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The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases., Author(s): Feng Yue [1, 2]; Yong Cheng [3]; Alessandra Breschi [4]; Jeff Vierstra [5]; Weisheng Wu [6]; Tyrone Ryba [7]; Richard Sandstrom [5]; Zhihai Ma [3]; Carrie Davis [8]; Benjamin [...]

Gene expression differs among individuals and populations and is thought to be a major determinant of phenotypic variation. Although variation and genetic loci responsible for RNA expression levels have been analysed extensively in human populations (1-5), our knowledge is limited regarding the differences in human protein abundance and the genetic basis for this difference. Variation in messenger RNA expression is not a perfect surrogate for protein expression because the latter is influenced by an array of post-transcriptional regulatory mechanisms, and, empirically, the correlation between protein and mRNA levels is generally modest (6,7). Here we used isobaric tag-based quantitative mass spectrometry to determine relative protein levels of 5,953 genes in lymphoblastoid cell lines from 95 diverse individuals genotyped in the HapMap Project (8,9). We found that protein levels are heritable molecular phenotypes that exhibit considerable variation between individuals, populations and sexes. Levels of specific sets of proteins involved in the same biological process covary among individuals, indicating that these processes are tightly regulated at the protein level. We identified cis-pQTLs (protein quantitative trait loci), including variants not detected by previous transcriptome studies. This study demonstrates the feasibility of high-throughput human proteome quantification that, when integrated with DNA variation and transcriptome information, adds a new dimension to the characterization of gene expression regulation., We used isobaric tandem mass tag (TMT)-based quantitative mass spectrometry to determine protein expression variation of lymphoblastoid cell lines (LCLs) derived from 95 ethnically diverse individuals genotyped in the HapMap [...]

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1-4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other., Whereas chimpanzees are widespread across equatorial Africa, bonobos live only south of the Congo River in the Democratic Republic of Congo (Fig. 1a). As a result of their relatively small [...]

The 546-base pair enhancer of limb expression HACNS1, which is highly constrained in all terrestrial vertebrates, has accumulated 16 human-specific changes after the human-chimpanzee split. There has been discussion whether this process was driven by positive selection or biased gene conversion, without considering population data. We studied 83 South Amerindian, 11 Eskimo, 35 Europeans, 37 Bantu, and non-Bantu Sub-Saharan speakers, and 28 Brazilian mestizo samples and found no variation in this DNA region. Similar lack of variability in this region was found in four Africans, five Europeans or Euro-derived, two Asians, one Paleo-Eskimo, and one Neandertal sequence, whose whole genomes are publicly available. No difference was found. This result favors the interpretation of past positive and present conservative selection, as would expected in a region which influences Homo-specific traits as important as opposable thumbs, manual dexterity, and bipedal walking. Am J Phys Anthropol 143:478-481, 2010. [c] 2010 Wiley-Liss, Inc. KEY WORDS human evolution; Native Americans; morphological adaptations DOI 10.1002/ajpa.21378

Osseous and dental nonmetric (discrete) traits have long been used to assess population variability and affinity in anthropological and archaeological contexts. However, the full extent to which nonmetric traits can reliably be used as a proxy for genetic data when assessing close or familial relationships is currently poorly understood. This study represents the unique opportunity to directly compare genetic and nonmetric data for the same individuals excavated from the Egyin Gol necropolis, Mongolia. These data were analyzed to consider the general efficacy of nonmetric traits for detecting familial groupings in the absence of available genetic data. The results showed that the Egyin Gol population is quite homogenous both metrically and genetically confirming a previous suggestion that the same people occupied the necropolis throughout the five centuries of its existence. Kinship analysis detected the presence of potential family burials in the necropolis. Moreover, individuals buried in one sector of the necropolis were differentiated from other sectors on the basis of nonmetric data. This separation is likely due to an outside Turkish influence in the paternal line, as indicated by the results of Y-chromosome analysis. Affinity matrices based on nonmetric and genetic data were correlated demonstrating the potential of nonmetric traits for detecting relationships in the absence of genetic data. However, the strengths of the correlations were relatively low, cautioning against the use of nonmetric traits when the resolution of the familial relationships is low. Am J Phys Anthropol 143:355-364, 2010. [c] 2010 Wiley-Liss, Inc. KEY WORDS nonmetric traits; ancient DNA; kinship; Egyin Gol DOI 10.1002/ajpa.21322

