patients with CFS defined by Centers for Disease Control criteria, and 248 controls were recruited. Sequencing and restriction enzyme testing of the CBG gene coding region allowed detection of severe CBG gene mutations and a common exon 3 polymorphism (c.825G-->T, Ala-Ser224). Plasma CBG levels were measured in 125 CFS patients and 198 controls by radioimmunoassay. Total and free (calculated and measured) cortisol levels were ascertained in single samples between 8-10 a.m. The age of onset (mid 30s) and gender ratio (2.2:1, female:male) of the patients were similar to those reported in U.S. epidemiologic studies. A trend toward a preponderance of serine224 homozygosity among the CFS patients was noted, compared with controls (chi2 = 5.31, P = 0.07). Immunoreactive-CBG (IR-CBG) levels were higher in Serine/Alanine (Ser/Ala) than Ala/Ala subjects and higher again in Ser/Ser subjects, this effect was strongest in controls; Ser/Ser: 46.1+/-1.8 (n = 31, P = 0.03) vs. Ser/Ala: 42.4+/-1.0 (n = 56, P = 0.05) vs. Ala/Ala: 40.8+/-1.7 microg/mL (n = 21). Despite higher CBG levels, there was a nonsignificant trend toward lower total and free plasma cortisol in serine allele positive patients, total cortisol: Ser/Ser: 13.3+/-1.4 (n = 34) vs. Ser/Ala: 14.0+/-0.7 (n = 66) vs. Ala/Ala: 15.4+/-1.0 (n = 23). Homozygosity for the serine allele of the CBG gene may predispose to CFS, perhaps due to an effect on hypothalamic-pituitary-adrenal axis function related to altered CBG-cortisol transport function or immune-cortisol interactions.

The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution

The complete sequence of the MC1R locus has been assembled, the coding region of the gene is intronless and placed within a 12 kb region flanked by the NULP1 and TUBB4 genes. The immediate promoter region has an E-box site with homology to the M-box consensus known to bind the microphthalmia transcription factor (MITF); however, promoter deletion analysis and transactivation studies have failed to show activation through this element by MITF. Polymorphism within the coding region, immediate 5' promoter region and a variable number tandem repeat (VNTR) minisatellite within the locus have been examined in a collection of Caucasian families and African individuals. Haplotype analysis shows linkage disequilibrium between the VNTR and MC1R coding region red hair variant alleles which can be used to estimate the age of these missense changes. Assuming a mean VNTR mutation rate of 1% and a star phylogeny, we estimate the Arg151Cys variant arose 7500 years before the present day, suggesting these variants may have arisen in the Caucasian population more recently than previously thought.

Differential expression of the actin-binding proteins, alpha-actinin-2 and -3, in different species: implications for the evolution of functional redundancy

The alpha-actinins are a multigene family of four actin-binding proteins related to dystrophin. The two skeletal muscle isoforms of alpha-actinin (ACTN2 and ACTN3) are major structural components of the Z-line involved in anchoring the actin-containing thin filaments. In humans, ACTN2 is expressed in all muscle fibres, while ACTN3 expression is restricted to a subset of type 2 fibres. We have recently demonstrated that alpha-actinin-3 is absent in approximately 18% of individuals in a range of human populations, and that homozygosity for a premature stop codon (577X) accounts for most cases of true alpha-actinin-3 deficiency. Absence of alpha-actinin-3 is not associated with an obvious disease phenotype, raising the possibility that ACTN3 is functionally redundant in humans, and that alpha-actinin-2 is able to compensate for alpha-actinin-3 deficiency. We now present data concerning the expression of ACTN3 in other species. Genotyping of non-human primates indicates that the 577X null mutation has likely arisen in humans. The mouse genome contains four orthologues which all map to evolutionarily conserved syntenic regions for the four human genes. Murine Actn2 and Actn3 are differentially expressed, spatially and temporally, during embryonic development and, in contrast to humans, alpha-actinin-2 expression does not completely overlap alpha-actinin-3 in postnatal skeletal muscle, suggesting independent function. Furthermore, sequence comparison of human, mouse and chicken alpha-actinin genes demonstrates that ACTN3 has been conserved over a long period of evolutionary time, implying a constraint on evolutionary rate imposed by continued function of the gene. These observations provide a real framework in which to test theoretical models of genetic redundancy as they apply to human populations. In addition we highlight the need for caution in making conclusions about gene function from the phenotypic consequences of loss-of-function mutations in animal knockout models.

