A natural history of the human mind: tracing evolutionary changes in brain and cognition

PubMed Central

Sherwood, Chet C; Subiaul, Francys; Zawidzki, Tadeusz W

2008-01-01

Since the last common ancestor shared by modern humans, chimpanzees and bonobos, the lineage leading to Homo sapiens has undergone a substantial change in brain size and organization. As a result, modern humans display striking differences from the living apes in the realm of cognition and linguistic expression. In this article, we review the evolutionary changes that occurred in the descent of Homo sapiens by reconstructing the neural and cognitive traits that would have characterized the last common ancestor and comparing these with the modern human condition. The last common ancestor can be reconstructed to have had a brain of approximately 300–400 g that displayed several unique phylogenetic specializations of development, anatomical organization, and biochemical function. These neuroanatomical substrates contributed to the enhancement of behavioral flexibility and social cognition. With this evolutionary history as precursor, the modern human mind may be conceived as a mosaic of traits inherited from a common ancestry with our close relatives, along with the addition of evolutionary specializations within particular domains. These modern human-specific cognitive and linguistic adaptations appear to be correlated with enlargement of the neocortex and related structures. Accompanying this general neocortical expansion, certain higher-order unimodal and multimodal cortical areas have grown disproportionately relative to primary cortical areas. Anatomical and molecular changes have also been identified that might relate to the greater metabolic demand and enhanced synaptic plasticity of modern human brain's. Finally, the unique brain growth trajectory of modern humans has made a significant contribution to our species’ cognitive and linguistic abilities. PMID:18380864

Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains

PubMed Central

Bennett, Brian J.; Davis, Richard C.; Civelek, Mete; Orozco, Luz; Wu, Judy; Qi, Hannah; Pan, Calvin; Packard, René R. Sevag; Eskin, Eleazar; Yan, Mujing; Kirchgessner, Todd; Wang, Zeneng; Li, Xinmin; Gregory, Jill C.; Hazen, Stanley L.; Gargalovic, Peter S.; Lusis, Aldons J.

2015-01-01

Common forms of atherosclerosis involve multiple genetic and environmental factors. While human genome-wide association studies have identified numerous loci contributing to coronary artery disease and its risk factors, these studies are unable to control environmental factors or examine detailed molecular traits in relevant tissues. We now report a study of natural variations contributing to atherosclerosis and related traits in over 100 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP). The mice were made hyperlipidemic by transgenic expression of human apolipoprotein E-Leiden (APOE-Leiden) and human cholesteryl ester transfer protein (CETP). The mice were examined for lesion size and morphology as well as plasma lipid, insulin and glucose levels, and blood cell profiles. A subset of mice was studied for plasma levels of metabolites and cytokines. We also measured global transcript levels in aorta and liver. Finally, the uptake of acetylated LDL by macrophages from HMDP mice was quantitatively examined. Loci contributing to the traits were mapped using association analysis, and relationships among traits were examined using correlation and statistical modeling. A number of conclusions emerged. First, relationships among atherosclerosis and the risk factors in mice resemble those found in humans. Second, a number of trait-loci were identified, including some overlapping with previous human and mouse studies. Third, gene expression data enabled enrichment analysis of pathways contributing to atherosclerosis and prioritization of candidate genes at associated loci in both mice and humans. Fourth, the data provided a number of mechanistic inferences; for example, we detected no association between macrophage uptake of acetylated LDL and atherosclerosis. Fifth, broad sense heritability for atherosclerosis was much larger than narrow sense heritability, indicating an important role for gene-by-gene interactions. Sixth, stepwise linear regression showed that the combined variations in plasma metabolites, including LDL/VLDL-cholesterol, trimethylamine N-oxide (TMAO), arginine, glucose and insulin, account for approximately 30 to 40% of the variation in atherosclerotic lesion area. Overall, our data provide a rich resource for studies of complex interactions underlying atherosclerosis. PMID:26694027

The evolution of human warfare.

PubMed

Pitman, George R

2011-01-01

Here we propose a new theory for the origins and evolution of human warfare as a complex social phenomenon involving several behavioral traits, including aggression, risk taking, male bonding, ingroup altruism, outgroup xenophobia, dominance and subordination, and territoriality, all of which are encoded in the human genome. Among the family of great apes only chimpanzees and humans engage in war; consequently, warfare emerged in their immediate common ancestor that lived in patrilocal groups who fought one another for females. The reasons for warfare changed when the common ancestor females began to immigrate into the groups of their choice, and again, during the agricultural revolution.

Punctuated Emergences of Genetic and Phenotypic Innovations in Eumetazoan, Bilaterian, Euteleostome, and Hominidae Ancestors

PubMed Central

Wenger, Yvan; Galliot, Brigitte

2013-01-01

Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans, bilaterians, euteleostomi (bony vertebrates), and hominidae, largely specific to each epoch, whereas early branching deuterostome and chordate phyla show very few innovations. Interestingly, groups of proteins that act together in their modern human functions often originated concomitantly, although the corresponding human phenotypes frequently emerged later. For example, the three cnidarians Acropora, Nematostella, and Hydra express a highly similar protein inventory, and their protein innovations can be affiliated either to traits shared by all eumetazoans (gut differentiation, neurogenesis); or to bilaterian traits present in only some cnidarians (eyes, striated muscle); or to traits not identified yet in this phylum (mesodermal layer, endocrine glands). The variable correspondence between phenotypes predicted from protein enrichments and observed phenotypes suggests that a parallel mechanism repeatedly produce similar phenotypes, thanks to novel regulatory events that independently tie preexisting conserved genetic modules. PMID:24065732

Systems genetics approaches to understand complex traits

PubMed Central

Civelek, Mete; Lusis, Aldons J.

2014-01-01

Systems genetics is an approach to understand the flow of biological information that underlies complex traits. It uses a range of experimental and statistical methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels, in populations that vary for traits of interest. Systems genetics studies have provided the first global view of the molecular architecture of complex traits and are useful for the identification of genes, pathways and networks that underlie common human diseases. Given the urgent need to understand how the thousands of loci that have been identified in genome-wide association studies contribute to disease susceptibility, systems genetics is likely to become an increasingly important approach to understanding both biology and disease. PMID:24296534

Hunter-Gatherers and the Origins of Religion.

PubMed

Peoples, Hervey C; Duda, Pavel; Marlowe, Frank W

2016-09-01

Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

PubMed

Astle, William J; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A; Lambourne, John J; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R; Daugherty, Louise C; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H A; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M; Staley, James R; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J; Ouwehand, Willem H; Butterworth, Adam S; Soranzo, Nicole

2016-11-17

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal. Copyright © 2016 Elsevier Inc. All rights reserved.

Maintenance of genetic variation in human personality: Testing evolutionary models by estimating heritability due to common causal variants and investigating the effect of distant inbreeding

PubMed Central

Verweij, Karin J.H.; Yang, Jian; Lahti, Jari; Veijola, Juha; Hintsanen, Mirka; Pulkki-Råback, Laura; Heinonen, Kati; Pouta, Anneli; Pesonen, Anu-Katriina; Widen, Elisabeth; Taanila, Anja; Isohanni, Matti; Miettunen, Jouko; Palotie, Aarno; Penke, Lars; Service, Susan K.; Heath, Andrew C.; Montgomery, Grant W.; Raitakari, Olli; Kähönen, Mika; Viikari, Jorma; Räikkönen, Katri; Eriksson, Johan G; Keltikangas-Järvinen, Liisa; Lehtimäki, Terho; Martin, Nicholas G.; Järvelin, Marjo-Riitta; Visscher, Peter M.; Keller, Matthew C.; Zietsch, Brendan P.

2012-01-01

Personality traits are basic dimensions of behavioural variation, and twin, family, and adoption studies show that around 30% of the between-individual variation is due to genetic variation. There is rapidly-growing interest in understanding the evolutionary basis of this genetic variation. Several evolutionary mechanisms could explain how genetic variation is maintained in traits, and each of these makes predictions in terms of the relative contribution of rare and common genetic variants to personality variation, the magnitude of nonadditive genetic influences, and whether personality is affected by inbreeding. Using genome-wide SNP data from >8,000 individuals, we estimated that little variation in the Cloninger personality dimensions (7.2% on average) is due to the combined effect of common, additive genetic variants across the genome, suggesting that most heritable variation in personality is due to rare variant effects and/or a combination of dominance and epistasis. Furthermore, higher levels of inbreeding were associated with less socially-desirable personality trait levels in three of the four personality dimensions. These findings are consistent with genetic variation in personality traits having been maintained by mutation-selection balance. PMID:23025612

Perceived importance of employees' traits in the service industry.

PubMed

Lange, Rense; Houran, James

2009-04-01

Selection assessments are common practice to help reduce employee turnover in the service industry, but as too little is known about employees' characteristics, which are valued most highly by human resources professionals, a sample of 108 managers and human resources professionals rated the perceived importance of 31 performance traits for Line, Middle, and Senior employees. Rasch scaling analyses indicated strong consensus among the respondents. Nonsocial skills, abilities, and traits such as Ethical Awareness, Self-motivation, Writing Skills, Verbal Ability, Creativity, and Problem Solving were rated as more important for higher level employees. By contrast, traits which directly affect the interaction with customers and coworkers (Service Orientation, Communication Style, Agreeableness, Sense of Humor, Sensitivity to Diversity, Group Process, and Team Building) were rated as more important for lower level employees. Respondents' age and sex did not substantially alter these findings. Results are discussed in terms of improving industry professionals' perceived ecological and external validities of generic and customized assessments of employee.

Genetic selection for temperament traits in dairy and beef cattle.

PubMed

Haskell, Marie J; Simm, Geoff; Turner, Simon P

2014-01-01

Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL) have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.

Genetic selection for temperament traits in dairy and beef cattle

PubMed Central

Haskell, Marie J.; Simm, Geoff; Turner, Simon P.

2014-01-01

Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL) have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection. PMID:25374582

Discretization of Gene Expression Data Unmasks Molecular Subgroups Recurring in Different Human Cancer Types.

PubMed

Beleut, Manfred; Soeldner, Robert; Egorov, Mark; Guenther, Rolf; Dehler, Silvia; Morys-Wortmann, Corinna; Moch, Holger; Henco, Karsten; Schraml, Peter

2016-01-01

Despite the individually different molecular alterations in tumors, the malignancy associated biological traits are strikingly similar. Results of a previous study using renal cell carcinoma (RCC) as a model pointed towards cancer-related features, which could be visualized as three groups by microarray based gene expression analysis. In this study, we used a mathematic model to verify the presence of these groups in RCC as well as in other cancer types. We developed an algorithm for gene-expression deviation profiling for analyzing gene expression data of a total of 8397 patients with 13 different cancer types and normal tissues. We revealed three common Cancer Transcriptomic Profiles (CTPs) which recurred in all investigated tumors. Additionally, CTPs remained robust regardless of the functions or numbers of genes analyzed. CTPs may represent common genetic fingerprints, which potentially reflect the closely related biological traits of human cancers.

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

PubMed Central

Eriksson, Nicholas; Macpherson, J. Michael; Tung, Joyce Y.; Hon, Lawrence S.; Naughton, Brian; Saxonov, Serge; Avey, Linda; Wojcicki, Anne; Pe'er, Itsik; Mountain, Joanna

2010-01-01

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. The identification of novel associations for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A; and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability to smell the methanethiol produced after eating asparagus (rs4481887, near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and rs11856995, near NR2F2) illustrates the power of the approach. PMID:20585627

A Genetic Basis for Mechanosensory Traits in Humans

PubMed Central

Frenzel, Henning; Bohlender, Jörg; Pinsker, Katrin; Wohlleben, Bärbel; Tank, Jens; Lechner, Stefan G.; Schiska, Daniela; Jaijo, Teresa; Rüschendorf, Franz; Saar, Kathrin; Jordan, Jens; Millán, José M.; Gross, Manfred; Lewin, Gary R.

2012-01-01

In all vertebrates hearing and touch represent two distinct sensory systems that both rely on the transformation of mechanical force into electrical signals. There is an extensive literature describing single gene mutations in humans that cause hearing impairment, but there are essentially none for touch. Here we first asked if touch sensitivity is a heritable trait and second whether there are common genes that influence different mechanosensory senses like hearing and touch in humans. Using a classical twin study design we demonstrate that touch sensitivity and touch acuity are highly heritable traits. Quantitative phenotypic measures of different mechanosensory systems revealed significant correlations between touch and hearing acuity in a healthy human population. Thus mutations in genes causing deafness genes could conceivably negatively influence touch sensitivity. In agreement with this hypothesis we found that a proportion of a cohort of congenitally deaf young adults display significantly impaired measures of touch sensitivity compared to controls. In contrast, blind individuals showed enhanced, not diminished touch acuity. Finally, by examining a cohort of patients with Usher syndrome, a genetically well-characterized deaf-blindness syndrome, we could show that recessive pathogenic mutations in the USH2A gene influence touch acuity. Control Usher syndrome cohorts lacking demonstrable pathogenic USH2A mutations showed no impairment in touch acuity. Our study thus provides comprehensive evidence that there are common genetic elements that contribute to touch and hearing and has identified one of these genes as USH2A. PMID:22563300

Global genetic architecture of an erythroid quantitative trait locus, HMIP-2.

PubMed

Menzel, Stephan; Rooks, Helen; Zelenika, Diana; Mtatiro, Siana N; Gnanakulasekaran, Akshala; Drasar, Emma; Cox, Sharon; Liu, Li; Masood, Mariam; Silver, Nicholas; Garner, Chad; Vasavda, Nisha; Howard, Jo; Makani, Julie; Adekile, Adekunle; Pace, Betty; Spector, Tim; Farrall, Martin; Lathrop, Mark; Thein, Swee Lay

2014-11-01

HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed "A" and "B." These typically occurred together ("A-B") on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for "A" and "B," we interrogated public population datasets. Haplotypes carrying only "A" or "B" were typical for populations in Sub-Saharan Africa. The "A-B" combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene-environment interaction during human migration and adaptation. © 2014 The Authors. Annals of Human Genetics published by University College London (UCL) and John Wiley & Sons Ltd.

[Progress in genetic research of human height].

PubMed

Chen, Kaixu; Wang, Weilan; Zhang, Fuchun; Zheng, Xiufen

2015-08-01

It is well known that both environmental and genetic factors contribute to adult height variation in general population. However, heritability studies have shown that the variation in height is more affected by genetic factors. Height is a typical polygenic trait which has been studied by traditional linkage analysis and association analysis to identify common DNA sequence variation associated with height, but progress has been slow. More recently, with the development of genotyping and DNA sequencing technologies, tremendous achievements have been made in genetic research of human height. Hundreds of single nucleotide polymorphisms (SNPs) associated with human height have been identified and validated with the application of genome-wide association studies (GWAS) methodology, which deepens our understanding of the genetics of human growth and development and also provides theoretic basis and reference for studying other complex human traits. In this review, we summarize recent progress in genetic research of human height and discuss problems and prospects in this research area which may provide some insights into future genetic studies of human height.

Continuing Commentary.

ERIC Educational Resources Information Center

Burgess, R. L.; Molenaar, P. C. M.

1993-01-01

Comments on an earlier paper by Lerner and von Eye on sociobiology and human development; general theory in science, especially evolutionary theory; adaptation and behavior plasticity; and modern behavior genetics. Examines assertion that "heritability says nothing about the extent to which a trait is commonly inherited." Discusses…

Phenotyping common beans for adaptation to drought

PubMed Central

Beebe, Stephen E.; Rao, Idupulapati M.; Blair, Matthew W.; Acosta-Gallegos, Jorge A.

2013-01-01

Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation. PMID:23507928

Geological Substrates Shape Tree Species and Trait Distributions in African Moist Forests

PubMed Central

Fayolle, Adeline; Engelbrecht, Bettina; Freycon, Vincent; Mortier, Frédéric; Swaine, Michael; Réjou-Méchain, Maxime; Doucet, Jean-Louis; Fauvet, Nicolas; Cornu, Guillaume; Gourlet-Fleury, Sylvie

2012-01-01

Background Understanding the factors that shape the distribution of tropical tree species at large scales is a central issue in ecology, conservation and forest management. The aims of this study were to (i) assess the importance of environmental factors relative to historical factors for tree species distributions in the semi-evergreen forests of the northern Congo basin; and to (ii) identify potential mechanisms explaining distribution patterns through a trait-based approach. Methodology/Principal Findings We analyzed the distribution patterns of 31 common tree species in an area of more than 700,000 km2 spanning the borders of Cameroon, the Central African Republic, and the Republic of Congo using forest inventory data from 56,445 0.5-ha plots. Spatial variation of environmental (climate, topography and geology) and historical factors (human disturbance) were quantified from maps and satellite records. Four key functional traits (leaf phenology, shade tolerance, wood density, and maximum growth rate) were extracted from the literature. The geological substrate was of major importance for the distribution of the focal species, while climate and past human disturbances had a significant but lesser impact. Species distribution patterns were significantly related to functional traits. Species associated with sandy soils typical of sandstone and alluvium were characterized by slow growth rates, shade tolerance, evergreen leaves, and high wood density, traits allowing persistence on resource-poor soils. In contrast, fast-growing pioneer species rarely occurred on sandy soils, except for Lophira alata. Conclusions/Significance The results indicate strong environmental filtering due to differential soil resource availability across geological substrates. Additionally, long-term human disturbances in resource-rich areas may have accentuated the observed patterns of species and trait distributions. Trait differences across geological substrates imply pronounced differences in population and ecosystem processes, and call for different conservation and management strategies. PMID:22905127

Curcumin and aging

USDA-ARS?s Scientific Manuscript database

Curcumin has been used commonly as a spice, food additive, and an herbal medicine worldwide. Known as a bioactive polyphenolic, curcumin has a broad range of beneficial properties to human health. Recently, active research on curcumin with respect to aging and related traits in model organisms has d...

Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

PubMed

Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

2018-06-01

Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.

Skeletal variation among early Holocene North American humans: implications for origins and diversity in the Americas.

PubMed

Auerbach, Benjamin M

2012-12-01

The movement of humans into the Americas remains a major topic of debate among scientific disciplines. Central to this discussion is ascertaining the timing and migratory routes of the earliest colonizers, in addition to understanding their ancestry. Molecular studies have recently argued that the colonizing population was isolated from other Asian populations for an extended period before proceeding to colonize the Americas. This research has suggested that Beringia was the location of this "incubation," though archaeological and skeletal data have not yet supported this hypothesis. This study employs the remains of the five most complete North American male early Holocene skeletons to examine patterns of human morphology at the earliest observable time period. Stature, body mass, body breadth, and limb proportions are examined in the context of male skeletal samples representing the range of morphological variation in North America in the last two millennia of the Holocene. These are also compared with a global sample. Results indicate that early Holocene males have variable postcranial morphologies, but all share the common trait of wide bodies. This trait, which is retained in more recent indigenous North American groups, is associated with adaptations to cold climates. Peoples from the Americas exhibit wider bodies than other populations sampled globally. This pattern suggests the common ancestral population of all of these indigenous American groups had reduced morphological variation in this trait. Furthermore, this provides support for a single, possibly high latitude location for the genetic isolation of ancestors of the human colonizers of the Americas. Copyright © 2012 Wiley Periodicals, Inc.

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes.

PubMed

Albrechtsen, A; Grarup, N; Li, Y; Sparsø, T; Tian, G; Cao, H; Jiang, T; Kim, S Y; Korneliussen, T; Li, Q; Nie, C; Wu, R; Skotte, L; Morris, A P; Ladenvall, C; Cauchi, S; Stančáková, A; Andersen, G; Astrup, A; Banasik, K; Bennett, A J; Bolund, L; Charpentier, G; Chen, Y; Dekker, J M; Doney, A S F; Dorkhan, M; Forsen, T; Frayling, T M; Groves, C J; Gui, Y; Hallmans, G; Hattersley, A T; He, K; Hitman, G A; Holmkvist, J; Huang, S; Jiang, H; Jin, X; Justesen, J M; Kristiansen, K; Kuusisto, J; Lajer, M; Lantieri, O; Li, W; Liang, H; Liao, Q; Liu, X; Ma, T; Ma, X; Manijak, M P; Marre, M; Mokrosiński, J; Morris, A D; Mu, B; Nielsen, A A; Nijpels, G; Nilsson, P; Palmer, C N A; Rayner, N W; Renström, F; Ribel-Madsen, R; Robertson, N; Rolandsson, O; Rossing, P; Schwartz, T W; Slagboom, P E; Sterner, M; Tang, M; Tarnow, L; Tuomi, T; van't Riet, E; van Leeuwen, N; Varga, T V; Vestmar, M A; Walker, M; Wang, B; Wang, Y; Wu, H; Xi, F; Yengo, L; Yu, C; Zhang, X; Zhang, J; Zhang, Q; Zhang, W; Zheng, H; Zhou, Y; Altshuler, D; 't Hart, L M; Franks, P W; Balkau, B; Froguel, P; McCarthy, M I; Laakso, M; Groop, L; Christensen, C; Brandslund, I; Lauritzen, T; Witte, D R; Linneberg, A; Jørgensen, T; Hansen, T; Wang, J; Nielsen, R; Pedersen, O

2013-02-01

Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) >1% with common metabolic phenotypes. The study comprised three stages. We performed medium-depth (8×) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI >27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. Exome sequencing identified 70,182 polymorphisms with MAF >1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 × 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 × 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 × 10(-10)). We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.

Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits

PubMed Central

Petersen, Ann-Kristin; Zeilinger, Sonja; Kastenmüller, Gabi; Römisch-Margl, Werner; Brugger, Markus; Peters, Annette; Meisinger, Christine; Strauch, Konstantin; Hengstenberg, Christian; Pagel, Philipp; Huber, Fritz; Mohney, Robert P.; Grallert, Harald; Illig, Thomas; Adamski, Jerzy; Waldenberger, Melanie; Gieger, Christian; Suhre, Karsten

2014-01-01

Previously, we reported strong influences of genetic variants on metabolic phenotypes, some of them with clinical relevance. Here, we hypothesize that DNA methylation may have an important and potentially independent effect on human metabolism. To test this hypothesis, we conducted what is to the best of our knowledge the first epigenome-wide association study (EWAS) between DNA methylation and metabolic traits (metabotypes) in human blood. We assess 649 blood metabolic traits from 1814 participants of the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) population study for association with methylation of 457 004 CpG sites, determined on the Infinium HumanMethylation450 BeadChip platform. Using the EWAS approach, we identified two types of methylome–metabotype associations. One type is driven by an underlying genetic effect; the other type is independent of genetic variation and potentially driven by common environmental and life-style-dependent factors. We report eight CpG loci at genome-wide significance that have a genetic variant as confounder (P = 3.9 × 10−20 to 2.0 × 10−108, r2 = 0.036 to 0.221). Seven loci display CpG site-specific associations to metabotypes, but do not exhibit any underlying genetic signals (P = 9.2 × 10−14 to 2.7 × 10−27, r2 = 0.008 to 0.107). We further identify several groups of CpG loci that associate with a same metabotype, such as 4-vinylphenol sulfate and 4-androsten-3-beta,17-beta-diol disulfate. In these cases, the association between CpG-methylation and metabotype is likely the result of a common external environmental factor, including smoking. Our study shows that analysis of EWAS with large numbers of metabolic traits in large population cohorts are, in principle, feasible. Taken together, our data suggest that DNA methylation plays an important role in regulating human metabolism. PMID:24014485

3 CFR 8655 - Proclamation 8655 of April 14, 2011. Education and Sharing Day, U.S.A., 2011

Code of Federal Regulations, 2012 CFR

2012-01-01

... generations the values that will help them write the next proud chapter of the American story—a dedication to... extraordinary challenge and our dedication to our common humanity. We must nurture these traits in our children...

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy.

PubMed

Byars, Sean G; Huang, Qin Qin; Gray, Lesley-Ann; Bakshi, Andrew; Ripatti, Samuli; Abraham, Gad; Stearns, Stephen C; Inouye, Michael

2017-06-01

Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.

Genetic and environmental influences on female sexual orientation, childhood gender typicality and adult gender identity.

PubMed

Burri, Andrea; Cherkas, Lynn; Spector, Timothy; Rahman, Qazi

2011-01-01

Human sexual orientation is influenced by genetic and non-shared environmental factors as are two important psychological correlates--childhood gender typicality (CGT) and adult gender identity (AGI). However, researchers have been unable to resolve the genetic and non-genetic components that contribute to the covariation between these traits, particularly in women. Here we performed a multivariate genetic analysis in a large sample of British female twins (N = 4,426) who completed a questionnaire assessing sexual attraction, CGT and AGI. Univariate genetic models indicated modest genetic influences on sexual attraction (25%), AGI (11%) and CGT (31%). For the multivariate analyses, a common pathway model best fitted the data. This indicated that a single latent variable influenced by a genetic component and common non-shared environmental component explained the association between the three traits but there was substantial measurement error. These findings highlight common developmental factors affecting differences in sexual orientation.

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. CNVs represent an important type of genetic variation among cattle breeds and even individual animals; however, only low-resolution maps of cattle CNVs currently exis...

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

PubMed

Taylor, D Leland; Knowles, David A; Scott, Laura J; Ramirez, Andrea H; Casale, Francesco Paolo; Wolford, Brooke N; Guan, Li; Varshney, Arushi; Albanus, Ricardo D'Oliveira; Parker, Stephen C J; Narisu, Narisu; Chines, Peter S; Erdos, Michael R; Welch, Ryan P; Kinnunen, Leena; Saramies, Jouko; Sundvall, Jouko; Lakka, Timo A; Laakso, Markku; Tuomilehto, Jaakko; Koistinen, Heikki A; Stegle, Oliver; Boehnke, Michael; Birney, Ewan; Collins, Francis S

2018-01-01

From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)-genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.

A Thomistic appraisal of human enhancement technologies.

PubMed

Eberl, Jason T

2014-08-01

Debate concerning human enhancement often revolves around the question of whether there is a common "nature" that all human beings share and which is unwarrantedly violated by enhancing one's capabilities beyond the "species-typical" norm. I explicate Thomas Aquinas's influential theory of human nature, noting certain key traits commonly shared among human beings that define each as a "person" who possesses inviolable moral status. Understanding the specific qualities that define the nature of human persons, which includes self-conscious awareness, capacity for intellective thought, and volitional autonomy, informs the ethical assessment of various forms of enhancement. Some forms of cognitive and physical enhancement may be desirable from the perspective of what constitutes the "flourishing" of human persons in our fundamental nature; while other forms of enhancement, such as emotive or so-called "moral" enhancement, run the risk of detracting from human flourishing when evaluated from the virtue-theoretic perspective Aquinas promotes.

Ontogenetic study of the skull in modern humans and the common chimpanzees: neotenic hypothesis reconsidered with a tridimensional Procrustes analysis.

PubMed

Penin, Xavier; Berge, Christine; Baylac, Michel

2002-05-01

Heterochronic studies compare ontogenetic trajectories of an organ in different species: here, the skulls of common chimpanzees and modern humans. A growth trajectory requires three parameters: size, shape, and ontogenetic age. One of the great advantages of the Procrustes method is the precise definition of size and shape for whole organs such as the skull. The estimated ontogenetic age (dental stages) is added to the plot to give a graphical representation to compare growth trajectories. We used the skulls of 41 Homo sapiens and 50 Pan troglodytes at various stages of growth. The Procrustes superimposition of all specimens was completed by statistical procedures (principal component analysis, multivariate regression, and discriminant function) to calculate separately size-related shape changes (allometry common to chimpanzees and humans), and interspecific shape differences (discriminant function). The results confirm the neotenic theory of the human skull (sensu Gould [1977] Ontogeny and Phylogeny, Cambridge: Harvard University Press; Alberch et al. [1979] Paleobiology 5:296-317), but modify it slightly. Human growth is clearly retarded in terms of both the magnitude of changes (size-shape covariation) and shape alone (size-shape dissociation) with respect to the chimpanzees. At the end of growth, the adult skull in humans reaches an allometric shape (size-related shape) which is equivalent to that of juvenile chimpanzees with no permanent teeth, and a size which is equivalent to that of adult chimpanzees. Our results show that human neoteny involves not only shape retardation (paedomorphosis), but also changes in relative growth velocity. Before the eruption of the first molar, human growth is accelerated, and then strongly decelerated, relative to the growth of the chimpanzee as a reference. This entails a complex process, which explains why these species reach the same overall (i.e., brain + face) size in adult stage. The neotenic traits seem to concern primarily the function of encephalization, but less so other parts of the skull. Our results, based on the discriminant function, reveal that additional structural traits (corresponding to the nonallometric part of the shape which is specific to humans) are rather situated in the other part of the skull. They mainly concern the equilibrium of the head related to bipedalism, and the respiratory and masticatory functions. Thus, the reduced prognathism, the flexed cranial base (forward position of the foramen magnum which is brought closer to the palate), the reduced anterior portion of the face, the reduced glabella, and the prominent nose mainly correspond to functional innovations which have nothing to do with a neotenic process in human evolution. The statistical analysis used here gives us the possibility to point out that some traits, which have been classically described as paedomorphic because they superficially resemble juvenile traits, are in reality independent of growth. Copyright 2002 Wiley-Liss, Inc.

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

PubMed Central

Yang, Jian; Bakshi, Andrew; Zhu, Zhihong; Hemani, Gibran; Vinkhuyzen, Anna A.E.; Lee, Sang Hong; Robinson, Matthew R.; Perry, John R.B.; Nolte, Ilja M.; van Vliet-Ostaptchouk, Jana V.; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hamsten, Anders; Magnusson, Patrik K.E.; Pedersen, Nancy L.; Ingelsson, Erik; Soranzo, Nicole; Keller, Matthew C.; Wray, Naomi R.; Goddard, Michael E.; Visscher, Peter M.

2015-01-01

We propose a method (GREML-LDMS) to estimate heritability for human complex traits in unrelated individuals using whole-genome sequencing (WGS) data. We demonstrate using simulations based on WGS data that ~97% and ~68% of variation at common and rare variants, respectively, can be captured by imputation. Using the GREML-LDMS method, we estimate from 44,126 unrelated individuals that all ~17M imputed variants explain 56% (s.e. = 2.3%) of variance for height and 27% (s.e. = 2.5%) for body mass index (BMI), and find evidence that height- and BMI-associated variants have been under natural selection. Considering imperfect tagging of imputation and potential overestimation of heritability from previous family-based studies, heritability is likely to be 60–70% for height and 30–40% for BMI. Therefore, missing heritability is small for both traits. For further gene discovery of complex traits, a design with SNP arrays followed by imputation is more cost-effective than WGS at current prices. PMID:26323059

Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation.

PubMed

Xia, Charley; Amador, Carmen; Huffman, Jennifer; Trochet, Holly; Campbell, Archie; Porteous, David; Hastie, Nicholas D; Hayward, Caroline; Vitart, Veronique; Navarro, Pau; Haley, Chris S

2016-02-01

Genome-wide association studies have successfully identified thousands of loci for a range of human complex traits and diseases. The proportion of phenotypic variance explained by significant associations is, however, limited. Given the same dense SNP panels, mixed model analyses capture a greater proportion of phenotypic variance than single SNP analyses but the total is generally still less than the genetic variance estimated from pedigree studies. Combining information from pedigree relationships and SNPs, we examined 16 complex anthropometric and cardiometabolic traits in a Scottish family-based cohort comprising up to 20,000 individuals genotyped for ~520,000 common autosomal SNPs. The inclusion of related individuals provides the opportunity to also estimate the genetic variance associated with pedigree as well as the effects of common family environment. Trait variation was partitioned into SNP-associated and pedigree-associated genetic variation, shared nuclear family environment, shared couple (partner) environment and shared full-sibling environment. Results demonstrate that trait heritabilities vary widely but, on average across traits, SNP-associated and pedigree-associated genetic effects each explain around half the genetic variance. For most traits the recently-shared environment of couples is also significant, accounting for ~11% of the phenotypic variance on average. On the other hand, the environment shared largely in the past by members of a nuclear family or by full-siblings, has a more limited impact. Our findings point to appropriate models to use in future studies as pedigree-associated genetic effects and couple environmental effects have seldom been taken into account in genotype-based analyses. Appropriate description of the trait variation could help understand causes of intra-individual variation and in the detection of contributing loci and environmental factors.

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. Prior studies in cattle have produced low-resolution CNV maps. We constructed a draft, high-resolution map of cattle CNVs based on whole genome sequencing data from 7...

Genome-wide association study for nutritional composition traits in cooked common bean seeds

USDA-ARS?s Scientific Manuscript database

Seed nutrients in legumes are important for human health, particularly in developing countries with heavy reliance on plant-based diets, and amongst vegetarians in developed nations. Here we report on our efforts to uncover the genetic basis underlying the phenotypic variation for protein, zinc, cal...

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama

PubMed Central

Matterson, Kenan O.; Freeman, Christopher J.; Archer, Stephanie K.; Thacker, Robert W.

2015-01-01

Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyll a concentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities. PMID:26587347

Directional dominance on stature and cognition in diverse human populations.