Although adipose tissue is an expandable and readily attainable source of proliferating, multipotent stem cells, its potential for use in regenerative medicine has not been extensively explored. Here we report that adult human and mouse adipose-derived stem cells can be reprogrammed to induced pluripotent stem (iPS) cells with substantially higher efficiencies than those reported for human and mouse fibroblasts. Unexpectedly, both human and mouse iPS cells can be obtained in feeder-free conditions. We discovered that adipose-derived stem cells intrinsically express high levels of pluripotency factors such as basic FGF, TGF[beta], fibronectin, and vitronectin and can serve as feeders for both autologous and heterologous pluripotent cells. These results demonstrate a great potential for adipose-derived cells in regenerative therapeutics and as a model for studying the molecular mechanisms of feeder-free iPS generation and maintenance. adipose stem cell | mesenchymal stem cells | pre-adipocytes | iPS cells | metabolism doi/10.1073/pnas.0910172106

Human and mouse subjects tried to anticipate at which of 2 locations a reward would appear. On a randomly scheduled fraction of the trials, it appeared with a short latency at one location; on the complementary fraction, it appeared after a longer latency at the other location. Subjects of both species accurately assessed the exogenous uncertainty (the probability of a short versus a long trial) and the endogenous uncertainty (from the scalar variability in their estimates of an elapsed duration) to compute the optimal target latency for a switch from the short- to the long-latency location. The optimal latency was arrived at so rapidly that there was no reliably discernible improvement over trials. Under these nonverbal conditions, humans and mice accurately assess risks and behave nearly optimally. That this capacity is well-developed in the mouse opens up the possibility of a genetic approach to the neurobiological mechanisms underlying risk assessment. genetics | human | interval timing | optimality | statistical decision theory

The order in which ectocranial sutures undergo fusion displays species-specific variation among primates. However, the precise relationship between suture closure and phylogenetic affinities is poorly understood. In this study, we used Guttman Scaling to determine if the modal progression of suture closure differs among Homo sapiens, Pan troglodytes, and Gorilla gorilla. Because DNA sequence homologies strongly suggest that P. troglodytes and Homo sapiens share a more recent common ancestor than either does with G. gorilla, we hypothesized that this phylogenetic relationship would be reflected in the suture closure patterns of these three taxa. Results indicated that while all three species do share a similar lateral-anterior closure pattern, G. gorilla exhibits a unique vault pattern, which, unlike humans and P. troglodytes, follows a strong posterior-to-anterior gradient. P. troglodytes is therefore more like Homo sapiens in suture synostosis. KEY WORDS cranial suture; synostosis; variation; phylogeny; Guttman analysis

Most phenotypic differences between human and chimpanzee are likely to result from differences in gene regulation, rather than changes to protein-coding regions. To date, however, only a handful of human-chimpanzee nucleotide differences leading to changes in gene regulation have been identified. To hone in on differences in regulatory elements between human and chimpanzee, we focused on 10 genes that were previously found to be differentially expressed between the two species. We then designed reporter gene assays for the putative human and chimpanzee promoters of the 10 genes. Of seven promoters that we found to be active in human liver cell lines, human and chimpanzee promoters had significantly different activity in four cases, three of which recapitulated the gene expression difference seen in the microarray experiment. For these three genes, we were therefore able to demonstrate that a change in cis influences expression differences between humans and chimpanzees. Moreover, using site-directed mutagenesis on one construct, the promoter for the DDA3 gene, we were able to identify three nucleotides that together lead to a cis regulatory difference between the species. High-throughput application of this approach can provide a map of regulatory element differences between humans and our close evolutionary relatives.

In humans, telomere length in proliferating tissues shortens with age--a process accelerated with age-related diseases. Thus, telomere length and attrition with age in the nonhuman primate may serve as a useful paradigm for understanding telomere biology in humans. We examined telomere parameters in tissues of young and old Macaca fascicularis and compared them with several tissues from humans. Macaque telomeres were variable in length and exhibited partial synchrony (equivalence) within animals. They were longer than humans, partially because of longer subtelomeric segments. As skeletal muscle telomere length was unchanged with age, we used it as an internal reference to offset interanimal variation in telomere length. We identified age-dependent telomere attrition in lung, pancreas, skin, and thyroid. Similar to humans, telomerase activity was detected in spleen, thymus, digestive tract, and gonads. We conclude that factors that modify telomere attrition and aging in humans may also operate in the macaque.