Association of a polymorphism of the dopamine transporter gene with externalizing behavior problems and associated temperament traits: a longitudinal study from infancy to the mid-teens

There have been reports that a variable number of tandem repeats (VNTR) polymorphism situated in the 3' untranslated region of the dopamine transporter gene is associated with attention-deficit hyperactivity disorder. On the basis of these findings, we predicted an association of this polymorphism with hyperactivity, other externalizing behavior problems, and related temperament traits in a general population sample. The association was investigated using children participating in a longitudinal study of childhood temperament and development. DNA was taken from 660 children who had been assessed for temperament from 4-8 months to 15-16 years, and for behavior problems from 3-4 to 15-16 years. No significant associations were found at any age. There are a number of methodological differences from earlier studies that might explain the lack of associations with hyperactivity. It is also possible that the earlier findings are not replicable.

Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins

DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [ approximately 60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) "anatomically modern" human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins.

Association of a functional polymorphism of the serotonin transporter gene with anxiety-related temperament and behavior problems in children: a longitudinal study from infancy to the mid-teens

A polymorphism in the promoter region of the serotonin transporter gene (5-HTTLPR) has been associated with anxiety-related personality traits in adults. Initial studies showed that the short allele was associated with higher neuroticism, anxiety and harm avoidance. However, most attempts to replicate these findings have been negative. Because the association of candidate polymorphisms with behavioral traits may vary with stage of development, we investigated the association using participants in a longitudinal study of childhood temperament. DNA was available for 660 children who had been assessed for temperament from 4-8 months to 15-16 years, and for behaviour problems from 3-4 years to 15-16 years. No significant associations were found at most ages. However, at ages 13-14 years and 15-16 years, the long/long genotype was associated with higher anxiety. These findings do not support an association of the short allele with anxiety-related traits in early life.

Identification, characterization, and crystal structure of the Omega class glutathione transferases

A new class of glutathione transferases has been discovered by analysis of the expressed sequence tag data base and sequence alignment. Glutathione S-transferases (GSTs) of the new class, named Omega, exist in several mammalian species and Caenorhabditis elegans. In humans, GSTO 1-1 is expressed in most tissues and exhibits glutathione-dependent thiol transferase and dehydroascorbate reductase activities characteristic of the glutaredoxins. The structure of GSTO 1-1 has been determined at 2.0-A resolution and has a characteristic GST fold (Protein Data Bank entry code ). The Omega class GSTs exhibit an unusual N-terminal extension that abuts the C terminus to form a novel structural unit. Unlike other mammalian GSTs, GSTO 1-1 appears to have an active site cysteine that can form a disulfide bond with glutathione.

Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study

Mutations in BRCA1 (ref. 1) confer an increased risk of female breast cancer. In a genome-wide scan of linkage disequilibrium (LD), a high level of LD was detected among microsatellite markers flanking BRCA1 (ref. 3), raising the prospect that positive natural selection may have acted on this gene. We have used the predictions of evolutionary genetic theory to investigate this further. Using phylogeny-based maximum likelihood analysis of the BRCA1 sequences from primates and other mammals, we found that the ratios of replacement to silent nucleotide substitutions on the human and chimpanzee lineages were not different from one another (P=0.8), were different from those of other primate lineages (P=0.004) and were greater than 1 (P=0.04). This is consistent with the historic occurrence of positive darwinian selection pressure on the BRCA1 protein in the human and chimpanzee lineages. Analysis of genetic variation in a sample of female Australians of Northern European origin showed evidence for Hardy-Weinberg (HW) disequilibrium at polymorphic sites in BRCA1, consistent with the possibility that natural selection is affecting genotype frequencies in modern Europeans. The clustering of between-species variation in the region of the gene encoding the RAD51-interaction domain of BRCA1 suggests the maintenance of genomic integrity as a possible target of selection.