PubMed

Joshi, Peter K; Esko, Tonu; Mattsson, Hannele; Eklund, Niina; Gandin, Ilaria; Nutile, Teresa; Jackson, Anne U; Schurmann, Claudia; Smith, Albert V; Zhang, Weihua; Okada, Yukinori; Stančáková, Alena; Faul, Jessica D; Zhao, Wei; Bartz, Traci M; Concas, Maria Pina; Franceschini, Nora; Enroth, Stefan; Vitart, Veronique; Trompet, Stella; Guo, Xiuqing; Chasman, Daniel I; O'Connel, Jeffery R; Corre, Tanguy; Nongmaithem, Suraj S; Chen, Yuning; Mangino, Massimo; Ruggiero, Daniela; Traglia, Michela; Farmaki, Aliki-Eleni; Kacprowski, Tim; Bjonnes, Andrew; van der Spek, Ashley; Wu, Ying; Giri, Anil K; Yanek, Lisa R; Wang, Lihua; Hofer, Edith; Rietveld, Cornelius A; McLeod, Olga; Cornelis, Marilyn C; Pattaro, Cristian; Verweij, Niek; Baumbach, Clemens; Abdellaoui, Abdel; Warren, Helen R; Vuckovic, Dragana; Mei, Hao; Bouchard, Claude; Perry, John R B; Cappellani, Stefania; Mirza, Saira S; Benton, Miles C; Broeckel, Ulrich; Medland, Sarah E; Lind, Penelope A; Malerba, Giovanni; Drong, Alexander; Yengo, Loic; Bielak, Lawrence F; Zhi, Degui; van der Most, Peter J; Shriner, Daniel; Mägi, Reedik; Hemani, Gibran; Karaderi, Tugce; Wang, Zhaoming; Liu, Tian; Demuth, Ilja; Zhao, Jing Hua; Meng, Weihua; Lataniotis, Lazaros; van der Laan, Sander W; Bradfield, Jonathan P; Wood, Andrew R; Bonnefond, Amelie; Ahluwalia, Tarunveer S; Hall, Leanne M; Salvi, Erika; Yazar, Seyhan; Carstensen, Lisbeth; de Haan, Hugoline G; Abney, Mark; Afzal, Uzma; Allison, Matthew A; Amin, Najaf; Asselbergs, Folkert W; Bakker, Stephan J L; Barr, R Graham; Baumeister, Sebastian E; Benjamin, Daniel J; Bergmann, Sven; Boerwinkle, Eric; Bottinger, Erwin P; Campbell, Archie; Chakravarti, Aravinda; Chan, Yingleong; Chanock, Stephen J; Chen, Constance; Chen, Y-D Ida; Collins, Francis S; Connell, John; Correa, Adolfo; Cupples, L Adrienne; Smith, George Davey; Davies, Gail; Dörr, Marcus; Ehret, Georg; Ellis, Stephen B; Feenstra, Bjarke; Feitosa, Mary F; Ford, Ian; Fox, Caroline S; Frayling, Timothy M; Friedrich, Nele; Geller, Frank; Scotland, Generation; Gillham-Nasenya, Irina; Gottesman, Omri; Graff, Misa; Grodstein, Francine; Gu, Charles; Haley, Chris; Hammond, Christopher J; Harris, Sarah E; Harris, Tamara B; Hastie, Nicholas D; Heard-Costa, Nancy L; Heikkilä, Kauko; Hocking, Lynne J; Homuth, Georg; Hottenga, Jouke-Jan; Huang, Jinyan; Huffman, Jennifer E; Hysi, Pirro G; Ikram, M Arfan; Ingelsson, Erik; Joensuu, Anni; Johansson, Åsa; Jousilahti, Pekka; Jukema, J Wouter; Kähönen, Mika; Kamatani, Yoichiro; Kanoni, Stavroula; Kerr, Shona M; Khan, Nazir M; Koellinger, Philipp; Koistinen, Heikki A; Kooner, Manraj K; Kubo, Michiaki; Kuusisto, Johanna; Lahti, Jari; Launer, Lenore J; Lea, Rodney A; Lehne, Benjamin; Lehtimäki, Terho; Liewald, David C M; Lind, Lars; Loh, Marie; Lokki, Marja-Liisa; London, Stephanie J; Loomis, Stephanie J; Loukola, Anu; Lu, Yingchang; Lumley, Thomas; Lundqvist, Annamari; Männistö, Satu; Marques-Vidal, Pedro; Masciullo, Corrado; Matchan, Angela; Mathias, Rasika A; Matsuda, Koichi; Meigs, James B; Meisinger, Christa; Meitinger, Thomas; Menni, Cristina; Mentch, Frank D; Mihailov, Evelin; Milani, Lili; Montasser, May E; Montgomery, Grant W; Morrison, Alanna; Myers, Richard H; Nadukuru, Rajiv; Navarro, Pau; Nelis, Mari; Nieminen, Markku S; Nolte, Ilja M; O'Connor, George T; Ogunniyi, Adesola; Padmanabhan, Sandosh; Palmas, Walter R; Pankow, James S; Patarcic, Inga; Pavani, Francesca; Peyser, Patricia A; Pietilainen, Kirsi; Poulter, Neil; Prokopenko, Inga; Ralhan, Sarju; Redmond, Paul; Rich, Stephen S; Rissanen, Harri; Robino, Antonietta; Rose, Lynda M; Rose, Richard; Sala, Cinzia; Salako, Babatunde; Salomaa, Veikko; Sarin, Antti-Pekka; Saxena, Richa; Schmidt, Helena; Scott, Laura J; Scott, William R; Sennblad, Bengt; Seshadri, Sudha; Sever, Peter; Shrestha, Smeeta; Smith, Blair H; Smith, Jennifer A; Soranzo, Nicole; Sotoodehnia, Nona; Southam, Lorraine; Stanton, Alice V; Stathopoulou, Maria G; Strauch, Konstantin; Strawbridge, Rona J; Suderman, Matthew J; Tandon, Nikhil; Tang, Sian-Tsun; Taylor, Kent D; Tayo, Bamidele O; Töglhofer, Anna Maria; Tomaszewski, Maciej; Tšernikova, Natalia; Tuomilehto, Jaakko; Uitterlinden, Andre G; Vaidya, Dhananjay; van Hylckama Vlieg, Astrid; van Setten, Jessica; Vasankari, Tuula; Vedantam, Sailaja; Vlachopoulou, Efthymia; Vozzi, Diego; Vuoksimaa, Eero; Waldenberger, Melanie; Ware, Erin B; Wentworth-Shields, William; Whitfield, John B; Wild, Sarah; Willemsen, Gonneke; Yajnik, Chittaranjan S; Yao, Jie; Zaza, Gianluigi; Zhu, Xiaofeng; Project, The BioBank Japan; Salem, Rany M; Melbye, Mads; Bisgaard, Hans; Samani, Nilesh J; Cusi, Daniele; Mackey, David A; Cooper, Richard S; Froguel, Philippe; Pasterkamp, Gerard; Grant, Struan F A; Hakonarson, Hakon; Ferrucci, Luigi; Scott, Robert A; Morris, Andrew D; Palmer, Colin N A; Dedoussis, George; Deloukas, Panos; Bertram, Lars; Lindenberger, Ulman; Berndt, Sonja I; Lindgren, Cecilia M; Timpson, Nicholas J; Tönjes, Anke; Munroe, Patricia B; Sørensen, Thorkild I A; Rotimi, Charles N; Arnett, Donna K; Oldehinkel, Albertine J; Kardia, Sharon L R; Balkau, Beverley; Gambaro, Giovanni; Morris, Andrew P; Eriksson, Johan G; Wright, Margie J; Martin, Nicholas G; Hunt, Steven C; Starr, John M; Deary, Ian J; Griffiths, Lyn R; Tiemeier, Henning; Pirastu, Nicola; Kaprio, Jaakko; Wareham, Nicholas J; Pérusse, Louis; Wilson, James G; Girotto, Giorgia; Caulfield, Mark J; Raitakari, Olli; Boomsma, Dorret I; Gieger, Christian; van der Harst, Pim; Hicks, Andrew A; Kraft, Peter; Sinisalo, Juha; Knekt, Paul; Johannesson, Magnus; Magnusson, Patrik K E; Hamsten, Anders; Schmidt, Reinhold; Borecki, Ingrid B; Vartiainen, Erkki; Becker, Diane M; Bharadwaj, Dwaipayan; Mohlke, Karen L; Boehnke, Michael; van Duijn, Cornelia M; Sanghera, Dharambir K; Teumer, Alexander; Zeggini, Eleftheria; Metspalu, Andres; Gasparini, Paolo; Ulivi, Sheila; Ober, Carole; Toniolo, Daniela; Rudan, Igor; Porteous, David J; Ciullo, Marina; Spector, Tim D; Hayward, Caroline; Dupuis, Josée; Loos, Ruth J F; Wright, Alan F; Chandak, Giriraj R; Vollenweider, Peter; Shuldiner, Alan; Ridker, Paul M; Rotter, Jerome I; Sattar, Naveed; Gyllensten, Ulf; North, Kari E; Pirastu, Mario; Psaty, Bruce M; Weir, David R; Laakso, Markku; Gudnason, Vilmundur; Takahashi, Atsushi; Chambers, John C; Kooner, Jaspal S; Strachan, David P; Campbell, Harry; Hirschhorn, Joel N; Perola, Markus; Polašek, Ozren; Wilson, James F

2015-07-23

Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

Directional dominance on stature and cognition in diverse human populations

PubMed Central

Mattsson, Hannele; Eklund, Niina; Gandin, Ilaria; Nutile, Teresa; Jackson, Anne U.; Schurmann, Claudia; Smith, Albert V.; Zhang, Weihua; Okada, Yukinori; Stančáková, Alena; Faul, Jessica D.; Zhao, Wei; Bartz, Traci M.; Concas, Maria Pina; Franceschini, Nora; Enroth, Stefan; Vitart, Veronique; Trompet, Stella; Guo, Xiuqing; Chasman, Daniel I.; O’Connel, Jeffery R.; Corre, Tanguy; Nongmaithem, Suraj S.; Chen, Yuning; Mangino, Massimo; Ruggiero, Daniela; Traglia, Michela; Farmaki, Aliki-Eleni; Kacprowski, Tim; Bjonnes, Andrew; van der Spek, Ashley; Wu, Ying; Giri, Anil K.; Yanek, Lisa R.; Wang, Lihua; Hofer, Edith; Rietveld, Cornelius A.; McLeod, Olga; Cornelis, Marilyn C.; Pattaro, Cristian; Verweij, Niek; Baumbach, Clemens; Abdellaoui, Abdel; Warren, Helen R.; Vuckovic, Dragana; Mei, Hao; Bouchard, Claude; Perry, John R.B.; Cappellani, Stefania; Mirza, Saira S.; Benton, Miles C.; Broeckel, Ulrich; Medland, Sarah E.; Lind, Penelope A.; Malerba, Giovanni; Drong, Alexander; Yengo, Loic; Bielak, Lawrence F.; Zhi, Degui; van der Most, Peter J.; Shriner, Daniel; Mägi, Reedik; Hemani, Gibran; Karaderi, Tugce; Wang, Zhaoming; Liu, Tian; Demuth, Ilja; Zhao, Jing Hua; Meng, Weihua; Lataniotis, Lazaros; van der Laan, Sander W.; Bradfield, Jonathan P.; Wood, Andrew R.; Bonnefond, Amelie; Ahluwalia, Tarunveer S.; Hall, Leanne M.; Salvi, Erika; Yazar, Seyhan; Carstensen, Lisbeth; de Haan, Hugoline G.; Abney, Mark; Afzal, Uzma; Allison, Matthew A.; Amin, Najaf; Asselbergs, Folkert W.; Bakker, Stephan J.L.; Barr, R. Graham; Baumeister, Sebastian E.; Benjamin, Daniel J.; Bergmann, Sven; Boerwinkle, Eric; Bottinger, Erwin P.; Campbell, Archie; Chakravarti, Aravinda; Chan, Yingleong; Chanock, Stephen J.; Chen, Constance; Chen, Y.-D. Ida; Collins, Francis S.; Connell, John; Correa, Adolfo; Cupples, L. Adrienne; Smith, George Davey; Davies, Gail; Dörr, Marcus; Ehret, Georg; Ellis, Stephen B.; Feenstra, Bjarke; Feitosa, Mary F.; Ford, Ian; Fox, Caroline S.; Frayling, Timothy M.; Friedrich, Nele; Geller, Frank; Scotland, Generation; Gillham-Nasenya, Irina; Gottesman, Omri; Graff, Misa; Grodstein, Francine; Gu, Charles; Haley, Chris; Hammond, Christopher J.; Harris, Sarah E.; Harris, Tamara B.; Hastie, Nicholas D.; Heard-Costa, Nancy L.; Heikkilä, Kauko; Hocking, Lynne J.; Homuth, Georg; Hottenga, Jouke-Jan; Huang, Jinyan; Huffman, Jennifer E.; Hysi, Pirro G.; Ikram, M. Arfan; Ingelsson, Erik; Joensuu, Anni; Johansson, Åsa; Jousilahti, Pekka; Jukema, J. Wouter; Kähönen, Mika; Kamatani, Yoichiro; Kanoni, Stavroula; Kerr, Shona M.; Khan, Nazir M.; Koellinger, Philipp; Koistinen, Heikki A.; Kooner, Manraj K.; Kubo, Michiaki; Kuusisto, Johanna; Lahti, Jari; Launer, Lenore J.; Lea, Rodney A.; Lehne, Benjamin; Lehtimäki, Terho; Liewald, David C.M.; Lind, Lars; Loh, Marie; Lokki, Marja-Liisa; London, Stephanie J.; Loomis, Stephanie J.; Loukola, Anu; Lu, Yingchang; Lumley, Thomas; Lundqvist, Annamari; Männistö, Satu; Marques-Vidal, Pedro; Masciullo, Corrado; Matchan, Angela; Mathias, Rasika A.; Matsuda, Koichi; Meigs, James B.; Meisinger, Christa; Meitinger, Thomas; Menni, Cristina; Mentch, Frank D.; Mihailov, Evelin; Milani, Lili; Montasser, May E.; Montgomery, Grant W.; Morrison, Alanna; Myers, Richard H.; Nadukuru, Rajiv; Navarro, Pau; Nelis, Mari; Nieminen, Markku S.; Nolte, Ilja M.; O’Connor, George T.; Ogunniyi, Adesola; Padmanabhan, Sandosh; Palmas, Walter R.; Pankow, James S.; Patarcic, Inga; Pavani, Francesca; Peyser, Patricia A.; Pietilainen, Kirsi; Poulter, Neil; Prokopenko, Inga; Ralhan, Sarju; Redmond, Paul; Rich, Stephen S.; Rissanen, Harri; Robino, Antonietta; Rose, Lynda M.; Rose, Richard; Sala, Cinzia; Salako, Babatunde; Salomaa, Veikko; Sarin, Antti-Pekka; Saxena, Richa; Schmidt, Helena; Scott, Laura J.; Scott, William R.; Sennblad, Bengt; Seshadri, Sudha; Sever, Peter; Shrestha, Smeeta; Smith, Blair H.; Smith, Jennifer A.; Soranzo, Nicole; Sotoodehnia, Nona; Southam, Lorraine; Stanton, Alice V.; Stathopoulou, Maria G.; Strauch, Konstantin; Strawbridge, Rona J.; Suderman, Matthew J.; Tandon, Nikhil; Tang, Sian-Tsun; Taylor, Kent D.; Tayo, Bamidele O.; Töglhofer, Anna Maria; Tomaszewski, Maciej; Tšernikova, Natalia; Tuomilehto, Jaakko; Uitterlinden, Andre G.; Vaidya, Dhananjay; van Hylckama Vlieg, Astrid; van Setten, Jessica; Vasankari, Tuula; Vedantam, Sailaja; Vlachopoulou, Efthymia; Vozzi, Diego; Vuoksimaa, Eero; Waldenberger, Melanie; Ware, Erin B.; Wentworth-Shields, William; Whitfield, John B.; Wild, Sarah; Willemsen, Gonneke; Yajnik, Chittaranjan S.; Yao, Jie; Zaza, Gianluigi; Zhu, Xiaofeng; Project, The BioBank Japan; Salem, Rany M.; Melbye, Mads; Bisgaard, Hans; Samani, Nilesh J.; Cusi, Daniele; Mackey, David A.; Cooper, Richard S.; Froguel, Philippe; Pasterkamp, Gerard; Grant, Struan F.A.; Hakonarson, Hakon; Ferrucci, Luigi; Scott, Robert A.; Morris, Andrew D.; Palmer, Colin N.A.; Dedoussis, George; Deloukas, Panos; Bertram, Lars; Lindenberger, Ulman; Berndt, Sonja I.; Lindgren, Cecilia M.; Timpson, Nicholas J.; Tönjes, Anke; Munroe, Patricia B.; Sørensen, Thorkild I.A.; Rotimi, Charles N.; Arnett, Donna K.; Oldehinkel, Albertine J.; Kardia, Sharon L.R.; Balkau, Beverley; Gambaro, Giovanni; Morris, Andrew P.; Eriksson, Johan G.; Wright, Margie J.; Martin, Nicholas G.; Hunt, Steven C.; Starr, John M.; Deary, Ian J.; Griffiths, Lyn R.; Tiemeier, Henning; Pirastu, Nicola; Kaprio, Jaakko; Wareham, Nicholas J.; Pérusse, Louis; Wilson, James G.; Girotto, Giorgia; Caulfield, Mark J.; Raitakari, Olli; Boomsma, Dorret I.; Gieger, Christian; van der Harst, Pim; Hicks, Andrew A.; Kraft, Peter; Sinisalo, Juha; Knekt, Paul; Johannesson, Magnus; Magnusson, Patrik K.E.; Hamsten, Anders; Schmidt, Reinhold; Borecki, Ingrid B.; Vartiainen, Erkki; Becker, Diane M.; Bharadwaj, Dwaipayan; Mohlke, Karen L.; Boehnke, Michael; van Duijn, Cornelia M.; Sanghera, Dharambir K.; Teumer, Alexander; Zeggini, Eleftheria; Metspalu, Andres; Gasparini, Paolo; Ulivi, Sheila; Ober, Carole; Toniolo, Daniela; Rudan, Igor; Porteous, David J.; Ciullo, Marina; Spector, Tim D.; Hayward, Caroline; Dupuis, Josée; Loos, Ruth J.F.; Wright, Alan F.; Chandak, Giriraj R.; Vollenweider, Peter; Shuldiner, Alan; Ridker, Paul M.; Rotter, Jerome I.; Sattar, Naveed; Gyllensten, Ulf; North, Kari E.; Pirastu, Mario; Psaty, Bruce M.; Weir, David R.; Laakso, Markku; Gudnason, Vilmundur; Takahashi, Atsushi; Chambers, John C.; Kooner, Jaspal S.; Strachan, David P.; Campbell, Harry; Hirschhorn, Joel N.; Perola, Markus

2015-01-01

Homozygosity has long been associated with rare, often devastating, Mendelian disorders1 and Darwin was one of the first to recognise that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity, ROH), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3,4. Here we use ROH to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts and find statistically significant associations between summed runs of homozygosity (SROH) and four complex traits: height, forced expiratory lung volume in 1 second (FEV1), general cognitive ability (g) and educational attainment (nominal p<1 × 10−300, 2.1 × 10−6, 2.5 × 10−10, 1.8 × 10−10). In each case increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing convincing evidence for the first time that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5,6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein (LDL) cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been. PMID:26131930

Behavioural Susceptibility Theory: Professor Jane Wardle and the Role of Appetite in Genetic Risk of Obesity.

PubMed

Llewellyn, Clare H; Fildes, Alison

2017-03-01

There is considerable variability in human body weight, despite the ubiquity of the 'obesogenic' environment. Human body weight has a strong genetic basis and it has been hypothesised that genetic susceptibility to the environment explains variation in human body weight, with differences in appetite being implicated as the mediating mechanism; so-called 'behavioural susceptibility theory' (BST), first described by Professor Jane Wardle. This review summarises the evidence for the role of appetite as a mediator of genetic risk of obesity. Variation in appetitive traits is observable from infancy, drives early weight gain and is highly heritable in infancy and childhood. Obesity-related common genetic variants identified through genome-wide association studies show associations with appetitive traits, and appetite mediates part of the observed association between genetic risk and adiposity. Obesity results from an interaction between genetic susceptibility to overeating and exposure to an 'obesogenic' food environment.

A GWA study reveals genetic loci for body conformation traits in Chinese Laiwu pigs and its implications for human BMI.

PubMed

Zhou, Lisheng; Ji, Jiuxiu; Peng, Song; Zhang, Zhen; Fang, Shaoming; Li, Lin; Zhu, Yaling; Huang, Lusheng; Chen, Congying; Ma, Junwu

2016-12-01

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10 -5 ) and 88 SNPs had suggestive (P < 10 -4 ) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.

Meta-analysis of sex-specific genome-wide association studies.

PubMed

Magi, Reedik; Lindgren, Cecilia M; Morris, Andrew P

2010-12-01

Despite the success of genome-wide association studies, much of the genetic contribution to complex human traits is still unexplained. One potential source of genetic variation that may contribute to this "missing heritability" is that which differs in magnitude and/or direction between males and females, which could result from sexual dimorphism in gene expression. Such sex-differentiated effects are common in model organisms, and are becoming increasingly evident in human complex traits through large-scale male- and female-specific meta-analyses. In this article, we review the methodology for meta-analysis of sex-specific genome-wide association studies, and propose a sex-differentiated test of association with quantitative or dichotomous traits, which allows for heterogeneity of allelic effects between males and females. We perform detailed simulations to compare the power of the proposed sex-differentiated meta-analysis with the more traditional "sex-combined" approach, which is ambivalent to gender. The results of this study highlight only a small loss in power for the sex-differentiated meta-analysis when the allelic effects of the causal variant are the same in males and females. However, over a range of models of heterogeneity in allelic effects between genders, our sex-differentiated meta-analysis strategy offers substantial gains in power, and thus has the potential to discover novel loci contributing effects to complex human traits with existing genome-wide association data. © 2010 Wiley-Liss, Inc.

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

PubMed Central

Byars, Sean G.; Gray, Lesley-Ann; Ripatti, Samuli; Stearns, Stephen C.; Inouye, Michael

2017-01-01

Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD. PMID:28640878

All about Mammals. Animal Life for Children. [Videotape].

ERIC Educational Resources Information Center

2000

In this videotape, students learn more about the characteristics of common warm-blooded mammals and what makes them different from other animals. Children also find out how humans are more advanced in structure than other mammals, but how they still share the same basic traits. This videotape correlates to the following National Science Education…

Identification of quantitative trait loci associated with seed iron in the legumes Lotus japonicus and Medicago truncatula

USDA-ARS?s Scientific Manuscript database

Iron deficiency is one of the leading micronuntrient deficiencies in humans, and increasing the amount of bioavailable iron in commonly consumed plant foods has been proposed as a means to ameliorate this deficiency. This approach seems especially beneficial in developing countries where plant food...

Genetic Factors Influence Serological Measures of Common Infections

PubMed Central

Rubicz, Rohina; Leach, Charles T.; Kraig, Ellen; Dhurandhar, Nikhil V.; Duggirala, Ravindranath; Blangero, John; Yolken, Robert; Göring, Harald H.H.

2011-01-01

Background/Aims Antibodies against infectious pathogens provide information on past or present exposure to infectious agents. While host genetic factors are known to affect the immune response, the influence of genetic factors on antibody levels to common infectious agents is largely unknown. Here we test whether antibody levels for 13 common infections are significantly heritable. Methods IgG antibodies to Chlamydophila pneumoniae, Helicobacter pylori, Toxoplasma gondii, adenovirus 36 (Ad36), hepatitis A virus, influenza A and B, cytomegalovirus, Epstein-Barr virus, herpes simplex virus (HSV)-1 and −2, human herpesvirus-6, and varicella zoster virus were determined for 1,227 Mexican Americans. Both quantitative and dichotomous (seropositive/seronegative) traits were analyzed. Influences of genetic and shared environmental factors were estimated using variance components pedigree analysis, and sharing of underlying genetic factors among traits was investigated using bivariate analyses. Results Serological phenotypes were significantly heritable for most pathogens (h2 = 0.17–0.39), except for Ad36 and HSV-2. Shared environment was significant for several pathogens (c2 = 0.10–0.32). The underlying genetic etiology appears to be largely different for most pathogens. Conclusions Our results demonstrate, for the first time for many of these pathogens, that individual genetic differences of the human host contribute substantially to antibody levels to many common infectious agents, providing impetus for the identification of underlying genetic variants, which may be of clinical importance. PMID:21996708

A subjective domestic cat (Felis silvestris catus) temperament assessment results in six independent dimensions.

PubMed

Ha, Daniel; Ha, James

2017-08-01

The study of personality or temperament is well developed in many species, but in domestic cats (Felis silvestris catus) it has lagged behind. We applied one common methodology, subjective surveys, performed by their owners, to investigate the dimensions of cat temperament. To do this, we developed an eighteen question survey covering common behavioral traits of cats, and had the evaluators rank their cat on a seven point Likert scale for trait. The responses were analyzed with factor analysis, and resulted in six significant dimensions of temperament across the 251 surveys. The six dimensions, in order of importance, are: Cat Social, Active, Human Nonsocial, Human Aggressive, and Intense. Supplemental questions were also included in all the surveys, and MANOVA analysis of these showed that outdoor usage, feeding style (ad-lib vs. meal fed), living with other cats, sex, duration of ownership, and previous history as a stray all had effects on at least one of the dimensions of cat temperament. Future work is clearly needed to fully validate our model and to further investigate our findings. Copyright © 2017 Elsevier B.V. All rights reserved.

Incremental Validity of the DSM-5 Section III Personality Disorder Traits With Respect to Psychosocial Impairment.

PubMed

Simms, Leonard J; Calabrese, William R

2016-02-01

Traditional personality disorders (PDs) are associated with significant psychosocial impairment. DSM-5 Section III includes an alternative hybrid personality disorder (PD) classification approach, with both type and trait elements, but relatively little is known about the impairments associated with Section III traits. Our objective was to study the incremental validity of Section III traits--compared to normal-range traits, traditional PD criterion counts, and common psychiatric symptomatology--in predicting psychosocial impairment. To that end, 628 current/recent psychiatric patients completed measures of PD traits, normal-range traits, traditional PD criteria, psychiatric symptomatology, and psychosocial impairments. Hierarchical regressions revealed that Section III PD traits incrementally predicted psychosocial impairment over normal-range personality traits, PD criterion counts, and common psychiatric symptomatology. In contrast, the incremental effects for normal-range traits, PD symptom counts, and common psychiatric symptomatology were substantially smaller than for PD traits. These findings have implications for PD classification and the impairment literature more generally.

Sexual dimorphism in human cranial trait scores: effects of population, age, and body size.

PubMed

Garvin, Heather M; Sholts, Sabrina B; Mosca, Laurel A

2014-06-01

Sex estimation from the skull is commonly performed by physical and forensic anthropologists using a five-trait scoring system developed by Walker. Despite the popularity of this method, validation studies evaluating its accuracy across a variety of samples are lacking. Furthermore, it remains unclear what other intrinsic or extrinsic variables are related to the expression of these traits. In this study, cranial trait scores and postcranial measurements were collected from four diverse population groups (U.S. Whites, U.S. Blacks, medieval Nubians, and Arikara Native Americans) following Walker's protocols (total n = 499). Univariate and multivariate analyses were utilized to evaluate the accuracy of these traits in sex estimation, and to test for the effects of population, age, and body size on trait expressions. Results revealed significant effects of population on all trait scores. Sample-specific correct sex classification rates ranged from 74% to 94%, with an overall accuracy of 85% for the pooled sample. Classification performance varied among the traits (best for glabella and mastoid scores and worst for nuchal scores). Furthermore, correlations between traits were weak or nonsignificant, suggesting that different factors may influence individual traits. Some traits displayed correlations with age and/or postcranial size that were significant but weak, and within-population analyses did not reveal any consistent relationships between these traits across all groups. These results indicate that neither age nor body size plays a large role in trait expression, and thus does not need to be incorporated into sex estimation methods. Copyright © 2014 Wiley Periodicals, Inc.

Genetic and Environmental Influences on Female Sexual Orientation, Childhood Gender Typicality and Adult Gender Identity

PubMed Central

Burri, Andrea; Cherkas, Lynn; Spector, Timothy; Rahman, Qazi

2011-01-01

Background Human sexual orientation is influenced by genetic and non-shared environmental factors as are two important psychological correlates – childhood gender typicality (CGT) and adult gender identity (AGI). However, researchers have been unable to resolve the genetic and non-genetic components that contribute to the covariation between these traits, particularly in women. Methodology/Principal Findings Here we performed a multivariate genetic analysis in a large sample of British female twins (N = 4,426) who completed a questionnaire assessing sexual attraction, CGT and AGI. Univariate genetic models indicated modest genetic influences on sexual attraction (25%), AGI (11%) and CGT (31%). For the multivariate analyses, a common pathway model best fitted the data. Conclusions/Significance This indicated that a single latent variable influenced by a genetic component and common non-shared environmental component explained the association between the three traits but there was substantial measurement error. These findings highlight common developmental factors affecting differences in sexual orientation. PMID:21760939

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index.

PubMed

Yang, Jian; Bakshi, Andrew; Zhu, Zhihong; Hemani, Gibran; Vinkhuyzen, Anna A E; Lee, Sang Hong; Robinson, Matthew R; Perry, John R B; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hamsten, Anders; Magnusson, Patrik K E; Pedersen, Nancy L; Ingelsson, Erik; Soranzo, Nicole; Keller, Matthew C; Wray, Naomi R; Goddard, Michael E; Visscher, Peter M

2015-10-01

We propose a method (GREML-LDMS) to estimate heritability for human complex traits in unrelated individuals using whole-genome sequencing data. We demonstrate using simulations based on whole-genome sequencing data that ∼97% and ∼68% of variation at common and rare variants, respectively, can be captured by imputation. Using the GREML-LDMS method, we estimate from 44,126 unrelated individuals that all ∼17 million imputed variants explain 56% (standard error (s.e.) = 2.3%) of variance for height and 27% (s.e. = 2.5%) of variance for body mass index (BMI), and we find evidence that height- and BMI-associated variants have been under natural selection. Considering the imperfect tagging of imputation and potential overestimation of heritability from previous family-based studies, heritability is likely to be 60-70% for height and 30-40% for BMI. Therefore, the missing heritability is small for both traits. For further discovery of genes associated with complex traits, a study design with SNP arrays followed by imputation is more cost-effective than whole-genome sequencing at current prices.

GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

PubMed

Chande, Aroon T; Wang, Lu; Rishishwar, Lavanya; Conley, Andrew B; Norris, Emily T; Valderrama-Aguirre, Augusto; Jordan, I King

2018-05-18

Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

PubMed

Ishikawa, Akira

2017-11-27

Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

Plant-animal interactions in suburban environments: implications for floral evolution.

PubMed

Irwin, Rebecca E; Warren, Paige S; Carper, Adrian L; Adler, Lynn S

2014-03-01

Plant interactions with mutualists and antagonists vary remarkably across space, and have played key roles in the ecology and evolution of flowering plants. One dominant form of spatial variation is human modification of the landscape, including urbanization and suburbanization. Our goal was to assess how suburbanization affected plant-animal interactions in Gelsemium sempervirens in the southeastern United States, including interactions with mutualists (pollination) and antagonists (nectar robbing and florivory). Based on differences in plant-animal interactions measured in multiple replicate sites, we then developed predictions for how these differences would affect patterns of natural selection, and we explored the patterns using measurements of floral and defensive traits in the field and in a common garden. We found that Gelsemium growing in suburban sites experienced more robbing and florivory as well as more heterospecific but not conspecific pollen transfer. Floral traits, particularly corolla length and width, influenced the susceptibility of plants to particular interactors. Observational data of floral traits measured in the field and in a common garden provided some supporting but also some conflicting evidence for the hypothesis that floral traits evolved in response to differences in species interactions in suburban vs. wild sites. However, the degree to which plants can respond to any one interactor may be constrained by correlations among floral morphological traits. Taken together, consideration of the broader geographic context in which organisms interact, in both suburban and wild areas, is fundamental to our understanding of the forces that shape contemporary plant-animal interactions and selection pressures in native species.

Marmosets as model species in neuroscience and evolutionary anthropology.

PubMed

Burkart, Judith M; Finkenwirth, Christa

2015-04-01

Marmosets are increasingly used as model species by both neuroscientists and evolutionary anthropologists, but with a different rationale for doing so. Whereas neuroscientists stress that marmosets share many cognitive traits with humans due to common descent, anthropologists stress those traits shared with marmosets - and callitrichid monkeys in general - due to convergent evolution, as a consequence of the cooperative breeding system that characterizes both humans and callitrichids. Similarities in socio-cognitive abilities due to convergence, rather than homology, raise the question whether these similarities also extend to the proximate regulatory mechanisms, which is particularly relevant for neuroscientific investigations. In this review, we first provide an overview of the convergent adaptations to cooperative breeding at the psychological and cognitive level in primates, which bear important implications for our understanding of human cognitive evolution. In the second part, we zoom in on two of these convergent adaptations, proactive prosociality and social learning, and compare their proximate regulation in marmosets and humans with regard to oxytocin and cognitive top down regulation. Our analysis suggests considerable similarity in these regulatory mechanisms presumably because the convergent traits emerged due to small motivational changes that define how pre-existing cognitive mechanisms are quantitatively combined. This finding reconciles the prima facie contradictory rationale for using marmosets as high priority model species in neuroscience and anthropology. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Impulsivity and behaviour problems in dogs: A Reinforcement Sensitivity Theory perspective.

PubMed

Piotti, Patrizia; Satchell, Liam Paul; Lockhart, Tom Steven

2018-06-01

Trait impulsivity is an increasingly relevant topic for human and non-human animal personality research. There are similarities in dog and human manifestations of trait impulsivity at the behavioural, genetic, and neurobiological level. We investigated a well-validated measure of dog impulsivity and responsivity (the Dog Impulsivity Assessment Scale, DIAS) and a neuropsychological theory of human trait approach and avoidance (the Reinforcement Sensitivity Theory of personality, RST). Owners reported their dogs' dispositional behaviour on the DIAS, an RST scale modified to describe dogs' behaviour, and a list of common dog behaviour problems. In a sample of 730 dogs, we observed convergence between the RST and the DIAS. There was a negative correlation between RST 'Behaviour Inhibition System' and DIAS impulsivity factor ('Behavioural Regulation'). RST 'Behavioural Approach System' correlated positively with DIAS 'Responsiveness'. The RST 'Fight-Flight-Freeze System' (FFFS) and the DIAS 'Aggression and response to novelty factor were both distinct from other factors. However, the DIAS 'Aggression and response to novelty' factor and the RST FFFS explained different aspects of dog behaviour problems. Importantly, whilst the DIAS factors indicated tendencies towards avoidant behaviours, the FFFS discriminated between active and passive avoidance. The findings suggest a partial overlapping between the DIAS and RST scales, and highlights the utility of personality models in investigating behaviour problems in dogs. Copyright © 2018 Elsevier B.V. All rights reserved.

Porcine response to a multidrug-resistant Salmonella enterica serovar I 4,[5],12:i:- outbreak isolate

USDA-ARS?s Scientific Manuscript database

Salmonella enterica serovar I 4,[5],12:i:- has emerged as a common nontyphoidal Salmonella serovar to cause human foodborne illness. An interesting trait of serovar I 4,[5],12:i:- is it only expresses the fliC gene for bacterial motility (i.e. monophasic), while most Salmonella strains alternately e...

Genetics of common forms of heart failure: challenges and potential solutions.

PubMed

Rau, Christoph D; Lusis, Aldons J; Wang, Yibin

2015-05-01

In contrast to many other human diseases, the use of genome-wide association studies (GWAS) to identify genes for heart failure (HF) has had limited success. We will discuss the underlying challenges as well as potential new approaches to understanding the genetics of common forms of HF. Recent research using intermediate phenotypes, more detailed and quantitative stratification of HF symptoms, founder populations and novel animal models has begun to allow researchers to make headway toward explaining the genetics underlying HF using GWAS techniques. By expanding analyses of HF to improved clinical traits, additional HF classifications and innovative model systems, the intractability of human HF GWAS should be ameliorated significantly.

Psychological foundations of xenophilia: the role of major personality traits in predicting favorable attitudes toward cross-cultural contact and exploration.

PubMed

Stürmer, Stefan; Benbow, Alison E F; Siem, Birte; Barth, Markus; Bodansky, Alexander N; Lotz-Schmitt, Katharina

2013-11-01

Building on an integration of research findings on intergroup behavior from multiple fields of scientific inquiry (biological and cultural paleoanthropology, social psychology), as well as research on the HEXACO personality framework (e.g., Ashton & Lee, 2007), 3 independent studies (total N = 1,007) were conducted to introduce and test a fresh personality perspective on human xenophilia. Even though the studies focused on different criteria (Study 1: favorable attitudes toward contact with immigrants, Study 2: habitual cross-cultural exploration, Study 3: favorable attitudes toward contact with indigenous people) and employed different operationalizations of major personality traits (the HEXACO Personality Inventory-Revised [HEXACO-PI-R], the 10-item Big Five Inventory [BFI-10]) results were remarkably similar. First, path analyses confirmed that major personality traits were significant and direct predictors of xenophilia that were independent of the contributions of individual differences commonly predicting xenophobic reactions across studies. Second, and in line with the authors' more specific hypotheses, hierarchical regression analyses also corroborated that individual differences in the levels of endeavor-related personality traits (i.e., eXtraversion, Openness, and Conscientiousness) had a substantially greater power in predicting individual differences in xenophilia than individual differences in levels of altruism/cooperation-related traits (i.e., Honesty-Humility, Emotionality, and Agreeableness). The implications of these findings for more general psychological theorizing on human sociality are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved

It's not all about us: evolution and maintenance of Cryptococcus virulence requires selection outside the human host.

PubMed

Gerstein, Aleeza C; Nielsen, Kirsten

2017-04-01

Cryptococcus is predominantly an AIDS-related pathogen that causes significant morbidity and mortality in immunocompromised patients. Research studies have historically focused on understanding how the organism causes human disease through the use of in vivo and in vitro model systems to identify virulence factors. Cryptococcus is not an obligate pathogen, however, as human-human transmission is either absent or rare. Selection in the environment must thus be invoked to shape the evolution of this taxa, and directly influences genotypic and trait diversity. Importantly, the evolution and maintenance of pathogenicity must also stem directly from environmental selection. To that end, here we examine abiotic and biotic stresses in the environment, and discuss how they could shape the factors that are commonly identified as important virulence traits. We identify a number of important unanswered questions about Cryptococcus diversity and evolution that are critical for understanding this deadly pathogen, and discuss how implementation of modern sampling and genomic tools could be utilized to answer these questions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Expansion of a globally pervasive grass occurs without substantial trait differences between home and away populations.

PubMed

Leifso, A; MacDougall, A S; Husband, B; Hierro, J L; Köchy, M; Pärtel, M; Peltzer, D A

2012-12-01

The global expansion of species beyond their ancestral ranges can derive from mechanisms that are trait-based (e.g., post-establishment evolved differences compared to home populations) or circumstantial (e.g., propagule pressure, with no trait-based differences). These mechanisms can be difficult to distinguish following establishment, but each makes unique predictions regarding trait similarity between ancestral ('home') and introduced ('away') populations. Here, we tested for trait-based population differences across four continents for the globally distributed grass Dactylis glomerata, to assess the possible role of trait evolution in its worldwide expansion. We used a common-environment glasshouse experiment to quantify trait differences among home and away populations, and the potential relevance of these differences for competitive interactions. Few significant trait differences were found among continents, suggesting minimal change during global expansion. All populations were polyploids, with similar foliar carbon:nitrogen ratios (a proxy for defense), chlorophyll content, and biomass. Emergence time and growth rate favored home populations, resulting in their competitive superiority over away populations. Small but significant trait differences among away populations suggest different introductory histories or local adaptive responses following establishment. In summary, the worldwide distribution of this species appears to have arisen from its pre-adapted traits promoting growth, and its repeated introduction with cultivation and intense propagule pressure. Global expansion can thus occur without substantial shifts in growth, reproduction, or defense. Rather than focusing strictly on the invader, invasion success may also derive from the traits found (or lacking) in the recipient community and from environmental context including human disturbance.

Neural Basis of Interpersonal Traits in Neurodegenerative Diseases

PubMed Central

Sollberger, Marc; Stanley, Christine M.; Wilson, Stephen M.; Gyurak, Anett; Beckman, Victoria; Growdon, Matthew; Jang, Jung; Weiner, Michael W.; Miller, Bruce L.; Rankin, Katherine P.