The article discusses the evolutionary relationships among the proteins of the eukaryotes from comparison of eight different species.

The insertion of two transposon-like DNA sequences in the human prolactin gene, which together function as an alternative promoter directing extrapituitary pituitary hormone prolactin (PRL) expression, is reported. It is supposed that the transposon insertion event has resulted in divergent expression of prolactin in primates, and in differential actions of pituitary versus extrapituitary prolactin in lactation versus pregnancy respectively.

The reference human and chimpanzee genomes are compared to determine the magnitude of the recombination between Alu elements in the human lineage since the human-chimpanzee divergence ~6 million years ago. It is found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome.

An overview of function of spalt genes in the development of vertebrates and also diseases in humans is presented.

Much evidence from studies in humans and animals supports the hypothesis that alcohol addiction is a complex disease with both hereditary and environmental influences. Molecular determinants of excessive alcohol consumption are difficult to study in humans. However, several rodent models show a high or low degree of alcohol preference, which provides a unique opportunity to approach the molecular complexities underlying the genetic predisposition to drink alcohol. Microarray analyses of brain gene expression in three selected lines, and six isogenic strains of mice known to differ markedly in voluntary alcohol consumption provided >4.5 million data points for a meta-analysis. A total of 107 arrays were obtained and arranged into six experimental data sets, allowing the identification of 3,800 unique genes significantly and consistently changed between all models of high or low amounts of alcohol consumption. Several functional groups, including mitogen-activated protein kinase signaling and transcription regulation pathways, were found to be significantly overrepresented and may play an important role in establishing a high level of voluntary alcohol drinking in these mouse models. Data from the general meta-analysis was further filtered by a congenic strain microarray set, from which cis-regulated candidate genes for an alcohol preference quantitative trait locus on chromosome 9 were identified: Arhgef12, Carm1, Cryab, Cox5a, Dlat, Fxyd6, Limd1, Nicn1, Nmnat3, Pknox2, Rbp1, Sc5d, Scn4b, Tcf12, Vps11, and Zfp291 and four ESTs. The present study demonstrates the use of (i) a microarray meta-analysis to analyze a behavioral phenotype (in this case, alcohol preference) and (ii) a congenic strain for identification of cis regulation. alcoholism | gene expression | microarray

A comparison of segmental duplications in humans and chimpanzees is presented as they might help in understanding the origins of phenotypic difference between humans and their closest relatives. Comparisons revealed that a total of approximately 80 Mb of segmentally duplicated DNA in humans and 65 Mb in chimpanzees.

Multiprobe oligonucleotide arrays are a widely used type of expression microarray with the attractive feature that numerous probes are used to represent each transcript. An 'expression index' is a statistic used to represent expression level for a particular gene that is estimated from the probe hybridization intensities. We show that a popular model-based expression index proposed by Li and Wong has an interpretation as a component of the singular value decomposition (SVD) of the probe intensity matrix. Following this observation, we propose a new SVD model that accounts for differing variance structure across probes. We also propose that nonlinearity in intensity response to expression can be corrected to some extent through a data transformation, which is guided by an SVD entropy measure. The methods are demonstrated with simulation and applications to two real datasets. KEY WORDS: Characteristic mode; Entropy; Expression index; Oligonucleotide array; Singular value decomposition.