Association of smoking and personality with a polymorphism of the dopamine transporter gene: results from a community survey

In studies that used mixed volunteer samples, Lerman et al. [1999: Health Psychol 18:14-20] and Sabol et al. [1999: Health Psychol 18:7-13] reported on an association of smoking with a polymorphism of the dopamine transporter gene. We attempted to replicate this association in a nonvolunteer community sample of 861 Caucasians. No associations were found with either smoking initiation or smoking cessation. Sabol et al. [1999] also reported on an association of the dopamine transporter polymorphism with the personality trait of novelty seeking. However, we failed to find any associations with a range of personality traits, including a scale of fun seeking that correlates with novelty seeking. These negative findings suggest that either the original associations are not replicable or that any association is very small.

Evolutionary rate acceleration of cytochrome c oxidase subunit I in simian primates

We present an analysis of the evolutionary rates of the cytochrome c oxidase subunit I genes of primates and other mammals. Five primate genes were sequenced, and this information was combined with published data from other species. The sequences from simian primates show approximately twofold increases in their nonsynonymous substitution rate compared to those from other primates and other mammals. The species range and the overall magnitude of this rate increase are similar to those previously identified for the cytochrome c oxidase subunit II and cytochrome b genes.

Association of a functional polymorphism of the monoamine oxidase A gene promoter with personality and psychiatric symptoms

A functional polymorphism in the promoter of the monoamine oxidase gene has recently been described by Sabol et al. This polymorphism is a strong candidate for associations with personality traits and psychiatric symptoms. We report relevant data from a general population sample of 850 Caucasian Australians. We found no associations with anxiety and depression symptoms, with personality traits that predispose to anxiety (neuroticism, behavioral inhibition, negative affect) or to a personality trait related to antisocial behavior (psychoticism).

How important is DNA replication for mutagenesis?

Rates of mutation and substitution in mammals are generally greater in the germ lines of males. This is usually explained as resulting from the larger number of germ cell divisions during spermatogenesis compared with oogenesis, with the assumption made that mutations occur primarily during DNA replication. However, the rate of cell division is not the only difference between male and female germ lines, and mechanisms are known that can give rise to mutations independently of DNA replication. We investigate the possibility that there are other causes of male-biased mutation. First, we show that patterns of variation at approximately 5,200 short tandem repeat (STR) loci indicate a higher mutation rate in males. We estimate a ratio of male-to-female mutation rates of approximately 1.9. This is significantly greater than 1 and supports a greater rate of mutation in males, affecting the evolution of these loci. Second, we show that there are chromosome-specific patterns of nucleotide and dinucleotide composition in mammals that have been shaped by mutation at CpG dinucleotides. Comparable patterns occur in birds. In mammals, male germ lines are more methylated than female germ lines, and these patterns indicate that differential methylation has played a role in male-biased vertebrate evolution. However, estimates of male mutation bias obtained from both classes of mutation are substantially lower than estimates of cell division bias from anatomical data. This discrepancy, along with published data indicating slipped-strand mispairing arising at STR loci in nonreplicating DNA, suggests that a substantial percentage of mutation may occur in nonreplicating DNA.

TrExML: a maximum-likelihood approach for extensive tree-space exploration

MOTIVATION

Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified.

RESULTS

This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs.

