[show abstract][hide abstract] ABSTRACT: Reports an error in "Interactions between serotonin transporter gene haplotypes and quality of mothers' parenting predict the development of children's noncompliance" by Michael J. Sulik, Nancy Eisenberg, Kathryn Lemery-Chalfant, Tracy L. Spinrad, Kassondra M. Silva, Natalie D. Eggum, Jennifer A. Betkowski, Anne Kupfer, Cynthia L. Smith, Bridget Gaertner, Daryn A. Stover and Brian C. Verrelli (Developmental Psychology, 2012[May], Vol 48, 740-754). The haplotype combinations for Group 1 and 2 (under the subheading SLC6A4 haplotype groups) are incorrectly described. The true haplotype combinations for Group 1 and 2 are given in the correction. (The following abstract of the original article appeared in record 2011-25157-001.) The LPR and STin2 polymorphisms of the serotonin transporter gene (SLC6A4) were combined into haplotypes that, together with quality of maternal parenting, were used to predict initial levels and linear change in children's (N = 138) noncompliance and aggression from age 18-54 months. Quality of mothers' parenting behavior was observed when children were 18 months old, and nonparental caregivers' reports of noncompliance and aggression were collected annually from 18 to 54 months of age. Quality of early parenting was negatively related to the slope of noncompliance only for children with the LPR-S/STin2-10 haplotype and to 18-month noncompliance only for children with haplotypes that did not include LPR-S. The findings support the notion that SLC6A4 haplotypes index differential susceptibility to variability in parenting quality, with certain haplotypes showing greater reactivity to both supportive and unsupportive environments. These different genetic backgrounds likely reflect an evolutionary response to variation in the parenting environment. (PsycINFO Database Record (c) 2013 APA, all rights reserved).
[show abstract][hide abstract] ABSTRACT: The LPR and STin2 polymorphisms of the serotonin transporter gene (SLC6A4) were combined into haplotypes that, together with quality of maternal parenting, were used to predict initial levels and linear change in children's (
N = 138) noncompliance and aggression from age 18–54 months. Quality of mothers' parenting behavior was observed when children were 18 months old, and nonparental caregivers' reports of noncompliance and aggression were collected annually from 18 to 54 months of age. Quality of early parenting was negatively related to the slope of noncompliance only for children with the LPR-S/STin2-10 haplotype and to 18-month noncompliance only for children with haplotypes that did not include LPR-S. The findings support the notion that SLC6A4 haplotypes index differential susceptibility to variability in parenting quality, with certain haplotypes showing greater reactivity to both supportive and unsupportive environments. These different genetic backgrounds likely reflect an evolutionary response to variation in the parenting environment. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
[show abstract][hide abstract] ABSTRACT: In the vertebrate embryo, skeletal muscle is derived from the myotome of the somites. Notch1-3 demonstrate overlapping and distinct expression patterns in mouse somites. Notch1 and Notch2 have been shown to be inhibitors of skeletal myogenesis. The current data demonstrate that Notch3 also is an effective inhibitor of MyoD induced myogenesis. Numb, an adaptor protein that promotes Notch degradation by recruiting the E3 ubiquitin ligase, Itch, is limited in expression to dividing cells of the dorsal medial lip of the dermomyotome and the myotome itself. Here the specificity of the four protein isoforms of Numb for the Notch receptors was examined. In transcription and myogenic differentiation assays, Notch1 was consistently negatively regulated by all four Numb isoforms, and Notch3 was not a target for Numb. Notch2 however was variably affected. Subsequent analyses showed that unlike Notch1, that Notch3 was not polyubiquitinated, nor degraded when co-expressed in cells with Numb. These data provide the first observations that Notch receptors are variably affected by Numb and will be important for the interpretation of the function of Notch and Numb interactions during the development of many different cells and tissues.