2009-01-01

Several functional and structural imaging studies have investigated the neural basis of personality in healthy adults, but human lesions studies are scarce. Personality changes are a common symptom in patients with neurodegenerative diseases like frontotemporal dementia (FTD) and semantic dementia (SD), allowing a unique window into the neural basis of personality. In this study, we used the Interpersonal Adjective Scales to investigate the structural basis of eight interpersonal traits (dominance, arrogance, coldness, introversion, submissiveness, ingenuousness, warmth, and extraversion) in 257 subjects: 214 patients with neurodegenerative diseases such as FTD, SD, progressive non-fluent aphasia, Alzheimer’s disease, amnestic mild cognitive impairment, corticobasal degeneration, and progressive supranuclear palsy and 43 healthy elderly people. Measures of interpersonal traits were correlated with regional atrophy pattern using voxel-based morphometry (VBM) analysis of structural MR images. Interpersonal traits mapped onto distinct brain regions depending on the degree to which they involved agency and affiliation. Interpersonal traits high in agency related to left dorsolateral prefrontal and left lateral frontopolar regions, whereas interpersonal traits high in affiliation related to right ventromedial prefrontal and right anteromedial temporal regions. Consistent with the existing literature on neural networks underlying social cognition, these results indicate that brain regions related to externally-focused, executive control-related processes underlie agentic interpersonal traits such as dominance, whereas brain regions related to internally-focused, emotion- and reward-related processes underlie affiliative interpersonal traits such as warmth. In addition, these findings indicate that interpersonal traits are subserved by complex neural networks rather than discrete anatomic areas. PMID:19540253

Common genetic variation drives molecular heterogeneity in human iPSCs.

PubMed

Kilpinen, Helena; Goncalves, Angela; Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard; Stegle, Oliver; Gaffney, Daniel J

2017-06-15

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.

An intrinsic DFF40/CAD endonuclease deficiency impairs oligonucleosomal DNA hydrolysis during caspase-dependent cell death: a common trait in human glioblastoma cells

PubMed Central

Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Martínez-Soler, Fina; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Velasco, Roser; Plans, Gerard; Vidal, Noemi; Tortosa, Avelina; Barcia, Carlos; Bruna, Jordi; Yuste, Victor J.

2016-01-01

Background Glioblastoma (GBM) or grade IV astrocytoma is one of the most devastating human cancers. The loss of DFF40/CAD, the key endonuclease that triggers oligonucleosomal DNA fragmentation during apoptosis, has been linked to genomic instability and cell survival after radiation. Despite the near inevitability of GBM tumor recurrence after treatment, the relationship between DFF40/CAD and GBM remains unexplored. Methods We studied the apoptotic behavior of human GBM-derived cells after apoptotic insult. We analyzed caspase activation and the protein levels and subcellular localization of DFF40/CAD apoptotic endonuclease. DFF40/CAD was also evaluated in histological sections from astrocytic tumors and nontumoral human brain. Results We showed that GBM cells undergo incomplete apoptosis without generating oligonucleosomal DNA degradation despite the correct activation of executioner caspases. The major defect of GBM cells relied on the improper accumulation of DFF40/CAD at the nucleoplasmic subcellular compartment. Supporting this finding, DFF40/CAD overexpression allowed GBM cells to display oligonucleosomal DNA degradation after apoptotic challenge. Moreover, the analysis of histological slices from astrocytic tumors showed that DFF40/CAD immunoreactivity in tumoral GFAP-positive cells was markedly reduced when compared with nontumoral samples. Conclusions Our data highlight the low expression levels of DFF40/CAD and the absence of DNA laddering as common molecular traits in GBM. These findings could be of major importance for understanding the malignant behavior of remaining tumor cells after radiochemotherapy. PMID:26755073

Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population.

PubMed

Yousri, Noha A; Fakhro, Khalid A; Robay, Amal; Rodriguez-Flores, Juan L; Mohney, Robert P; Zeriri, Hassina; Odeh, Tala; Kader, Sara Abdul; Aldous, Eman K; Thareja, Gaurav; Kumar, Manish; Al-Shakaki, Alya; Chidiac, Omar M; Mohamoud, Yasmin A; Mezey, Jason G; Malek, Joel A; Crystal, Ronald G; Suhre, Karsten

2018-01-23

Metabolomics-genome-wide association studies (mGWAS) have uncovered many metabolic quantitative trait loci (mQTLs) influencing human metabolic individuality, though predominantly in European cohorts. By combining whole-exome sequencing with a high-resolution metabolomics profiling for a highly consanguineous Middle Eastern population, we discover 21 common variant and 12 functional rare variant mQTLs, of which 45% are novel altogether. We fine-map 10 common variant mQTLs to new metabolite ratio associations, and 11 common variant mQTLs to putative protein-altering variants. This is the first work to report common and rare variant mQTLs linked to diseases and/or pharmacological targets in a consanguineous Arab cohort, with wide implications for precision medicine in the Middle East.

Statistical power and utility of meta-analysis methods for cross-phenotype genome-wide association studies.

PubMed

Zhu, Zhaozhong; Anttila, Verneri; Smoller, Jordan W; Lee, Phil H

2018-01-01

Advances in recent genome wide association studies (GWAS) suggest that pleiotropic effects on human complex traits are widespread. A number of classic and recent meta-analysis methods have been used to identify genetic loci with pleiotropic effects, but the overall performance of these methods is not well understood. In this work, we use extensive simulations and case studies of GWAS datasets to investigate the power and type-I error rates of ten meta-analysis methods. We specifically focus on three conditions commonly encountered in the studies of multiple traits: (1) extensive heterogeneity of genetic effects; (2) characterization of trait-specific association; and (3) inflated correlation of GWAS due to overlapping samples. Although the statistical power is highly variable under distinct study conditions, we found the superior power of several methods under diverse heterogeneity. In particular, classic fixed-effects model showed surprisingly good performance when a variant is associated with more than a half of study traits. As the number of traits with null effects increases, ASSET performed the best along with competitive specificity and sensitivity. With opposite directional effects, CPASSOC featured the first-rate power. However, caution is advised when using CPASSOC for studying genetically correlated traits with overlapping samples. We conclude with a discussion of unresolved issues and directions for future research.

Adiposity, compared with masculinity, serves as a more valid cue to immunocompetence in human mate choice.

PubMed

Rantala, Markus J; Coetzee, Vinet; Moore, Fhionna R; Skrinda, Ilona; Kecko, Sanita; Krama, Tatjana; Kivleniece, Inese; Krams, Indrikis

2013-01-22

According to the 'good genes' hypothesis, females choose males based on traits that indicate the male's genetic quality in terms of disease resistance. The 'immunocompetence handicap hypothesis' proposed that secondary sexual traits serve as indicators of male genetic quality, because they indicate that males can contend with the immunosuppressive effects of testosterone. Masculinity is commonly assumed to serve as such a secondary sexual trait. Yet, women do not consistently prefer masculine looking men, nor is masculinity consistently related to health across studies. Here, we show that adiposity, but not masculinity, significantly mediates the relationship between a direct measure of immune response (hepatitis B antibody response) and attractiveness for both body and facial measurements. In addition, we show that circulating testosterone is more closely associated with adiposity than masculinity. These findings indicate that adiposity, compared with masculinity, serves as a more important cue to immunocompetence in female mate choice.

Trait conscientiousness and the personality meta-trait stability are associated with regional white matter microstructure.

PubMed

Lewis, Gary J; Cox, Simon R; Booth, Tom; Muñoz Maniega, Susana; Royle, Natalie A; Valdés Hernández, Maria; Wardlaw, Joanna M; Bastin, Mark E; Deary, Ian J

2016-08-01

Establishing the neural bases of individual differences in personality has been an enduring topic of interest. However, while a growing literature has sought to characterize grey matter correlates of personality traits, little attention to date has been focused on regional white matter correlates of personality, especially for the personality traits agreeableness, conscientiousness and openness. To rectify this gap in knowledge we used a large sample (n > 550) of older adults who provided data on both personality (International Personality Item Pool) and white matter tract-specific fractional anisotropy (FA) from diffusion tensor MRI. Results indicated that conscientiousness was associated with greater FA in the left uncinate fasciculus (β = 0.17, P < 0.001). We also examined links between FA and the personality meta-trait 'stability', which is defined as the common variance underlying agreeableness, conscientiousness, and neuroticism/emotional stability. We observed an association between left uncinate fasciculus FA and stability (β = 0.27, P < 0.001), which fully accounted for the link between left uncinate fasciculus FA and conscientiousness. In sum, these results provide novel evidence for links between regional white matter microstructure and key traits of human personality, specifically conscientiousness and the meta-trait, stability. Future research is recommended to replicate and address the causal directions of these associations. © The Author (2016). Published by Oxford University Press.

Patients with Gilles de la Tourette syndrome have widespread personality differences.

PubMed

Trillini, Morounke O; Müller-Vahl, Kirsten R

2015-08-30

Only little is known about pathological personality traits in patients with Gilles de la Tourette syndrome (GTS). The aim of this study was to further investigate the prevalence of personality traits in adults with GTS. We used a variety of rating scales to assess not only personality traits, but also severity of tics, quality of life, and comorbidities (obsessive-compulsive disorder (OCD), attention deficit hyperactivity disorder (ADHD), depression), in a large group (n=50) of patients. Our major finding was that pathological personality traits are very common in patients with GTS encompassing a wide range of different personality traits, but most typically personality traits related to cluster C. Demand-anxious was the most common personality trait, while histrionic personality trait was absent. Patients' quality of life was more impaired by personality traits than comorbidities. Personality traits were more common in patients with comorbid OCD and depression, while comorbid ADHD had no influence. Our findings, therefore, corroborate the hypothesis that GTS plus OCD represents a more severe subtype of GTS, and support the assumption that OCD and depression, but not ADHD, are part of the GTS spectrum. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Comparative Genomic Analysis of Pathogenic and Probiotic Enterococcus faecalis Isolates, and Their Transcriptional Responses to Growth in Human Urine

PubMed Central

Snipen, Lars; Nes, Ingolf F.; Brede, Dag A.

2010-01-01

Urinary tract infection (UTI) is the most common infection caused by enterococci, and Enterococcus faecalis accounts for the majority of enterococcal infections. Although a number of virulence related traits have been established, no comprehensive genomic or transcriptomic studies have been conducted to investigate how to distinguish pathogenic from non-pathogenic E. faecalis in their ability to cause UTI. In order to identify potential genetic traits or gene regulatory features that distinguish pathogenic from non-pathogenic E. faecalis with respect to UTI, we have performed comparative genomic analysis, and investigated growth capacity and transcriptome profiling in human urine in vitro. Six strains of different origins were cultivated and all grew readily in human urine. The three strains chosen for transcriptional analysis showed an overall similar response with respect to energy and nitrogen metabolism, stress mechanism, cell envelope modifications, and trace metal acquisition. Our results suggest that citrate and aspartate are significant for growth of E. faecalis in human urine, and manganese appear to be a limiting factor. The majority of virulence factors were either not differentially regulated or down-regulated. Notably, a significant up-regulation of genes involved in biofilm formation was observed. Strains from different origins have similar capacity to grow in human urine. The overall similar transcriptional responses between the two pathogenic and the probiotic strain suggest that the pathogenic potential of a certain E. faecalis strain may to a great extent be determined by presence of fitness and virulence factors, rather than the level of expression of such traits. PMID:20824220

Zoonoses-With Friends Like This, Who Needs Enemies?

PubMed Central

Baum, Stephen G.

2008-01-01

Zoonoses are infections that are spread from animals to humans. Most often, humans are “dead-end” hosts, meaning that there is no subsequent human-to-human transmission. If one considers most of the emerging infections that were recognized at the end of the last century and the beginning of this century, they would fall into the category of zoonoses. One of the most important common traits exhibited by infections that have been or can be eliminated from the face of the earth (e.g. smallpox, measles, polio) is the absence of any host other than humans. Therefore, zoonses represent infections that can never be eliminated and must be considered as permanent and recurrent factors to be dealt with in protecting human health. PMID:18596867

Zoonoses-with friends like this, who needs enemies?

PubMed

Baum, Stephen G

2008-01-01

Zoonoses are infections that are spread from animals to humans. Most often, humans are "dead-end" hosts, meaning that there is no subsequent human-to-human transmission. If one considers most of the emerging infections that were recognized at the end of the last century and the beginning of this century, they would fall into the category of zoonoses. One of the most important common traits exhibited by infections that have been or can be eliminated from the face of the earth (e.g. smallpox, measles, polio) is the absence of any host other than humans. Therefore, zoonses represent infections that can never be eliminated and must be considered as permanent and recurrent factors to be dealt with in protecting human health.

Genetics of Lipid and Lipoprotein Disorders and Traits.

PubMed

Dron, Jacqueline S; Hegele, Robert A

2016-01-01

Plasma lipids, namely cholesterol and triglyceride, and lipoproteins, such as low-density lipoprotein (LDL) and high-density lipoprotein, serve numerous physiological roles. Perturbed levels of these traits underlie monogenic dyslipidemias, a diverse group of multisystem disorders. We are on the verge of having a relatively complete picture of the human dyslipidemias and their components. Recent advances in genetics of plasma lipids and lipoproteins include the following: (1) expanding the range of genes causing monogenic dyslipidemias, particularly elevated LDL cholesterol; (2) appreciating the role of polygenic effects in such traits as familial hypercholesterolemia and combined hyperlipidemia; (3) accumulating a list of common variants that determine plasma lipids and lipoproteins; (4) applying exome sequencing to identify collections of rare variants determining plasma lipids and lipoproteins that via Mendelian randomization have also implicated gene products such as NPC1L1 , APOC3 , LDLR , APOA5 , and ANGPTL4 as causal for atherosclerotic cardiovascular disease; and (5) using naturally occurring genetic variation to identify new drug targets, including inhibitors of apolipoprotein (apo) C-III, apo(a), ANGPTL3, and ANGPTL4. Here, we compile this disparate range of data linking human genetic variation to plasma lipids and lipoproteins, providing a "one stop shop" for the interested reader.

Common genetic variation drives molecular heterogeneity in human iPSCs

PubMed Central

Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard

2017-01-01

Induced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterisation of many existing iPSC lines limits their potential use for research and therapy. Here, we describe the systematic generation, genotyping and phenotyping of 711 iPSC lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative (HipSci: http://www.hipsci.org). Our study outlines the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of rare, genomic copy number mutations that are repeatedly observed in iPSC reprogramming and present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells. PMID:28489815

A Comprehensive Phenotypic Investigation of the "Pod-Shattering Syndrome" in Common Bean.

PubMed

Murgia, Maria L; Attene, Giovanna; Rodriguez, Monica; Bitocchi, Elena; Bellucci, Elisa; Fois, Davide; Nanni, Laura; Gioia, Tania; Albani, Diego M; Papa, Roberto; Rau, Domenico

2017-01-01

Seed shattering in crops is a key domestication trait due to its relevance for seed dispersal, yield, and fundamental questions in evolution (e.g., convergent evolution). Here, we focused on pod shattering in common bean ( Phaseolus vulgaris L.), the most important legume crop for human consuption in the world. With this main aim, we developed a methodological pipeline that comprises a thorough characterization under field conditions, including also the chemical composition and histological analysis of the pod valves. The pipeline was developed based on the assumption that the shattering trait itself can be treated in principle as a "syndrome" (i.e., a set of correlated different traits) at the pod level. We characterized a population of 267 introgression lines that were developed ad-hoc to study shattering in common bean. Three main objectives were sought: (1) to dissect the shattering trait into its "components," of level (percentage of shattering pods per plant) and mode (percentage of pods with twisting or non-twisting valves); (2) to test whether shattering is associated to the chemical composition and/or the histological characteristics of the pod valves; and (3) to test the associations between shattering and other plant traits. We can conclude the following: Very high shattering levels can be achieved in different modes; shattering resistance is mainly a qualitative trait; and high shattering levels is correlated with high carbon and lignin contents of the pod valves and with specific histological charaterstics of the ventral sheath and the inner fibrous layer of the pod wall. Our data also suggest that shattering comes with a "cost," as it is associated with low pod size, low seed weight per pod, high pod weight, and low seed to pod-valves ratio; indeed, it can be more exaustively described as a syndrome at the pod level. Our work suggests that the valve chemical composition (i.e., carbon and lignin content) can be used for a high troughput phenotyping procedures for shattering phenotyping. Finally, we believe that the application of our pipeline will greatly facilitate comparative studies among legume crops, and gene tagging.

Genetics of human body size and shape: pleiotropic and independent genetic determinants of adiposity.

PubMed

Livshits, G; Yakovenko, K; Ginsburg, E; Kobyliansky, E

1998-01-01

The present study utilized pedigree data from three ethnically different populations of Kirghizstan, Turkmenia and Chuvasha. Principal component analysis was performed on a matrix of genetic correlations between 22 measures of adiposity, including skinfolds, circumferences and indices. Findings are summarized as follows: (1) All three genetic matrices were not positive definite and the first four factors retained even after exclusion RG > or = 1.0, explained from 88% to 97% of the total additive genetic variation in the 22 trials studied. This clearly emphasizes the massive involvement of pleiotropic gene effects in the variability of adiposity traits. (2) Despite the quite natural differences in pairwise correlations between the adiposity traits in the three ethnically different samples under study, factor analysis revealed a common basic pattern of covariability for the adiposity traits. In each of the three samples, four genetic factors were retained, namely, the amount of subcutaneous fat, the total body obesity, the pattern of distribution of subcutaneous fat and the central adiposity distribution. (3) Genetic correlations between the retained four factors were virtually non-existent, suggesting that several independent genetic sources may be governing the variation of adiposity traits. (4) Variance decomposition analysis on the obtained genetic factors leaves no doubt regarding the substantial familial and (most probably genetic) effects on variation of each factor in each studied population. The similarity of results in the three different samples indicates that the findings may be deemed valid and reliable descriptions of the genetic variation and covariation pattern of adiposity traits in the human species.

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

PubMed

Lv, Weihua; Zheng, Xianhu; Kuang, Youyi; Cao, Dingchen; Yan, Yunqin; Sun, Xiaowen

2016-05-05

Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.

PubMed

Arboleya, Silvia; Bottacini, Francesca; O'Connell-Motherway, Mary; Ryan, C Anthony; Ross, R Paul; van Sinderen, Douwe; Stanton, Catherine

2018-01-08

Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.

The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect.

PubMed

Sniegula, Szymon; Golab, Maria J; Drobniak, Szymon M; Johansson, Frank

2018-06-01

Seasonal time constraints are usually stronger at higher than lower latitudes and can exert strong selection on life-history traits and the correlations among these traits. To predict the response of life-history traits to environmental change along a latitudinal gradient, information must be obtained about genetic variance in traits and also genetic correlation between traits, that is the genetic variance-covariance matrix, G. Here, we estimated G for key life-history traits in an obligate univoltine damselfly that faces seasonal time constraints. We exposed populations to simulated native temperatures and photoperiods and common garden environmental conditions in a laboratory set-up. Despite differences in genetic variance in these traits between populations (lower variance at northern latitudes), there was no evidence for latitude-specific covariance of the life-history traits. At simulated native conditions, all populations showed strong genetic and phenotypic correlations between traits that shaped growth and development. The variance-covariance matrix changed considerably when populations were exposed to common garden conditions compared with the simulated natural conditions, showing the importance of environmentally induced changes in multivariate genetic structure. Our results highlight the importance of estimating variance-covariance matrixes in environments that mimic selection pressures and not only trait variances or mean trait values in common garden conditions for understanding the trait evolution across populations and environments. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Activation of the germ-cell potential of human bone marrow-derived cells by a chemical carcinogen

PubMed Central

Liu, Chunfang; Ma, Zhan; Xu, Songtao; Hou, Jun; Hu, Yao; Yu, Yinglu; Liu, Ruilai; Chen, Zhihong; Lu, Yuan

2014-01-01

Embryonic/germ cell traits are common in malignant tumors and are thought to be involved in malignant tumor behaviors. The reasons why tumors show strong embryonic/germline traits (displaced germ cells or gametogenic programming reactivation) are controversial. Here, we show that a chemical carcinogen, 3-methyl-cholanthrene (3-MCA), can trigger the germ-cell potential of human bone marrow-derived cells (hBMDCs). 3-MCA promoted the generation of germ cell-like cells from induced hBMDCs that had undergone malignant transformation, whereas similar results were not observed in the parallel hBMDC culture at the same time point. The malignant transformed hBMDCs spontaneously and more efficiently generated into germ cell-like cells even at the single-cell level. The germ cell-like cells from induced hBMDCs were similar to natural germ cells in many aspects, including morphology, gene expression, proliferation, migration, further development, and teratocarcinoma formation. Therefore, our results demonstrate that a chemical carcinogen can reactivate the germline phenotypes of human somatic tissue-derived cells, which might provide a novel idea to tumor biology and therapy. PMID:24998261

A HapMap harvest of insights into the genetics of common disease

PubMed Central

Manolio, Teri A.; Brooks, Lisa D.; Collins, Francis S.

2008-01-01

The International HapMap Project was designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases. This expectation has been amply fulfilled with just the initial output of genome-wide association studies, identifying nearly 100 loci for nearly 40 common diseases and traits. These associations provided new insights into pathophysiology, suggesting previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. In addition, HapMap-based discoveries have shed new light on the impact of evolutionary pressures on the human genome, suggesting multiple loci important for adapting to disease-causing pathogens and new environments. In this review we examine the origin, development, and current status of the HapMap; its prospects for continued evolution; and its current and potential future impact on biomedical science. PMID:18451988

[Genetic and epigenetic news in gerontology].

PubMed

Baranov, V S; Glotov, O S; Baranova, E V

2014-01-01

The overview represents the recent most conspicuous findings in aging studies. It includes new data on the whole genome association studies (GWAS) in big cohort of centenaries, recently found mutation protecting from Alzheimer disease, discovery of hypothalamus as a command center of human aging, very important data on the negative effect of common antioxidants in the treatment of lung cancer as well as new data concerning antiaging and anticancer effects of common drugs such as rapamycine and metformin. Substantial part of the review is devoted to the epigenetic problems of senescence and feasible impact of basic epigenetic mechanisms (methylation of DNA and histone proteins, DNA heterochromatization) in regulation of gene expression, long-term genome reprogramming during early childhood, and transgeneration transmission of epigenetic traits. The necessity of transition from molecular studies of dormant human genome (anatomy of human genome) to genome in action (dynamic genome) and thus with special emphasis to epigenetic medicine is stressed.

Trait space of rare plants in a fire-dependent ecosystem.

PubMed

Ames, Gregory M; Wall, Wade A; Hohmann, Matthew G; Wright, Justin P

2017-08-01

The causes of species rarity are of critical concern because of the high extinction risk associated with rarity. Studies examining individual rare species have limited generality, whereas trait-based approaches offer a means to identify functional causes of rarity that can be applied to communities with disparate species pools. Differences in functional traits between rare and common species may be indicative of the functional causes of species rarity and may therefore be useful in crafting species conservation strategies. However, there is a conspicuous lack of studies comparing the functional traits of rare species and co-occurring common species. We measured 18 important functional traits for 19 rare and 134 common understory plant species from North Carolina's Sandhills region and compared their trait distributions to determine whether there are significant functional differences that may explain species rarity. Flowering, fire, and tissue-chemistry traits differed significantly between rare and common, co-occurring species. Differences in specific traits suggest that fire suppression has driven rarity in this system and that changes to the timing and severity of prescribed fire may improve conservation success. Our method provides a useful tool to prioritize conservation efforts in other systems based on the likelihood that rare species are functionally capable of persisting. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Intronic SNP in ESR1 encoding human estrogen receptor alpha is associated with brain ESR1 mRNA isoform expression and behavioral traits.

PubMed

Pinsonneault, Julia K; Frater, John T; Kompa, Benjamin; Mascarenhas, Roshan; Wang, Danxin; Sadee, Wolfgang

2017-01-01

Genetic variants of ESR1 have been implicated in multiple diseases, including behavioral disorders, but causative variants remain uncertain. We have searched for regulatory variants affecting ESR1 expression in human brain, measuring allelic ESR1 mRNA expression in human brain tissues with marker SNPs in exon4 representing ESR1-008 (or ESRα-36), and in the 3'UTR of ESR1-203, two main ESR1 isoforms in brain. In prefrontal cortex from subjects with bipolar disorder, schizophrenia, and controls (n = 35 each; Stanley Foundation brain bank), allelic ESR1 mRNA ratios deviated from unity up to tenfold at the exon4 marker SNP, with large allelic ratios observed primarily in bipolar and schizophrenic subjects. SNP scanning and targeted sequencing identified rs2144025, associated with large allelic mRNA ratios (p = 1.6E10-6). Moreover, rs2144025 was significantly associated with ESR1 mRNA levels in the Brain eQTL Almanac and in brain regions in the Genotype-Tissue Expression project. In four GWAS cohorts, rs2104425 was significantly associated with behavioral traits, including: hypomanic episodes in female bipolar disorder subjects (GAIN bipolar disorder study; p = 0.0004), comorbid psychological symptoms in both males and females with attention deficit hyperactivity disorder (GAIN ADHD, p = 0.00002), psychological diagnoses in female children (eMERGE study of childhood health, subject age ≥9, p = 0.0009), and traits in schizophrenia (e.g., grandiose delusions, GAIN schizophrenia, p = 0.0004). The first common ESR1 variant (MAF 12-33% across races) linked to regulatory functions, rs2144025 appears conditionally to affect ESR1 mRNA expression in the brain and modulate traits in behavioral disorders.

Intronic SNP in ESR1 encoding human estrogen receptor alpha is associated with brain ESR1 mRNA isoform expression and behavioral traits

PubMed Central

Kompa, Benjamin; Mascarenhas, Roshan; Wang, Danxin; Sadee, Wolfgang

2017-01-01

Genetic variants of ESR1 have been implicated in multiple diseases, including behavioral disorders, but causative variants remain uncertain. We have searched for regulatory variants affecting ESR1 expression in human brain, measuring allelic ESR1 mRNA expression in human brain tissues with marker SNPs in exon4 representing ESR1-008 (or ESRα-36), and in the 3’UTR of ESR1-203, two main ESR1 isoforms in brain. In prefrontal cortex from subjects with bipolar disorder, schizophrenia, and controls (n = 35 each; Stanley Foundation brain bank), allelic ESR1 mRNA ratios deviated from unity up to tenfold at the exon4 marker SNP, with large allelic ratios observed primarily in bipolar and schizophrenic subjects. SNP scanning and targeted sequencing identified rs2144025, associated with large allelic mRNA ratios (p = 1.6E10-6). Moreover, rs2144025 was significantly associated with ESR1 mRNA levels in the Brain eQTL Almanac and in brain regions in the Genotype-Tissue Expression project. In four GWAS cohorts, rs2104425 was significantly associated with behavioral traits, including: hypomanic episodes in female bipolar disorder subjects (GAIN bipolar disorder study; p = 0.0004), comorbid psychological symptoms in both males and females with attention deficit hyperactivity disorder (GAIN ADHD, p = 0.00002), psychological diagnoses in female children (eMERGE study of childhood health, subject age ≥9, p = 0.0009), and traits in schizophrenia (e.g., grandiose delusions, GAIN schizophrenia, p = 0.0004). The first common ESR1 variant (MAF 12–33% across races) linked to regulatory functions, rs2144025 appears conditionally to affect ESR1 mRNA expression in the brain and modulate traits in behavioral disorders. PMID:28617822

Common genetic factors among sexual orientation, gender nonconformity, and number of sex partners in female twins: implications for the evolution of homosexuality.

PubMed

Burri, Andrea; Spector, Tim; Rahman, Qazi

2015-04-01

Homosexuality is a stable population-level trait in humans that lowers direct fitness and yet is substantially heritable, resulting in a so-called Darwinian "paradox." Evolutionary models have proposed that polymorphic genes influencing homosexuality confer a reproductive benefit to heterosexual carriers, thus offsetting the fitness costs associated with persistent homosexuality. This benefit may consist of a "sex typicality" intermediate phenotype. However, there are few empirical tests of this hypothesis using genetically informative data in humans. This study aimed to test the hypothesis that common genetic factors can explain the association between measures of sex typicality, mating success, and homosexuality in a Western (British) sample of female twins. Here, we used data from 996 female twins (498 twin pairs) comprising 242 full dizygotic pairs and 256 full monozygotic pairs (mean age 56.8) and 1,555 individuals whose co-twin did not participate. Measures of sexual orientation, sex typicality (recalled childhood gender nonconformity), and mating success (number of lifetime sexual partners) were completed. Variables were subject to multivariate variance component analysis. We found that masculine women are more likely to be nonheterosexual, report more sexual partners, and, when heterosexual, also report more sexual partners. Multivariate twin modeling showed that common genetic factors explained the relationship between sexual orientation, sex typicality, and mating success through a shared latent factor. Our findings suggest that genetic factors responsible for nonheterosexuality are shared with genetic factors responsible for the number of lifetime sexual partners via a latent sex typicality phenotype in human females. These results may have implications for evolutionary models of homosexuality but are limited by potential mediating variables (such as personality traits) and measurement issues. © 2015 International Society for Sexual Medicine.

Human heart failure with preserved ejection versus feline cardiomyopathy: what can we learn from both veterinary and human medicine?

PubMed

Prat, Valentine; Rozec, Bertrand; Gauthier, Chantal; Lauzier, Benjamin

2017-11-01

Cardiovascular affections are a growing health burden in human populations. Recent advances in cardiology have improved treatments and outcomes for myocardial infarction and arrhythmias, but other conditions still remain poorly understood. To date, the classical approach to study cardiovascular diseases involves rodent models, despite their strong differences with human cardiac physiology. In this context, this review will focus on the common traits between human and feline cardiac diseases, namely heart failure with preserved ejection fraction and feline cardiomyopathies, respectively. These two affections share similar pathological patterns and epidemiological characteristics. An improved knowledge would be of interest for both human and feline patients and could lead to the establishment of a more accurate treatment and therapeutic strategy for medical doctors and veterinary practitioners.

Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility.

PubMed

Nashef, A; Qabaja, R; Salaymeh, Y; Botzman, M; Munz, M; Dommisch, H; Krone, B; Hoffmann, P; Wellmann, J; Laudes, M; Berger, K; Kocher, T; Loos, B; van der Velde, N; Uitterlinden, A G; de Groot, L C P G M; Franke, A; Offenbacher, S; Lieb, W; Divaris, K; Mott, R; Gat-Viks, I; Wiess, E; Schaefer, A; Iraqi, F A; Haddad, Y H

2018-05-01

Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro-computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (-log P = 5.3; false discovery rate = 0.06) on chromosomes 1 ( Perio3) and 14 ( Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes ( CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.

Children's Thinking about Traits: Implications for Judgments of the Self and Others.

ERIC Educational Resources Information Center

Heyman, Gail D.; Dweck, Carol S.

1998-01-01

Investigated the relation between 7- and 8-year-olds' interpretations of human behavior and children's beliefs about the stability of human traits. Found that the belief that traits are stable predicted a greater tendency to make trait judgments in the academic and sociomoral domains, and an increased focus on outcomes such as performance and…

A cybernetic model of global personality traits.

PubMed

Van Egeren, Lawrence F

2009-05-01

Neurobehavioral studies of human and animal temperament have shed light on how individual personality traits influence human actions. This approach, however, leaves open questions about how the entire system of traits and temperaments function together to exercise control. To address this key issue, I describe a cybernetic model of control and then apply it to the Big Five (B5) personality traits. Employing evidence from descriptive trait terms, temperamental behavioral processes associated with traits, and empirical correlates of traits, I relate distinct cybernetic processes of self-regulation to the B5 traits. The B5 traits broadly parallel basic cybernetic self-regulation processes. For example, the core behavior activation property of the B5 Extraversion trait can be mapped onto the device output function of automated cybernetic control systems. Implications and limitations of interpreting personality traits in self-regulation terms are discussed.

Combining a weed traits database with a population dynamics model predicts shifts in weed communities.

PubMed

Storkey, J; Holst, N; Bøjer, O Q; Bigongiali, F; Bocci, G; Colbach, N; Dorner, Z; Riemens, M M; Sartorato, I; Sønderskov, M; Verschwele, A

2015-04-01

A functional approach to predicting shifts in weed floras in response to management or environmental change requires the combination of data on weed traits with analytical frameworks that capture the filtering effect of selection pressures on traits. A weed traits database (WTDB) was designed, populated and analysed, initially using data for 19 common European weeds, to begin to consolidate trait data in a single repository. The initial choice of traits was driven by the requirements of empirical models of weed population dynamics to identify correlations between traits and model parameters. These relationships were used to build a generic model, operating at the level of functional traits, to simulate the impact of increasing herbicide and fertiliser use on virtual weeds along gradients of seed weight and maximum height. The model generated 'fitness contours' (defined as population growth rates) within this trait space in different scenarios, onto which two sets of weed species, defined as common or declining in the UK, were mapped. The effect of increasing inputs on the weed flora was successfully simulated; 77% of common species were predicted to have stable or increasing populations under high fertiliser and herbicide use, in contrast with only 29% of the species that have declined. Future development of the WTDB will aim to increase the number of species covered, incorporate a wider range of traits and analyse intraspecific variability under contrasting management and environments.

Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility

PubMed Central

Zeller, Tanja; Wild, Philipp; Szymczak, Silke; Rotival, Maxime; Schillert, Arne; Castagne, Raphaele; Maouche, Seraya; Germain, Marine; Lackner, Karl; Rossmann, Heidi; Eleftheriadis, Medea; Sinning, Christoph R.; Schnabel, Renate B.; Lubos, Edith; Mennerich, Detlev; Rust, Werner; Perret, Claire; Proust, Carole; Nicaud, Viviane; Loscalzo, Joseph; Hübner, Norbert; Tregouet, David; Münzel, Thomas; Ziegler, Andreas; Tiret, Laurence

2010-01-01

Background Variability of gene expression in human may link gene sequence variability and phenotypes; however, non-genetic variations, alone or in combination with genetics, may also influence expression traits and have a critical role in physiological and disease processes. Methodology/Principal Findings To get better insight into the overall variability of gene expression, we assessed the transcriptome of circulating monocytes, a key cell involved in immunity-related diseases and atherosclerosis, in 1,490 unrelated individuals and investigated its association with >675,000 SNPs and 10 common cardiovascular risk factors. Out of 12,808 expressed genes, 2,745 expression quantitative trait loci were detected (P<5.78×10−12), most of them (90%) being cis-modulated. Extensive analyses showed that associations identified by genome-wide association studies of lipids, body mass index or blood pressure were rarely compatible with a mediation by monocyte expression level at the locus. At a study-wide level (P<3.9×10−7), 1,662 expression traits (13.0%) were significantly associated with at least one risk factor. Genome-wide interaction analyses suggested that genetic variability and risk factors mostly acted additively on gene expression. Because of the structure of correlation among expression traits, the variability of risk factors could be characterized by a limited set of independent gene expressions which may have biological and clinical relevance. For example expression traits associated with cigarette smoking were more strongly associated with carotid atherosclerosis than smoking itself. Conclusions/Significance This study demonstrates that the monocyte transcriptome is a potent integrator of genetic and non-genetic influences of relevance for disease pathophysiology and risk assessment. PMID:20502693

Medial prefrontal cortex subserves diverse forms of self-reflection.

PubMed

Jenkins, Adrianna C; Mitchell, Jason P

2011-01-01

The ability to think about oneself--to self--reflect--is one of the defining features of the human mind. Recent research has suggested that this ability may be subserved by a particular brain region: the medial prefrontal cortex (MPFC). However, although humans can contemplate a variety of different aspects of themselves, including their stable personality traits, current feelings, and physical attributes, no research has directly examined the extent to which these different forms of self-reflection are subserved by common mechanisms. To address this question, participants were scanned using functional magnetic resonance imaging (fMRI) while making judgments about their own personality traits, current mental states, and physical attributes as well as those of another person. Whereas some brain regions responded preferentially during only one form of self-reflection, a robust region of MPFC was engaged preferentially during self-reflection across all three types of judgment. These results suggest that--although dissociable--diverse forms of self-referential thought draw on a shared cognitive process subserved by MPFC.

Recent Mitochondrial DNA Mutations Increase the Risk of Developing Common Late-Onset Human Diseases

PubMed Central

Hudson, Gavin; Gomez-Duran, Aurora; Wilson, Ian J.; Chinnery, Patrick F.

2014-01-01

Mitochondrial DNA (mtDNA) is highly polymorphic at the population level, and specific mtDNA variants affect mitochondrial function. With emerging evidence that mitochondrial mechanisms are central to common human diseases, it is plausible that mtDNA variants contribute to the “missing heritability” of several complex traits. Given the central role of mtDNA genes in oxidative phosphorylation, the same genetic variants would be expected to alter the risk of developing several different disorders, but this has not been shown to date. Here we studied 38,638 individuals with 11 major diseases, and 17,483 healthy controls. Imputing missing variants from 7,729 complete mitochondrial genomes, we captured 40.41% of European mtDNA variation. We show that mtDNA variants modifying the risk of developing one disease also modify the risk of developing other diseases, thus providing independent replication of a disease association in different case and control cohorts. High-risk alleles were more common than protective alleles, indicating that mtDNA is not at equilibrium in the human population, and that recent mutations interact with nuclear loci to modify the risk of developing multiple common diseases. PMID:24852434

Personality disorder traits, family environment, and alcohol misuse: a multivariate behavioural genetic analysis.