AVAILABILITY

TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

COMT and DRD3 polymorphisms, environmental exposures, and personality traits related to common mental disorders

In a community sample of 2,327 Caucasians, we tested the hypotheses that polymorphisms in the COMT and DRD3 genes are associated with personality traits conferring vulnerability to anxiety, depression, or alcohol misuse, or with current symptoms of these; and that the association is stronger in persons who also have been exposed to stressor experiences. To conserve resources and to allow replication, the genetic analysis was undertaken in two stages. For the COMT polymorphism, no statistically significant associations were found in the first sample of 862 persons. The remainder of the sample was therefore not analysed for that gene. For the DRD3 polymorphism, those in the first sample with at least one of the Ser(9) alleles had significantly higher scores in neuroticism (p=0.006) and behavioral inhibition (p=0.003). There was a trend, failing to meet the 1% significance criterion, for those with this genotype also to have higher depression and anxiety. The groups did not differ in alcohol use. In persons with the Ser(9) allele who were also exposed to stressors, there was a higher level of depression at the 5% level; and the depression level was higher in homozygotes. But when the remainder of the sample (1,465) was analysed, none of the associations reached statistical significance. We conclude that neither the COMT nor DRD3 polymorphisms are associated with anxiety, depression, or alcohol abuse. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:102-107, 2000

Assessing candidate genes as risk factors for mental disorders: the value of population-based epidemiological studies

BACKGROUND

It is now possible to routinely collect DNA for the investigation of genetic risk factors in psychiatric epidemiology. However, concerns have been raised about the investigation of genetic risk factors in population surveys and in case-control studies with population controls, because of spurious associations arising through population stratification. To overcome this problem, some geneticists advocate the use of family controls and studies on isolated populations. However, such approaches may not be the best for psychiatric epidemiology.

METHOD

A critical analysis is made of arguments against the investigation of genetic risk factors in studies with population controls.

RESULTS

It is argued that concerns about population stratification have been overblown. It is simply a form of confounding and can occur in studies of environmental as well as genetic risk factors. Epidemiologists have traditionally dealt with this and other types of confounding by matching on potential confounders in the design of the study, or stratification by confounders in the analysis. Family controls overcome population stratification, but not other forms of confounding. They are a good choice when the sole interest is genetic risk factors, but psychiatric epidemiologists are typically interested in both genetic and environmental factors. Family controls are poor for examining environmental risk factors because they can give rise to over-matching. Isolated populations may produce genetic associations that do not generalize to other populations, and they may have a restricted range of environments.

CONCLUSION

We conclude that population surveys and case-control studies using population controls are suitable for the investigation of both genetic and environmental risk factors and have greater public health relevance than alternative designs.

Molecular evidence for the early divergence of placental mammals

Paleontological and molecular data suggest quite different patterns for the early evolution of placental mammals. Paleontological evidence indicates a radiation, with most of the extant orders diverging at approximately the same time, close to the Cretaceous-Tertiary boundary, 65 Myr ago. Molecular evidence suggests a branching pattern of evolution that started much earlier. Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely to be correct. If it is correct then either: 1) A diversity of placental mammals remains to be sampled from the Cretaceous, or 2) The placental orders diverged phylogenetically long before they diversified morphologically, implying a decoupling of the evolutionary processes associated with speciation and adaptation. The adaptive diversification of placental mammals may have required the demise of the dinosaurs at the end of the Cretaceous, but it occurred in lineages that had a long prior history of independent existence. 1999.

Evolution of HLA class II molecules: Allelic and amino acid site variability across populations

Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations.

Evolution of class I alcohol dehydrogenase genes in catarrhine primates: gene conversion, substitution rates, and gene regulation

The three class I alcohol dehydrogenases (ADHs) in humans comprise homo- and heterodimers of three subunits (alpha, beta, and gamma) with greater than 90% sequence identity. These are encoded by distinct genes (ADH1, ADH2, and ADH3, respectively) and are all expressed in the liver. In baboons, only the beta ADH subunit is expressed in liver. A second class I ADH is expressed in the kidney; we isolated, cloned, and sequenced the cDNA corresponding to this ADH and conclude that it is of the gamma ADH lineage. We also amplified and sequenced the 5' noncoding regions of all three class I baboon ADH genes and the rhesus monkey ADH1 gene and compared their nucleotide sequences with the corresponding human sequences. There is clear evidence that the evolution of these genes has been reticulate. At least three gene conversion events, affecting the coding and 3' noncoding regions of the genes, are inferred from compatibility and partition matrices and phylogenetic analysis of the sequences. Our estimation of the evolutionary history of these genes provides a framework for the investigation of relative substitution rates and functional variation among the sequences. Relative-rate tests, designed to account for the reticulate evolution of these genes, indicate no difference in substitution rate either between genes encoding different subunits or between human and Old World monkey lineages. The human and baboon gamma ADH sequences do not show clear differences at functionally important sites within the coding region, but they do differ at a number of sites in regions previously proposed to be regulatory sites for transcriptional control. This variation may explain the different patterns of gene expression in humans and baboons.

Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium

A hyperthermophilic and amylolytic prokaryote, designated Rt3, was isolated from a thermal spring near Rotorua, New Zealand. The 16S rRNA gene of Rt3 was cloned and sequenced with the aim of determining its phylogenetic affiliations. The phylogenetic analysis of this sequence, which included a selection of archaebacterial and eubacterial 16S rRNA sequences, indicates that Rt3 most likely belongs to the archaebacterial order Thermococcales. An amylase gene (amyA) from Rt3, encoding a highly thermostable amylase activity, was cloned and its DNA sequence determined. Transcriptional signals typical of archaebacteria were evident in this sequence. The sequence is homologous to a broad range of enzymes from the AMY superfamily and contains a typical N-terminal signal peptide. Phylogenetic analysis and comparison of structural features with other AMY superfamily enzymes reveals that, firstly, the closest homologues of the Rt3 amylase are members of the Bacillus and Plant alpha-amylase groups; and secondly, that the Rt3 amylase is closely related to only one other currently known archaebacterial enzyme, i.e. an (AMY superfamily) alpha-amylase from Natronococcus.

Patterns of reticulate evolution for the classical class I and II HLA loci

Some alleles of the major histocompatibility complex (MHC) genes have a reticulate pattern of evolution, probably resulting from the exchange of segments by gene conversion or recombination. Here we compare the extent and patterns of reticulate evolution among the classical class I and class II loci of the human MHC using the recently developed compatibility and partition matrix methods. A complex pattern is revealed with substantial differences among loci in the extent and pattern of reticulation. Extremely high levels of reticulation are observed at HLA-B and HLA-DPB1, high levels at HLA-A and HLA-DRB1, moderate levels at HLA-C and HLA-DQB1, and low levels at HLA-DQA1. The reticulate events are concentrated in the exons encoding the highly variable, peptide-binding domains, suggesting that the sequence combinations produced by these events are maintained by natural selection.

Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins?

We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.

Determination of a common genetic variant of luteinizing hormone using DNA hybridization and immunoassays

OBJECTIVE

An immunologically anomalous form of LH, due to two point mutations in codons 8 and 15 of the LH beta gene, has previously been described. LH status, i.e. the discrimination between wild-type (WT) and variant (V) LH, is usually determined by immunoassays, which can be unreliable at low serum concentrations of LH. A DNA hybridization assay was therefore developed to score the LH genotype in all subjects, independent of their serum LH concentrations. To evaluate the performance of the hybridization method, and to expand our observations of the worldwide occurrence of the V-LH, we determined its frequency in additional populations. To confirm the connection between the anomalous immunoreactivity and the V-LH beta gene, we also sequenced the LH beta subunit gene of a homozygous person.

DESIGN

According to the ratio of two immunoassays, one detecting only WT-LH and the other detecting equally WT and V-LH, individuals can be classified as homozygotes for the V-LH beta allele, heterozygotes or WT. DNA samples from persons with known LH status, according to the immunoassays, were used for the development and evaluation of a new allele-specific DNA hybridization assay. This assay, and PCR and restriction fragment length polymorphism analysis, were used to determine the frequency of the V-LH beta allele in DNA samples obtained from eight populations.

PATIENTS

Ambulatory adult men and women, apparently healthy and with no endocrine disorders.

RESULTS

The LH genotyping by immunoassays and by the new hybridization method gave identical results with all samples analysed (n = 25). The V-LH beta subunit was observed to always have the two point mutations, and to be identical with the ones previously reported. The V-LH beta carrier frequency in the DNA samples collected from various populations varied between 0 and 53.5%.