Mechanisms of development 02/2011; 128(5-6):247-57. · 2.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: Collagen type I alpha 1 (COL1a1), which encodes the primary subunit of type I collagen, the main structural and most abundant protein in vertebrates, harbors hundreds of mutations linked to human diseases like osteoporosis and osteogenesis imperfecta. Previous studies have attempted to predict the phenotypic severity associated with type I collagen mutations, yet an evolutionary analysis that compares historical and recent selective pressures, including across noncoding regions, has never been conducted. Here, we use a comparative genomic and species evolutionary analysis representing ∼450 My of vertebrate history to investigate functional constraints associated with both exons and introns of the >17-kb COL1a1 gene. We find that although the COL1a1 amino acid sequence is highly conserved, there are both spatial and temporal signatures of varying selective constraint across protein domains. Furthermore, sites of high evolutionary constraint significantly correlate with the location of disease-associated mutations, the latter of which also cluster with respect to specific severity classes typically categorized in clinical studies. Finally, we find that COL1a1 introns are significantly short in length with high GC content, patterns that are shared across highly diverged vertebrates, and which may be a signature of strong stabilizing selection for high COL1a1 gene expression. In conclusion, although previous studies focused on COL1a1 coding regions, the current results implicate introns as areas of high selective constraint and targets of bone-related phenotypic variation. From a broader perspective, our comparative evolutionary approach provides further resolution to models predicting mutations associated with bone-related function and disease severity.
Molecular Biology and Evolution 01/2011; 28(1):533-42. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Genetic variation in the human serotonin system has long-been studied because of its functional consequences and links to various behavior-related disorders and it being routinely targeted in research and development for drug therapy. However, aside from clinical studies, little is known about this genetic diversity and how it differs within and between human populations with respect to haplotype structure, which can greatly impact phenotype association studies. In addition, no evolutionary approach among humans and other primates has examined how long- and short-term selective pressures explain existing serotonin variation. Here, we examine DNA sequence variation in natural population samples of 192 human and 40 chimpanzee chromosome sequences for the most commonly implicated approximately 38-kb serotonin transporter (SLC6A4) and approximately 63-kb serotonin 2A receptor (HTR2A) genes. Our comparative population genetic analyses find significant linkage disequilibrium associated with functionally relevant variants in humans, as well as geographic variation for these haplotypes, at both loci. In addition, although amino acid divergence is consistent with purifying selection, promoter and untranslated regions exhibit significantly high divergence in both species lineages. These evolutionary analyses imply that the serotonin system may have accumulated significant regulatory variation over both recent and ancient periods of time in both humans and chimpanzees. We discuss the implications of this variation for disease association studies and for the evolution of behavior-related phenotypes during the divergence of humans and our closest primate relatives.
Molecular Biology and Evolution 07/2010; 27(7):1518-29. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Some of the earliest evidence for modern human behavior has been recovered from the Western Cape Province, South Africa. Archaeological and paleontological sites in the Western Cape are typically described as “glacial” or “interglacial” in aspect based on the numbers of grazers found in the faunal assemblage, as glacial periods are often thought to have been characterized by spreading C4 grasslands that replaced endemic C3 shrubland vegetation found in the Western Cape today. Here, we test the hypothesis that glacial and interglacial time periods were associated with a predictable change in large mammal trophic adaptations by analyzing the proportions of grazing larger mammals from 118 levels of 15 Western Cape fossil assemblages sampling marine isotope stage (MIS) 6 to the present time to determine whether there is a change in composition in these communities that might reflect a shift in ecology and habitat. Our results indicate that trophic proportions did not significantly change over time in the Western Cape as a whole, and thus the hypothesis for habitat changes affecting the subsistence ecology of modern humans during the development of modern behavior is not supported. However, our results show that the southwestern subregion of the Western Cape was characterized by the presence of more grazing species through time than the western subregion. Thus, if ecological and population isolation during glacial periods were integral to catalyzing the development of modern behaviors in the Western Cape region of South Africa, then a complex model including the development of possible mosaic habitats is needed.
[show abstract][hide abstract] ABSTRACT: This study was designed to statistically evaluate the independent and interacting effects of biological and environmental risk factors that influence lateralization of deformational plagiocephaly (DP) in an attempt to provide future guidance for clinical treatment.
A database of >20000 children treated for DP was examined by using 2- and 3-way factor analyses for categorical frequency data, representing the largest statistical analysis of DP to date. Data on parity, zygosity, intrauterine presentation, birth number and weight, sleep position, lateralization, and sex were collected from parents of children with DP who were treated at Cranial Technologies, Inc, from 1990 to 2007.
As with most DP studies, male patients were significantly overrepresented. Nonetheless, after statistically accounting for sex in our analyses, DP is significantly correlated with primiparity, fewer vertex but more breech and transverse intrauterine presentations, twinning (specifically, dizygosity), and, finally, right-sided lateralization. Additional analyses revealed that several factors correlated with DP, such as intrauterine presentation, sleep position, and lateralization, are not easily explained by an underlying biological factor. Instead, sleep position was the single greatest predictor of lateralization.