PubMed

Jang, K L; Vernon, P A; Livesley, W J

2000-06-01

This study seeks to estimate the extent to which a common genetic and environmental basis is shared between (i) traits delineating specific aspects of antisocial personality and alcohol misuse, and (ii) childhood family environments, traits delineating broad domains of personality pathology and alcohol misuse. Postal survey data were collected from monozygotic and dizygotic twin pairs. Twin pairs were recruited from Vancouver, British Columbia and London, Ontario, Canada using newspaper advertisements, media stories and twin clubs. Data obtained from 324 monozygotic and 335 dizygotic twin pairs were used to estimate the extent to which traits delineating specific antisocial personality traits and alcohol misuse shared a common genetic and environmental aetiology. Data from 81 monozygotic and 74 dizygotic twin pairs were used to estimate the degree to which traits delineating personality pathology, childhood family environment and alcohol misuse shared a common aetiology. Current alcohol misuse and personality pathology were measured using scales contained in the self-report Dimensional Assessment of Personality Pathology. Perceptions of childhood family environment were measured using the self-report Family Environment Scale. Multivariate genetic analyses showed that a subset of traits delineating components of antisocial personality (i.e. grandiosity, attention-seeking, failure to adopt social norms, interpersonal violence and juvenile antisocial behaviours) are influenced by genetic factors in common to alcohol misuse. Genetically based perceptions of childhood family environment had little relationship with alcohol misuse. Heritable personality factors that influence the perception of childhood family environment play only a small role in the liability to alcohol misuse. Instead, liability to alcohol misuse is related to genetic factors common a specific subset of antisocial personality traits describing conduct problems, narcissistic and stimulus-seeking behaviour.

The Prediction of Empathetic Tendency and Characteristic Trait of Collaboration on Humane Values in Secondary Education Students and the Examining to Those Characteristics

ERIC Educational Resources Information Center

Dereli, Esra; Aypay, Ayse

2012-01-01

The purpose of this study was to investigate the relationships among the empathic tendency, collaboration character trait, human values of student high school and whether high school students' empathic tendency, character trait of collaboration, human values differ based on qualifications of personnel ( gender, class levels, mother and father…

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish.

PubMed

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-08-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change - an important component of biological conservation and ecosystem management.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish

PubMed Central

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-01-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management. PMID:26240605

What can genes tell us about the relationship between education and health?

PubMed

Boardman, Jason D; Domingue, Benjamin W; Daw, Jonathan

2015-02-01

We use genome wide data from respondents of the Health and Retirement Study (HRS) to evaluate the possibility that common genetic influences are associated with education and three health outcomes: depression, self-rated health, and body mass index. We use a total of 1.7 million single nucleotide polymorphisms obtained from the Illumina HumanOmni2.5-4v1 chip from 4233 non-Hispanic white respondents to characterize genetic similarities among unrelated persons in the HRS. We then used the Genome Wide Complex Trait Analysis (GCTA) toolkit, to estimate univariate and bivariate heritability. We provide evidence that education (h(2) = 0.33), BMI (h(2) = 0.43), depression (h(2) = 0.19), and self-rated health (h(2) = 0.18) are all moderately heritable phenotypes. We also provide evidence that some of the correlation between depression and education as well as self-rated health and education is due to common genetic factors associated with one or both traits. We find no evidence that the correlation between education and BMI is influenced by common genetic factors. Copyright © 2014 Elsevier Ltd. All rights reserved.

"Touching Triton": Building Student Understanding of Complex Disease Risk.

PubMed

Loftin, Madelene; East, Kelly; Hott, Adam; Lamb, Neil

2016-01-01

Life science classrooms often emphasize the exception to the rule when it comes to teaching genetics, focusing heavily on rare single-gene and Mendelian traits. By contrast, the vast majority of human traits and diseases are caused by more complicated interactions between genetic and environmental factors. Research indicates that students have a deterministic view of genetics, generalize Mendelian inheritance patterns to all traits, and have unrealistic expectations of genetic technologies. The challenge lies in how to help students analyze complex disease risk with a lack of curriculum materials. Providing open access to both content resources and an engaging storyline can be achieved using a "serious game" model. "Touching Triton" was developed as a serious game in which students are asked to analyze data from a medical record, family history, and genomic report in order to develop an overall lifetime risk estimate of six common, complex diseases. Evaluation of student performance shows significant learning gains in key content areas along with a high level of engagement.

Translational Insight Into Polycystic Ovary Syndrome (PCOS) From Female Monkeys with PCOS-like Traits

PubMed Central

Abbott, D.H.; Levine, J.E.; Dumesic, D.A.

2017-01-01

Genetics-based studies of women with polycystic ovary syndrome (PCOS) implicate >20 PCOS risk genes that collectively account for <10% of PCOS. Clinicians now consider that either rare alleles or non-genetic, potentially epigenetic, developmental origins may contribute key pathogenic components to >90% of PCOS cases. Animal models convincingly demonstrate excess fetal testosterone exposure in females as a reliable, epigenetic, developmental origin for PCOS-like traits. In particular, nonhuman primates (NHPs) provide the most faithful emulation of PCOS-like pathophysiology, likely because of close similarities to humans in genomic, developmental, reproductive and metabolic characteristics, as well as aging. Recent appreciation of potential molecular mechanisms contributing to enhanced LH action in both PCOS women (GWAS-based) and PCOS-like monkeys (DNA methylation-based) suggest commonality in pathogenic origins. This review examines the translational relevance of NHP studies to PCOS, identifying characteristics of newborn females at risk for PCOS-like traits and potential prepubertal treatment interventions to ameliorate PCOS onset. PMID:27426126

Adiposity, compared with masculinity, serves as a more valid cue to immunocompetence in human mate choice

PubMed Central

Rantala, Markus J.; Coetzee, Vinet; Moore, Fhionna R.; Skrinda, Ilona; Kecko, Sanita; Krama, Tatjana; Kivleniece, Inese; Krams, Indrikis

2013-01-01

According to the ‘good genes’ hypothesis, females choose males based on traits that indicate the male's genetic quality in terms of disease resistance. The ‘immunocompetence handicap hypothesis’ proposed that secondary sexual traits serve as indicators of male genetic quality, because they indicate that males can contend with the immunosuppressive effects of testosterone. Masculinity is commonly assumed to serve as such a secondary sexual trait. Yet, women do not consistently prefer masculine looking men, nor is masculinity consistently related to health across studies. Here, we show that adiposity, but not masculinity, significantly mediates the relationship between a direct measure of immune response (hepatitis B antibody response) and attractiveness for both body and facial measurements. In addition, we show that circulating testosterone is more closely associated with adiposity than masculinity. These findings indicate that adiposity, compared with masculinity, serves as a more important cue to immunocompetence in female mate choice. PMID:23193134

Translational Insight Into Polycystic Ovary Syndrome (PCOS) From Female Monkeys with PCOS-like Traits.

PubMed

Abbott, David H; Levine, Jon E; Dumesic, Daniel A

2016-01-01

Genetics-based studies of women with polycystic ovary syndrome (PCOS) implicate >20 PCOS risk genes that collectively account for <10% of PCOS. Clinicians now consider that either rare alleles or non-genetic, potentially epigenetic, developmental origins may contribute key pathogenic components to >90% of PCOS cases. Animal models convincingly demonstrate excess fetal testosterone exposure in females as a reliable, epigenetic, developmental origin for PCOS-like traits. In particular, nonhuman primates (NHPs) provide the most faithful emulation of PCOS-like pathophysiology, likely because of close similarities to humans in genomic, developmental, reproductive and metabolic characteristics, as well as aging. Recent appreciation of potential molecular mechanisms contributing to enhanced LH action in both PCOS women (GWAS-based) and PCOS-like monkeys (DNA methylation-based) suggest commonality in pathogenic origins. This review examines the translational relevance of NHP studies to PCOS, identifying characteristics of newborn females at risk for PCOS-like traits and potential prepubertal treatment interventions to ameliorate PCOS onset.

Belongingness as a core personality trait: how social exclusion influences social functioning and personality expression.

PubMed

DeWall, C Nathan; Deckman, Timothy; Pond, Richard S; Bonser, Ian

2011-12-01

People have a fundamental need for positive and lasting relationships. This need to belong is rooted in evolutionary history and gave rise to the development of traits that enable individuals to gain acceptance and to avoid rejection. Because belongingness is a core component of human functioning, social exclusion should influence many cognitive, emotional, and behavioral outcomes and personality expression. This article summarizes recent evidence that social exclusion causes an assortment of outcomes, many of which depend on whether the excluded can gain acceptance or forestall possible distress. It highlights common overlap in physical and social pain systems and how a physical painkiller can reduce the pain of social exclusion. Finally, it shows how social exclusion moderates the effects of traits on cognition, emotion, and behavior. To appreciate personality processes in social contexts, scientists should consider how people respond to social exclusion and how the need to belong influences personality expression. © 2010 The Authors. Journal of Personality © 2011, Wiley Periodicals, Inc.

The landscape of sex-differential transcriptome and its consequent selection in human adults.

PubMed

Gershoni, Moran; Pietrokovski, Shmuel

2017-02-07

The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes. This can impact human evolution by differential selection on mutations with dissimilar effects on the two sexes. We comprehensively mapped human sex-differential genetic architecture across 53 tissues. Analyzing available RNA-sequencing data from 544 adults revealed thousands of genes differentially expressed in the reproductive tracts and tissues common to both sexes. Sex-differential genes are related to various biological systems, and suggest new insights into the pathophysiology of diverse human diseases. We also identified a significant association between sex-specific gene transcription and reduced selection efficiency and accumulation of deleterious mutations, which might affect the prevalence of different traits and diseases. Interestingly, many of the sex-specific genes that also undergo reduced selection efficiency are essential for successful reproduction in men or women. This seeming paradox might partially explain the high incidence of human infertility. This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Power and Autistic Traits

PubMed Central

Overskeid, Geir

2016-01-01

Autistic traits can help people gain and sustain power, and has probably done so throughout history, says the present paper. A number of testable claims follow from this assumption. First, the powerful should have more autistic traits than others – which they do appear to have. Among other things, powerful people, and those with many autistic traits, tend to prefer solitary activities and are often aloof. Moreover, they are often rigid and socially insensitive, low on empathy and with low scores on the trait of agreeableness – and as a rule they do not have many friends. Both groups are also more self-centered than others, more honest, less submissive, more sensitive to slights, and with a stronger tendency to engage in abstract thinking. They tend to behave in bossy or dominant ways, and their moral judgment is more based on rules than on feelings. In addition to experimental evidence, I cite biographies showing that a surprising number of presidents, prime ministers and other powerful people seem to have had traits like those in question – and interestingly, in animals, leaders are often rigid and insensitive to group members’ needs and feelings, mostly acting the way they are themselves inclined to, not responding much to others. Problem solving is important in leadership, and people with many autistic traits appear often to be better thinkers than typical subjects with similar IQs. However, these and other congruities could be coincidences. Hence the question of whether traits the two groups have in common also have a common cause constitutes a strong test of the paper’s thesis – and a common cause does appear to exist, in the form of testosterone’s effects on the central nervous system. Finally, there is evidence that, other things equal, powerful men have more reproductive success than others. If men wielding power do indeed have more autistic traits than those less powerful, this will lead to, other things equal, such traits becoming more common – which can help explain the prevalence of autistic traits. PMID:27630593

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus.

PubMed

Whitney, Kenneth D; Randell, Rebecca A; Rieseberg, Loren H

2010-07-01

*Adaptive trait introgression is increasingly recognized as common. However, it is unclear whether adaptive genetic exchanges typically affect only a single trait, or instead affect multiple aspects of the phenotype. Here, we examine introgression of abiotic tolerance traits between two hybridizing North American sunflower species, Helianthus annuus and Helianthus debilis. *In two common gardens in the hybrid range, we measured 10 ecophysiological, phenological, and architectural traits for parents and their natural and artificial hybrids, and examined how fitness covaried with trait values. *Eight of the 10 traits showed patterns consistent with introgression from H. debilis into H. annuus, and suggested that H. debilis-like traits allowing rapid growth and reproduction before summer heat and drought have been favored in the hybrid range. Natural selection currently favors BC(1) hybrids with H. debilis-like branching traits. *We demonstrate that introgression has altered multiple aspects of the H. annuus phenotype in an adaptive manner, has affected traits relevant to both biotic and abiotic environments, and may have aided expansion of the H. annuus range into central Texas, USA.

Sex-specific genetic architecture of human fatness in Chinese: the SAPPHIRe Study.

PubMed

Chiu, Y-F; Chuang, L-M; Kao, H-Y; Shih, K-C; Lin, M-W; Lee, W-J; Quertermous, T; Curb, J D; Chen, I; Rodriguez, B L; Hsiung, C A

2010-11-01

To dissect the genetic architecture of sexual dimorphism in obesity-related traits, we evaluated the sex-genotype interaction, sex-specific heritability and genome-wide linkages for seven measurements related to obesity. A total of 1,365 non-diabetic Chinese subjects from the family study of the Stanford Asia-Pacific Program of Hypertension and Insulin Resistance were used to search for quantitative trait loci (QTLs) responsible for the obesity-related traits. Pleiotropy and co-incidence effects from the QTLs were also examined using the bivariate linkage approach. We found that sex-specific differences in heritability and the genotype-sex interaction effects were substantially significant for most of these traits. Several QTLs with strong linkage evidence were identified after incorporating genotype by sex (G × S) interactions into the linkage mapping, including one QTL for hip circumference [maximum LOD score (MLS) = 4.22, empirical p = 0.000033] and two QTLs: for BMI on chromosome 12q with MLS 3.37 (empirical p = 0.0043) and 3.10 (empirical p = 0.0054). Sex-specific analyses demonstrated that these linkage signals all resulted from females rather than males. Most of these QTLs for obesity-related traits replicated the findings in other ethnic groups. Bivariate linkage analyses showed several obesity traits were influenced by a common set of QTLs. All regions with linkage signals were observed in one gender, but not in the whole sample, suggesting the genetic architecture of obesity-related traits does differ by gender. These findings are useful for further identification of the liability genes for these phenotypes through candidate genes or genome-wide association analysis.

An intrinsic DFF40/CAD endonuclease deficiency impairs oligonucleosomal DNA hydrolysis during caspase-dependent cell death: a common trait in human glioblastoma cells.

PubMed

Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Martínez-Soler, Fina; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Velasco, Roser; Plans, Gerard; Vidal, Noemi; Tortosa, Avelina; Barcia, Carlos; Bruna, Jordi; Yuste, Victor J

2016-07-01

Glioblastoma (GBM) or grade IV astrocytoma is one of the most devastating human cancers. The loss of DFF40/CAD, the key endonuclease that triggers oligonucleosomal DNA fragmentation during apoptosis, has been linked to genomic instability and cell survival after radiation. Despite the near inevitability of GBM tumor recurrence after treatment, the relationship between DFF40/CAD and GBM remains unexplored. We studied the apoptotic behavior of human GBM-derived cells after apoptotic insult. We analyzed caspase activation and the protein levels and subcellular localization of DFF40/CAD apoptotic endonuclease. DFF40/CAD was also evaluated in histological sections from astrocytic tumors and nontumoral human brain. We showed that GBM cells undergo incomplete apoptosis without generating oligonucleosomal DNA degradation despite the correct activation of executioner caspases. The major defect of GBM cells relied on the improper accumulation of DFF40/CAD at the nucleoplasmic subcellular compartment. Supporting this finding, DFF40/CAD overexpression allowed GBM cells to display oligonucleosomal DNA degradation after apoptotic challenge. Moreover, the analysis of histological slices from astrocytic tumors showed that DFF40/CAD immunoreactivity in tumoral GFAP-positive cells was markedly reduced when compared with nontumoral samples. Our data highlight the low expression levels of DFF40/CAD and the absence of DNA laddering as common molecular traits in GBM. These findings could be of major importance for understanding the malignant behavior of remaining tumor cells after radiochemotherapy. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

CLCA1 and TMEM16A: the link towards a potential cure for airway diseases.

PubMed

Brett, Tom J

2015-10-01

The hallmark traits of chronic obstructive airway diseases are inflammation, airway constriction due to hyperreactivity and mucus overproduction. The current common treatments for asthma and chronic obstructive pulmonary disease target the first two traits with none currently targeting mucus overproduction. The main source of obstructive mucus production is mucus cell metaplasia (MCM), the transdifferentiation of airway epithelial cells into mucus-producing goblet cells, in the small airways. Our current understanding of MCM is profusely incomplete. Few of the molecular players involved in driving MCM in humans have been identified and for many of those that have, their functions and mechanisms are unknown. This fact has limited the development of therapeutics that target mucus overproduction by inhibiting MCM. Current work in the field is aiming to change that.

Sex-Linked Behavior: Evolution, Stability, and Variability.

PubMed

Fine, Cordelia; Dupré, John; Joel, Daphna

2017-07-29

Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sex-Linked Behavior: Evolution, Stability, and Variability.

PubMed

Fine, Cordelia; Dupré, John; Joel, Daphna

2017-09-01

Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the relationship between phylogenetic diversity and trait diversity.

PubMed

Tucker, Caroline M; Davies, T Jonathan; Cadotte, Marc W; Pearse, William D

2018-05-21

Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so-called functional trait diversity, FD); the second quantifies the amount of time or evolutionary history captured by a group of species (phylogenetic diversity, PD). It is often-but controversially-assumed that these putative measures of niche space are at a minimum correlated and perhaps redundant, since more evolutionary time allows for greater accumulation of trait changes. This theoretical expectation remains surprisingly poorly evaluated, particularly in the context of multivariate measures of trait diversity. We evaluated the relationship between phylogenetic diversity and trait diversity using analytical and simulation-based methods across common models of trait evolution. We show that PD correlates with FD increasingly strongly as more traits are included in the FD measure. Our results indicate that phylogenetic diversity can be a useful surrogate for high-dimensional trait diversity, but we also show that the correlation weakens when the underlying process of trait evolution includes variation in rate and optima. © 2018 by the Ecological Society of America.

Erythro-megakaryocytic transcription factors associated with hereditary anemia

PubMed Central

Weiss, Mitchell J.

2014-01-01

Most heritable anemias are caused by mutations in genes encoding globins, red blood cell (RBC) membrane proteins, or enzymes in the glycolytic and hexose monophosphate shunt pathways. A less common class of genetic anemia is caused by mutations that alter the functions of erythroid transcription factors (TFs). Many TF mutations associated with heritable anemia cause truncations or amino acid substitutions, resulting in the production of functionally altered proteins. Characterization of these mutant proteins has provided insights into mechanisms of gene expression, hematopoietic development, and human disease. Mutations within promoter or enhancer regions that disrupt TF binding to essential erythroid genes also cause anemia and heritable variations in RBC traits, such as fetal hemoglobin content. Defining the latter may have important clinical implications for de-repressing fetal hemoglobin synthesis to treat sickle cell anemia and β thalassemia. Functionally important alterations in genes encoding TFs or their cognate cis elements are likely to occur more frequently than currently appreciated, a hypothesis that will soon be tested through ongoing genome-wide association studies and the rapidly expanding use of global genome sequencing for human diagnostics. Findings obtained through such studies of RBCs and associated diseases are likely generalizable to many human diseases and quantitative traits. PMID:24652993

Can Neglected Tropical Diseases Compromise Human Wellbeing in Sex-, Age-, and Trait-Specific Ways?

PubMed Central

Geary, David C.

2016-01-01

Traits that facilitate competition for reproductive resources or that influence mate choice have evolved to signal resilience to infectious disease and other stressors. As a result, the dynamics of competition and choice can, in theory, be used to generate predictions about sex-, age-, and trait-specific vulnerabilities for any sexually reproducing species, including humans. These dynamics and associated vulnerabilities are reviewed for nonhuman species, focusing on traits that are compromised by exposure to parasites. Using the same approach, sex-, age-, and trait-specific vulnerabilities to parasitic disease are illustrated for children’s and adolescent’s physical growth and fitness. Suggestions are then provided for widening the assessment of human vulnerabilities to include age-appropriate measures of behavioral (e.g., children’s play) and cognitive (e.g., language fluency) traits. These are traits that are likely to be compromised by infection in age- and sex-specific ways. Inclusion of these types of measures in studies of neglected tropic diseases has the potential to provide a more nuanced understanding of how these diseases undermine human wellbeing and may provide a useful means to study the efficacy of associated treatments. PMID:27077746

Complex Genetics and the Etiology of Human Congenital Heart Disease

PubMed Central

Gelb, Bruce D.; Chung, Wendy K.

2014-01-01

Congenital heart disease (CHD) is the most common birth defect. Despite considerable advances in care, CHD remains a major contributor to newborn mortality and is associated with substantial morbidities and premature death. Genetic abnormalities appear to be the primary cause of CHD, but identifying precise defects has proven challenging, principally because CHD is a complex genetic trait. Mainly because of recent advances in genomic technology such as next-generation DNA sequencing, scientists have begun to identify the genetic variants underlying CHD. In this article, the roles of modifier genes, de novo mutations, copy number variants, common variants, and noncoding mutations in the pathogenesis of CHD are reviewed. PMID:24985128

Exploring the unknown: assumptions about allelic architecture and strategies for susceptibility variant discovery.

PubMed

McCarthy, Mark I

2009-07-03

Identification of common-variant associations for many common disorders has been highly effective, but the loci detected so far typically explain only a small proportion of the genetic predisposition to disease. Extending explained genetic variance is one of the major near-term goals of human genetic research. Next-generation sequencing technologies offer great promise, but optimal strategies for their deployment remain uncertain, not least because we lack a clear view of the characteristics of the variants being sought. Here, I discuss what can and cannot be inferred about complex trait disease architecture from the information currently available and review the implications for future research strategies.

Functional linear models for association analysis of quantitative traits.

PubMed

Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

2013-11-01

Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY PERIODICALS, INC.

Sexual selection for indicators of intelligence.

PubMed

Miller, G

2000-01-01

Many traits in many species have evolved through sexual selection specifically to function as 'fitness indicators' that reveal good genes and good health. Sexually selected fitness indicators typically show (1) higher coefficients of phenotypic and genetic variation than survival traits, (2) at least moderate genetic heritabilities and (3) positive correlations with many aspects of an animal's general condition, including body size, body symmetry, parasite resistance, longevity and freedom from deleterious mutations. These diagnostic criteria also appear to describe human intelligence (the g factor). This paper argues that during human evolution, mate choice by both sexes focused increasingly on intelligence as a major heritable component of biological fitness. Many human-specific behaviours (such as conversation, music production, artistic ability and humour) may have evolved principally to advertise intelligence during courtship. Though these mental adaptations may be modular at the level of psychological functioning, their efficiencies may be tightly intercorrelated because they still tap into common genetic and neurophysiological variables associated with fitness itself. Although the g factor (like the superordinate factor of fitness itself) probably exists in all animal species, humans evolved an unusually high degree of interest in assessing each other's intelligence during courtship and other social interactions--and, consequently, a unique suite of highly g-loaded mental adaptations for advertising their intelligence to one another through linguistic and cultural interaction. This paper includes nine novel, testable predictions about human intelligence derived from sexual selection theory.

Common genetic variants of the human UMOD gene are functional on transcription and predict plasma uric acid in two distinct populations

PubMed Central

Han, Jia; Liu, Ying; Rao, Fangwen; Nievergelt, Caroline M.; O’Connor, Daniel T.; Wang, Xingyu; Liu, Lisheng; Bu, Dingfang; Liang, Yu; Wang, Fang; Zhang, Luxia; Zhang, Hong; Chen, Yuqing; Wang, Haiyan

2013-01-01

Uromodulin (UMOD) genetic variants cause familial juvenile hyperuricemic nephropathy, characterized by hyperuricemia, decreased renal excretion of UMOD and uric acid; such findings suggest a role for UMOD in the regulation of plasma uric acid. We screened common variants across the UMOD locus in two populations, one from a community-based Chinese population, the other from California twins and siblings. Transcriptional activity of promoter variants was estimated in luciferase reporter plasmids transfected into HEK293 cells and mlMCD3 cells. By variance components in twin pairs, uric acid concentration and excretion were heritable traits. In the primary population from Beijing, we identified that carriers of haplotype GCC displayed higher plasma uric acid, and 3 UMOD promoter variants associated with plasma uric acid. UMOD promoter variants displayed reciprocal effects on urine uric acid excretion and plasma uric acid concentration, suggesting a primary effect on renal tubular handling of urate. These UMOD genetic marker-on-trait associations for uric acid were replicated in an independent American population sample. Site-directed mutagenesis at trait-associated UMOD promoter variants altered promoter activity in transfected luciferase reporter plasmids. These results suggest that UMOD promoter variants seem to initiate a cascade of transcriptional and biochemical changes influencing UMOD secretion, eventuating in elevation of plasma uric acid. PMID:23344472

The thinking ape: the enigma of human consciousness.

PubMed

Paulson, Steve; Chalmers, David; Kahneman, Daniel; Santos, Laurie; Schiff, Nicholas

2013-11-01

What is the origin and nature of consciousness? If consciousness is common to humans and animals alike, what are the defining traits of human consciousness? Moderated by Steve Paulson, executive producer and host of To the Best of Our Knowledge, Nobel laureate psychologist Daniel Kahneman, philosopher David Chalmers, expert in primate cognition Laurie Santos, and physician-scientist Nicholas Schiff discuss what it means to be conscious and examine the human capacities displayed in cognitive, aesthetic, and ethical behaviors, with a focus on the place and function of the mind within nature. The following is an edited transcript of the discussion that occurred October 10, 2012, 7:00-8:15 PM, at the New York Academy of Sciences in New York City. © 2013 New York Academy of Sciences.

Significance of functional disease-causal/susceptible variants identified by whole-genome analyses for the understanding of human diseases.

PubMed

Hitomi, Yuki; Tokunaga, Katsushi

2017-01-01

Human genome variation may cause differences in traits and disease risks. Disease-causal/susceptible genes and variants for both common and rare diseases can be detected by comprehensive whole-genome analyses, such as whole-genome sequencing (WGS), using next-generation sequencing (NGS) technology and genome-wide association studies (GWAS). Here, in addition to the application of an NGS as a whole-genome analysis method, we summarize approaches for the identification of functional disease-causal/susceptible variants from abundant genetic variants in the human genome and methods for evaluating their functional effects in human diseases, using an NGS and in silico and in vitro functional analyses. We also discuss the clinical applications of the functional disease causal/susceptible variants to personalized medicine.

Limited genetic covariance between autistic traits and intelligence: findings from a longitudinal twin study.

PubMed

Hoekstra, Rosa A; Happé, Francesca; Baron-Cohen, Simon; Ronald, Angelica

2010-07-01

Intellectual disability is common in individuals with autism spectrum conditions. However, the strength of the association between both conditions and its relevance to finding the underlying (genetic) causes of autism is unclear. This study aimed to investigate the longitudinal association between autistic traits and intelligence in a general population twin sample and to examine the etiology of this association. Parental ratings of autistic traits and performance on intelligence tests were collected in a sample of 8,848 twin pairs when the children were 7/8, 9, and 12 years old. Phenotypic and longitudinal correlations in the sample as a whole were compared to the associations in the most extreme scoring 5% of the population. The genetic and environmental influences on the overlap between autistic traits and IQ and on the stability of this relationship over time were estimated using structural equation modeling. Autistic traits were modestly negatively correlated to intellectual ability, both in the extreme scoring groups and among the full-range scores. The correlation was stable over time and was mainly explained by autistic trait items assessing communication difficulties. Genetic model fitting showed that autistic traits and IQ were influenced by a common set of genes and a common set of environmental influences that continuously affect these traits throughout childhood. The genetic correlation between autistic traits and IQ was only modest. These findings suggest that individual differences in autistic traits are substantially genetically independent of intellectual functioning. The relevance of these findings to future studies is discussed. (c) 2010 Wiley-Liss, Inc.

Neuropeptide Y gene-by-psychosocial stress interaction effect is associated with obesity in a Korean population.

PubMed

Kim, Hyun-Jin; Min, Kyoung-Bok; Min, Jin-Young

2016-07-01

Chronic psychosocial stress is a crucial risk factor in the development of many diseases including obesity. Neuropeptide Y (NPY), distributed throughout the peripheral and central nervous system, is believed to pay a role in the pathophysiologic relationship between stress and obesity. Although several animal studies have investigated the impact on obesity of interactions between NPY single nucleotide polymorphisms (SNPs) and stress, the same remains to be analyzed in humans. To identify NPY gene-by-stress interaction effects on human obesity, we analyzed the interaction between four NPY SNPs and stress with obesity-related traits, including visceral adipose tissue (VAT). A total of 1468 adult subjects were included for this analysis. In a SNP-only model without interaction with stress, no significant SNPs were found (pSNP>0.05). However, NPY SNPs-by-stress interaction effects were significantly linked to body mass index (BMI), waist circumference, and VAT (pint<0.05), even though a significant interaction effect for rs16135 on BMI was not identified. These significant interaction effects were also detected in interaction results for the binary traits of obesity. Among the obesity traits, mean changes of VAT by increased stress levels in homozygous risk allele carriers were the greatest (range of mean increases for four SNPs (min-max)=12.57cm(2)-29.86cm(2)). This study suggests that common polymorphisms for NPY were associated with human obesity by interacting with psychosocial stress, emphasizing the need for stress management in obesity prevention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transmission fidelity is the key to the build-up of cumulative culture

PubMed Central

Lewis, Hannah M.; Laland, Kevin N.

2012-01-01

Many animals have socially transmitted behavioural traditions, but human culture appears unique in that it is cumulative, i.e. human cultural traits increase in diversity and complexity over time. It is often suggested that high-fidelity cultural transmission is necessary for cumulative culture to occur through refinement, a process known as ‘ratcheting’, but this hypothesis has never been formally evaluated. We discuss processes of information transmission and loss of traits from a cognitive viewpoint alongside other cultural processes of novel invention (generation of entirely new traits), modification (refinement of existing traits) and combination (bringing together two established traits to generate a new trait). We develop a simple cultural transmission model that does not assume major evolutionary changes (e.g. in brain architecture) and show that small changes in the fidelity with which information is passed between individuals can lead to cumulative culture. In comparison, modification and combination have a lesser influence on, and novel invention appears unimportant to, the ratcheting process. Our findings support the idea that high-fidelity transmission is the key driver of human cumulative culture, and that progress in cumulative culture depends more on trait combination than novel invention or trait modification. PMID:22734060

Transmission fidelity is the key to the build-up of cumulative culture.

PubMed

Lewis, Hannah M; Laland, Kevin N

2012-08-05

Many animals have socially transmitted behavioural traditions, but human culture appears unique in that it is cumulative, i.e. human cultural traits increase in diversity and complexity over time. It is often suggested that high-fidelity cultural transmission is necessary for cumulative culture to occur through refinement, a process known as 'ratcheting', but this hypothesis has never been formally evaluated. We discuss processes of information transmission and loss of traits from a cognitive viewpoint alongside other cultural processes of novel invention (generation of entirely new traits), modification (refinement of existing traits) and combination (bringing together two established traits to generate a new trait). We develop a simple cultural transmission model that does not assume major evolutionary changes (e.g. in brain architecture) and show that small changes in the fidelity with which information is passed between individuals can lead to cumulative culture. In comparison, modification and combination have a lesser influence on, and novel invention appears unimportant to, the ratcheting process. Our findings support the idea that high-fidelity transmission is the key driver of human cumulative culture, and that progress in cumulative culture depends more on trait combination than novel invention or trait modification.

Identification of genetic loci shared between schizophrenia and the Big Five personality traits.

PubMed

Smeland, Olav B; Wang, Yunpeng; Lo, Min-Tzu; Li, Wen; Frei, Oleksandr; Witoelar, Aree; Tesli, Martin; Hinds, David A; Tung, Joyce Y; Djurovic, Srdjan; Chen, Chi-Hua; Dale, Anders M; Andreassen, Ole A

2017-05-22

Schizophrenia is associated with differences in personality traits, and recent studies suggest that personality traits and schizophrenia share a genetic basis. Here we aimed to identify specific genetic loci shared between schizophrenia and the Big Five personality traits using a Bayesian statistical framework. Using summary statistics from genome-wide association studies (GWAS) on personality traits in the 23andMe cohort (n = 59,225) and schizophrenia in the Psychiatric Genomics Consortium cohort (n = 82,315), we evaluated overlap in common genetic variants. The Big Five personality traits neuroticism, extraversion, openness, agreeableness and conscientiousness were measured using a web implementation of the Big Five Inventory. Applying the conditional false discovery rate approach, we increased discovery of genetic loci and identified two loci shared between neuroticism and schizophrenia and six loci shared between openness and schizophrenia. The study provides new insights into the relationship between personality traits and schizophrenia by highlighting genetic loci involved in their common genetic etiology.

HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers

PubMed Central

Stadhouders, Ralph; Aktuna, Suleyman; Thongjuea, Supat; Aghajanirefah, Ali; Pourfarzad, Farzin; van IJcken, Wilfred; Lenhard, Boris; Rooks, Helen; Best, Steve; Menzel, Stephan; Grosveld, Frank; Thein, Swee Lay; Soler, Eric

2014-01-01

Genetic studies have identified common variants within the intergenic region (HBS1L-MYB) between GTP-binding elongation factor HBS1L and myeloblastosis oncogene MYB on chromosome 6q that are associated with elevated fetal hemoglobin (HbF) levels and alterations of other clinically important human erythroid traits. It is unclear how these noncoding sequence variants affect multiple erythrocyte characteristics. Here, we determined that several HBS1L-MYB intergenic variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We found that several HBS1L-MYB intergenic variants reduce transcription factor binding, affecting long-range interactions with MYB and MYB expression levels. These data provide a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity. PMID:24614105

The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

PubMed Central

Lohmueller, Kirk E.

2014-01-01

Population genetic studies have found evidence for dramatic population growth in recent human history. It is unclear how this recent population growth, combined with the effects of negative natural selection, has affected patterns of deleterious variation, as well as the number, frequency, and effect sizes of mutations that contribute risk to complex traits. Because researchers are performing exome sequencing studies aimed at uncovering the role of low-frequency variants in the risk of complex traits, this topic is of critical importance. Here I use simulations under population genetic models where a proportion of the heritability of the trait is accounted for by mutations in a subset of the exome. I show that recent population growth increases the proportion of nonsynonymous variants segregating in the population, but does not affect the genetic load relative to a population that did not expand. Under a model where a mutation's effect on a trait is correlated with its effect on fitness, rare variants explain a greater portion of the additive genetic variance of the trait in a population that has recently expanded than in a population that did not recently expand. Further, when using a single-marker test, for a given false-positive rate and sample size, recent population growth decreases the expected number of significant associations with the trait relative to the number detected in a population that did not expand. However, in a model where there is no correlation between a mutation's effect on fitness and the effect on the trait, common variants account for much of the additive genetic variance, regardless of demography. Moreover, here demography does not affect the number of significant associations detected. These findings suggest recent population history may be an important factor influencing the power of association tests and in accounting for the missing heritability of certain complex traits. PMID:24875776

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

PubMed

Morris, C A; Pitchford, W S; Cullen, N G; Esmailizadeh, A K; Hickey, S M; Hyndman, D; Dodds, K G; Afolayan, R A; Crawford, A M; Bottema, C D K

2009-10-01

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant (P < 0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.

Outcrossing and crossbreeding recovers deteriorated traits in laboratory cultured Steinernema carpocapsae nematodes

PubMed Central

Chaston, John M.; Dillman, Adler R.; Shapiro-Ilan, David I.; Bilgrami, Anwar L.; Gaugler, Randy; Hopper, Keith R.; Adams, Byron J.

2011-01-01

The nematode Steinernema carpocapsae infects and kills many pest insects in agroecosystems and is commonly used in biocontrol of these pests. Growth of the nematodes prior to distribution for biocontrol commonly results in deterioration of traits that are essential for nematode persistence in field applications. To better understand the mechanisms underlying trait deterioration of the efficacy of natural parasitism in entomopathogenic nematodes, we explored the maintenance of fitness related traits including reproductive capacity, heat tolerance, virulence to insects and `tail standing' (formerly called nictation) among laboratory-cultured lines derived from natural, randomly mating populations of S. carpocapsae. Laboratory cultured nematode lines with fitness-related trait values below wild-type levels regained wild-type levels of reproductive and heat tolerance traits when outcrossed with a non-deteriorated line, while virulence and `tail standing' did not deteriorate in our experiments. Crossbreeding two trait-deteriorated lines with each other also resulted in restoration of trait means to wild-type levels in most crossbred lines. Our results implicate inbreeding depression as the primary cause of trait deterioration in the laboratory cultured S. carpocapsae. We further suggest the possibility of creating inbred lines purged of deleterious alleles as founders in commercial nematode growth. PMID:21447341

Applications of the 1000 Genomes Project resources

PubMed Central

Zheng-Bradley, Xiangqun

2017-01-01

Abstract The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci, filtering non-pathogenic variants from exome, whole genome and cancer genome sequencing projects, and genetic analysis of population structure and molecular evolution. In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies. PMID:27436001

Reliability of the Walker Cranial Nonmetric Method and Implications for Sex Estimation.