CONCLUSIONS

The immunoassay technique and the hybridization assay can be used as alternatives to determine the LH status. A great variation in carrier frequency of the V-LH beta allele is observed in different populations.

An association study of a functional polymorphism of the serotonin transporter gene with personality and psychiatric symptoms

A functional polymorphism in the regulatory region of the serotonin transporter gene has been reported to be associated with anxiety-related personality traits. We attempted to replicate this finding in an association study involving 759 Caucasians selected from the general Australian population. We found no associations with personality traits (including neuroticism, negative affect and behavioral inhibition), anxiety and depressive symptoms, or alcohol misuse.

The hemochromatosis 845 G-->A and 187 C-->G mutations: prevalence in non-Caucasian populations

Hemochromatosis, the inherited disorder of iron metabolism, leads, if untreated, to progressive iron overload and premature death. The hemochromatosis gene, HFE, recently has been identified, and characterization of this gene has shown that it contains two mutations that result in amino acid substitutions-cDNA nucleotides 845 G-->A (C282Y) and 187 C-->G (H63D). Although hemochromatosis is common in Caucasians, affecting >=1/300 individuals of northern European origin, it has not been recognized in other populations. The present study used PCR and restriction-enzyme digestion to analyze the frequency of the 845 G-->A and 187 C-->G mutations in HLA-typed samples from non-Caucasian populations, comprising Australian Aboriginal, Chinese, and Pacific Islanders. Results showed that the 845 G-->A mutation was present in these populations (allele frequency 0.32%), and, furthermore, it was always seen in conjunction with HLA haplotypes common in Caucasians, suggesting that 845 G-->A may have been introduced into these populations by Caucasian admixture. 187 C-->G was present at an allele frequency of 2.68% in the two populations analyzed (Australian Aboriginal and Chinese). In the Australian Aboriginal samples, 187 C-->G was found to be associated with HLA haplotypes common in Caucasians, suggesting that it was introduced by recent admixture. In the Chinese samples analyzed, 187 C-->G was present in association with a wide variety of HLA haplotypes, showing this mutation to be widespread and likely to predate the more genetically restricted 845 G-->A mutation.

Correlating sequence variation with HLA-A allelic families: implications for T cell receptor binding specificities

Six families of HLA-A alleles have been previously proposed on the basis of nucleotide sequence and phylogenetic analysis. Here, sequence polymorphism has been examined at both the protein and DNA levels in a family specific manner and new minimal signatures for each of the families have been delineated. The DNA and protein sites that constitute these signatures are distributed throughout the length of the sequence and generally do not appear to act to promote structural or functional features of the molecules. This is explained by the fact that traditional signatures suffer biases where, for example, recombination products of low frequency can obscure one family's trend by introducing 'impurities' intrinsic to another family. In the absence of complete frequency data, a closer approximation of family signatures can be defined by sites that show strong correlation with the family groups. Using this description, the amino acid positions 62, 97 and 114, localized in the antigen-binding cleft are, in combination, sufficient to discriminate between the six families. Thus, while the composition of the whole cleft defines the details of antigen specificity, these sites in particular, play a key role in modulating supertype peptide specificity and T cell recognition.

Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees

To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as TAJIMA's D test, and the D and F tests proposed by FU and LI, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a "neutral" marker in evolutionary and population genetic studies.

Molecular genetics and the epidemiology of common mental disorders: new opportunities

AIM

To describe the rationale for introducing molecular genetic analyses to psychiatric epidemiology. This offers new possibilities for aetiological research on common mental disorders.

METHODS

In addition to the traditional variables used in field surveys, it is now possible to include molecular genetic information. This is currently done by looking for allelic associations rather than by linkage analysis, and can be directed either at traits conferring susceptibility or at states. The purpose is to identify quantitative trait loci (QTLs) by examining candidate genes. An alternative strategy is genome scanning, which can identify genes by their chromosomal position with increasing resolution.