This study investigated effects of prolonged submaximal exercise on [Na.sup.+]-[K.sup.+]-ATPase mRNA and protein expression, maximal activity, and content in human skeletal muscle. We also investigated the effects on mRNA expression of the transcription initiator gene, RNA polymerase II (RNAP II), and key genes involved in protein translation, eukaryotic initiation factor-4E (eIF-4E) and 4E-binding protein 1 (4E-BP1). Eleven subjects (6 men, 5 women) cycled at 75.5% (SD 4.8%) peak [O.sub.2] uptake and continued until fatigue. A vastus lateralis muscle biopsy was taken at rest, fatigue, and 3 and 24 h postexercise. We analyzed muscle for [Na.sup.+]-[K.sup.+]-ATPase [[alpha].sub.1], [[alpha].sub.2], [[alpha].sub.3], [[beta].sub.1], [[beta].sub.2], and [[beta].sub.3], as well for RNAP II, eIF-4E, and 4E-BP1 mRNA expression by real-time RT-PCR and [Na.sup.+]-[K.sup.+] -ATPase isoform protein abundance using immunoblotting. Muscle homogenate maximal [Na.sup.+]-[K.sup.+]-ATPase activity was determined by 3-O-methylfluorescein phosphatase activity and [Na.sup.+]-[K.sup.+] -ATPase content by [[sup.3]H]ouabain binding. Cycling to fatigue [54.5 (SD 20.6) min] immediately increased [[alpha].sub.3] (P = 0.044) and [[beta].sub.2] mRNA (P = 0.042) by 2.2- and 1.9-fold, respectively, whereas [[alpha].sub.1] mRNA was elevated by 2.0-fold at 24 h postexercise (P = 0.036) A significant time main effect was found for [[alpha].sup.3] protein abundance (P = 0.046). Exercise transiently depressed maximal [Na.sup.+]-[K.sup.+]-ATPase activity (P = 0.004), but [Na.sup.+]-[K.sup.+]-ATPase content was unaltered throughout recovery. Exercise immediately increased RNAP II mRNA by 2.6-fold (P = 0.011) but had no effect on eIF-4E and 4E-BPI mRNA. Thus a single bout of prolonged submaximal exercise induced isoform-specific [Na.sup.+]-[K.sup.+]-ATPase responses, increasing [[alpha].sub.1], [alpha].sub.3], and [[beta].sub.2] mRNA but only [[alpha].sub.3] protein expression. Exercise also increased mRNA expression of RNAP II, a gene initiating transcription, but not of eIF-4E and 4E-BP1, key genes initiating protein translation. gene expression; RNA polymerase II; 3-O-methylfluorescein phosphatase; [[sup.3]H]ouabain binding

Cytokines that use the common gamma chain [gamma]c are critical for lymphoid development and function. Mutations of the IL-7 receptor, [gamma]c, or its associated kinase, Jak3, are the major cause of human severe combined immunodeficiency. Although activated by IL-7, Stat5a/b (Stat, signal transducer and activator of transcription) have been thought to play limited roles in lymphoid development. However, we now show that mice completely deficient in Stat5a/b have severely impaired lymphoid development and differentiation. Absence of Stat5 also abrogates T cell receptor [gamma] rearrangement and survival of peripheral CD[8.sup.+] T cells. Thus, deficiency of Stat5 results in severe combined immunodeficiency, similar in many respects to deficiency of IL-7R, [gamma]c, and Jak3. cytokine | jak | lymphocyte | severe combined immunodeficiency | interleukin

Reproductive cloning is uniformly rejected as a valid technology in humans because of the severely abnormal phenotypes seen in cloned animals. Gene expression aberrations observed in tissues of cloned animals have also raised concerns regarding the therapeutic application of 'customized' embryonic stem (ES) cells derived by nuclear transplantation (NT) from a patient's somatic cells. Although previous experiments in mice have demonstrated that the developmental potential of ES cells derived from cloned blastocysts (NT-ES cells) is identical to that of ES cells derived from fertilized blastocysts, a systematic molecular characterization of NT-ES cell lines is lacking. To investigate whether transcriptional aberrations, similar to those observed in tissues of cloned mice, also occur in NT-ES cells, we have compared transcriptional profiles of 10 mouse NT- and fertilization-derived-ES cell lines. We report here that the ES cell lines derived from cloned and fertilized mouse blastocysts are indistinguishable based on their transcriptional profiles, consistent with their normal developmental potential. Our results indicate that, in contrast to embryonic and fetal development of clones, the process of NT-ES cell derivation rigorously selects for those immortal cells that have erased the 'epigenetic memory' of the donor nucleus and, thus, become functionally equivalent. Our findings support the notion that ES cell lines derived from cloned or fertilized blastocysts have an identical therapeutic potential. expression profiling | nuclear transfer

The preferential occurrence of meiotic recombination at certain regions called hot spots is essential for the generation of genetic diversity and proper segregation of chromosomes during meiosis. The recombination hot spots are the sites for initiation and resolution of both crossovers and conversion events.