PubMed

Lewis, Cheyenne J; Garvin, Heather M

2016-05-01

The cranial trait scoring method presented in Buikstra and Ubelaker (Standards for data collection from human skeletal remains. Fayetteville, AR: Arkansas Archeological Survey Research Series No. 44, 1994) and Walker (Am J Phys Anthropol, 136, 2008 and 39) is the most common nonmetric cranial sex estimation method utilized by physical and forensic anthropologists. As such, the reliability and accuracy of the method is vital to ensure its validity in forensic applications. In this study, inter- and intra-observer error rates for the Walker scoring method were calculated using a sample of U.S. White and Black individuals (n = 135). Cohen's weighted kappas, intraclass correlation coefficients, and percentage agreements indicate good agreement between trials and observers for all traits except the mental eminence. Slight disagreement in scoring, however, was found to impact sex classifications, leading to lower accuracy rates than those published by Walker. Furthermore, experience does appear to impact trait scoring and sex classification. The use of revised population-specific equations that avoid the mental eminence is highly recommended to minimize the potential for misclassifications. © 2016 American Academy of Forensic Sciences.

Be meek or be bold? A colony-level behavioural syndrome in ants

PubMed Central

Bengston, S. E.; Dornhaus, A.

2014-01-01

Consistent individual variation in animal behaviour is nearly ubiquitous and has important ecological and evolutionary implications. Additionally, suites of behavioural traits are often correlated, forming behavioural syndromes in both humans and other species. Such syndromes are often described by testing for variation in traits across commonly described dimensions (e.g. aggression and neophobia), independent of whether this variation is ecologically relevant to the focal species. Here, we use a variety of ecologically relevant behavioural traits to test for a colony-level behavioural syndrome in rock ants (Temnothorax rugatulus). Specifically, we combine field and laboratory assays to measure foraging effort, how colonies respond to different types of resources, activity level, response to threat and aggression level. We find evidence for a colony level syndrome that suggests colonies consistently differ in coping style—some are more risk-prone, whereas others are more risk-averse. Additionally, by collecting data across the North American range of this species, we show that environmental variation may affect how different populations maintain consistent variation in colony behaviour. PMID:25100691

Hairless mutation: a driving force of humanization from a human–ape common ancestor by enforcing upright walking while holding a baby with both hands

PubMed Central

Sutou, Shizuyo

2012-01-01

Three major characteristics distinguish humans from other primates: bipedality, practical nakedness, and the family as a social unit. A hairless mutation introduced into the chimpanzee/human last common ancestor (CLCA) 6 million years ago (Mya) diverged hairless human and hairy chimpanzee lineages. All primates except humans can carry their babies without using their hands. A hairless mother would be forced to stand and walk upright. Her activities would be markedly limited. The male partner would have to collect food and carry it to her by hand to keep her and their baby from starving; irresponsible and selfish males could not have left their offspring. The mother would have sexually accepted her partner at any time as a reward for food. Sexual relations irrespective of estrus cycles might have strengthened the pair bond. Molecular and paleontological dating indicates that CLCA existed 6 Mya, and early hominin fossils show that they were bipeds, indicating that humanization from CLCA occurred rapidly. A single mutation in animals with scalp hair is known to induce hairless phenotype (ectodermal dysplasia). Bipedalism and hairlessness are disadvantageous traits; only those who could survive trials and tribulations in cooperation with family members must have been able to evolve as humans. PMID:22404045

Personality traits affecting judgement bias task performance in dogs (Canis familiaris).

PubMed

Barnard, Shanis; Wells, Deborah L; Milligan, Adam D S; Arnott, Gareth; Hepper, Peter G

2018-04-27

Certain personality traits (e.g. anxiousness, fearfulness), are known to affect the cognitive processing of environmental stimuli, such as the judgement of ambiguous stimuli (judgement bias). Our aim was to assess if personality traits are predictive of a more or less 'pessimistic' or 'optimistic' judgement bias in the domestic dog. We assessed dog personality (N = 31) using two validated protocols: the Dog Mentality Assessment (standardised battery test) and the CBARQ (owner-based survey). We used a common task based on the animals' latency to approach a bowl placed in one of three ambiguous positions (Near Positive, Middle, Near Negative) between a baited (Positive) and a non-baited food bowl (Negative) to assess judgement bias. Linear Mixed Model analyses revealed that dogs scoring higher on sociability, excitability and non-social-fear had shorter response latencies to bowls in an ambiguous location, indicating a more 'optimistic' bias. In contrast, dogs scoring higher on separation-related-behaviour and dog-directed-fear/aggression traits were more likely to judge an ambiguous stimulus as leading to a negative outcome, indicating a more 'pessimistic' bias. Results, partially consistent with previous findings in humans, indicate that personality plays a role in the cognitive processing of environmental stimuli in the domestic dog.

Disruption of the Aortic Elastic Lamina and Medial Calcification Share Genetic Determinants in Mice

PubMed Central

Wang, Susanna S.; Martin, Lisa J.; Schadt, Eric E.; Meng, Haijin; Wang, Xuping; Zhao, Wei; Ingram-Drake, Leslie; Nebohacova, Martina; Mehrabian, Margarete; Drake, Thomas A.; Lusis, Aldons J.

2010-01-01

Background Disruption of the elastic lamina, as an early indicator of aneurysm formation, and vascular calcification frequently occur together in atherosclerotic lesions of humans. Methods and Results We now report evidence of shared genetic basis for disruption of the elastic lamina (medial disruption) and medial calcification in an F2 mouse intercross between C57BL/6J and C3H/HeJ on a hyperlipidemic apolipoprotein E (ApoE−/−) null background. We identified 3 quantitative trait loci (QTLs) on chromosomes 6, 13, and 18, which are common to both traits, and 2 additional QTLs for medial calcification on chromosomes 3 and 7. Medial disruption, including severe disruptions leading to aneurysm formation, and medial calcification were highly correlated and occurred concomitantly in the cross. The chromosome 18 locus showed a striking male sex-specificity for both traits. To identify candidate genes, we integrated data from microarray analysis, genetic segregation, and clinical traits. The chromosome 7 locus contains the Abcc6 gene, known to mediate myocardial calcification. Using transgenic complementation, we show that Abcc6 also contributes to aortic medial calcification. Conclusions Our data indicate that calcification, though possibly contributory, does not always lead to medial disruption and that in addition to aneurysm formation, medial disruption may be the precursor to calcification. PMID:20031637

Sticking with the nice guy: trait warmth information impairs learning and modulates person perception brain network activity.

PubMed

Lee, Victoria K; Harris, Lasana T

2014-12-01

Social learning requires inferring social information about another person, as well as evaluating outcomes. Previous research shows that prior social information biases decision making and reduces reliance on striatal activity during learning (Delgado, Frank, & Phelps, Nature Neuroscience 8 (11): 1611-1618, 2005). A rich literature in social psychology on person perception demonstrates that people spontaneously infer social information when viewing another person (Fiske & Taylor, 2013) and engage a network of brain regions, including the medial prefrontal cortex, temporal parietal junction, superior temporal sulcus, and precuneus (Amodio & Frith, Nature Reviews Neuroscience, 7(4), 268-277, 2006; Haxby, Gobbini, & Montgomery, 2004; van Overwalle Human Brain Mapping, 30, 829-858, 2009). We investigate the role of these brain regions during social learning about well-established dimensions of person perception-trait warmth and trait competence. We test the hypothesis that activity in person perception brain regions interacts with learning structures during social learning. Participants play an investment game where they must choose an agent to invest on their behalf. This choice is guided by cues signaling trait warmth or trait competence based on framing of monetary returns. Trait warmth information impairs learning about human but not computer agents, while trait competence information produces similar learning rates for human and computer agents. We see increased activation to warmth information about human agents in person perception brain regions. Interestingly, activity in person perception brain regions during the decision phase negatively predicts activity in the striatum during feedback for trait competence inferences about humans. These results suggest that social learning may engage additional processing within person perception brain regions that hampers learning in economic contexts.

Genome-wide association analysis of symbiotic nitrogen fixation in common bean

USDA-ARS?s Scientific Manuscript database

A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean diversity panel (ADP) comprised of 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in...

Methods for meta-analysis of multiple traits using GWAS summary statistics.

PubMed

Ray, Debashree; Boehnke, Michael

2018-03-01

Genome-wide association studies (GWAS) for complex diseases have focused primarily on single-trait analyses for disease status and disease-related quantitative traits. For example, GWAS on risk factors for coronary artery disease analyze genetic associations of plasma lipids such as total cholesterol, LDL-cholesterol, HDL-cholesterol, and triglycerides (TGs) separately. However, traits are often correlated and a joint analysis may yield increased statistical power for association over multiple univariate analyses. Recently several multivariate methods have been proposed that require individual-level data. Here, we develop metaUSAT (where USAT is unified score-based association test), a novel unified association test of a single genetic variant with multiple traits that uses only summary statistics from existing GWAS. Although the existing methods either perform well when most correlated traits are affected by the genetic variant in the same direction or are powerful when only a few of the correlated traits are associated, metaUSAT is designed to be robust to the association structure of correlated traits. metaUSAT does not require individual-level data and can test genetic associations of categorical and/or continuous traits. One can also use metaUSAT to analyze a single trait over multiple studies, appropriately accounting for overlapping samples, if any. metaUSAT provides an approximate asymptotic P-value for association and is computationally efficient for implementation at a genome-wide level. Simulation experiments show that metaUSAT maintains proper type-I error at low error levels. It has similar and sometimes greater power to detect association across a wide array of scenarios compared to existing methods, which are usually powerful for some specific association scenarios only. When applied to plasma lipids summary data from the METSIM and the T2D-GENES studies, metaUSAT detected genome-wide significant loci beyond the ones identified by univariate analyses. Evidence from larger studies suggest that the variants additionally detected by our test are, indeed, associated with lipid levels in humans. In summary, metaUSAT can provide novel insights into the genetic architecture of a common disease or traits. © 2017 WILEY PERIODICALS, INC.

Computational analysis of gene-gene interactions using multifactor dimensionality reduction.

PubMed

Moore, Jason H

2004-11-01

Understanding the relationship between DNA sequence variations and biologic traits is expected to improve the diagnosis, prevention and treatment of common human diseases. Success in characterizing genetic architecture will depend on our ability to address nonlinearities in the genotype-to-phenotype mapping relationship as a result of gene-gene interactions, or epistasis. This review addresses the challenges associated with the detection and characterization of epistasis. A novel strategy known as multifactor dimensionality reduction that was specifically designed for the identification of multilocus genetic effects is presented. Several case studies that demonstrate the detection of gene-gene interactions in common diseases such as atrial fibrillation, Type II diabetes and essential hypertension are also discussed.

Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies

USDA-ARS?s Scientific Manuscript database

Despite large variation in root traits among species, we have limited understanding of how traits are related to diverse soil resource acquisition strategies. We examined root trait variation among 33 species co-existing in Northeastern US forests that form the two most common mutualisms with mycorr...

Psychometric Properties of the ASPeCT-DD: Measuring Positive Traits in Persons with Developmental Disabilities

ERIC Educational Resources Information Center

Woodard, Cooper

2009-01-01

Background: The Assessment Scale for Positive Character Traits-Developmental Disabilities (ASPeCT-DD) was designed to measure the presence and strength of selected positive or strength-based traits in persons with developmental disabilities. These traits may help to determine level of happiness or value associated with the more commonly measured…

Personality Traits of Minority Arab Teachers in the Arab Educational System in Israel

ERIC Educational Resources Information Center

Abu Hussain, Jamal; Abu Hussain, Nadia

2017-01-01

The present research examined the personality traits prevalent among Arab teachers as a minority in the Arab educational system in Israel. Personality traits has much significance in the prediction of human behavior in various situations. Personality traits affect a person's behavior. Usually personality traits do not change, and they are…

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

PubMed Central

Ranciaro, Alessia; Campbell, Michael C.; Hirbo, Jibril B.; Ko, Wen-Ya; Froment, Alain; Anagnostou, Paolo; Kotze, Maritha J.; Ibrahim, Muntaser; Nyambo, Thomas; Omar, Sabah A.; Tishkoff, Sarah A.

2014-01-01

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa. PMID:24630847

Metabolic syndrome-related composite factors over 5 years in the STANISLAS family study: genetic heritability and common environmental influences.

PubMed

Herbeth, Bernard; Samara, Anastasia; Ndiaye, Coumba; Marteau, Jean-Brice; Berrahmoune, Hind; Siest, Gérard; Visvikis-Siest, Sophie

2010-06-03

We estimated genetic heritability and common environmental influences for various traits related to metabolic syndrome in young families from France. At entrance and after 5 years, nineteen traits related to metabolic syndrome were measured in a sample of families drawn from the STANISLAS study. In addition, 5 aggregates of these traits were identified using factor analysis. At entrance, genetic heritability was high (20 to 44%) for plasma lipids and lipoproteins, uric acid, fasting glucose, and the related clusters "risk lipids" and "protective lipids". Intermediate or low genetic heritability (less than 20%) was shown for triglycerides, adiposity indices, blood pressure, hepatic enzyme activity, inflammatory makers and the related clusters: "liver enzymes", "adiposity/blood pressure" and "inflammation". Moreover, common environmental influences were significant for all the parameters. With regard to 5-year changes, polygenic variance was low and not statistically significant for any of the individual variables or clusters whereas shared environment influence was significant. In these young families, genetic heritability of metabolic syndrome-related traits was generally lower than previously reported while the common environmental influences were greater. In addition, only shared environment contributed to short-term changes of these traits. Copyright 2010 Elsevier B.V. All rights reserved.

The circle of life: A cross-cultural comparison of children's attribution of life-cycle traits.

PubMed

Burdett, Emily R R; Barrett, Justin L

2016-06-01

Do children attribute mortality and other life-cycle traits to all minded beings? The present study examined whether culture influences young children's ability to conceptualize and differentiate human beings from supernatural beings (such as God) in terms of life-cycle traits. Three-to-5-year-old Israeli and British children were questioned whether their mother, a friend, and God would be subject to various life-cycle processes: Birth, death, ageing, existence/longevity, and parentage. Children did not anthropomorphize but differentiated among human and supernatural beings, attributing life-cycle traits to humans, but not to God. Although 3-year-olds differentiated significantly among agents, 5-year-olds attributed correct life-cycle traits more consistently than younger children. The results also indicated some cross-cultural variation in these attributions. Implications for biological conceptual development are discussed. © 2015 The British Psychological Society.

Phylogenetics Exercise Using Inherited Human Traits

ERIC Educational Resources Information Center

Tuimala, Jarno

2006-01-01

A bioinformatics laboratory exercise based on inherited human morphological traits is presented. It teaches how morphological characters can be used to study the evolutionary history of humans using parsimony. The exercise can easily be used in a pen-and-paper laboratory, but if computers are available, a more versatile analysis can be carried…

Deafness, genetics and dysgenics.

PubMed

Nunes, Rui

2006-01-01

It has been argued by some authors that our reaction to deaf parents who choose deafness for their children ought to be compassion, not condemnation. Although I agree with the reasoning proposed I suggest that this practice could be regarded as unethical. In this article, I shall use the term "dysgenic" as a culturally imposed genetic selection not to achieve any improvement of the human person but to select genetic traits that are commonly accepted as a disabling condition by the majority of the social matrix; in short as a handicap. As in eugenics, dysgenics can be achieved in a positive and a negative way. Positive dysgenics intends to increase the overall number of people with a particular genetic trait. Marriage between deaf people or conceiving deaf children through reproductive technology are examples of positive dysgenics. Negative dysgenics can be obtained through careful prenatal or pre-implantation selection and abortion (or discarding) of normal embryos and foetuses. Only deaf children would be allowed to live. If dysgenics is seen as a programmed genetic intervention that undesirably shapes the human condition--like deliberately creating deaf or dwarf people--the professionals involved in reproductive technologies should answer the question if this should be an accepted ethical practice because the basic human right to an open future is violated.

Effects of playing video games on perceptions of one's humanity.

PubMed

Greitemeyer, Tobias

2013-01-01

According to self-perception theory, individuals infer their characteristics by observing their own behavior. In the present research, the hypothesis is examined whether helping behavior increases perceptions of one's own humanity even when help is given that does not benefit a real person. In fact, two studies revealed that playing a prosocial video game (where the goal is to help and care for other game characters) led to increased perceptions of the player's own humanity (in particular, for positive humanity traits). Results also revealed that playing a violent, relative to a neutral, video game decreased perceptions of humanity on positive humanity traits and increased perceptions of humanity on negative humanity traits. Taken together, it appears that being helpful while playing video games leads to the perception of being more human, whereas being harmful while playing video games leads players to perceive themselves negatively.

Heteroscedastic Latent Trait Models for Dichotomous Data.

PubMed

Molenaar, Dylan

2015-09-01

Effort has been devoted to account for heteroscedasticity with respect to observed or latent moderator variables in item or test scores. For instance, in the multi-group generalized linear latent trait model, it could be tested whether the observed (polychoric) covariance matrix differs across the levels of an observed moderator variable. In the case that heteroscedasticity arises across the latent trait itself, existing models commonly distinguish between heteroscedastic residuals and a skewed trait distribution. These models have valuable applications in intelligence, personality and psychopathology research. However, existing approaches are only limited to continuous and polytomous data, while dichotomous data are common in intelligence and psychopathology research. Therefore, in present paper, a heteroscedastic latent trait model is presented for dichotomous data. The model is studied in a simulation study, and applied to data pertaining alcohol use and cognitive ability.

Confirming Testlet Effects

ERIC Educational Resources Information Center

DeMars, Christine E.

2012-01-01

A testlet is a cluster of items that share a common passage, scenario, or other context. These items might measure something in common beyond the trait measured by the test as a whole; if so, the model for the item responses should allow for this testlet trait. But modeling testlet effects that are negligible makes the model unnecessarily…

A statistical approach to root system classification

PubMed Central

Bodner, Gernot; Leitner, Daniel; Nakhforoosh, Alireza; Sobotik, Monika; Moder, Karl; Kaul, Hans-Peter

2013-01-01

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for “plant functional type” identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential. PMID:23914200

A statistical approach to root system classification.

PubMed

Bodner, Gernot; Leitner, Daniel; Nakhforoosh, Alireza; Sobotik, Monika; Moder, Karl; Kaul, Hans-Peter

2013-01-01

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for "plant functional type" identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential.

Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

DOE PAGES

Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Jr., Marcio F. R.; ...

2016-09-06

Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genesmore » in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. Lastly, these polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.« less

DSM-5 pathological personality traits and the personality assessment inventory.

PubMed

Hopwood, Christopher J; Wright, Aidan G C; Krueger, Robert F; Schade, Nick; Markon, Kristian E; Morey, Leslie C

2013-06-01

Section 3 of the DSM-5 will include a pathological personality trait system rooted in the quantitative epistemology of personality and clinical psychology. This system has the potential to enhance the clinical utility of the diagnostic nosology by providing a means for the dimensional assessment of individuals with psychopathology. However, there is limited research on the associations of DSM-5 traits with common mental disorders and related clinical phenomena as measured by currently popular assessment instruments. The purpose of this article was to evaluate the convergence of the DSM-5 trait system with a well-validated broadband clinical instrument, the Personality Assessment Inventory (PAI). Bivariate correlations were examined and factor analytic methods were used to examine the degree to which the DSM-5 traits and PAI capture common variance in personality and mental health. In a student sample (N = 1,001), we found broad convergence between the DSM-5 traits and PAI, which could be organized effectively using five factors. The implications of these findings for using traits to address issues related to diagnostic co-occurrence and heterogeneity in routine clinical assessment are discussed.

Nonmetric traits of permanent posterior teeth in Kerala population: A forensic overview

PubMed Central

Baby, Tibin K; Sunil, S; Babu, Sharlene Sara

2017-01-01

Introduction: Dental morphology is a highly heritable characteristic which is stable with time and has a fairly high state of preservation. Nonmetric dental traits have crucial role in ethnic classifications of a population that helps in forensic racial identification purposes. Aims and Objectives: To determine the frequency and variability of possible nonmetric tooth traits using extracted permanent posterior teeth from Kerala population for discerning racial ethnicity. Materials and Methods: This qualitative, cross-sectional study was carried out using 1743 extracted intact permanent posterior teeth collected from different dental clinics situated all over Kerala. Results: The more common features on premolars were multiple lingual cusps (31.21%), distal accessary ridges (16.28%) and Tom's root (17.9%). In upper first molars, Carabelli trait expression was 17.78% and other common features included metaconulo, cusp 5 and enamel extensions. Conclusion: Posterior tooth traits had variable expression in the study population. Low prevalence rate of Carabelli trait in this study is characteristic of Asian population. This research explored new elements of invaluable tooth traits values to understand racial ethnicity of Kerala population. PMID:28932045

Higher sensory processing sensitivity, introversion and ectomorphism: New biomarkers for human creativity in developing rural areas

PubMed Central

Rizzo-Sierra, Carlos V; Leon-S, Martha E; Leon-Sarmiento, Fidias E

2012-01-01

The highly sensitive trait present in animals, has also been proposed as a human neurobiological trait. People having such trait can process larger amounts of sensory information than usual, making it an excellent attribute that allows to pick up subtle environmental details and cues. Furthermore, this trait correlates to some sort of giftedness such as higher perception, inventiveness, imagination and creativity. We present evidences that support the existance of key neural connectivity between the mentioned trait, higher sensory processing sensitivity, introversion, ectomorphism and creativity. The neurobiological and behavioral implications that these biomarkers have in people living in developing rural areas are discussed as well. PMID:22865969

Differences in forest plant functional trait distributions across land-use and productivity gradients

Treesearch

Margaret M. Mayfield; John M. Dwyer; Loic Chalmandrier; Jessie A. Wells; Stephen P. Bonser; Carla P. Catterall; Fabrice DeClerck; Yi Ding; Jennifer M. Fraterrigo; Daniel J. Metcalfe; Cibele Queiroz; Peter A. Vesk; John W. Morgan

2013-01-01

• Premise of study: Plant functional traits are commonly used as proxies for plant responses to environmental challenges, yet few studies have explored how functional trait distributions differ across gradients of land-use change. By comparing trait distributions in intact forests with those across land-use change gradients, we can improve our understanding of the ways...

Genome-Wide Copy Number Variation Association Analyses for Age at Menarche

PubMed Central

Li, Jian; Pan, Rong; Shen, Hui; Tian, Qing; Zhou, Yu; Liu, Yong-Jun

2012-01-01

Context: Menarche is a significant physiological event for women. Age at menarche (AAM) is a heritable trait associated with many common female diseases. The genetic basis and the mechanism for AAM are largely unknown. Copy number variation (CNV) is a common type of genetic variation underlying human complex traits. The importance of CNV to AAM variation is unclear. Objective: The objective of the study was to identify CNV important to AAM variation. Design: We performed the first genome-wide CNV study of AAM in 1654 Caucasian females using Affymetrix human single-nucleotide polymorphism 6.0 array. We also replicated our findings in another Chinese cohort containing 752 women. Results: We identified a CNV, variation_38399, in the 2q14.2 region, for association with AAM (P = 1.03 × 10−3). The CNV has two variants (one copy and two copy), with a mean AAM of 14.00 yr and 12.90 yr, respectively. Interestingly, in a Chinese sample containing 752 women, this CNV has been replicated both with a marginally significant P = 0.090 and with a same direction of effect (a lower copy number for a later AAM). The CNV is located approximately 75 kb upstream of the diazepam binding inhibitor (DBI), a gene known to regulate estrogen levels, a key factor for menarche. Conclusion: Our findings for the first time identified a novel CNV and suggested the DBI-mediated endocrinological pathway as a potential mechanism for AAM regulation. PMID:22904172

Differences in the 2nd to 4th digit length ratio in humans reflect shifts along the common allometric line

PubMed Central

Kratochvíl, Lukáš; Flegr, Jaroslav

2009-01-01

Ratios often lead to biased conclusions concerning the actual relationships between examined traits and comparisons of the relative size of traits among groups. Therefore, the use of ratios has been abandoned in most comparative studies. However, ratios such as body mass index and waist-to-hip ratio are widely used in evolutionary biology and medicine. One such, the ratio of the 2nd to the 4th finger (2D : 4D), has been the subject of much recent interest in both humans and animals. Most studies agree that 2D : 4D is sexually dimorphic. In men, the 2nd digit tends to be shorter than the 4th, while in women the 2nd digit tends to be of the same size or slightly longer than the 4th. Nevertheless, here we demonstrate that the sexes do not greatly differ in the scaling between the 2nd and 4th digit. Sexual differences in 2D : 4D are mainly caused by the shift along the common allometric line with non-zero intercept, which means 2D : 4D necessarily decreases with increasing finger length, and the fact that men have longer fingers than women. We conclude that previously published results on the 2D : 4D ratio are biased by its covariation with finger length. We strongly recommend regression-based approaches for comparisons of hand shape among different groups. PMID:19553247

Outcrossing and crossbreeding recovers deteriorated traits in laboratory cultured Steinernema carpocapsae nematodes.

PubMed

Chaston, John M; Dillman, Adler R; Shapiro-Ilan, David I; Bilgrami, Anwar L; Gaugler, Randy; Hopper, Keith R; Adams, Byron J

2011-06-01

The nematode Steinernema carpocapsae infects and kills many pest insects in agro-ecosystems and is commonly used in biocontrol of these pests. Growth of the nematodes prior to distribution for biocontrol commonly results in deterioration of traits that are essential for nematode persistence in field applications. To better understand the mechanisms underlying trait deterioration of the efficacy of natural parasitism in entomopathogenic nematodes, we explored the maintenance of fitness related traits including reproductive capacity, heat tolerance, virulence to insects and 'tail standing' (formerly called nictation) among laboratory-cultured lines derived from natural, randomly mating populations of S. carpocapsae. Laboratory cultured nematode lines with fitness-related trait values below wild-type levels regained wild-type levels of reproductive and heat tolerance traits when outcrossed with a non-deteriorated line, while virulence and 'tail standing' did not deteriorate in our experiments. Crossbreeding two trait-deteriorated lines with each other also resulted in restoration of trait means to wild-type levels in most crossbred lines. Our results implicate inbreeding depression as the primary cause of trait deterioration in the laboratory cultured S. carpocapsae. We further suggest the possibility of creating inbred lines purged of deleterious alleles as founders in commercial nematode growth. Copyright © 2011 Australian Society for Parasitology Inc. All rights reserved.

Estimation of genetic parameters and selection of high-yielding, upright common bean lines with slow seed-coat darkening.

PubMed

Alvares, R C; Silva, F C; Melo, L C; Melo, P G S; Pereira, H S

2016-11-21

Slow seed coat darkening is desirable in common bean cultivars and genetic parameters are important to define breeding strategies. The aims of this study were to estimate genetic parameters for plant architecture, grain yield, grain size, and seed-coat darkening in common bean; identify any genetic association among these traits; and select lines that associate desirable phenotypes for these traits. Three experiments were set up in the winter 2012 growing season, in Santo Antônio de Goiás and Brasília, Brazil, including 220 lines obtained from four segregating populations and five parents. A triple lattice 15 x 15 experimental design was used. The traits evaluated were plant architecture, grain yield, grain size, and seed-coat darkening. Analyses of variance were carried out and genetic parameters such as heritability, gain expected from selection, and correlations, were estimated. For selection of superior lines, a "weight-free and parameter-free" index was used. The estimates of genetic variance, heritability, and gain expected from selection were high, indicating good possibility for success in selection of the four traits. The genotype x environment interaction was proportionally more important for yield than for the other traits. There was no strong genetic correlation observed among the four traits, which indicates the possibility of selection of superior lines with many traits. Considering simultaneous selection, it was not possible to join high genetic gains for the four traits. Forty-four lines that combined high yield, more upright plant architecture, slow darkening grains, and commercial grade size were selected.

Species climate range influences hydraulic and stomatal traits in Eucalyptus species.

PubMed

Bourne, Aimee E; Creek, Danielle; Peters, Jennifer M R; Ellsworth, David S; Choat, Brendan

2017-07-01

Plant hydraulic traits influence the capacity of species to grow and survive in water-limited environments, but their comparative study at a common site has been limited. The primary aim of this study was to determine whether selective pressures on species originating in drought-prone environments constrain hydraulic traits among related species grown under common conditions. Leaf tissue water relations, xylem anatomy, stomatal behaviour and vulnerability to drought-induced embolism were measured on six Eucalyptus species growing in a common garden to determine whether these traits were related to current species climate range and to understand linkages between the traits. Hydraulically weighted xylem vessel diameter, leaf turgor loss point, the water potential at stomatal closure and vulnerability to drought-induced embolism were significantly ( P < 0·05) correlated with climate parameters from the species range. There was a co-ordination between stem and leaf parameters with the water potential at turgor loss, 12 % loss of conductivity and the point of stomatal closure significantly correlated. The correlation of hydraulic, stomatal and anatomical traits with climate variables from the species' original ranges suggests that these traits are genetically constrained. The conservative nature of xylem traits in Eucalyptus trees has important implications for the limits of species responses to changing environmental conditions and thus for species survival and distribution into the future, and yields new information for physiological models. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Phenotypic and genetic relations between the HEXACO dimensions and trait emotional intelligence.

PubMed

Veselka, Livia; Petrides, K V; Schermer, Julie Aitken; Cherkas, Lynn F; Spector, Tim D; Vernon, Philip A

2010-02-01

The present study investigated the location of trait emotional intelligence (trait EI or trait emotional self-efficacy) within the context of the HEXACO model - a more comprehensive personality framework than the conventional Big Five structure. A total of 666 MZ and 526 DZ adult twin pairs from the United Kingdom completed the short form of the Trait Emotional Intelligence Questionnaire (TEIQue-SF) and the short form of the HEXACO Personality Inventory (HEXACO-60). Many significant phenotypic correlations between the TEIQue-SF and the HEXACO-60 were obtained, which were strongest for HEXACO Extraversion, and weakest for HEXACO Honesty-Humility. As was expected, Emotionality was the only HEXACO dimension to correlate negatively with TEIQue-SF scores. Bivariate behavioral genetic analyses revealed that all phenotypic correlations were attributable to common genetic and common nonshared environmental factors. The study confirms the validity of trait EI as a constellation of emotional self-perceptions located at the lower levels of personality.

A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure.

PubMed

Frayling, Timothy M; Beaumont, Robin N; Jones, Samuel E; Yaghootkar, Hanieh; Tuke, Marcus A; Ruth, Katherine S; Casanova, Francesco; West, Ben; Locke, Jonathan; Sharp, Seth; Ji, Yingjie; Thompson, William; Harrison, Jamie; Etheridge, Amy S; Gallins, Paul J; Jima, Dereje; Wright, Fred; Zhou, Yihui; Innocenti, Federico; Lindgren, Cecilia M; Grarup, Niels; Murray, Anna; Freathy, Rachel M; Weedon, Michael N; Tyrrell, Jessica; Wood, Andrew R

2018-04-10

Fibroblast growth factor 21 (FGF21) is a hormone that has insulin-sensitizing properties. Some trials of FGF21 analogs show weight loss and lipid-lowering effects. Recent studies have shown that a common allele in the FGF21 gene alters the balance of macronutrients consumed, but there was little evidence of an effect on metabolic traits. We studied a common FGF21 allele (A:rs838133) in 451,099 people from the UK Biobank study, aiming to use the human allele to inform potential adverse and beneficial effects of targeting FGF21. We replicated the association between the A allele and higher percentage carbohydrate intake. We then showed that this allele is more strongly associated with higher blood pressure and waist-hip ratio, despite an association with lower total body-fat percentage, than it is with BMI or type 2 diabetes. These human phenotypes of variation in the FGF21 gene will inform research into FGF21's mechanisms and therapeutic potential. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Axon guidance pathways served as common targets for human speech/language evolution and related disorders.

PubMed

Lei, Huimeng; Yan, Zhangming; Sun, Xiaohong; Zhang, Yue; Wang, Jianhong; Ma, Caihong; Xu, Qunyuan; Wang, Rui; Jarvis, Erich D; Sun, Zhirong

2017-11-01

Human and several nonhuman species share the rare ability of modifying acoustic and/or syntactic features of sounds produced, i.e. vocal learning, which is the important neurobiological and behavioral substrate of human speech/language. This convergent trait was suggested to be associated with significant genomic convergence and best manifested at the ROBO-SLIT axon guidance pathway. Here we verified the significance of such genomic convergence and assessed its functional relevance to human speech/language using human genetic variation data. In normal human populations, we found the affected amino acid sites were well fixed and accompanied with significantly more associated protein-coding SNPs in the same genes than the rest genes. Diseased individuals with speech/language disorders have significant more low frequency protein coding SNPs but they preferentially occurred outside the affected genes. Such patients' SNPs were enriched in several functional categories including two axon guidance pathways (mediated by netrin and semaphorin) that interact with ROBO-SLITs. Four of the six patients have homozygous missense SNPs on PRAME gene family, one youngest gene family in human lineage, which possibly acts upon retinoic acid receptor signaling, similarly as FOXP2, to modulate axon guidance. Taken together, we suggest the axon guidance pathways (e.g. ROBO-SLIT, PRAME gene family) served as common targets for human speech/language evolution and related disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Testing the lexical hypothesis: are socially important traits more densely reflected in the English lexicon?

PubMed

Wood, Dustin

2015-02-01

Using a set of 498 English words identified by Saucier (1997) as common person-descriptor adjectives or trait terms, I tested 3 instantiations of the lexical hypothesis, which posit that more socially important person descriptors show greater density in the lexicon. Specifically, I explored whether trait terms that have greater relational impact (i.e., more greatly influence how others respond to a person) have more synonyms, are more frequently used, and are more strongly correlated with other trait terms. I found little evidence to suggest that trait terms rated as having greater relational impact were more frequently used or had more synonyms. However, these terms correlated more strongly with other trait terms in the set. Conversely, a trait term's loadings on structural factors (e.g., the Big Five, HEXACO) were extremely good predictors of the term's relational impact. The findings suggest that the lexical hypothesis may not be strongly supported in some ways it is commonly understood but is supported in the manner most important to investigations of trait structure. Specifically, trait terms with greater relational impact tend to more strongly correlate with other terms in lexical sets and thus have a greater role in driving the location of factors in analyses of trait structure. Implications for understanding the meaning of lexical factors such as the Big Five are discussed. PsycINFO Database Record (c) 2015 APA, all rights reserved.

LncRNA, a new component of expanding RNA-protein regulatory network important for animal sperm development.

PubMed

Zhang, Chenwang; Gao, Liuze; Xu, Eugene Yujun

2016-11-01

Spermatogenesis is one of the fundamental processes of sexual reproduction, present in almost all metazoan animals. Like many other reproductive traits, developmental features and traits of spermatogenesis are under strong selective pressure to change, both at morphological and underlying molecular levels. Yet evidence suggests that some fundamental features of spermatogenesis may be ancient and conserved among metazoan species. Identifying the underlying conserved molecular mechanisms could reveal core components of metazoan spermatogenic machinery and provide novel insight into causes of human infertility. Conserved RNA-binding proteins and their interacting RNA network emerge to be a common theme important for animal sperm development. We review research on the recent addition to the RNA family - Long non-coding RNA (lncRNA) and its roles in spermatogenesis in the context of the expanding RNA-protein network. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genetic parameters for linear type traits and milk, fat, and protein production in holstein cows in Brazil.

PubMed

Campos, Rafael Viegas; Cobuci, Jaime Araujo; Kern, Elisandra Lurdes; Costa, Cláudio Napolis; McManus, Concepta Margaret

2015-04-01

The objective of this study was to estimate genetic and phenotypic parameters for linear type traits, as well as milk yield (MY), fat yield (FY) and protein yield (PY) in 18,831 Holstein cows reared in 495 herds in Brazil. Restricted maximum likelihood with a bivariate model was used for estimation genetic parameters, including fixed effects of herd-year of classification, period of classification, classifier and stage of lactation for linear type traits and herd-year of calving, season of calving and lactation order effects for production traits. The age of cow at calving was fitted as a covariate (with linear and quadratic terms), common to both models. Heritability estimates varied from 0.09 to 0.38 for linear type traits and from 0.17 to 0.24 for production traits, indicating sufficient genetic variability to achieve genetic gain through selection. In general, estimates of genetic correlations between type and production traits were low, except for udder texture and angularity that showed positive genetic correlations (>0.29) with MY, FY, and PY. Udder depth had the highest negative genetic correlation (-0.30) with production traits. Selection for final score, commonly used by farmers as a practical selection tool to improve type traits, does not lead to significant improvements in production traits, thus the use of selection indices that consider both sets of traits (production and type) seems to be the most adequate to carry out genetic selection of animals in the Brazilian herd.