RESULTS

Some associations have already been reported in the literature, linking personality traits with particular alleles extraversion or novelty-seeking with a polymorphism of the dopamine DRD4 receptor gene; and neuroticism with a polymorphism of the serotonin transporter gene.

CONCLUSIONS

These findings are of major interest, but cannot yet be looked upon as confirmed. What is significant for epidemiology is the opportunity to link behavioural and psychiatric variables with genes influencing biochemical and physiological processes in the brain, and to do so at the population level. For further allelic association studies, there are four principal requirements: valid measures of phenotypes; replication of findings across diverse populations; more candidate genes; and exploration of the interaction between genotype and environmental exposures from conception to late life. Through such research, psychiatric epidemiology can now investigate biopsychosocial phenomena.

Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees

Restriction mapping and sequencing have shown that humans have substantially lower levels of mitochondrial genome diversity (d) than chimpanzees. In contrast, humans have substantially higher levels of heterozygosity (H) at protein-coding loci, suggesting a higher level of diversity in the nuclear genome. To investigate the discrepancy further, we sequenced a segment of the mitochondrial genome control region (CR) from 49 chimpanzees. The majority of these were from the Pan troglodytes versus subspecies, which was underrepresented in previous studies. We also estimated the average heterozygosity at 60 short tandem repeat (STR) loci in both species. For a total sample of 115 chimpanzees, d = 0.075 +/0 0.037, compared to 0.020 +/- 0.011 for a sample of 1,554 humans. The heterozygosity of human STR loci is significantly higher than that of chimpanzees. Thus, the higher level of nuclear genome diversity relative to mitochondrial genome diversity in humans is not restricted to protein-coding loci. It seems that humans, not chimpanzees, have an unusual d/H ratio, since the ratio in chimpanzees is similar to that in other catarrhines. This discrepancy in the relative levels of nuclear and mitochondrial genome diversity in the two species cannot be explained by differences in mutation rate. However, it may result from a combination of factors such as a difference in the extent of sex ratio disparity, the greater effect of population subdivision on mitochondrial than on nuclear genome diversity, a difference in the relative levels of male and female migration among subpopulations, diversifying selection acting to increase variation in the nuclear genome, and/or directional selection acting to reduce variation in the mitochondrial genome.

The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments

The partition matrix is a graphical tool for comparative analysis of nucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence regions undergoing reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of aligned sequences with the binary partitions inferred from the sequences. Since the linear order of sites is maintained, the matrix can be used to assess whether the distribution of sites either supporting or conflicting with particular partitions changes along the length of the alignment. The usefulness of the matrix in allowing visual identification of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering schemes are proposed. We demonstrate the use of the partition matrix in interpreting the evolution of the pseudoautosomal boundary region on the sex chromosome of catarrhine primates. Its routine use should help to avoid attempts to derive single phylogenies from sequences whose evolution has been reticulate and to identify the gene conversion or recombination events underlying the reticulation. The method is relatively fast. It is exploratory, and it can form the basis for more formal analysis, which we discuss.

Correlating patterns in alignments of polymorphic sequences with experimental assays

A general algorithm is presented for identifying sets of positions in multiple sequence alignments that best characterize an a priori partitioning such as those determined by inhibition studies or other experimental techniques. The algorithm explores combinations of polymorphic columns in the alignment and evaluates how well these sites reflect the original input partition. Partitions across the polymorphic columns are derived using a tree building procedure with conventional amino acid substitution matrices. Elucidation of those amino acids which govern the biochemical behaviour of a protein with a given substrate or inhibitor can provide insights towards an understanding of the tertiary conformation of the protein. Since it is likely that such positions will be spatially clustered in the protein fold, these positions may give rise to useful distance constraints for substantiating model protein structures. The method is exemplified using data for a set of human mu class glutathione S-transferases. A novel aspect for predicting the behaviour of new polymorphic sequences is also discussed.