Although previous studies have argued for both environmental and underlying biological factors associated with DP, we found that lateralization in children with DP could be largely explained by environmental factors such as sleep position.
[show abstract][hide abstract] ABSTRACT: A population genetic analysis of the long-wavelength opsin (OPN1LW, "red") color vision gene in a global sample of 236 human nucleotide sequences had previously discovered nine amino acid replacement single nucleotide polymorphisms, which were found at high frequencies in both African and non-African populations and associated with an unusual haplotype diversity. Although this pattern of nucleotide diversity is consistent with balancing selection, it has been argued that a recombination "hot spot" or gene conversion within and between X-linked color vision genes alone may explain these patterns. The current analysis investigates a closely related primate with trichromatism to determine whether color vision gene amino acid polymorphism and signatures of adaptive evolution are characteristic of humans alone. Our population sample of 56 chimpanzee (Pan troglodytes) OPN1LW sequences shows three singleton amino acid polymorphisms and no unusual recombination or linkage disequilibrium patterns across the approximately 5.5-kb region analyzed. Our comparative population genetic approach shows that the patterns of OPN1LW variation in humans and chimpanzees are consistent with positive and purifying selection within the two lineages, respectively. Although the complex role of color vision has been greatly documented in primate evolution in general, it is surprising that trichromatism has followed very different selective trajectories even between humans and our closest relatives.
Molecular Biology and Evolution 11/2008; 25(12):2735-43. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: While color vision perception is thought to be adaptively correlated with foraging efficiency for diurnal mammals, those that forage exclusively at night may not need color vision nor have the capacity for it. Indeed, although the basic condition for mammals is dichromacy, diverse nocturnal mammals have only monochromatic vision, resulting from functional loss of the short-wavelength sensitive opsin gene. However, many nocturnal primates maintain intact two opsin genes and thus have dichromatic capacity. The evolutionary significance of this surprising observation has not yet been elucidated. We used a molecular population genetics approach to test evolutionary hypotheses for the two intact opsin genes of the fully nocturnal aye-aye (Daubentonia madagascariensis), a highly unusual and endangered Madagascar primate. No evidence of gene degradation in either opsin gene was observed for any of 8 aye-aye individuals examined. Furthermore, levels of nucleotide diversity for opsin gene functional sites were lower than those for 15 neutrally evolving intergenic regions (>25 kb in total), which is consistent with a history of purifying selection on aye-aye opsin genes. The most likely explanation for these findings is that dichromacy is advantageous for aye-ayes despite their nocturnal activity pattern. We speculate that dichromatic nocturnal primates may be able to perceive color while foraging under moonlight conditions, and suggest that behavioral and ecological comparisons among dichromatic and monochromatic nocturnal primates will help to elucidate the specific activities for which color vision perception is advantageous.
Molecular Biology and Evolution 10/2007; 24(9):1963-70. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Recent studies have suggested that gene gain and loss may contribute significantly to the divergence between humans and chimpanzees. Initial comparisons of the human and chimpanzee Y-chromosomes indicate that chimpanzees have a disproportionate loss of Y-chromosome genes, which may have implications for the adaptive evolution of sex-specific as well as reproductive traits, especially because one of the genes lost in chimpanzees is critically involved in spermatogenesis in humans. Here we have characterized Y-chromosome sequences in gorilla, bonobo, and several chimpanzee subspecies for 7 chimpanzee gene-disruptive mutations. Our analyses show that 6 of these gene-disruptive mutations predate chimpanzee-bonobo divergence at approximately 1.8 MYA, which indicates significant Y-chromosome change in the chimpanzee lineage relatively early in the evolutionary divergence of humans and chimpanzees.
Molecular Biology and Evolution 04/2007; 24(3):853-9. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: The initial human and chimpanzee genome sequences have been published, and additional primate genomes, including those of gorilla and orang-utan, are in progress. With these new resources, we can now address what makes our species unique, by focusing on the underlying genetic differences associated with phenotypes. Comparative primate population genomics, including studies of structural changes, mobile elements, gene expression and functional analyses, will shed light on how natural selection and population demography are involved in the processes that lead to differences among great apes. Historically, this research has focused on the human perspective; however, we will learn much about ourselves with a focus on genomic diversity in hominoids as a group.