Genetic Parameters for Linear Type Traits and Milk, Fat, and Protein Production in Holstein Cows in Brazil

PubMed Central

Campos, Rafael Viegas; Cobuci, Jaime Araujo; Kern, Elisandra Lurdes; Costa, Cláudio Napolis; McManus, Concepta Margaret

2015-01-01

The objective of this study was to estimate genetic and phenotypic parameters for linear type traits, as well as milk yield (MY), fat yield (FY) and protein yield (PY) in 18,831 Holstein cows reared in 495 herds in Brazil. Restricted maximum likelihood with a bivariate model was used for estimation genetic parameters, including fixed effects of herd-year of classification, period of classification, classifier and stage of lactation for linear type traits and herd-year of calving, season of calving and lactation order effects for production traits. The age of cow at calving was fitted as a covariate (with linear and quadratic terms), common to both models. Heritability estimates varied from 0.09 to 0.38 for linear type traits and from 0.17 to 0.24 for production traits, indicating sufficient genetic variability to achieve genetic gain through selection. In general, estimates of genetic correlations between type and production traits were low, except for udder texture and angularity that showed positive genetic correlations (>0.29) with MY, FY, and PY. Udder depth had the highest negative genetic correlation (−0.30) with production traits. Selection for final score, commonly used by farmers as a practical selection tool to improve type traits, does not lead to significant improvements in production traits, thus the use of selection indices that consider both sets of traits (production and type) seems to be the most adequate to carry out genetic selection of animals in the Brazilian herd. PMID:25656190

Exploring the Robustness of a Unidimensional Item Response Theory Model with Empirically Multidimensional Data

ERIC Educational Resources Information Center

Anderson, Daniel; Kahn, Joshua D.; Tindal, Gerald

2017-01-01

Unidimensionality and local independence are two common assumptions of item response theory. The former implies that all items measure a common latent trait, while the latter implies that responses are independent, conditional on respondents' location on the latent trait. Yet, few tests are truly unidimensional. Unmodeled dimensions may result in…

Personality from a cognitive-biological perspective

NASA Astrophysics Data System (ADS)

Neuman, Yair

2014-12-01

The term "personality" is used to describe a distinctive and relatively stable set of mental traits that aim to explain the organism's behavior. The concept of personality that emerged in human psychology has been also applied to the study of non-human organisms from birds to horses. In this paper, I critically review the concept of personality from an interdisciplinary perspective, and point to some ideas that may be used for developing a cognitive-biological theory of personality. Integrating theories and research findings from various fields such as cognitive ethnology, clinical psychology, and neuroscience, I argue that the common denominator of various personality theories are neural systems of threat/trust management and their emotional, cognitive, and behavioral dimensions. In this context, personality may be also conceived as a meta-heuristics both human and non-human organisms apply to model and predict the behavior of others. The paper concludes by suggesting a minimal computational model of personality that may guide future research.

Identification of female-specific QTLs affecting an emotionality-related behavior in rats.

PubMed

Ramos, A; Moisan, M P; Chaouloff, F; Mormède, C; Mormède, P

1999-09-01

The influence of genetic factors on psychological traits and disorders has been repeatedly demonstrated; however, the molecular mechanisms underlying such an influence remain largely unknown. Anxiety-related disorders constitute the most common class of mental disorder in humans, with women being diagnosed far more frequently than men. A better understanding of the genetic and gender-related mechanisms mediating anxiety traits should enable the development of more rational methods for preventing and treating anxiety disorders. In this study we have aimed to identify, for the first time, quantitative trait loci (QTL) influencing anxiety/emotionality-related traits in rats. To this end, two strains-Lewis (LEW) and Spontaneously Hypertensive Rats (SHR)-that differ for several behavioral measures of anxiety/emotionality were intercrossed. A QTL analysis of the F2 population revealed suggestive loci for various traits, including behaviors in the elevated plus-maze and blood pressure. In addition, one major QTL explaining 50.4% of the total variance (LOD = 7.22) was identified on chromosome 4 for the locomotion in the central and aversive area of the open field. Two other relevant QTLs have been recently mapped near this chromosomic region in the rat, which also harbors Tac1r, the gene encoding for the substance P receptor. Our major QTL affected females but not males and its effect depended on the type of cross (LEW or SHR grandmothers). The present results reveal a complex genetic basis underlying emotional behaviors and they confirm the existence of interactions between genetic factors and sex for this kind of trait. Further investigation of the loci identified herein may give clues to the pathophysiology of psychiatric disorders such as anxiety-related ones.

Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children.

PubMed

Butte, Nancy F; Voruganti, V Saroja; Cole, Shelley A; Haack, Karin; Comuzzie, Anthony G; Muzny, Donna M; Wheeler, David A; Chang, Kyle; Hawes, Alicia; Gibbs, Richard A

2011-09-22

Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5' and 3' flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3'-UTR, and 2 in the 5'-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001-0.009) were associated with obesity-related traits (P = 0.01-0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77-0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children.

CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits.

PubMed

Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick; Kristiansson, Kati; Mattsson, Hannele; Nõukas, Margit; Sapkota, Yadav; Schick, Ursula; Porcu, Eleonora; Rüeger, Sina; McDaid, Aaron F; Porteous, David; Winkler, Thomas W; Salvi, Erika; Shrine, Nick; Liu, Xueping; Ang, Wei Q; Zhang, Weihua; Feitosa, Mary F; Venturini, Cristina; van der Most, Peter J; Rosengren, Anders; Wood, Andrew R; Beaumont, Robin N; Jones, Samuel E; Ruth, Katherine S; Yaghootkar, Hanieh; Tyrrell, Jessica; Havulinna, Aki S; Boers, Harmen; Mägi, Reedik; Kriebel, Jennifer; Müller-Nurasyid, Martina; Perola, Markus; Nieminen, Markku; Lokki, Marja-Liisa; Kähönen, Mika; Viikari, Jorma S; Geller, Frank; Lahti, Jari; Palotie, Aarno; Koponen, Päivikki; Lundqvist, Annamari; Rissanen, Harri; Bottinger, Erwin P; Afaq, Saima; Wojczynski, Mary K; Lenzini, Petra; Nolte, Ilja M; Sparsø, Thomas; Schupf, Nicole; Christensen, Kaare; Perls, Thomas T; Newman, Anne B; Werge, Thomas; Snieder, Harold; Spector, Timothy D; Chambers, John C; Koskinen, Seppo; Melbye, Mads; Raitakari, Olli T; Lehtimäki, Terho; Tobin, Martin D; Wain, Louise V; Sinisalo, Juha; Peters, Annette; Meitinger, Thomas; Martin, Nicholas G; Wray, Naomi R; Montgomery, Grant W; Medland, Sarah E; Swertz, Morris A; Vartiainen, Erkki; Borodulin, Katja; Männistö, Satu; Murray, Anna; Bochud, Murielle; Jacquemont, Sébastien; Rivadeneira, Fernando; Hansen, Thomas F; Oldehinkel, Albertine J; Mangino, Massimo; Province, Michael A; Deloukas, Panos; Kooner, Jaspal S; Freathy, Rachel M; Pennell, Craig; Feenstra, Bjarke; Strachan, David P; Lettre, Guillaume; Hirschhorn, Joel; Cusi, Daniele; Heid, Iris M; Hayward, Caroline; Männik, Katrin; Beckmann, Jacques S; Loos, Ruth J F; Nyholt, Dale R; Metspalu, Andres; Eriksson, Johan G; Weedon, Michael N; Salomaa, Veikko; Franke, Lude; Reymond, Alexandre; Frayling, Timothy M; Kutalik, Zoltán

2017-09-29

There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at 1q21.1, 3q29, 7q11.23, 11p14.2, and 18q21.32 and confirms two known loci at 16p11.2 and 22q11.21, implicating at least one anthropometric trait. The discovered CNVs are recurrent and rare (0.01-0.2%), with large effects on height (>2.4 cm), weight (>5 kg), and body mass index (BMI) (>3.5 kg/m 2 ). Burden analysis shows a 0.41 cm decrease in height, a 0.003 increase in waist-to-hip ratio and increase in BMI by 0.14 kg/m 2 for each Mb of total deletion burden (P = 2.5 × 10 -10 , 6.0 × 10 -5 , and 2.9 × 10 -3 ). Our study provides evidence that the same genes (e.g., MC4R, FIBIN, and FMO5) harbor both common and rare variants affecting body size and that anthropometric traits share genetic loci with developmental and psychiatric disorders.Individual SNPs have small effects on anthropometric traits, yet the impact of CNVs has remained largely unknown. Here, Kutalik and co-workers perform a large-scale genome-wide meta-analysis of structural variation and find rare CNVs associated with height, weight and BMI with large effect sizes.

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

PubMed Central

O'Meara, Brian C.; Smith, Stacey D.; Armbruster, W. Scott; Harder, Lawrence D.; Hardy, Christopher R.; Hileman, Lena C.; Hufford, Larry; Litt, Amy; Magallón, Susana; Smith, Stephen A.; Stevens, Peter F.; Fenster, Charles B.; Diggle, Pamela K.

2016-01-01

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years. PMID:27147092

A metastructural model of mental disorders and pathological personality traits.

PubMed

Wright, A G C; Simms, L J

2015-08-01

Psychiatric co-morbidity is extensive in both psychiatric settings and the general population. Such co-morbidity challenges whether DSM-based mental disorders serve to effectively carve nature at its joints. In response, a substantial literature has emerged showing that a small number of broad dimensions - internalizing, externalizing and psychoticism - can account for much of the observed covariation among common mental disorders. However, the location of personality disorders within this emerging metastructure has only recently been studied, and no studies have yet examined where pathological personality traits fit within such a broad metastructural framework. We conducted joint structural analyses of common mental disorders, personality disorders and pathological personality traits in a sample of 628 current or recent psychiatric out-patients. Bridging across the psychopathology and personality trait literatures, the results provide evidence for a robust five-factor metastructure of psychopathology, including broad domains of symptoms and features related to internalizing, disinhibition, psychoticism, antagonism and detachment. These results reveal evidence for a psychopathology metastructure that (a) parsimoniously accounts for much of the observed covariation among common mental disorders, personality disorders and related personality traits, and (b) provides an empirical basis for the organization and classification of mental disorder.

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.

PubMed

O'Meara, Brian C; Smith, Stacey D; Armbruster, W Scott; Harder, Lawrence D; Hardy, Christopher R; Hileman, Lena C; Hufford, Larry; Litt, Amy; Magallón, Susana; Smith, Stephen A; Stevens, Peter F; Fenster, Charles B; Diggle, Pamela K

2016-05-11

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years. © 2016 The Author(s).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Jr., Marcio F. R.

Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genesmore » in a population of 391 unrelated individuals. To increase power to detect associations with low-frequency variants, multiple-marker association tests were used in combination with single-marker association tests. Significant associations were discovered for all phenotypes and are indicative that low-frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low-frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. Lastly, these polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.« less

Androgen receptor polyglutamine repeat length (AR-CAGn) modulates the effect of testosterone on androgen-associated somatic traits in Filipino young adult men.

PubMed

Ryan, Calen P; Georgiev, Alexander V; McDade, Thomas W; Gettler, Lee T; Eisenberg, Dan T A; Rzhetskaya, Margarita; Agustin, Sonny S; Hayes, M Geoffrey; Kuzawa, Christopher W

2017-06-01

The androgen receptor (AR) mediates expression of androgen-associated somatic traits such as muscle mass and strength. Within the human AR is a highly variable glutamine short-tandem repeat (AR-CAGn), and CAG repeat number has been inversely correlated to AR transcriptional activity in vitro. However, evidence for an attenuating effect of long AR-CAGn on androgen-associated somatic traits has been inconsistent in human populations. One possible explanation for this lack of consistency is that the effect of AR-CAGn on AR bioactivity in target tissues likely varies in relation to circulating androgen levels. We tested whether relationships between AR-CAGn and several androgen-associated somatic traits (waist circumference, lean mass, arm muscle area, and grip strength) were modified by salivary (waking and pre-bed) and circulating (total) testosterone (T) levels in young adult males living in metropolitan Cebu, Philippines (n = 675). When men's waking T was low, they had a reduction in three out of four androgen-associated somatic traits with lengthening AR-CAGn (p < .1), consistent with in vitro research. However, when waking T was high, we observed the opposite effect-lengthening AR-CAGn was associated with an increase in these same somatic traits. Our finding that longer AR-CAGn predicts greater androgen-associated trait expression among high-T men runs counter to in vitro work, but is generally consistent with the few prior studies to evaluate similar interactions in human populations. Collectively, these results raise questions about the applicability of findings derived from in vitro AR-CAGn studies to the receptor's role in maintaining androgen-associated somatic traits in human populations. © 2017 Wiley Periodicals, Inc.

Applications of the 1000 Genomes Project resources.

PubMed

Zheng-Bradley, Xiangqun; Flicek, Paul

2017-05-01

The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci, filtering non-pathogenic variants from exome, whole genome and cancer genome sequencing projects, and genetic analysis of population structure and molecular evolution. In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies. © The Author 2016. Published by Oxford University Press.

Eating traits questionnaires as a continuum of a single concept. Uncontrolled eating.

PubMed

Vainik, Uku; Neseliler, Selin; Konstabel, Kenn; Fellows, Lesley K; Dagher, Alain

2015-07-01

Research on eating behaviour has identified several potentially relevant eating-related traits captured by different questionnaires. Often, these questionnaires predict Body Mass Index (BMI), but the relationship between them has not been explicitly studied. We studied the unity and diversity of questionnaires capturing five common eating-related traits: Power of Food, Eating Impulsivity, emotional eating, Disinhibition, and binge eating in women from Estonia (n = 740) and Canada (n = 456). Using bifactor analysis, we showed that a) these questionnaires are largely explained by a single factor, and b) relative to this shared factor, only some questionnaires offered additional variance in predicting BMI. Hence, these questionnaires seemed to characterise a common factor, which we label Uncontrolled Eating. Item Response Theory techniques were then applied to demonstrate that c) within this common factor, the questionnaires could be placed on a continuum of Uncontrolled Eating. That is, Eating Impulsivity focused on the milder degree, Power of Food Scale, emotional eating scales, and Disinhibition on intermediate degrees, and the Binge Eating Scale on the most severe degrees of Uncontrolled Eating. In sum, evidence from two samples showed that questionnaires capturing five common BMI-related traits largely reflected the same underlying latent trait - Uncontrolled Eating. In Estonia, some questionnaires focused on different severities of this common construct, supporting a continuum model of Uncontrolled Eating. These findings provide a starting point for developing better questionnaires of the neurobehavioural correlates of obesity, and provide a unifying perspective from which to view the existing literature. R scripts and data used for the analysis are provided. Copyright © 2015 Elsevier Ltd. All rights reserved.

Signatures of negative selection in the genetic architecture of human complex traits.

PubMed

Zeng, Jian; de Vlaming, Ronald; Wu, Yang; Robinson, Matthew R; Lloyd-Jones, Luke R; Yengo, Loic; Yap, Chloe X; Xue, Angli; Sidorenko, Julia; McRae, Allan F; Powell, Joseph E; Montgomery, Grant W; Metspalu, Andres; Esko, Tonu; Gibson, Greg; Wray, Naomi R; Visscher, Peter M; Yang, Jian

2018-05-01

We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.

Quantitative genetics of human morphology and obesity-related phenotypes in nuclear families from the Greater Bilbao (Spain): comparison with other populations.

PubMed

Jelenkovic, Aline; Poveda, Alaitz; Rebato, Esther

2011-07-01

It is well established that variation of soft-tissue traits is less influenced by the genetic component than skeletal traits. However, it is still unclear whether heritabilities (h(2)) of obesity-related phenotypes present a common pattern across populations. To estimate familial resemblance and heritability of body size, shape and composition phenotypes and to compare these results with those from other populations. The subject group consisted of 533 nuclear families living in Greater Bilbao and included 1702 individuals aged 2-61 years. Familial correlations and h(2) were estimated for 29 anthropometric phenotypes (19 simple measures, three derived factors, four obesity indices and the three Heath-Carter somatotype components) using MAN and SOLAR programmes. All phenotypes were influenced by additive genetic factors with narrow sense heritabilities ranging from 0.28-0.69. In general, skeletal traits exhibited the highest h(2), whereas phenotypes defining the amount of adipose tissue, particularly central fat, were less determined by genetic factors. Familial correlations and heritability estimates of body morphology and composition from the Greater Bilbao sample were within the range observed in other studies. The lower heritability detected for central fat has also been found in some other populations, but further investigations in different populations using the same anthropometric traits and estimation methods are needed in order to obtain more robust conclusions.

The Sima de los Huesos crania (Sierra de Atapuerca, Spain). A comparative study.

PubMed

Arsuaga, J L; Martínez, I; Gracia, A; Lorenzo, C

1997-01-01

The Sima de los Huesos (Sierra de Atapuerca) cranial remains found up to and including the 1995 field season are described and compared with other fossils in order to assess their evolutionary relationships. The phenetic affinities of the Sima de los Huesos crania and a large sample of Homo fossils are investigated through principal component analyses. Metrical comparisons of the Sima de los Huesos and other European and African Middle Pleistocene fossils with Neandertals are performed using Z-scores relative to the Neandertal sample statistics. The most relevant cranial traits are metrically and morphologically analyzed and cladistically evaluated. The Sima de los Huesos crania exhibit a number of primitive traits lost in Upper Pleistocene Neandertals (especially in the braincase, but also in the facial skeleton), as well as other traits that are transitional to the Neandertal morphology (particularly in the occipital bone), and features close to what is found in Neandertals (as the supraorbital morphology and midfacial prognathism). Different combinations of primitive and derived traits (shared with Neandertals) are also displayed by the other European Middle Pleistocene fossils. In conclusion, the Sima de los Huesos sample is evolutionarily related to Neandertals as well as to the other European Middle Pleistocene fossils. In our opinion, all the European Middle Pleistocene fossils belong to the Neandertal lineage, and none can be included in an Afroeuropean common ancestor of Neandertals and modern humans.

Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression

PubMed Central

Tzeng, Jung-Ying; Zhang, Daowen; Pongpanich, Monnat; Smith, Chris; McCarthy, Mark I.; Sale, Michèle M.; Worrall, Bradford B.; Hsu, Fang-Chi; Thomas, Duncan C.; Sullivan, Patrick F.

2011-01-01

Genomic association analyses of complex traits demand statistical tools that are capable of detecting small effects of common and rare variants and modeling complex interaction effects and yet are computationally feasible. In this work, we introduce a similarity-based regression method for assessing the main genetic and interaction effects of a group of markers on quantitative traits. The method uses genetic similarity to aggregate information from multiple polymorphic sites and integrates adaptive weights that depend on allele frequencies to accomodate common and uncommon variants. Collapsing information at the similarity level instead of the genotype level avoids canceling signals that have the opposite etiological effects and is applicable to any class of genetic variants without the need for dichotomizing the allele types. To assess gene-trait associations, we regress trait similarities for pairs of unrelated individuals on their genetic similarities and assess association by using a score test whose limiting distribution is derived in this work. The proposed regression framework allows for covariates, has the capacity to model both main and interaction effects, can be applied to a mixture of different polymorphism types, and is computationally efficient. These features make it an ideal tool for evaluating associations between phenotype and marker sets defined by linkage disequilibrium (LD) blocks, genes, or pathways in whole-genome analysis. PMID:21835306

Are Autistic Traits Measured Equivalently in Individuals with and without an Autism Spectrum Disorder? An Invariance Analysis of the Autism Spectrum Quotient Short Form

ERIC Educational Resources Information Center

Murray, Aja L.; Booth, Tom; McKenzie, Karen; Kuenssberg, Renate; O'Donnell, Michael

2014-01-01

It is common to administer measures of autistic traits to those without autism spectrum disorders (ASDs) with, for example, the aim of understanding autistic personality characteristics in non-autistic individuals. Little research has examined the extent to which measures of autistic traits actually measure the same traits in the same way across…

Do pioneers have r-selected traits? Life history patterns among colonizing terrestrial gastropods.

PubMed

Bengtsson, J; Baur, B

1993-05-01

We examine whether pioneer species of terrestrial gastropods (snails and slugs) possess particular life history traits commonly associated with r-selection, using data on gastropod colonization in four areas in north-west Europe (the Kvarken and Tvärminne archipelagos in the Baltic, polder woods in IJsselmeer, and a rehabilitated quarry near Maastricht). Data on age at first reproduction, longevity, clutch size, egg size and lifetime fecundity were gathered from the literature. In order to control for potentially confounding effects of body size on life history traits, we compared the residuals from the allometric relations between life history traits and body size for pioneers and non-pioneers. In snails, all life history traits examined were related to body size. In slugs, all traits except age at first reproduction scaled with body size. Body sizes did not differ between pioneers and non-pioneers in any area. In all four areas, there were no significant differences between pioneers and non-pioneers in any of the life history traits examined, after body size had been taken into account. This indicates that pioneer terrestrial gastropods generally cannot be regarded as r-selected. Pioneer species may possess any of several life history strategies, and the combinations of traits shown by them may have little in common with the r-K selection concept.

Novel Applications of Multi-task Learning and Multiple Output Regression to Multiple Genetic Trait Prediction

USDA-ARS?s Scientific Manuscript database

Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait predicti...

Can Chimpanzee Biology Highlight Human Origin and Evolution?

PubMed Central

Roffman, Itai; Nevo, Eviatar

2010-01-01

The closest living relatives of humans are their chimpanzee/bonobo (Pan) sister species, members of the same subfamily “Homininae”. This classification is supported by over 50 years of research in the fields of chimpanzee cultural diversity, language competency, genomics, anatomy, high cognition, psychology, society, self-consciousness and relation to others, tool use/production, as well as Homo level emotions, symbolic competency, memory recollection, complex multifaceted problem-solving capabilities, and interspecies communication. Language competence and symbolism can be continuously bridged from chimpanzee to man. Emotions, intercommunity aggression, body language, gestures, facial expressions, and vocalization of intonations seem to parallel between the sister taxa Homo and Pan. The shared suite of traits between Pan and Homo genus demonstrated in this article integrates old and new information on human–chimpanzee evolution, bilateral informational and cross-cultural exchange, promoting the urgent need for Pan cultures in the wild to be protected, as they are part of the cultural heritage of mankind. Also, we suggest that bonobos, Pan paniscus, based on shared traits with Australopithecus, need to be included in Australopithecine’s subgenus, and may even represent living-fossil Australopithecines. Unfolding bonobo and chimpanzee biology highlights our common genetic and cultural evolutionary origins. PMID:23908781

Social Monogamy in Nonhuman Primates: Phylogeny, Phenotype, and Physiology.

PubMed

French, Jeffrey A; Cavanaugh, Jon; Mustoe, Aaryn C; Carp, Sarah B; Womack, Stephanie L

Monogamy as a social system has been both a scientific puzzle and a sociocultural issue for decades. In this review, we examine social monogamy from a comparative perspective with a focus on primates, our closest genetic relatives. We break down monogamy into component elements, including pair-bonding and partner preference, mate guarding or jealousy, social attachment, and biparental care. Our survey of primates shows that not all features are present in species classified as socially monogamous, in the same way that human monogamous relationships may not include all elements-a perspective we refer to as "monogamy à la carte." Our review includes a survey of the neurobiological correlates of social monogamy in primates, exploring unique or common pathways for the elemental components of monogamy. This compilation reveals that the components of monogamy are modulated by a suite of androgenic steroids, glucocorticoid hormones, the nonapeptide hormones oxytocin and vasopressin, and other neurotransmitter systems (e.g., dopamine and opioids). We propose that efforts to understand the biological underpinnings of complex human and animal sociosexual relationships will be well served by exploring individual phenotypic traits, as opposed to pursuing these questions with the assumption that monogamy is a unitary trait or a species-specific characteristic.

Personality Traits: A View From the Animal Kingdom.

PubMed

Weiss, Alexander

2018-02-01

Given their backgrounds in classical ethology and in comparative psychology, researchers who study animal personality in biology and psychology, respectively, differ in how they measure personality, what questions they see as important, and how they address these questions. Despite these differences, both comparative psychologists and biologists embrace personality traits. By doing so, they have solved empirical and conceptual problems in animal behavior. Studies of animal personality have provided answers to questions about the evolution of human personality and have presented conceptual and empirical anomalies for sociocognitive theories. Animal personality research does not break from trait theories of personality. Instead, it enriches trait theories by conceiving of traits as not belonging to a species, but as expressed, with some modifications, across species. Broadening trait theory in this way has the potential to further enhance its ability to answer questions related to animal and human personality. © 2017 The Authors. Journal of Personality published by Wiley Periodicals, Inc.

Phenotypic evaluation and genome wide association studies of two common bean (Phaseolus vulgaris) diversity panels in multiple locations highlight evaluation techniques, traits and lines useful for trait based selection

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris) productivity is constrained by abiotic soil conductions including drought and low fertility as well as by high temperature. High temperature primarily impacts pollen viability and growth. Soil water content and nutrients occur heterogeneously and often in a stratif...

Prediction of human adaptation and performance in underwater environments.

PubMed

Colodro Plaza, Joaquín; Garcés de los Fayos Ruiz, Enrique J; López García, Juan J; Colodro Conde, Lucía

2014-01-01

Environmental stressors require the professional diver to undergo a complex process of psychophysiological adaptation in order to overcome the demands of an extreme environment and carry out effective and efficient work under water. The influence of cognitive and personality traits in predicting underwater performance and adaptation has been a common concern for diving psychology, and definitive conclusions have not been reached. In this ex post facto study, psychological and academic data were analyzed from a large sample of personnel participating in scuba diving courses carried out in the Spanish Navy Diving Center. In order to verify the relevance of individual differences in adaptation to a hostile environment, we evaluated the predictive validity of general mental ability and personality traits with regression techniques. The data indicated the existence of psychological variables that can predict the performance ( R² = .30, p <.001) and adaptation ( R²(N) = .51, p <.001) of divers in underwater environment. These findings support the hypothesis that individual differences are related to the probability of successful adaptation and effective performance in professional diving. These results also verify that dispositional traits play a decisive role in diving training and are significant factors in divers' psychological fitness.

Comparing GWAS Results of Complex Traits Using Full Genetic Model and Additive Models for Revealing Genetic Architecture

PubMed Central

Monir, Md. Mamun; Zhu, Jun

2017-01-01

Most of the genome-wide association studies (GWASs) for human complex diseases have ignored dominance, epistasis and ethnic interactions. We conducted comparative GWASs for total cholesterol using full model and additive models, which illustrate the impacts of the ignoring genetic variants on analysis results and demonstrate how genetic effects of multiple loci could differ across different ethnic groups. There were 15 quantitative trait loci with 13 individual loci and 3 pairs of epistasis loci identified by full model, whereas only 14 loci (9 common loci and 5 different loci) identified by multi-loci additive model. Again, 4 full model detected loci were not detected using multi-loci additive model. PLINK-analysis identified two loci and GCTA-analysis detected only one locus with genome-wide significance. Full model identified three previously reported genes as well as several new genes. Bioinformatics analysis showed some new genes are related with cholesterol related chemicals and/or diseases. Analyses of cholesterol data and simulation studies revealed that the full model performs were better than the additive-model performs in terms of detecting power and unbiased estimations of genetic variants of complex traits. PMID:28079101

Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub.

PubMed

Carlson, Jane E; Adams, Christopher A; Holsinger, Kent E

2016-01-01

Trait-environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub Protea repens. Specifically, the study examines whether broad-scale patterns of trait variation are consistent with spatial differences in selection and ecophysiology in the wild. In a common garden study of plants sourced from 19 populations, associations were measured between five morphological traits and three axes describing source climates. Trait-trait and trait-environment associations were analysed in a multi-response model. Within two focal populations in the wild, selection and path analyses were used to test associations between traits, fecundity and physiological performance. Across 19 populations in a common garden, stomatal density increased with the source population's mean annual temperature and decreased with its average amount of rainfall in midsummer. Concordantly, selection analysis in two natural populations revealed positive selection on stomatal density at the hotter, drier site, while failing to detect selection at the cooler, moister site. Dry-site plants with high stomatal density also had higher stomatal conductances, cooler leaf temperatures and higher light-saturated photosynthetic rates than those with low stomatal density, but no such relationships were present among wet-site plants. Leaf area, stomatal pore index and specific leaf area in the garden also co-varied with climate, but within-population differences were not associated with fitness in either wild population. The parallel patterns of broad-scale variation, differences in selection and differences in trait-ecophysiology relationships suggest a mechanism for adaptive differentiation in stomatal density. Densely packed stomata may improve performance by increasing transpiration and cooling, but predominately in drier, hotter climates. This study uniquely shows context-dependent benefits of stomatal density--a trait rarely linked to local adaptation in plants. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds.

PubMed

Ramayo-Caldas, Yuliaxis; Renand, Gilles; Ballester, Maria; Saintilan, Romain; Rocha, Dominique

2016-04-23

Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds. Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context.

Exploring the folkbiological conception of human nature

PubMed Central

Linquist, Stefan; Machery, Edouard; Griffiths, Paul E.; Stotz, Karola

2011-01-01

Integrating the study of human diversity into the human evolutionary sciences requires substantial revision of traditional conceptions of a shared human nature. This process may be made more difficult by entrenched, ‘folkbiological’ modes of thought. Earlier work by the authors suggests that biologically naive subjects hold an implicit theory according to which some traits are expressions of an animal's inner nature while others are imposed by its environment. In this paper, we report further studies that extend and refine our account of this aspect of folkbiology. We examine biologically naive subjects' judgments about whether traits of an animal are ‘innate’, ‘in its DNA’ or ‘part of its nature’. Subjects do not understand these three descriptions to be equivalent. Both innate and in its DNA have the connotation that the trait is species-typical. This poses an obstacle to the assimilation of the biology of polymorphic and plastic traits by biologically naive audiences. Researchers themselves may not be immune to the continuing pull of folkbiological modes of thought. PMID:21199848

Quantitative trait loci affecting response to crowding stress in an F2 generation of rainbow trout produced through phenotypic selection

USDA-ARS?s Scientific Manuscript database

Selective breeding programs for salmonids typically aim to improve traits associated with growth and disease resistance. It has been established that stressors common to production environments can adversely affect these and other traits which are important to producers and consumers. Previously,...

Personality disorders as maladaptive, extreme variants of normal personality: borderline personality disorder and neuroticism in a substance using sample.

PubMed

Samuel, Douglas B; Carroll, Kathleen M; Rounsaville, Bruce J; Ball, Samuel A

2013-10-01

Although the current diagnostic manual conceptualizes personality disorders (PDs) as categorical entities, an alternative perspective is that PDs represent maladaptive extreme versions of the same traits that describe normal personality. Existing evidence indicates that normal personality traits, such as those assessed by the five-factor model (FFM), share a common structure and obtain reasonably predictable correlations with the PDs. However, very little research has investigated whether PDs are more extreme than normal personality traits. Utilizing item-response theory analyses, the authors of the current study extend previous research to demonstrate that the diagnostic criterion for borderline personality disorder and FFM neuroticism could be fit along a single latent dimension. Furthermore, the authors' findings indicate that the borderline criteria assessed the shared latent trait at a level that was more extreme (d = 1.11) than FFM neuroticism. This finding provides further evidence for dimensional understanding of personality pathology and suggests that a trait model in DSM-5 should span normal and abnormal personality functioning, but focus on the extremes of these common traits.

Common and distinct modulation of electrophysiological indices of feedback processing by autistic and psychopathic traits.

PubMed

Carter Leno, Virginia; Naples, Adam; Cox, Anthony; Rutherford, Helena; McPartland, James C

2016-01-01

Both autism spectrum disorder (ASD) and psychopathy are primarily characterized by social dysfunction; overlapping phenotypic features may reflect altered function in common brain mechanisms. The current study examined the degree to which neural response to social and nonsocial feedback is modulated by autistic versus psychopathic traits in a sample of typically developing adults (N = 31, 11 males, 18-52 years). Event-related potentials were recorded whilst participants completed a behavioral task and received feedback on task performance. Both autistic and psychopathic traits were associated with alterations in the neural correlates of feedback processing. Sensitivity to specific forms of feedback (social, nonsocial, positively valenced, negatively valenced) differed between the two traits. Autistic traits were associated with decreased sensitivity to social feedback. In contrast, the antisocial domain of psychopathic traits was associated with an overall decrease in sensitivity to feedback, and the interpersonal manipulation domain was associated with preserved processing of positively valenced feedback. Results suggest distinct alterations within specific mechanisms of feedback processing may underlie similar difficulties in social behavior.

Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses.

PubMed

François, Yoannah; Vignal, Alain; Molette, Caroline; Marty-Gasset, Nathalie; Davail, Stéphane; Liaubet, Laurence; Marie-Etancelin, Christel

2017-04-19

The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified. One hundred and seventy-six pQTL and 80 phenotypic QTL were detected at the 5% chromosome-wide significance threshold. The great majority of the identified pQTL were trans-acting and localized on a chromosome other than that carrying the coding gene. The most significant pQTL (1% genome-wide significance) were found for alpha-enolase on APL18 and fatty acid synthase on APL24. Some proteins were associated with numerous pQTL (for example, 17 and 14 pQTL were detected for alpha-enolase and apolipoprotein A1, respectively) and pQTL hotspots were observed on some chromosomes (APL18, 24, 25 and 29). We detected 66 co-localized phenotypic QTL and pQTL for which the significance of the two-trait QTL (2t-QTL) analysis was higher than that of the strongest QTL using a single-trait approach. Among these, 16 2t-QTL were pleiotropic. For example, on APL15, melting rate and abundance of two alpha-enolase spots appeared to be impacted by a single locus that is involved in the glycolytic process. On APLZ, we identified a pleiotropic QTL that modified both the blood level of glucose at the beginning of the force-feeding period and the concentration of glutamate dehydrogenase, which, in humans, is involved in increased glucose absorption by the liver when the glutamate dehydrogenase 1 gene is mutated. We identified pleiotropic loci that affect metabolic pathways linked to glycolysis or lipogenesis, and in the end to fatty liver quality. Further investigation, via transcriptomics and metabolomics approaches, is required to confirm the biomarkers that were found to impact the genetic variability of these phenotypic traits.

Evolution of human brain functions: the functional structure of human consciousness.

PubMed

Cloninger, C Robert

2009-11-01

The functional structure of self-aware consciousness in human beings is described based on the evolution of human brain functions. Prior work on heritable temperament and character traits is extended to account for the quantum-like and holographic properties (i.e. parts elicit wholes) of self-aware consciousness. Cladistic analysis is used to identify the succession of ancestors leading to human beings. The functional capacities that emerge along this lineage of ancestors are described. The ecological context in which each cladogenesis occurred is described to illustrate the shifting balance of evolution as a complex adaptive system. Comparative neuroanatomy is reviewed to identify the brain structures and networks that emerged coincident with the emergent brain functions. Individual differences in human temperament traits were well developed in the common ancestor shared by reptiles and humans. Neocortical development in mammals proceeded in five major transitions: from early reptiles to early mammals, early primates, simians, early Homo, and modern Homo sapiens. These transitions provide the foundation for human self-awareness related to sexuality, materiality, emotionality, intellectuality, and spirituality, respectively. The functional structure of human self-aware consciousness is concerned with the regulation of five planes of being: sexuality, materiality, emotionality, intellectuality, and spirituality. Each plane elaborates neocortical functions organized around one of the five special senses. The interactions among these five planes gives rise to a 5 x 5 matrix of subplanes, which are functions that coarsely describe the focus of neocortical regulation. Each of these 25 neocortical functions regulates each of five basic motives or drives that can be measured as temperaments or basic emotions related to fear, anger, disgust, surprise, and happiness/sadness. The resulting 5 x 5 x 5 matrix of human characteristics provides a general and testable model of the functional structure of human consciousness that includes personality, physicality, emotionality, cognition, and spirituality in a unified developmental framework.

To what extent is altitudinal variation of functional traits driven by genetic adaptation in European oak and beech?

PubMed

Bresson, Caroline C; Vitasse, Yann; Kremer, Antoine; Delzon, Sylvain

2011-11-01

The phenotypic responses of functional traits in natural populations are driven by genetic diversity and phenotypic plasticity. These two mechanisms enable trees to cope with rapid climate change. We studied two European temperate tree species (sessile oak and European beech), focusing on (i) in situ variations of leaf functional traits (morphological and physiological) along two altitudinal gradients and (ii) the extent to which these variations were under environmental and/or genetic control using a common garden experiment. For all traits, altitudinal trends tended to be highly consistent between species and transects. For both species, leaf mass per area displayed a positive linear correlation with altitude, whereas leaf size was negatively correlated with altitude. We also observed a significant increase in leaf physiological performance with increasing altitude: populations at high altitudes had higher maximum rates of assimilation, stomatal conductance and leaf nitrogen content than those at low altitudes. In the common garden experiment, genetic differentiation between populations accounted for 0-28% of total phenotypic variation. However, only two traits (leaf mass per area and nitrogen content) exhibited a significant cline. The combination of in situ and common garden experiments used here made it possible to demonstrate, for both species, a weaker effect of genetic variation than of variations in natural conditions, suggesting a strong effect of the environment on leaf functional traits. Finally, we demonstrated that intrapopulation variability was systematically higher than interpopulation variability, whatever the functional trait considered, indicating a high potential capacity to adapt to climate change.