Human EBV-transformed B lymphocyte cell lines (LCLs) were used to measure the apoptotic response of individuals to [gamma] radiation. The responses form a normal distribution around a median of 35.5% apoptosis with a range of 12-58%. This heterogeneous response has a genetic basis. LCLs from Caucasian donors and African American donors form distinct distributions of apoptotic response; all of the 11 LCLs comprising the lowest responding group (exhibiting between 12-20% apoptosis) are from Caucasian donors. The assay is capable of detecting significant effects of SNPs in two genes, MDM2 and AKT1, whose products are involved in controlling the p53 pathway and cellular response to DNA damage, suggesting that these data and this assay can be used to identify novel SNPs in other genes whose products impact the cellular response to radiation. Finally, the LCLs in the lowest apoptotic response group have the highest concentration of AKT1 protein and all harbor a haplotype in AKT1 that is present in Caucasians but absent in African Americans. AKT1 | MDM2 | p53

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations. ethnogenetics | human evolution | sex-bias dispersal

The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex. In this report we describe the isolation of the wild-type Homo sapiens (Hs)ORC and variants containing a Walker A motif mutation in the Orc1, Orc4, or Orc5 subunit using the baculovirus-expression system. Coexpression of all six HsORC subunits yielded a stable complex containing HsOrc subunits 1-5 (HsORC1-5) with virtually no Orc6 protein (Orc6p). We examined the ATPase, DNA-binding, and replication activities of these complexes. Similar to other eukaryotic ORCs, wild-type HsORC1-5 possesses ATPase activity that is stimulated only 2-fold by single-stranded DNA. HsORC1-5 with a mutated Walker A motif in Orc1p contains no ATPase activity, whereas a similar mutation of either the Orc4 or Orc5 subunit did not affect this activity. The DNA-binding activity of HsORC1-5, using lamin B2 DNA as substrate, is stimulated by ATP 3- to 5-fold. Mutations in the Walker A motif of Orclp, Orc4p, or Orc5p reduced the binding efficiency of HsORC1-5 modestly (2- to 5-fold). Xenopus laevis ORC-depleted extracts supplemented with HsORC1-5 supported prereplication complex formation and X. laevis sperm DNA replication, whereas the complex with a mutation in the Walker A motif of the Orc1, Orc4, or Orc5 subunit did not. These studies indicate that the ATP-binding motifs of Orc1, Orc4, and Orc5 are all essential for the replication activity associated with HsORC. ATP | replication

Byline: A. A. Ivonin (1), M. N. Tsitseroshin (2), A. A. Pogosyan (2), V. T. Shuvaev (1) Keywords: brain; genetics; bioelectrical activity; humans Abstract: The contribution of genetic factors to the formation of the neurophysiological mechanisms of cortical-subcortical integration was studied in 12 pairs of monozygotic and five pairs of dizygotic twins (aged 18--25 years). Intrapair similarity of the nature of spatial interactions between bioelectrical activity in the cerebral cortex, assessed from different combinations of statistical interactions of EEG from 16 monopolar recordings, was assessed in each pair of twins (and among 544 non-related pairs of subjects in both groups). The results suggest a high level of general population invariance and relatively small inherited and phenotypic variability in the morphofunctional systems making up the major neurophysiological mechanisms of brain integration as a whole. The ontogenetic formation of stem and subcortical regulatory structures, which have a leading role in the systems combination of different parts of the brain into a single formation, appears to occur in all individuals by the same principle, as disturbance can apparently affect the fundamental monomorphic features of the species. In turn, we might expect to find large interindividual variability in the establishment of interregional connections of the neocortex, the role of inherited and environmental factors being different in the processes forming long and relatively short intercortical interactions. Author Affiliation: (1) I. P. Pavlov Institute of Physiology, Russian Academy of Sciences, 6 Makarov Bank, 199034, St. Petersburg, Russia (2) I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 M. Torez Prospekt, 194223, St. Petersburg, Russia Article History: Registration Date: 18/10/2004