Molecular evidence from the nuclear genome for the time frame of human evolution

Evolutionary divergence times can be inferred from molecular distances if a molecular clock can be assumed and if the substitution rate can be estimated. We present new evidence from relative rate tests that the rate of substitution at fourfold degenerate sites of nuclear genome-coding DNA is uniform in primate and rodent lineages. We also review recent relative rate test results showing substitution rate uniformity in the nuclear genome of simian primates. DNA distances between a range of mammalian taxa shows that a molecular clock is inconsistent with many assumed divergence times irrespective of the assumed substitution rate. We find that the substitution rate that implies the best compromise fit with divergence times across the range of taxa is 2.0-2.25 x 10(-9). This range of substitution rates implies a divergence time of humans and chimpanzees of 4.0-3.6 million years ago. This postdates the occurrence of Ardipithecus ramidus and the earliest occurrence of Australopithecus afarensis, suggesting that the common ancestor of humans and chimpanzees was bipedal and that the trait has been lost in chimpanzees rather than gained in humans.

Structural comparison of major histocompatibility complex class I molecules and homology modelling of five distinct human leukocyte antigen-A alleles

The peptide complexes of 19 major histocompatibility complex class I alpha 1 and alpha 2 domains have been compared to identify similarities that can be interpreted as constraints necessary for the function or stability of the molecule. It was found that nearly half of the residues maintained their side-chain conformations (or had no side chain), with the remaining residues being highly solvent exposed and/or polymorphic. Seven hydrogen bonds between the molecule and peptide are conserved in all the structures and serve to orientate the ends of the peptide in the binding groove. Furthermore, the general orientations of most residue side chains in the peptide are similar. Based on these constraints, homology models for the distinct human leukocyte antigen-A alleles A*0302, A*2403, A*2603, A*3101 and A*8001 have been constructed and the implications for peptide binding discussed. The models provide a useful framework from which to engineer allele-specific peptides with a high binding affinity.

Relative rates of nuclear DNA evolution in human and Old World monkey lineages

Rates of substitution were compared between humans and Old World monkeys for sequences in or adjacent to 19 genes. The comparison of 21,299 sites in noncoding regions indicates that the substitution rate is approximately 43% greater in the Old World monkey lineage. However, 83% of the compared sites are in the region of the beta-globin gene family. Outside this region there is no consistent pattern of rate difference between the two lineages. Comparison of the coding regions of 16 genomically dispersed genes, involving 1,592 synonymous sites and 5,275 nonsynonymous sites, showed a faster rate of substitution in the human lineage at the nonsynonymous sites of the prion gene, but otherwise no evidence of rate difference between the two lineages. It is concluded that rate differences between these two lineages may be specific to certain regions of the genome rather than being a general phenomenon. This conclusion needs to be confirmed by comparison of a larger number of genomically dispersed sequences. It is, however, consistent with the results of DNA-DNA hybridization experiments, which show no difference in evolutionary rate between the two lineages.

Evolution of mammalian X-linked and autosomal Pgk and Pdh E1 alpha subunit genes

The phylogeny and substitution rates of the mammalian X chromosome-located and autosomal phosphoglycerate kinase and pyruvate dehydrogenase genes were investigated. Compatibility analysis was used to show reticulate evolution in these genes. Analysis of the marsupial, mouse, and human phosphoglycerate kinase genes suggests that at least two recombination events have taken place, one occurring about the time of the placental-marsupial split involving exons 1-5 and the other before the primate-rodent split involving exons 9-10. Similar analysis of the pyruvate dehydrogenase genes indicates a recombination event involving exons 2-3 at a time before the primate-rodent split and a gene conversion between exons 3-4 in the human somatic and testis-specific pyruvate dehydrogenase genes after the primate-rodent split. This demonstrates that genetic exchange can occur between paralogous genes at widely separated chromosomal locations. Estimation of nucleotide substitution rates in these genes confirmed a higher substitution rate in the pyruvate dehydrogenase genes. In the phosphoglycerate kinase genes, there is no difference between the substitution rates in mice and humans and between the X chromosome- and autosome-located genes. A greater substitution rate was noted in the mouse autosomal pyruvate dehydrogenase gene when compared with the other mouse and human genes. This may be a result of either directional natural selection or a relaxation of functional constraint at this specific gene.