Stress Response as a Function of Task Relevance

DTIC Science & Technology

2010-12-01

be benchmarked for validity and reliability. The State-Trait Anxiety Index (or STAI; Spielberger and Sydeman, 1994) is a popular self-report...and human performance. In J.E. Driskell & E. Salas (Eds.), Stress and Human Performance Spielberger , C.D. and Sydeman, S.J. (1994). State-Trait

Genomic Regions Associated with Root Traits under Drought Stress in Tropical Maize (Zea mays L.)

PubMed Central

Zaidi, P. H.; Krishna, Girish; Krishnamurthy, L.; Gajanan, S.; Babu, Raman; Zerka, M.; Vinayan, M. T.; Vivek, B. S.

2016-01-01

An association mapping panel, named as CIMMYT Asia association mapping (CAAM) panel, involving 396 diverse tropical maize lines were phenotyped for various structural and functional traits of roots under drought and well-watered conditions. The experiment was conducted during Kharif (summer-rainy) season of 2012 and 2013 in root phenotyping facility at CIMMYT-Hyderabad, India. The CAAM panel was genotyped to generate 955, 690 SNPs through GBS v2.7 using Illumina Hi-seq 2000/2500 at Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. GWAS analysis was carried out using 331,390 SNPs filtered from the entire set of SNPs revealed a total of 50 and 67 SNPs significantly associated for root functional (transpiration efficiency, flowering period water use) and structural traits (rooting depth, root dry weight, root length, root volume, root surface area and root length density), respectively. In addition to this, 37 SNPs were identified for grain yield and shoot biomass under well-watered and drought stress. Though many SNPs were found to have significant association with the traits under study, SNPs that were common for more than one trait were discussed in detail. A total 18 SNPs were found to have common association with more than one trait, out of which 12 SNPs were found within or near the various gene functional regions. In this study we attempted to identify the trait specific maize lines based on the presence of favorable alleles for the SNPs associated with multiple traits. Two SNPs S3_128533512 and S7_151238865 were associated with transpiration efficiency, shoot biomass and grain yield under well-watered condition. Based on favorable allele for these SNPs seven inbred lines were identified. Similarly, four lines were identified for transpiration efficiency and shoot biomass under drought stress based on the presence of favorable allele for the common SNPs S1_211520521, S2_20017716, S3_57210184 and S7_130878458 and three lines were identified for flowering period water-use, transpiration efficiency, root dry weight and root volume based on the presence of favorable allele for the common SNPs S3_162065732 and S3_225760139. PMID:27768702

Humanity in a Dish: Population Genetics with iPSCs.

PubMed

Warren, Curtis R; Cowan, Chad A

2018-01-01

Induced pluripotent stem cells (iPSCs) are powerful tools for investigating the relationship between genotype and phenotype. Recent publications have described iPSC cohort studies of common genetic variants and their effects on gene expression and cellular phenotypes. These in vitro quantitative trait locus (QTL) studies are the first experiments in a new paradigm with great potential: iPSC-based functional population genetic studies. iPSC collections from large cohorts are currently under development to facilitate the next wave of these studies, which have the potential to discover the effects of common genetic variants on cellular phenotypes and to uncover the molecular basis of common genetic diseases. Here, we describe the recent advances in this developing field, and provide a road map for future in vitro functional population genetic studies and trial-in-a-dish experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

The end of life, the ends of life: an anthropological view.

PubMed

Varisco, Daniel Martin

2011-12-01

All known human societies have a worldview that deserves to be called religion; all religions must explain death. Anthropologists study the diversity of religious systems, present and past, in order to understand what is common to humanity. Rather than starting from the view of a particular revelation or set of doctrines, the anthropologist tries to step outside his or her own subjective worldview and identify patterns in the evolution of human thinking about the reality of physical death. Are humans the only animals that are conscious of death, or do we share sentiments observable in our closest living relatives, the chimpanzees? At what point in history did the concept of an afterlife, life in some spiritual sense after physical death, appear? Is the religious explanation of life and death a mere reflection of a communal social fact, as the sociologist Emil Durkheim suggested, or a shared psychological trait, as more recent scholars assert? Can and should the modern scientist make a definitive statement about the finality of death and human consciousness?

A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data.

PubMed

Buchanan, Carrie C; Torstenson, Eric S; Bush, William S; Ritchie, Marylyn D

2012-01-01

Since publication of the human genome in 2003, geneticists have been interested in risk variant associations to resolve the etiology of traits and complex diseases. The International HapMap Consortium undertook an effort to catalog all common variation across the genome (variants with a minor allele frequency (MAF) of at least 5% in one or more ethnic groups). HapMap along with advances in genotyping technology led to genome-wide association studies which have identified common variants associated with many traits and diseases. In 2008 the 1000 Genomes Project aimed to sequence 2500 individuals and identify rare variants and 99% of variants with a MAF of <1%. To determine whether the 1000 Genomes Project includes all the variants in HapMap, we examined the overlap between single nucleotide polymorphisms (SNPs) genotyped in the two resources using merged phase II/III HapMap data and low coverage pilot data from 1000 Genomes. Comparison of the two data sets showed that approximately 72% of HapMap SNPs were also found in 1000 Genomes Project pilot data. After filtering out HapMap variants with a MAF of <5% (separately for each population), 99% of HapMap SNPs were found in 1000 Genomes data. Not all variants cataloged in HapMap are also cataloged in 1000 Genomes. This could affect decisions about which resource to use for SNP queries, rare variant validation, or imputation. Both the HapMap and 1000 Genomes Project databases are useful resources for human genetics, but it is important to understand the assumptions made and filtering strategies employed by these projects.

Cumulative role of rare and common putative functional genetic variants at NPAS3 in schizophrenia susceptibility.

PubMed

González-Peñas, Javier; Arrojo, Manuel; Paz, Eduardo; Brenlla, Julio; Páramo, Mario; Costas, Javier

2015-10-01

Schizophrenia may be considered a human-specific disorder arisen as a maladaptive by-product of human-specific brain evolution. Therefore, genetic variants involved in susceptibility to schizophrenia may be identified among those genes related to acquisition of human-specific traits. NPAS3, a transcription factor involved in central nervous system development and neurogenesis, seems to be implicated in the evolution of human brain, as it is the human gene with most human-specific accelerated elements (HAEs), i.e., .mammalian conserved regulatory sequences with accelerated evolution in the lineage leading to humans after human-chimpanzee split. We hypothesize that any nucleotide variant at the NPAS3 HAEs may lead to altered susceptibility to schizophrenia. Twenty-one variants at these HAEs detected by the 1000 genomes Project, as well as five additional variants taken from psychiatric genome-wide association studies, were genotyped in 538 schizophrenic patients and 539 controls from Galicia. Analyses at the haplotype level or based on the cumulative role of the variants assuming different susceptibility models did not find any significant association in spite of enough power under several plausible scenarios regarding direction of effect and the specific role of rare and common variants. These results suggest that, contrary to our hypothesis, the special evolution of the NPAS3 HAEs in Homo relaxed the strong constraint on sequence that characterized these regions during mammalian evolution, allowing some sequence changes without any effect on schizophrenia risk. © 2015 Wiley Periodicals, Inc.

Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

PubMed Central

2012-01-01

Background Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits. Results A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping. Conclusions The QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop. PMID:22873566

On the Flexibility of Basic Risk Attitudes in Monkeys.

PubMed

Farashahi, Shiva; Azab, Habiba; Hayden, Benjamin; Soltani, Alireza

2018-05-02

Monkeys and other animals appear to share with humans two risk attitudes predicted by prospect theory: an inverse-S-shaped probability-weighting (PW) function and a steeper utility curve for losses than for gains. These findings suggest that such preferences are stable traits with common neural substrates. We hypothesized instead that animals tailor their preferences to subtle changes in task contexts, making risk attitudes flexible. Previous studies used a limited number of outcomes, trial types, and contexts. To gain a broader perspective, we examined two large datasets of male macaques' risky choices: one from a task with real (juice) gains and another from a token task with gains and losses. In contrast to previous findings, monkeys were risk seeking for both gains and losses (i.e., lacked a reflection effect) and showed steeper gain than loss curves (loss seeking). Utility curves for gains were substantially different in the two tasks. Monkeys showed nearly linear PWs in one task and S-shaped ones in the other; neither task produced a consistent inverse-S-shaped curve. To account for these observations, we developed and tested various computational models of the processes involved in the construction of reward value. We found that adaptive differential weighting of prospective gamble outcomes could partially account for the observed differences in the utility functions across the two experiments and thus provide a plausible mechanism underlying flexible risk attitudes. Together, our results support the idea that risky choices are constructed flexibly at the time of elicitation and place important constraints on neural models of economic choice. SIGNIFICANCE STATEMENT We respond in reliable ways to risk, but are our risk preferences stable traits or ephemeral states? Using various computational models, we examined two large datasets of macaque risky choices in two different tasks. We observed several deviations from "classic" risk preferences seen in humans and monkeys: no reflection effect, loss seeking as opposed to loss aversion, and linear and S-shaped, as opposed to inverse-S-shaped, probability distortion. These results challenge the idea that our risk attitudes are evolved traits shared with the last common ancestor of macaques and humans, suggesting instead that behavioral flexibility is the hallmark of risky choice in primates. We show how this flexibility can emerge partly as a result of interactions between attentional and reward systems. Copyright © 2018 the authors 0270-6474/18/384383-16$15.00/0.

Positive Character Traits of Special Education Staff: Commonalities and Applications

ERIC Educational Resources Information Center

Korn, Maggie A.; Woodard, Cooper R.; Tucker, Chelsea A.

2016-01-01

The goal of the present study was to identify the positive character traits of staff working with a special education population and further understand how staff apply these traits in their work. Twenty-eight staff from a school/treatment program for students with autism and related developmental disorders completed the VIA Inventory of Strengths…

Higher Order Testlet Response Models for Hierarchical Latent Traits and Testlet-Based Items

ERIC Educational Resources Information Center

Huang, Hung-Yu; Wang, Wen-Chung

2013-01-01

Both testlet design and hierarchical latent traits are fairly common in educational and psychological measurements. This study aimed to develop a new class of higher order testlet response models that consider both local item dependence within testlets and a hierarchy of latent traits. Due to high dimensionality, the authors adopted the Bayesian…

Animal Models of Suicide Trait-Related Behaviors

PubMed Central

Malkesman, Oz; Pine, Daniel; Tragon, Tyson; Austin, Daniel R.; Henter, Ioline D.; Chen, Guang; Manji, Husseini K.

2009-01-01

Although antidepressants are at least moderately effective in treating major depressive disorder (MDD), concerns have arisen that selective serotonin reuptake inhibitors (SSRIs) are associated with suicidal thinking and behavior, especially in children, adolescents, and young adults. Virtually no experimental research in model systems has considered the mechanisms by which SSRIs may be associated with this potential side effect in some susceptible individuals. Suicide is a complex behavior that is, at best, complicated to study in humans and impossible to fully reproduce in an animal model. However, by investigating traits that show strong cross-species parallels as well as associations with suicide in humans, animal models may elucidate the mechanisms by which SSRIs are associated with suicidal thinking and behavior in the young. Traits linked with suicide in humans that can be successfully modeled in rodents include aggression, impulsivity, irritability, and hopelessness/helplessness. Differences in animal response to particular paradigms and to SSRIs across the lifespan are also discussed. Modeling these relevant traits in animals can help clarify the impact of SSRIs on these traits, suggesting avenues for reducing suicide risk in this vulnerable population. PMID:19269045

Sewage Reflects the Microbiomes of Human Populations

PubMed Central

Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

2015-01-01

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

Quantitative trait loci mapping for Gibberella ear rot resistance and associated agronomic traits using genotyping-by-sequencing in maize.

PubMed

Kebede, Aida Z; Woldemariam, Tsegaye; Reid, Lana M; Harris, Linda J

2016-01-01

Unique and co-localized chromosomal regions affecting Gibberella ear rot disease resistance and correlated agronomic traits were identified in maize. Dissecting the mechanisms underlying resistance to Gibberella ear rot (GER) disease in maize provides insight towards more informed breeding. To this goal, we evaluated 410 recombinant inbred lines (RIL) for GER resistance over three testing years using silk channel and kernel inoculation techniques. RILs were also evaluated for agronomic traits like days to silking, husk cover, and kernel drydown rate. The RILs showed significant genotypic differences for all traits with above average to high heritability estimates. Significant (P < 0.01) but weak genotypic correlations were observed between disease severity and agronomic traits, indicating the involvement of agronomic traits in disease resistance. Common QTLs were detected for GER resistance and kernel drydown rate, suggesting the existence of pleiotropic genes that could be exploited to improve both traits at the same time. The QTLs identified for silk and kernel resistance shared some common regions on chromosomes 1, 2, and 8 and also had some regions specific to each tissue on chromosomes 9 and 10. Thus, effective GER resistance breeding could be achieved by considering screening methods that allow exploitation of tissue-specific disease resistance mechanisms and include kernel drydown rate either in an index or as indirect selection criterion.

Gene flow does not prevent personality and morphological differentiation between two blue tit populations.

PubMed

Dubuc-Messier, Gabrielle; Caro, Samuel P; Perrier, Charles; van Oers, Kees; Réale, Denis; Charmantier, Anne

2018-05-23

Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to five years. We then compared adult phenotypes between the two populations, as well as trait-specific Q st and F st . Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Q st - F st comparisons revealed that the traits divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Q st - F st comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Quantitative genetics of disease traits.

PubMed

Wray, N R; Visscher, P M

2015-04-01

John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James' most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case-control data and review recent applications in human genetics. © 2015 Blackwell Verlag GmbH.

Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population

PubMed Central

Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E.; Lummaa, Virpi

2013-01-01

The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution. PMID:24107531

Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population.

PubMed

Bolund, Elisabeth; Bouwhuis, Sandra; Pettay, Jenni E; Lummaa, Virpi

2013-12-07

The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.

Psychological correlates of habitual diet in healthy adults.

PubMed

Stevenson, Richard J

2017-01-01

There are 3 motivations for studying the psychological correlates of habitual diet. First, diet is a major but modifiable cause of morbidity and mortality, and dietary interventions could be improved by knowing the psychological characteristics of consumers of healthy/unhealthy diets. Second, animal studies indicate that diet can impair cognition, stress responsiveness, and affective processing, but it is unclear whether this also happens in humans. Third, certain psychological traits are associated with obesity, but it is not known whether these precede and thus contribute to weight gain. Although many psychological correlates of diet have been identified, the literature is highly dispersed, and there has been no previous comprehensive narrative review. Organized here by psychological domain, studies linking diet with individual differences in perception, cognition, impulsivity, personality, affective processing, mental health, and attitudes, beliefs and values-in healthy adults-are reviewed. Although there is a growing literature on the psychological correlates of fruit/vegetable intake-the core of a healthy diet-consumers of unhealthy diets have characteristics that probably make them less responsive to education-based interventions. Diet may be a causal contributor to depression, and diet is consistently linked to impulsivity and certain personality traits. There are inconsistent and less explored links to perceptual, affective and cognitive processes, with several emerging parallels to the animal literature. Impulsivity and personality traits common to obese individuals also occur in lean consumers of unhealthy diets, suggesting these may contribute to weight gain. Diet-psychology correlates remain understudied even though this could significantly benefit human health. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Scaling up functional traits for ecosystem services with remote sensing: concepts and methods.

PubMed

Abelleira Martínez, Oscar J; Fremier, Alexander K; Günter, Sven; Ramos Bendaña, Zayra; Vierling, Lee; Galbraith, Sara M; Bosque-Pérez, Nilsa A; Ordoñez, Jenny C

2016-07-01

Ecosystem service-based management requires an accurate understanding of how human modification influences ecosystem processes and these relationships are most accurate when based on functional traits. Although trait variation is typically sampled at local scales, remote sensing methods can facilitate scaling up trait variation to regional scales needed for ecosystem service management. We review concepts and methods for scaling up plant and animal functional traits from local to regional spatial scales with the goal of assessing impacts of human modification on ecosystem processes and services. We focus our objectives on considerations and approaches for (1) conducting local plot-level sampling of trait variation and (2) scaling up trait variation to regional spatial scales using remotely sensed data. We show that sampling methods for scaling up traits need to account for the modification of trait variation due to land cover change and species introductions. Sampling intraspecific variation, stratification by land cover type or landscape context, or inference of traits from published sources may be necessary depending on the traits of interest. Passive and active remote sensing are useful for mapping plant phenological, chemical, and structural traits. Combining these methods can significantly improve their capacity for mapping plant trait variation. These methods can also be used to map landscape and vegetation structure in order to infer animal trait variation. Due to high context dependency, relationships between trait variation and remotely sensed data are not directly transferable across regions. We end our review with a brief synthesis of issues to consider and outlook for the development of these approaches. Research that relates typical functional trait metrics, such as the community-weighted mean, with remote sensing data and that relates variation in traits that cannot be remotely sensed to other proxies is needed. Our review narrows the gap between functional trait and remote sensing methods for ecosystem service management.

How scientists perceive the evolutionary origin of human traits: Results of a survey study.

PubMed

Tuomisto, Hanna; Tuomisto, Matleena; Tuomisto, Jouni T

2018-03-01

Various hypotheses have been proposed for why the traits distinguishing humans from other primates originally evolved, and any given trait may have been explained both as an adaptation to different environments and as a result of demands from social organization or sexual selection. To find out how popular the different explanations are among scientists, we carried out an online survey among authors of recent scientific papers in journals covering relevant fields of science (paleoanthropology, paleontology, ecology, evolution, human biology). Some of the hypotheses were clearly more popular among the 1,266 respondents than others, but none was universally accepted or rejected. Even the most popular of the hypotheses were assessed "very likely" by <50% of the respondents, but many traits had 1-3 hypotheses that were found at least moderately likely by >70% of the respondents. An ordination of the hypotheses identified two strong gradients. Along one gradient, the hypotheses were sorted by their popularity, measured by the average credibility score given by the respondents. The second gradient separated all hypotheses postulating adaptation to swimming or diving into their own group. The average credibility scores given for different subgroups of the hypotheses were not related to respondent's age or number of publications authored. However, (paleo)anthropologists were more critical of all hypotheses, and much more critical of the water-related ones, than were respondents representing other fields of expertise. Although most respondents did not find the water-related hypotheses likely, only a small minority found them unscientific. The most popular hypotheses were based on inherent drivers; that is, they assumed the evolution of a trait to have been triggered by the prior emergence of another human-specific behavioral or morphological trait, but opinions differed as to which of the traits came first.

On the Communicative Function of Body Odors.

PubMed

de Groot, Jasper H B; Semin, Gün R; Smeets, Monique A M

2017-03-01

Humans use multiple senses to navigate the social world, and the sense of smell is arguably the most underestimated one. An intriguing aspect of the sense of smell is its social communicative function. Research has shown that human odors convey information about a range of states (e.g., emotions, sickness) and traits (e.g., individuality, gender). Yet, what underlies the communicability of these states and traits via smell? We fill this explanatory gap with a framework that highlights the dynamic and flexible aspects of human olfactory communication. In particular, we explain how chemical profiles, associative learning (i.e., the systematic co-occurrence of chemical profiles with state- or trait-related information), and top-down contextual influences could interact to shape human odor perception. Our model not only helps to integrate past research on human olfactory communication but it also opens new avenues for future research on this fascinating, yet to date poorly understood, field.

Global genetic differentiation of complex traits shaped by natural selection in humans.

PubMed

Guo, Jing; Wu, Yang; Zhu, Zhihong; Zheng, Zhili; Trzaskowski, Maciej; Zeng, Jian; Robinson, Matthew R; Visscher, Peter M; Yang, Jian

2018-05-14

There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height ([Formula: see text]), waist-to-hip ratio ([Formula: see text]), and schizophrenia ([Formula: see text]) are significantly more differentiated among populations than matched "control" SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height ([Formula: see text]) and schizophrenia ([Formula: see text]) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations.

Culture and the Behavioral Manifestations of Traits: An Application of the Act Frequency Approach

PubMed Central

Church, A. Timothy; Katigbak, Marcia S.; Miramontes, Lilia G.; del Prado, Alicia M.

2009-01-01

The behavioral manifestations of Big Five traits were compared across cultures using the Act Frequency Approach. American (n = 176) and Filipino (n = 195) students completed a Big Five measure and act frequency ratings for behaviors performed during the past month. Acts for specific traits cohered to an equivalent degree across cultures. In both cultures, the structure of act composites resembled the Big Five and the strength of trait-behavior relationships was very similar. Many acts were multidimensional and analyses revealed cultural commonalities and differences in the relevance and prevalence of acts for the Big Five traits. The results were more consistent with trait than cultural psychology perspectives, because traits predicted behavior equally well, on average, in the two cultures. PMID:19865595

Evolution of cultural traits occurs at similar relative rates in different world regions.

PubMed

Currie, Thomas E; Mace, Ruth

2014-11-22

A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles.

The transformative potential of an integrative approach to pregnancy.

PubMed

Eidem, Haley R; McGary, Kriston L; Capra, John A; Abbot, Patrick; Rokas, Antonis

2017-09-01

Complex traits typically involve diverse biological pathways and are shaped by numerous genetic and environmental factors. Pregnancy-associated traits and pathologies are further complicated by extensive communication across multiple tissues in two individuals, interactions between two genomes-maternal and fetal-that obscure causal variants and lead to genetic conflict, and rapid evolution of pregnancy-associated traits across mammals and in the human lineage. Given the multi-faceted complexity of human pregnancy, integrative approaches that synthesize diverse data types and analyses harbor tremendous promise to identify the genetic architecture and environmental influences underlying pregnancy-associated traits and pathologies. We review current research that addresses the extreme complexities of traits and pathologies associated with human pregnancy. We find that successful efforts to address the many complexities of pregnancy-associated traits and pathologies often harness the power of many and diverse types of data, including genome-wide association studies, evolutionary analyses, multi-tissue transcriptomic profiles, and environmental conditions. We propose that understanding of pregnancy and its pathologies will be accelerated by computational platforms that provide easy access to integrated data and analyses. By simplifying the integration of diverse data, such platforms will provide a comprehensive synthesis that transcends many of the inherent challenges present in studies of pregnancy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution of cultural traits occurs at similar relative rates in different world regions

PubMed Central

Currie, Thomas E.; Mace, Ruth

2014-01-01

A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles PMID:25297866

Sex beyond the genitalia: The human brain mosaic

PubMed Central

Joel, Daphna; Berman, Zohar; Tavor, Ido; Wexler, Nadav; Gaber, Olga; Stein, Yaniv; Shefi, Nisan; Pool, Jared; Urchs, Sebastian; Margulies, Daniel S.; Liem, Franziskus; Hänggi, Jürgen; Jäncke, Lutz; Assaf, Yaniv

2015-01-01

Whereas a categorical difference in the genitals has always been acknowledged, the question of how far these categories extend into human biology is still not resolved. Documented sex/gender differences in the brain are often taken as support of a sexually dimorphic view of human brains (“female brain” or “male brain”). However, such a distinction would be possible only if sex/gender differences in brain features were highly dimorphic (i.e., little overlap between the forms of these features in males and females) and internally consistent (i.e., a brain has only “male” or only “female” features). Here, analysis of MRIs of more than 1,400 human brains from four datasets reveals extensive overlap between the distributions of females and males for all gray matter, white matter, and connections assessed. Moreover, analyses of internal consistency reveal that brains with features that are consistently at one end of the “maleness-femaleness” continuum are rare. Rather, most brains are comprised of unique “mosaics” of features, some more common in females compared with males, some more common in males compared with females, and some common in both females and males. Our findings are robust across sample, age, type of MRI, and method of analysis. These findings are corroborated by a similar analysis of personality traits, attitudes, interests, and behaviors of more than 5,500 individuals, which reveals that internal consistency is extremely rare. Our study demonstrates that, although there are sex/gender differences in the brain, human brains do not belong to one of two distinct categories: male brain/female brain. PMID:26621705

Human-aided admixture may fuel ecosystem transformation during biological invasions: theoretical and experimental evidence.

PubMed

Molofsky, Jane; Keller, Stephen R; Lavergne, Sébastien; Kaproth, Matthew A; Eppinga, Maarten B

2014-04-01

Biological invasions can transform our understanding of how the interplay of historical isolation and contemporary (human-aided) dispersal affects the structure of intraspecific diversity in functional traits, and in turn, how changes in functional traits affect other scales of biological organization such as communities and ecosystems. Because biological invasions frequently involve the admixture of previously isolated lineages as a result of human-aided dispersal, studies of invasive populations can reveal how admixture results in novel genotypes and shifts in functional trait variation within populations. Further, because invasive species can be ecosystem engineers within invaded ecosystems, admixture-induced shifts in the functional traits of invaders can affect the composition of native biodiversity and alter the flow of resources through the system. Thus, invasions represent promising yet under-investigated examples of how the effects of short-term evolutionary changes can cascade across biological scales of diversity. Here, we propose a conceptual framework that admixture between divergent source populations during biological invasions can reorganize the genetic variation underlying key functional traits, leading to shifts in the mean and variance of functional traits within invasive populations. Changes in the mean or variance of key traits can initiate new ecological feedback mechanisms that result in a critical transition from a native ecosystem to a novel invasive ecosystem. We illustrate the application of this framework with reference to a well-studied plant model system in invasion biology and show how a combination of quantitative genetic experiments, functional trait studies, whole ecosystem field studies and modeling can be used to explore the dynamics predicted to trigger these critical transitions.

A genome-wide association study of seed composition traits in wild soybean (Glycine soja).

PubMed

Leamy, Larry J; Zhang, Hengyou; Li, Changbao; Chen, Charles Y; Song, Bao-Hua

2017-01-05

Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits. We discovered 29 SNPs located on ten different chromosomes that are significantly associated with the seven seed composition traits in our wild soybean sample. Eight SNPs co-localized with QTLs previously uncovered in linkage or association mapping studies conducted with cultivated soybean samples, while the remaining SNPs appeared to be in novel locations. Twenty-four of the SNPs significantly associated with fatty acid variation, with the majority located on chromosomes 14 (6 SNPs) and seven (8 SNPs). Two SNPs were common for two or more fatty acids, suggesting loci with pleiotropic effects. We also identified some candidate genes that are involved in fatty acid metabolism and regulation. For each of the seven traits, most of the SNPs produced differences between the average phenotypic values of the two homozygotes of about one-half standard deviation and contributed over 3% of their total variability. This is the first GWA study conducted on seed composition traits solely in wild soybean populations, and a number of QTLs were found that have not been previously discovered. Some of these may be useful to breeders who select for increased protein/oil content or altered fatty acid ratios in the seeds. The results also provide additional insight into the genetic architecture of these traits in a large sample of wild soybean, and suggest some new candidate genes whose molecular effects on these traits need to be further studied.

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome.

PubMed

Power, Michelle L; Samuel, Angelingifta; Smith, James J; Stark, Jonathon S; Gillings, Michael R; Gordon, David M

2016-08-01

Discharge of untreated sewage into Antarctic environments presents a risk of introducing non-native microorganisms, but until now, adverse consequences have not been conclusively identified. Here we show that sewage disposal introduces human derived Escherichia coli carrying mobile genetic elements and virulence traits with the potential to affect the diversity and evolution of native Antarctic microbial communities. We compared E. coli recovered from environmental and animal sources in Antarctica to a reference collection of E. coli from humans and non-Antarctic animals. The distribution of phylogenetic groups and frequency of 11 virulence factors amongst the Antarctic isolates were characteristic of E. coli strains more commonly associated with humans. The rapidly emerging E. coli ST131 and ST95 clones were found amongst the Antarctic isolates, and ST95 was the predominant E. coli recovered from Weddell seals. Class 1 integrons were found in 15% of the Antarctic E. coli with 4 of 5 identified gene cassette arrays containing antibiotic resistance genes matching those common in clinical contexts. Disposing untreated sewage into the Antarctic environment does disseminate non-native microorganisms, but the extent of this impact and implications for Antarctic ecosystem health are, as yet, poorly understood. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transcriptomic Identification of ADH1B as a Novel Candidate Gene for Obesity and Insulin Resistance in Human Adipose Tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES)

PubMed Central

Winnier, Deidre A.; Fourcaudot, Marcel; Norton, Luke; Abdul-Ghani, Muhammad A.; Hu, Shirley L.; Farook, Vidya S.; Coletta, Dawn K.; Kumar, Satish; Puppala, Sobha; Chittoor, Geetha; Dyer, Thomas D.; Arya, Rector; Carless, Melanie; Lehman, Donna M.; Curran, Joanne E.; Cromack, Douglas T.; Tripathy, Devjit; Blangero, John; Duggirala, Ravindranath; Göring, Harald H. H.; DeFronzo, Ralph A.; Jenkinson, Christopher P.

2015-01-01

Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10-4) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10-60) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10-9), BMI (5.4 x 10-6), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits. PMID:25830378

Evolutionary and plastic responses of freshwater invertebrates to climate change: realized patterns and future potential.

PubMed

Stoks, Robby; Geerts, Aurora N; De Meester, Luc

2014-01-01

We integrated the evidence for evolutionary and plastic trait changes in situ in response to climate change in freshwater invertebrates (aquatic insects and zooplankton). The synthesis on the trait changes in response to the expected reductions in hydroperiod and increases in salinity indicated little evidence for adaptive, plastic, and genetic trait changes and for local adaptation. With respect to responses to temperature, there are many studies on temporal trait changes in phenology and body size in the wild that are believed to be driven by temperature increases, but there is a general lack of rigorous demonstration whether these trait changes are genetically based, adaptive, and causally driven by climate change. Current proof for genetic trait changes under climate change in freshwater invertebrates stems from a limited set of common garden experiments replicated in time. Experimental thermal evolution experiments and common garden warming experiments associated with space-for-time substitutions along latitudinal gradients indicate that besides genetic changes, also phenotypic plasticity and evolution of plasticity are likely to contribute to the observed phenotypic changes under climate change in aquatic invertebrates. Apart from plastic and genetic thermal adjustments, also genetic photoperiod adjustments are widespread and may even dominate the observed phenological shifts.

Human difference in the genomic era: Facilitating a socially responsible dialogue

PubMed Central

2010-01-01

Background The study of human genetic variation has been advanced by research such as genome-wide association studies, which aim to identify variants associated with common, complex diseases and traits. Significant strides have already been made in gleaning information on susceptibility, treatment, and prevention of a number of disorders. However, as genetic researchers continue to uncover underlying differences between individuals, there is growing concern that observed population-level differences will be inappropriately generalized as inherent to particular racial or ethnic groups and potentially perpetuate negative stereotypes. Discussion We caution that imprecision of language when conveying research conclusions, compounded by the potential distortion of findings by the media, can lead to the stigmatization of racial and ethnic groups. Summary It is essential that the scientific community and with those reporting and disseminating research findings continue to foster a socially responsible dialogue about genetic variation and human difference. PMID:20504336

The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges.

PubMed

Boonpeng, Hoh; Yusoff, Khalid

2013-03-01

The ultimate goal of human genetics is to understand the role of genome variation in elucidating human traits and diseases. Besides single nucleotide polymorphism (SNP), copy number variation (CNV), defined as gains or losses of a DNA segment larger than 1 kb, has recently emerged as an important tool in understanding heritable source of human genomic differences. It has been shown to contribute to genetic susceptibility of various common and complex diseases. Despite a handful of publications, its role in cardiovascular diseases remains largely unknown. Here, we deliberate on the currently available technologies for CNV detection. The possible utility and the potential roles of CNV in exploring the mechanisms of cardiac remodeling in hypertension will also be addressed. Finally, we discuss the challenges for investigations of CNV in cardiovascular diseases and its possible implications in diagnosis of hypertension-related left ventricular hypertrophy (LVH).

No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans

PubMed Central

Gómez-Robles, Aida; Bermúdez de Castro, José María; Arsuaga, Juan-Luis; Carbonell, Eudald; Polly, P. David

2013-01-01

A central problem in paleoanthropology is the identity of the last common ancestor of Neanderthals and modern humans ([N-MH]LCA). Recently developed analytical techniques now allow this problem to be addressed using a probabilistic morphological framework. This study provides a quantitative reconstruction of the expected dental morphology of the [N-MH]LCA and an assessment of whether known fossil species are compatible with this ancestral position. We show that no known fossil species is a suitable candidate for being the [N-MH]LCA and that all late Early and Middle Pleistocene taxa from Europe have Neanderthal dental affinities, pointing to the existence of a European clade originated around 1 Ma. These results are incongruent with younger molecular divergence estimates and suggest at least one of the following must be true: (i) European fossils and the [N-MH]LCA selectively retained primitive dental traits; (ii) molecular estimates of the divergence between Neanderthals and modern humans are underestimated; or (iii) phenotypic divergence and speciation between both species were decoupled such that phenotypic differentiation, at least in dental morphology, predated speciation. PMID:24145426

Genomic history of the origin and domestication of common bean unveils its closest sister species.

PubMed

Rendón-Anaya, Martha; Montero-Vargas, Josaphat M; Saburido-Álvarez, Soledad; Vlasova, Anna; Capella-Gutierrez, Salvador; Ordaz-Ortiz, José Juan; Aguilar, O Mario; Vianello-Brondani, Rosana P; Santalla, Marta; Delaye, Luis; Gabaldón, Toni; Gepts, Paul; Winkler, Robert; Guigó, Roderic; Delgado-Salinas, Alfonso; Herrera-Estrella, Alfredo

2017-03-29

Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

Approaches for vegetable and fruit quality trait improvement

USDA-ARS?s Scientific Manuscript database

Improving food quality traits has become a major goal of fruit and vegetable breeding due to the increasing public awareness of nutraceutical compounds to human nutrition and health. During domestication and breeding of modern varieties, many traits were left behind in the wild and in the primitive ...

The Logic of Fashion Cycles

PubMed Central

Acerbi, Alberto; Ghirlanda, Stefano; Enquist, Magnus

2012-01-01

Many cultural traits exhibit volatile dynamics, commonly dubbed fashions or fads. Here we show that realistic fashion-like dynamics emerge spontaneously if individuals can copy others' preferences for cultural traits as well as traits themselves. We demonstrate this dynamics in simple mathematical models of the diffusion, and subsequent abandonment, of a single cultural trait which individuals may or may not prefer. We then simulate the coevolution between many cultural traits and the associated preferences, reproducing power-law frequency distributions of cultural traits (most traits are adopted by few individuals for a short time, and very few by many for a long time), as well as correlations between the rate of increase and the rate of decrease of traits (traits that increase rapidly in popularity are also abandoned quickly and vice versa). We also establish that alternative theories, that fashions result from individuals signaling their social status, or from individuals randomly copying each other, do not satisfactorily reproduce these empirical observations. PMID:22412887

The logic of fashion cycles.

PubMed

Acerbi, Alberto; Ghirlanda, Stefano; Enquist, Magnus

2012-01-01

Many cultural traits exhibit volatile dynamics, commonly dubbed fashions or fads. Here we show that realistic fashion-like dynamics emerge spontaneously if individuals can copy others' preferences for cultural traits as well as traits themselves. We demonstrate this dynamics in simple mathematical models of the diffusion, and subsequent abandonment, of a single cultural trait which individuals may or may not prefer. We then simulate the coevolution between many cultural traits and the associated preferences, reproducing power-law frequency distributions of cultural traits (most traits are adopted by few individuals for a short time, and very few by many for a long time), as well as correlations between the rate of increase and the rate of decrease of traits (traits that increase rapidly in popularity are also abandoned quickly and vice versa). We also establish that alternative theories, that fashions result from individuals signaling their social status, or from individuals randomly copying each other, do not satisfactorily reproduce these empirical observations.

Midbrain dopamine receptor availability is inversely associated with novelty-seeking traits in humans.

PubMed

Zald, David H; Cowan, Ronald L; Riccardi, Patrizia; Baldwin, Ronald M; Ansari, M Sib; Li, Rui; Shelby, Evan S; Smith, Clarence E; McHugo, Maureen; Kessler, Robert M

2008-12-31

Novelty-seeking personality traits are a major risk factor for the development of drug abuse and other unsafe behaviors. Rodent models of temperament indicate that high novelty responding is associated with decreased inhibitory autoreceptor control of midbrain dopamine neurons. It has been speculated that individual differences in dopamine functioning also underlie the personality trait of novelty seeking in humans. However, differences in the dopamine system of rodents and humans, as well as the methods for assessing novelty responding/seeking across species leave unclear to what extent the animal models inform our understanding of human personality. In the present study we examined the correlation between novelty-seeking traits in humans and D(2)-like (D(2)/D(3)) receptor availability in the substantia nigra/ventral tegmental area. Based on the rodent literature we predicted that novelty seeking would be characterized by lowered levels of D(2)-like (auto)receptor availability in the midbrain. Thirty-four healthy adults (18 men, 16 women) completed the Tridimensional Personality Questionnaire-Novelty-Seeking Scale and PET scanning with the D(2)/D(3) ligand [(18)F]fallypride. Novelty-Seeking personality traits were inversely associated with D(2)-like receptor availability in the ventral midbrain, an effect that remained significant after controlling for age. We speculate that the lower midbrain (auto)receptor availability seen in high novelty seekers leads to accentuated dopaminergic responses to novelty and other conditions that induce dopamine release.