Surfactant protein A (SP-A) plays a role in innate host defense. Human SP-A is encoded by two functional genes (SP-A1 and SP-A2), and several alleles have been characterized for each gene. We assessed the effect of in vitro expressed human SP-A genetic variants, on TNF-[alpha] and IL-8 production by THP-1 cells in the presence of bleomycin, either before or after ozone-induced oxidation of the variants. The oligomerization of SP-A variants was also examined. We found 1) cytokine levels induced by SP-A2 (1A, [1A.sup.0]) were significantly higher than those by SP-AI ([6A.sup.2], [6A.sup.4]) in the presence of bleomycin. 2) In the presence of bleomycin, ozone-induced oxidation significantly decreased the ability of 1A and 1A/ [6A.sup.4], but not of [6A.sup.4], to stimulate TNF-[alpha] production. 3) The synergistic effect of bleomycin/SP-A, either before or after oxidation, can be inhibited to the level of bleomycin alone by surfactant lipids. 4) Differences in oligomerization were also observed between SP-A1 and SP-A2. The results indicate that differences among SP-A variants may partly explain the individual variability of pulmonary complications observed during bleomycin chemotherapy and/or in an environment that may promote protein oxidation. inflammation; enzyme-linked immunosorbent assay; oligomerization; ozone

The availability of both the mouse and human genome sequences allows for the systematic discovery of human gene function through the use of the mouse as a model system. To accelerate the genetic determination of gene function, we have developed a sequence-tagged gene-trap library of >270,000 mouse embryonic stem cell clones representing mutations in [approximately equal to] 60% of mammalian genes. Through the generation and phenotypic analysis of knockout mice from this resource, we are undertaking a functional screen to identify genes regulating physiological parameters such as blood pressure. As part of this screen, mice deficient for the Wnk1 kinase gene were generated and analyzed. Genetic studies in humans have shown that large intronic deletions in WNK1 lead to its overexpression and are responsible for pseudohypoaldosteronism type II, an autosomal dominant disorder characterized by hypertension, increased renal salt reabsorption, and impaired [K.sup.+] and [H.sup.+] excretion. Consistent with the human genetic studies, Wnk1 heterozygous mice displayed a significant decrease in blood pressure. Mice homozygous for the Wnk1 mutation died during embryonic development before day 13 of gestation. These results demonstrate that Wnk1 is a regulator of blood pressure critical for development and illustrate the utility of a functional screen driven by a sequence-based mutagenesis approach.

The frequency of rare mutant allele and the level of allelic association between this allele and one or several closely linked markers are freqeuntly measured in genetic epidemiology. Both quantities are related to the time elapsed since the appearance of the mutation in the population and the intrinsic growth rate of the mutation (which may be different from the average population growth rate). Here, we develop a method that uses these two kinds of genetic data to perform a joint estimation of the age of the mutation and the minimum growth rate that is compatible with its present frequency. In absence of demographic data, it provides a useful estimate of population growth rate. When such data are available, contrasts among estimates from several loci allow demographic processes, affecting all loci similarly, to be distinguished from selection, affecting loci differently. Testing these estimates on populations for which data are available for several disorders shows good congruence with demographic data in some cases whereas in others higher growth rates are obtained, which may be the result of selection or hidden demographic processes.

Human proteins containing polyalanine tracts tend to have runs of other amino acids and their open reading frames (ORFs) display a biased codon usage. Their alanine, glycine, proline, and histidine content strongly correlates with the GC content of the third codon base, suggesting that the compositional specificity of these proteins is dictated to a great extent by the evolution of their ORFs.

The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ~20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity ([pi]) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the [pi] value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The [pi] values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size ([N.sub.e]) in the human lineage after the human-chimpanzee divergence, because a reduction in [N.sub.e] has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima's D (FD) and Fu and Li's D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.

Classification of humans and other animals will be reconsidered when the human genome is completely sequenced, sometime in the next few years. Conserved elements common to primates and other eutherians and the elements that came later in evolution will be highlighted. Some of the very striking human features, among them the very enlarged brain and the prolonged childhood period in a socially nurturing society, have roots that go far back into evolutionary history. Neocortical parts of the brain increased in two emerging branches of anthropoid primates 30-40 mil years ago. In the catarrhine branch more marked enlargements came in the lineage that led to ancestors of modern hominids. In the most recent 3 mil years the largest neocortical increases came. Chimpanzees, bonobos and gorillas likely will not prove to be evolutionarily closer to orangutans than to humans. Chimpanzees and bonobos likely will be in the genus Homo.

The hypothesis that the putative introgression of an archaic hominin allele at the microcephalin gene in modern humans because it may have led to a brain morphology that results in more effective pragmatic thinking is examined.