Current Opinion in Genetics & Development 01/2007; 16(6):586-91. · 7.47 Impact Factor
[show abstract][hide abstract] ABSTRACT: Although mutations in the glucose-6-phosphate dehydrogenase (G6PD) gene result in several blood-related diseases in humans, they also confer resistance to malarial infection. This association between G6PD and malaria was supported by population genetic analyses of the G6PD locus, which indicated that these mutations may have recently risen in frequency in certain geographic regions as a result of positive selection. Here we characterize nucleotide sequence variation in a 5.2-kb region of the G6PD locus in a population sample of 56 chimpanzees, as well as among 7 other nonhuman primates, to compare with that in humans in determining whether other primates that are impacted by malaria also exhibit patterns of G6PD polymorphism or divergence consistent with positive selection. We find that chimpanzees have several amino acid variants but that the overall pattern at G6PD in chimpanzees, as well as in Old and New World primates in general, can be explained by recent purifying selection as well as strong functional constraint dating back to at least 30-40 MYA. These comparative analyses suggest that the recent signature of positive selection at G6PD in humans is unique.
Molecular Biology and Evolution 09/2006; 23(8):1592-601. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: A much-celebrated story of positive selection in the human genome is the 32-bp deletion in the chemokine receptor CCR5, a variant that confers resistance to AIDS. This variant was postulated to be a relatively recent response to plague or smallpox. New research shows that the frequency of CCR5-Delta32 in Bronze Age samples is similar to that seen today, pushing the observed age of the allele back to at least 3000 and possibly 5000 years ago. Interestingly, the extent of heterozygosity, differentiation across populations and linkage disequilibrium in the CCR5 region is not dissimilar to other human genomic regions, challenging claims of recent positive selection.
Trends in Genetics 07/2006; 22(6):293-6. · 9.77 Impact Factor
[show abstract][hide abstract] ABSTRACT: In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental genes, in a sample of 27 diverse primate species in order to identify coding or regulatory variation that may be associated with phenotypic diversity. Our analyses have identified four highly conserved noncoding sequences, including one that is conserved across primates and with dogs but not with mice. Although we find that substitution rates vary significantly across MSX1 exons, comparisons of nonsynonymous and synonymous substitution rates (dN/dS) suggest that, as a whole, MSX1 and PAX9 amino acid sequences have been under functional constraint throughout primate evolution. Compared to all other primates in our sample, our analysis of exon 1 in MSX1 finds an unusual pattern of amino acid substitution for Tarsius syrichta, a member of a lineage (tarsiers) that has many unique features among primates. For example, tarsiers are the only extant primates without deciduous incisors, and MSX1 is expressed exclusively in the incisor regions during the earliest stages of dental development. Our overall results provide insight into the utility of comparative species analyses of highly conserved developmental genes and their roles in the evolution of complex phenotypes.
Molecular Biology and Evolution 04/2006; 23(3):644-54. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: We describe the pattern of molecular evolution at a sarcomeric myosin gene, MYH16, using more than 30,000 bp of exon and intron sequence data from the chimpanzee and human genome sequencing projects to evaluate the timing and consequences of a human lineage-specific frameshift deletion. We estimate the age of the deletion at approximately 5.3 MYA. This estimate is consistent with the time of human and chimpanzee divergence and is significantly older than the first appearance of the genus Homo in the fossil record. We also find conflicting estimates of nonsynonymous fixation rates (d(N)) across different regions of this gene, revealing a complex pattern inconsistent with a simple model of pseudogene evolution for human MYH16.
Molecular Biology and Evolution 04/2005; 22(3):379-82. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Trichromatic color vision in humans results from the combination of red, green, and blue photopigment opsins. Although color vision genes have been the targets of active molecular and psychophysical research on color vision abnormalities, little is known about patterns of normal genetic variation in these genes among global human populations. The current study presents nucleotide sequence analyses and tests of neutrality for a 5.5-kb region of the X-linked long-wave "red" opsin gene (OPN1LW) in 236 individuals from ethnically diverse human populations. Our analysis of the recombination landscape across OPN1LW reveals an unusual haplotype structure associated with amino acid replacement variation in exon 3 that is consistent with gene conversion. Compared with the absence of OPN1LW amino acid replacement fixation since divergence from chimpanzee, the human population exhibits a significant excess of high-frequency OPN1LW replacements. Our results suggest that subtle changes in L-cone opsin wavelength absorption may have been adaptive during human evolution.
The American Journal of Human Genetics 10/2004; 75(3):363-75. · 11.20 Impact Factor