Midbrain dopamine receptor availability is inversely associated with novelty seeking traits in humans

PubMed Central

Zald, David H.; Cowan, Ronald L.; Riccardi, Patrizia; Baldwin, Ronald M.; Ansari, M. Sib; Li, Rui; Shelby, Evan S.; Smith, Clarence E.; McHugo, Maureen; Kessler, Robert M.

2009-01-01

Novelty seeking personality traits are a major risk factor for the development of drug abuse and other unsafe behaviors. Rodent models of temperament indicate that high novelty responding is associated with decreased inhibitory autoreceptor control of midbrain dopamine neurons. It has been speculated that individual differences in dopamine functioning also underlie the personality trait of novelty seeking in humans. However, differences in the dopamine system of rodents and humans, as well as the methods for assessing novelty responding/seeking across species leave unclear to what extent the animal models inform our understanding of human personality. In the present study we examined the correlation between novelty seeking traits in humans and D2-like (D2/D3) receptor availability in the substantia nigra/ventral tegmental area. Based on the rodent literature we predicted that novelty seeking would be characterized by lowered levels of D2-like (auto)receptor availability in the midbrain. 34 healthy adults (18 men, 16 women) completed the Tridimensional Personality Questionnaire-Novelty Seeking Scale and PET scanning with the D2/D3 ligand [18F]fallypride. Novelty seeking personality traits were inversely associated with D2-like receptor availability in the ventral midbrain, an effect that remained significant after controlling for age. We speculate that the lower midbrain (auto)receptor availability seen in high novelty seekers leads to accentuated dopaminergic responses to novelty and other conditions that induce DA release. PMID:19118170

The role of leadership in HRH development in challenging public health settings

PubMed Central

Schiffbauer, Judith; O'Brien, Julie Barrett; Timmons, Barbara K; Kiarie, William N

2008-01-01

As part of the special feature on leadership and human resources (HR), Management Sciences for Health profiles three leaders who have made a significance difference in the HR situation in their countries. By taking a comprehensive approach and working in partnership with stakeholders, these leaders demonstrate that strengthening health workforce planning, management, and training can have a positive effect on the performance of the health sector. Three profiles are presented, from Afghanistan, South Africa, and Southern Sudan, revealing common approaches and leadership traits while demonstrating the specificity of local contexts. PMID:18983671

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus).

PubMed

Feng, Xiu; Yu, Xiaomu; Fu, Beide; Wang, Xinhua; Liu, Haiyang; Pang, Meixia; Tong, Jingou

2018-04-02

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Representation matters: quantitative behavioral variation in wild worm strains

NASA Astrophysics Data System (ADS)

Brown, Andre

Natural genetic variation in populations is the basis of genome-wide association studies, an approach that has been applied in large studies of humans to study the genetic architecture of complex traits including disease risk. Of course, the traits you choose to measure determine which associated genes you discover (or miss). In large-scale human studies, the measured traits are usually taken as a given during the association step because they are expensive to collect and standardize. Working with the nematode worm C. elegans, we do not have the same constraints. In this talk I will describe how large-scale imaging of worm behavior allows us to develop alternative representations of behavior that vary differently across wild populations. The alternative representations yield novel traits that can be used for genome-wide association studies and may reveal basic properties of the genotype-phenotype map that are obscured if only a small set of fixed traits are used.

Selection on male sex pheromone composition contributes to butterfly reproductive isolation

PubMed Central

Bacquet, P. M. B.; Brattström, O.; Wang, H.-L.; Allen, C. E.; Löfstedt, C.; Brakefield, P. M.; Nieberding, C. M.

2015-01-01

Selection can facilitate diversification by inducing character displacement in mate choice traits that reduce the probability of maladaptive mating between lineages. Although reproductive character displacement (RCD) has been demonstrated in two-taxa case studies, the frequency of this process in nature is still debated. Moreover, studies have focused primarily on visual and acoustic traits, despite the fact that chemical communication is probably the most common means of species recognition. Here, we showed in a large, mostly sympatric, butterfly genus, a strong pattern of recurrent RCD for predicted male sex pheromone composition, but not for visual mate choice traits. Our results suggest that RCD is not anecdotal, and that selection for divergence in male sex pheromone composition contributed to reproductive isolation within the Bicyclus genus. We propose that selection may target olfactory mate choice traits as a more common sensory modality to ensure reproductive isolation among diverging lineages than previously envisaged. PMID:25740889

Introduction: revisiting the "negrito" hypothesis: a transdisciplinary approach to human prehistory in southeast Asia.

PubMed

Endicott, Phillip

2013-01-01

The "negrito" hypothesis predicts that a shared phenotype among various contemporary groups of hunter-gatherers in Southeast Asia--dark skin, short stature, tight curly hair--is due to common descent from a region-wide, pre-Neolithic substrate of humanity. The alternative is that their distinctive phenotype results from convergent evolution. The core issues of the negrito hypothesis are today more relevant than ever to studies of human evolution, including the out-of-Africa migration, admixture with Denisovans, and the effects of environment and ecology on life-history traits. Understanding the current distribution of the negrito phenotype dictates a wide-ranging remit for study, including the articulation of the relationship between foragers and farmers in the present, the development of settled agriculture in the mid-Holocene, and terminal Pleistocene population expansions. The consensus reached by the contributors to this special double issue of Human Biology is that there is not yet conclusive evidence either for or against the negrito hypothesis. Nevertheless, the process of revisiting the problem will benefit the knowledge of the human prehistory of Southeast Asia. Whether the term negrito accurately reflects the all-encompassing nature of the resulting inquiry is in itself questionable, but the publication of this double issue is testament to the enduring ability of this hypothesis to unite disparate academic disciplines in a common purpose. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

[Effect of an introgression from Aegilops cylindrica host on manifestation of productivity traits in winter common wheat F2 plants].

PubMed

Kozub, N A; Sozinov, I A; sozinov, A A

2004-12-01

The effect of introgression of a chromosome 1D segment from Aegilops cylindrica to winter common wheat on productivity traits in F2 plants was studied using storage protein loci as genetic markers. An allele of the gliadin-coding Gli-D1 locus served as a marker of the introgression. Using of two- and three-locus interaction models, it was shown that the introgression tagged with Gli-D1 affected the manifestation of productivity traits (productive tillering, grain weight per plant and grain number per plant) through interaction with other marker storage protein loci: Glu-B1, Glu-D1, and Gli-B2.

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

Estimating genetic effects and quantifying missing heritability explained by identified rare-variant associations.

PubMed

Liu, Dajiang J; Leal, Suzanne M

2012-10-05

Next-generation sequencing has led to many complex-trait rare-variant (RV) association studies. Although single-variant association analysis can be performed, it is grossly underpowered. Therefore, researchers have developed many RV association tests that aggregate multiple variant sites across a genetic region (e.g., gene), and test for the association between the trait and the aggregated genotype. After these aggregate tests detect an association, it is only possible to estimate the average genetic effect for a group of RVs. As a result of the "winner's curse," such an estimate can be biased. Although for common variants one can obtain unbiased estimates of genetic parameters by analyzing a replication sample, for RVs it is desirable to obtain unbiased genetic estimates for the study where the association is identified. This is because there can be substantial heterogeneity of RV sites and frequencies even among closely related populations. In order to obtain an unbiased estimate for aggregated RV analysis, we developed bootstrap-sample-split algorithms to reduce the bias of the winner's curse. The unbiased estimates are greatly important for understanding the population-specific contribution of RVs to the heritability of complex traits. We also demonstrate both theoretically and via simulations that for aggregate RV analysis the genetic variance for a gene or region will always be underestimated, sometimes substantially, because of the presence of noncausal variants or because of the presence of causal variants with effects of different magnitudes or directions. Therefore, even if RVs play a major role in the complex-trait etiologies, a portion of the heritability will remain missing, and the contribution of RVs to the complex-trait etiologies will be underestimated. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Gene-centric Association Signals for Lipids and Apolipoproteins Identified via the HumanCVD BeadChip

PubMed Central

Talmud, Philippa J.; Drenos, Fotios; Shah, Sonia; Shah, Tina; Palmen, Jutta; Verzilli, Claudio; Gaunt, Tom R.; Pallas, Jacky; Lovering, Ruth; Li, Kawah; Casas, Juan Pablo; Sofat, Reecha; Kumari, Meena; Rodriguez, Santiago; Johnson, Toby; Newhouse, Stephen J.; Dominiczak, Anna; Samani, Nilesh J.; Caulfield, Mark; Sever, Peter; Stanton, Alice; Shields, Denis C.; Padmanabhan, Sandosh; Melander, Olle; Hastie, Claire; Delles, Christian; Ebrahim, Shah; Marmot, Michael G.; Smith, George Davey; Lawlor, Debbie A.; Munroe, Patricia B.; Day, Ian N.; Kivimaki, Mika; Whittaker, John; Humphries, Steve E.; Hingorani, Aroon D.

2009-01-01

Blood lipids are important cardiovascular disease (CVD) risk factors with both genetic and environmental determinants. The Whitehall II study (n = 5592) was genotyped with the gene-centric HumanCVD BeadChip (Illumina). We identified 195 SNPs in 16 genes/regions associated with 3 major lipid fractions and 2 apolipoprotein components at p < 10−5, with the associations being broadly concordant with prior genome-wide analysis. SNPs associated with LDL cholesterol and apolipoprotein B were located in LDLR, PCSK9, APOB, CELSR2, HMGCR, CETP, the TOMM40-APOE-C1-C2-C4 cluster, and the APOA5-A4-C3-A1 cluster; SNPs associated with HDL cholesterol and apolipoprotein AI were in CETP, LPL, LIPC, APOA5-A4-C3-A1, and ABCA1; and SNPs associated with triglycerides in GCKR, BAZ1B, MLXIPL, LPL, and APOA5-A4-C3-A1. For 48 SNPs in previously unreported loci that were significant at p < 10−4 in Whitehall II, in silico analysis including the British Women's Heart and Health Study, BRIGHT, ASCOT, and NORDIL studies (total n > 12,500) revealed previously unreported associations of SH2B3 (p < 2.2 × 10−6), BMPR2 (p < 2.3 × 10−7), BCL3/PVRL2 (flanking APOE; p < 4.4 × 10−8), and SMARCA4 (flanking LDLR; p < 2.5 × 10−7) with LDL cholesterol. Common alleles in these genes explained 6.1%–14.7% of the variance in the five lipid-related traits, and individuals at opposite tails of the additive allele score exhibited substantial differences in trait levels (e.g., >1 mmol/L in LDL cholesterol [∼1 SD of the trait distribution]). These data suggest that multiple common alleles of small effect can make important contributions to individual differences in blood lipids potentially relevant to the assessment of CVD risk. These genes provide further insights into lipid metabolism and the likely effects of modifying the encoded targets therapeutically. PMID:19913121

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

NASA Astrophysics Data System (ADS)

Ha, Minsu; Nehm, Ross H.

2014-05-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or increase, they struggled to use it to convincingly account for cases of trait loss or decrease. This study examines Darwin's evolutionary writings about trait gain and loss in the Origin of Species (On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. D. Appleton, New York, 1859) and compares them to written evolutionary explanations for trait gain and loss in a large (n > 500), cross-cultural and cross-sectional sample (novices and experts from the USA and Korea). Findings indicate that significantly more students and experts applied natural selection to cases of trait gain, but like Darwin and his contemporaries, they more often applied `use and disuse' and `inheritance of acquired characteristics' to episodes of trait loss. Although the parallelism between Darwin's difficulties and students' struggles with trait loss are striking, significant differences also characterize explanatory model structure. Overall, however, students and scientists struggles to explain trait loss—which is a very common phenomenon in the history of life—appear to transcend time, place, and level of biological expertise. The significance of these findings for evolution education are discussed; in particular, the situated nature of biological reasoning, and the important role that the history of science can play in understanding cognitive constraints on science learning.

The evolution of offensive realism.

PubMed

Johnson, Dominic D P; Phil, D; Thayer, Bradley A

Offensive realism, a theory of international relations, holds that states are disposed to competition and conflict because they are self-interested, power maximizing, and fearful of other states. Moreover, it argues that states are obliged to behave this way because doing so favors survival in the international system. Debate continues as to whether modern states actually do, or should, behave in this way, but we are struck by a different question. In this article, we ask whether the three core assumptions about behavior in offensive realism-self-help, power maximization, and outgroup fear-have any basis in scientific knowledge about human behavioral evolution. We find that these precise traits are not only evolutionarily adaptive but also empirically common across the animal kingdom, especially in primate and human societies. Based on these findings, we hypothesize that states behave as offensive realists predict not just because of anarchy in the modern international system but also because of the legacy of our evolution. In short, offensive realism may really be describing the nature of the human species more than the nature of the international system. If our hypothesis is correct, then evolutionary theory offers the following: (1) a novel ultimate cause of offensive realist behavior; (2) an extension of offensive realism to any domain in which humans compete for power; and (3) an explanation for why individual leaders themselves, and not just states, seek power. However, a key insight from evolution is that the primacy of self-help, power maximization, and outgroup fear does not necessarily condemn individuals or groups to competition and conflict; rather, these traits can in themselves give rise to cooperation and alliances.

What is the relationship between trait anxiety and depressive symptoms, fatigue, and low sleep quality following breast cancer surgery?

PubMed

Lockefeer, J P M; De Vries, J

2013-05-01

Depressive symptoms, fatigue, and low sleep quality are common symptoms during and after breast cancer (BC) treatment. In the present study, the relationship between trait anxiety and these symptoms in a long follow-up period was examined. This was a prospective study. Participants, composed of 163 women with BC and 224 women with benign breast problems (BBPs), completed questionnaires on depressive symptoms, fatigue, and sleep quality before diagnosis and 1, 3, 6, 12, and 24 months after diagnosis (BBP group) or surgical treatment (BC group). In addition, patients completed a questionnaire on trait anxiety before diagnosis. Trait anxiety was the most significant predictor for depressive symptoms (p < 0.001) and lower sleep quality (p = 0.040) at 2-year follow-up. For fatigue, fatigue at baseline and trait anxiety together was the most important predictor (p < 0.001). Linear mixed model analyses showed that there was an interaction effect of time with trait anxiety and with diagnosis for depressive symptoms (p = 0.001 and p < 0.001) and fatigue (p = 0.004 and p < 0.001). There was no interaction effect of time with trait anxiety or diagnosis for sleep quality (p = 0.055 and p = 0.225). Together with diagnosis, trait anxiety was an important determinant of depressive symptoms, fatigue, and low sleep quality following diagnosis of BBP or BC and seemed to be a common factor in these persisting symptoms. Copyright © 2012 John Wiley & Sons, Ltd.

Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow.

PubMed

Richter-Boix, Alex; Teplitsky, Céline; Rogell, Björn; Laurila, Anssi

2010-02-01

In ectotherms, variation in life history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, as genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open-canopy or partially closed-canopy ponds. To separate local adaptation from genetic drift, we compared differentiation in quantitative genetic traits (Q(ST)) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (F(ST)). We found that R. temporaria populations differ in means and plasticities of life history traits in different temperatures at local, and in F(ST) at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature, the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure, but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among the populations, and that natural selection is strong in this system.

Integration of genome and phenotypic scanning gives evidence of genetic structure in Mesoamerican common bean (Phaseolus vulgaris L.) landraces from the southwest of Europe.

PubMed

Santalla, M; De Ron, A M; De La Fuente, M

2010-05-01

Southwestern Europe has been considered as a secondary centre of genetic diversity for the common bean. The dispersal of domesticated materials from their centres of origin provides an experimental system that reveals how human selection during cultivation and adaptation to novel environments affects the genetic composition. In this paper, our goal was to elucidate how distinct events could modify the structure and level of genetic diversity in the common bean. The genome-wide genetic composition was analysed at 42 microsatellite loci in individuals of 22 landraces of domesticated common bean from the Mesoamerican gene pool. The accessions were also characterised for phaseolin seed protein and for nine allozyme polymorphisms and phenotypic traits. One of this study's important findings was the complementary information obtained from all the polymorphisms examined. Most of the markers found to be potentially under the influence of selection were located in the proximity of previously mapped genes and quantitative trait loci (QTLs) related to important agronomic traits, which indicates that population genomics approaches are very efficient in detecting QTLs. As it was revealed by outlier simple sequence repeats, loci analysis with STRUCTURE software and multivariate analysis of phenotypic data, the landraces were grouped into three clusters according to seed size and shape, vegetative growth habit and genetic resistance. A total of 151 alleles were detected with an average of 4 alleles per locus and an average polymorphism information content of 0.31. Using a model-based approach, on the basis of neutral markers implemented in the software STRUCTURE, three clusters were inferred, which were in good agreement with multivariate analysis. Geographic and genetic distances were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Genomic scans using both markers linked to genes affected by selection (outlier) and neutral markers showed advantages relative to other approaches, since they help to create a more complete picture of how adaptation to environmental conditions has sculpted the common bean genomes in southern Europe. The use of outlier loci also gives a clue about what selective forces gave rise to the actual phenotypes of the analysed landraces.

Personality from a cognitive-biological perspective.

PubMed

Neuman, Yair

2014-12-01

The term "personality" is used to describe a distinctive and relatively stable set of mental traits that aim to explain the organism's behavior. The concept of personality that emerged in human psychology has been also applied to the study of non-human organisms from birds to horses. In this paper, I critically review the concept of personality from an interdisciplinary perspective, and point to some ideas that may be used for developing a cognitive-biological theory of personality. Integrating theories and research findings from various fields such as cognitive ethnology, clinical psychology, and neuroscience, I argue that the common denominator of various personality theories are neural systems of threat/trust management and their emotional, cognitive, and behavioral dimensions. In this context, personality may be also conceived as a meta-heuristics both human and non-human organisms apply to model and predict the behavior of others. The paper concludes by suggesting a minimal computational model of personality that may guide future research. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships.

PubMed

Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P L; Lund, Mogens Sandø; Sahana, Goutam

2016-08-17

There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map rare variants. Besides, livestock populations have large half-sib families and the occurrence of rare variants may be confounded with family structure, which makes it difficult to disentangle their effects from family mean effects. We compared the power of methods that are commonly applied in human genetics to map rare variants in cattle using whole-genome sequence data and simulated phenotypes. We also studied the power of mapping rare variants using linear mixed models (LMM), which are the method of choice to account for both family relationships and population structure in cattle. We observed that the power of the LMM approach was low for mapping a rare variant (defined as those that have frequencies lower than 0.01) with a moderate effect (5 to 8 % of phenotypic variance explained by multiple rare variants that vary from 5 to 21 in number) contributing to a QTL with a sample size of 1000. In contrast, across the scenarios studied, statistical methods that are specialized for mapping rare variants increased power regardless of whether multiple rare variants or a single rare variant underlie a QTL. Different methods for combining rare variants in the test single nucleotide polymorphism set resulted in similar power irrespective of the proportion of total genetic variance explained by the QTL. However, when the QTL variance is very small (only 0.1 % of the total genetic variance), these specialized methods for mapping rare variants and LMM generally had no power to map the variants within a gene with sample sizes of 1000 or 5000. We observed that the methods that combine multiple rare variants within a gene into a meta-variant generally had greater power to map rare variants compared to LMM. Therefore, it is recommended to use rare variant association mapping methods to map rare genetic variants that affect quantitative traits in livestock, such as bovine populations.

So, are we the massively lucky species?

PubMed

Penn, Derek C; Holyoak, Keith J; Povinelli, Daniel J

2012-08-01

We are in vehement agreement with most of Vaesen's key claims. But Vaesen fails to consider or rebut the possibility that there are deep causal dependencies among the various cognitive traits he identifies as uniquely human. We argue that "higher-order relational reasoning" is one such linchpin trait in the evolution of human tool use, social intelligence, language, and culture.

The TRPM8 Protein Is a Testosterone Receptor

PubMed Central

Asuthkar, Swapna; Demirkhanyan, Lusine; Sun, Xiaohui; Elustondo, Pia A.; Krishnan, Vivek; Baskaran, Padmamalini; Velpula, Kiran Kumar; Thyagarajan, Baskaran; Pavlov, Evgeny V.; Zakharian, Eleonora

2015-01-01

Testosterone is a key steroid hormone in the development of male reproductive tissues and the regulation of the central nervous system. The rapid signaling mechanism induced by testosterone affects numerous behavioral traits, including sexual drive, aggressiveness, and fear conditioning. However, the currently identified testosterone receptor(s) is not believed to underlie the fast signaling, suggesting an orphan pathway. Here we report that an ion channel from the transient receptor potential family, TRPM8, commonly known as the cold and menthol receptor is the major component of testosterone-induced rapid actions. Using cultured and primary cell lines along with the purified TRPM8 protein, we demonstrate that testosterone directly activates TRPM8 channel at low picomolar range. Specifically, testosterone induced TRPM8 responses in primary human prostate cells, PC3 prostate cancer cells, dorsal root ganglion neurons, and hippocampal neurons. Picomolar concentrations of testosterone resulted in full openings of the purified TRPM8 channel in planar lipid bilayers. Furthermore, acute applications of testosterone on human skin elicited a cooling sensation. Our data conclusively demonstrate that testosterone is an endogenous and highly potent agonist of TRPM8, suggesting a role of TRPM8 channels well beyond their well established function in somatosensory neurons. This discovery may further imply TRPM8 channel function in testosterone-dependent behavioral traits. PMID:25480785

Impact of an atrazine-based herbicide on an agrobiont wolf spider.

PubMed

Godfrey, Jake A; Rypstra, Ann L

2018-06-01

For animals that live in association with humans, a key ecological question is how anthropogenic factors influence their life history. While major negative effects are obvious, subtle non-lethal responses to anthropogenic stimuli may provide insight into the features that lead to the success of species that thrive in habitats heavily impacted by humans. Here we explored the influence of the herbicide atrazine on various life history traits of a wolf spider that thrives in agroecosystems where it is commonly applied. We found that exposure delayed maturation and increased the probability of having molting errors. Atrazine also decreased the probability of producing an egg sac after mating, but increased the average mass of the initial egg sacs that were produced while not impacting the average number of eggs inside. The total number of eggs produced from a single mating on the other hand, was increased in the presence of atrazine through the production of multiple egg sacs. Finally, adult lifespan was shortened with exposure to atrazine. These results suggest that the atrazine based herbicides that are routinely applied to agricultural fields result in altered life history traits, potentially through endocrine disruption, that may counteract one another to allow persistence. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language

PubMed Central

Scharff, Constance; Petri, Jana

2011-01-01

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the ‘evo-devo’ conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this ‘deep homology’. Recently, ‘evo-devo’ has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can ‘descend with modification’. PMID:21690130

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language.

PubMed

Scharff, Constance; Petri, Jana

2011-07-27

The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the 'evo-devo' conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this 'deep homology'. Recently, 'evo-devo' has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can 'descend with modification'.

Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23–24 × SEA 5 of Common Bean

PubMed Central

Polania, Jose; Rao, Idupulapati M.; Cajiao, Cesar; Grajales, Miguel; Rivera, Mariela; Velasquez, Federico; Raatz, Bodo; Beebe, Stephen E.

2017-01-01

Drought is the major abiotic stress factor limiting yield of common bean (Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23–24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod harvest index, and seed number per area could serve as useful selection criteria for assessing sink strength and for genetic improvement of drought resistance in common bean. PMID:28316609

Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress

PubMed Central

Asfaw, Asrat; Blair, Matthew W.; Struik, Paul C.

2012-01-01

Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance. PMID:22670228

Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23-24 × SEA 5 of Common Bean.

PubMed

Polania, Jose; Rao, Idupulapati M; Cajiao, Cesar; Grajales, Miguel; Rivera, Mariela; Velasquez, Federico; Raatz, Bodo; Beebe, Stephen E

2017-01-01

Drought is the major abiotic stress factor limiting yield of common bean ( Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23-24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod harvest index, and seed number per area could serve as useful selection criteria for assessing sink strength and for genetic improvement of drought resistance in common bean.

Multienvironment quantitative trait Loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress.

PubMed

Asfaw, Asrat; Blair, Matthew W; Struik, Paul C

2012-05-01

Many of the world's common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers' field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.

A nursing theory-guided framework for genetic and epigenetic research.

PubMed

Maki, Katherine A; DeVon, Holli A

2018-04-01

The notion that genetics, through natural selection, determines innate traits has led to much debate and divergence of thought on the impact of innate traits on the human phenotype. The purpose of this synthesis was to examine how innate theory informs genetic research and how understanding innate theory through the lens of Martha Rogers' theory of unitary human beings can offer a contemporary view of how innate traits can inform epigenetic and genetic research. We also propose a new conceptual model for genetic and epigenetic research. The philosophical, theoretical, and research literatures were examined for this synthesis. We have merged philosophical and conceptual phenomena from innate theory with the theory of unitary beings into the University of Illinois at Chicago model for genetic and epigenetic research. Innate traits are the cornerstone of the framework but may be modified epigenetically by biological, physiological, psychological, and social determinants as they are transcribed. These modifiers serve as important links between the concept of innate traits and epigenetic modifications, and, like the theory of unitary human beings, the process is understood in the context of individual and environmental interaction that has the potential to evolve as the determinants change. © 2018 John Wiley & Sons Ltd.

Decreased reward value of biological motion among individuals with autistic traits.

PubMed

Williams, Elin H; Cross, Emily S

2018-02-01

The Social Motivation Theory posits that a reduced sensitivity to the value of social stimuli, specifically faces, can account for social impairments in Autism Spectrum Disorders (ASD). Research has demonstrated that typically developing (TD) individuals preferentially orient towards another type of salient social stimulus, namely biological motion. Individuals with ASD, however, do not show this preference. While the reward value of faces to both TD and ASD individuals has been well-established, the extent to which individuals from these populations also find human motion to be rewarding remains poorly understood. The present study investigated the value assigned to biological motion by TD participants in an effort task, and further examined whether these values differed among individuals with more autistic traits. The results suggest that TD participants value natural human motion more than rigid, machine-like motion or non-human control motion, but this preference is attenuated among individuals reporting more autistic traits. This study provides the first evidence to suggest that individuals with more autistic traits find a broader conceptualisation of social stimuli less rewarding compared to individuals with fewer autistic traits. By quantifying the social reward value of human motion, the present findings contribute an important piece to our understanding of social motivation in individuals with and without social impairments. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Serotonergic, Brain Volume and Attentional Correlates of Trait Anxiety in Primates

PubMed Central

Mikheenko, Yevheniia; Shiba, Yoshiro; Sawiak, Stephen; Braesicke, Katrin; Cockcroft, Gemma; Clarke, Hannah; Roberts, Angela C

2015-01-01

Trait anxiety is a risk factor for the development and maintenance of affective disorders, and insights into the underlying brain mechanisms are vital for improving treatment and prevention strategies. Translational studies in non-human primates, where targeted neurochemical and genetic manipulations can be made, are critical in view of their close neuroanatomical similarity to humans in brain regions implicated in trait anxiety. Thus, we characterised the serotonergic and regional brain volume correlates of trait-like anxiety in the marmoset monkey. Low- and high-anxious animals were identified by behavioral responses to a human intruder (HI) that are known to be sensitive to anxiolytic drug treatment. Extracellular serotonin levels within the amygdala were measured with in vivo microdialysis, at baseline and in response to challenge with the selective serotonin reuptake inhibitor, citalopram. Regional brain volume was assessed by structural magnetic resonance imaging. Anxious individuals showed persistent, long-term fearful responses to both a HI and a model snake, alongside sustained attention (vigilance) to novel cues in a context associated with unpredictable threat. Neurally, high-anxious marmosets showed reduced amygdala serotonin levels, and smaller volumes in a closely connected prefrontal region, the dorsal anterior cingulate cortex. These findings highlight behavioral and neural similarities between trait-like anxiety in marmosets and humans, and set the stage for further investigation of the processes contributing to vulnerability and resilience to affective disorders. PMID:25586542

The cultural evolution of emergent group-level traits.

PubMed

Smaldino, Paul E

2014-06-01

Many of the most important properties of human groups - including properties that may give one group an evolutionary advantage over another - are properly defined only at the level of group organization. Yet at present, most work on the evolution of culture has focused solely on the transmission of individual-level traits. I propose a conceptual extension of the theory of cultural evolution, particularly related to the evolutionary competition between cultural groups. The key concept in this extension is the emergent group-level trait. This type of trait is characterized by the structured organization of differentiated individuals and constitutes a unit of selection that is qualitatively different from selection on groups as defined by traditional multilevel selection (MLS) theory. As a corollary, I argue that the traditional focus on cooperation as the defining feature of human societies has missed an essential feature of cooperative groups. Traditional models of cooperation assume that interacting with one cooperator is equivalent to interacting with any other. However, human groups involve differential roles, meaning that receiving aid from one individual is often preferred to receiving aid from another. In this target article, I discuss the emergence and evolution of group-level traits and the implications for the theory of cultural evolution, including ramifications for the evolution of human cooperation, technology, and cultural institutions, and for the equivalency of multilevel selection and inclusive fitness approaches.

Emerging roles of microRNAs as molecular switches in the integrated circuit of the cancer cell

PubMed Central

Sotiropoulou, Georgia; Pampalakis, Georgios; Lianidou, Evi; Mourelatos, Zissimos

2009-01-01

Transformation of normal cells into malignant tumors requires the acquisition of six hallmark traits, e.g., self-sufficiency in growth signals, insensitivity to antigrowth signals and self-renewal, evasion of apoptosis, limitless replication potential, angiogenesis, invasion, and metastasis, which are common to all cancers (Hanahan and Weinberg 2000). These new cellular traits evolve from defects in major regulatory microcircuits that are fundamental for normal homeostasis. The discovery of microRNAs (miRNAs) as a new class of small non-protein-coding RNAs that control gene expression post-transcriptionally by binding to various mRNA targets suggests that these tiny RNA molecules likely act as molecular switches in the extensive regulatory web that involves thousands of transcripts. Most importantly, accumulating evidence suggests that numerous microRNAs are aberrantly expressed in human cancers. In this review, we discuss the emergent roles of microRNAs as switches that function to turn on/off known cellular microcircuits. We outline recent compelling evidence that deregulated microRNA-mediated control of cellular microcircuits cooperates with other well-established regulatory mechanisms to confer the hallmark traits of the cancer cell. Furthermore, these exciting insights into aberrant microRNA control in cancer-associated circuits may be exploited for cancer therapies that will target deregulated miRNA switches. PMID:19561119

Dissociable patterns of brain activity for mentalizing about known others: a role for attachment

PubMed Central

Laurita, Anne C.; Hazan, Cindy

2017-01-01

Abstract The human brain tracks dynamic changes within the social environment, forming and updating representations of individuals in our social milieu. This mechanism of social navigation builds an increasingly complex map of persons with whom we are familiar and form attachments to guide adaptive social behaviors. We examined the neural representation of known others along a continuum of attachment using fMRI. Heterosexual adults (N = 29, 16 females), in romantic relationships for more than 2 years, made trait judgments for a romantic partner, parent, close friend, familiar acquaintance and self-during scanning. Multivariate analysis, partial least squares, was used to identify whole-brain patterns of brain activation associated with trait judgments of known others across a continuum of attachment. Across conditions, trait judgments engaged the default network and lateral prefrontal cortex. Judgments about oneself and a partner were associated with a common activation pattern encompassing anterior and middle cingulate, posterior superior temporal sulcus, as well as anterior insula. Parent and close friend judgments engaged medial and anterior temporal lobe regions. These results provide novel evidence that mentalizing about known familiar others results in differential brain activity. We provide initial evidence that the representation of adult attachment is a distinguishing feature of these differences. PMID:28407150

Constraints on the evolution of tolerance to herbicide in the common morning glory: resistance and tolerance are mutually exclusive.

PubMed

Baucom, Regina S; Mauricio, Rodney

2008-11-01

Evolutionary biologists explain the maintenance of intermediate levels of defense in plant populations as being due to trade-offs, or negative genetic covariances among ecologically important traits. Attempts at detecting trade-offs as constraints on the evolution of defense have not always been successful, leading some to conclude that such trade-offs rarely explain current levels of defense in the population. Using the agricultural pest Ipomoea purpurea, we measured correlations between traits involved in defense to glyphosate, the active ingredient in Roundup, a widely used herbicide. We found significant allocation costs of tolerance, as well as trade-offs between resistance and two measures of tolerance to glyphosate. Selection on resistance and tolerance exhibited differing patterns: tolerance to leaf damage was under negative directional selection, whereas resistance was under positive directional selection. The joint pattern of selection on resistance and tolerance to leaf damage indicated the presence of alternate peaks in the fitness landscape such that a combination of either high tolerance and low resistance, or high resistance and low tolerance was favored. The widespread use of this herbicide suggests that it is likely an important selective agent on weed populations. Understanding the evolutionary dynamics of herbicide defense traits is thus of increasing importance in the context of human-mediated evolution.

Genetic Architecture of Vitamin B12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets

PubMed Central

Thorleifsson, Gudmar; Ahluwalia, Tarunveer S.; Steinthorsdottir, Valgerdur; Bjarnason, Helgi; Gudbjartsson, Daniel F.; Magnusson, Olafur T.; Sparsø, Thomas; Albrechtsen, Anders; Kong, Augustine; Masson, Gisli; Tian, Geng; Cao, Hongzhi; Nie, Chao; Kristiansen, Karsten; Husemoen, Lise Lotte; Thuesen, Betina; Li, Yingrui; Nielsen, Rasmus; Linneberg, Allan; Olafsson, Isleifur; Eyjolfsson, Gudmundur I.; Jørgensen, Torben; Wang, Jun; Hansen, Torben; Thorsteinsdottir, Unnur; Stefánsson, Kari; Pedersen, Oluf

2013-01-01

Genome-wide association studies have mainly relied on common HapMap sequence variations. Recently, sequencing approaches have allowed analysis of low frequency and rare variants in conjunction with common variants, thereby improving the search for functional variants and thus the understanding of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined samples of 45,576 and 37,341 individuals with serum B12 and folate measurements, respectively. We found six novel loci associating with serum B12 (CD320, TCN2, ABCD4, MMAA, MMACHC) or folate levels (FOLR3) and confirmed seven loci for these traits (TCN1, FUT6, FUT2, CUBN, CLYBL, MUT, MTHFR). Conditional analyses established that four loci contain additional independent signals. Interestingly, 13 of the 18 identified variants were coding and 11 of the 13 target genes have known functions related to B12 and folate pathways. Contrary to epidemiological studies we did not find consistent association of the variants with cardiovascular diseases, cancers or Alzheimer's disease although some variants demonstrated pleiotropic effects. Although to some degree impeded by low statistical power for some of these conditions, these data suggest that sequence variants that contribute to the population diversity in serum B12 or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations. PMID:23754956

Good genes, complementary genes and human mate preferences.

PubMed

Roberts, S Craig; Little, Anthony C

2008-03-01

The past decade has witnessed a rapidly growing interest in the biological basis of human mate choice. Here we review recent studies that demonstrate preferences for traits which might reveal genetic quality to prospective mates, with potential but still largely unknown influence on offspring fitness. These include studies assessing visual, olfactory and auditory preferences for potential good-gene indicator traits, such as dominance or bilateral symmetry. Individual differences in these robust preferences mainly arise through within and between individual variation in condition and reproductive status. Another set of studies have revealed preferences for traits indicating complementary genes, focussing on discrimination of dissimilarity at genes in the major histocompatibility complex (MHC). As in animal studies, we are only just beginning to understand how preferences for specific traits vary and inter-relate, how consideration of good and compatible genes can lead to substantial variability in individual mate choice decisions and how preferences expressed in one sensory modality may reflect those in another. Humans may be an ideal model species in which to explore these interesting complexities.

Good genes, complementary genes and human mate preferences.

PubMed

Roberts, S Craig; Little, Anthony C

2008-09-01

The past decade has witnessed a rapidly growing interest in the biological basis of human mate choice. Here we review recent studies that demonstrate preferences for traits which might reveal genetic quality to prospective mates, with potential but still largely unknown influence on offspring fitness. These include studies assessing visual, olfactory and auditory preferences for potential good-gene indicator traits, such as dominance or bilateral symmetry. Individual differences in these robust preferences mainly arise through within and between individual variation in condition and reproductive status. Another set of studies have revealed preferences for traits indicating complementary genes, focussing on discrimination of dissimilarity at genes in the major histocompatibility complex (MHC). As in animal studies, we are only just beginning to understand how preferences for specific traits vary and inter-relate, how consideration of good and compatible genes can lead to substantial variability in individual mate choice decisions and how preferences expressed in one sensory modality may reflect those in another. Humans may be an ideal model species in which to explore these interesting complexities.

A human model for primate personality

PubMed Central

2017-01-01

In this article, I review the literature to determine how successful the latent trait theory model of personality from differential psychology has been for studying personality in non-human primates. The evidence for the success of this model is quite good, and offers insights and directions for personality research in primates and other animals. This, I conclude, stems from (i) the human trait model's simplicity, and (ii) the fact that the human differential model of personality developed in the face of harsh criticism, which led researchers to test and refine their models. PMID:29021170

Mapping QTLs of yield-related traits using RIL population derived from common wheat and Tibetan semi-wild wheat.

PubMed

Liu, Gang; Jia, Lijia; Lu, Lahu; Qin, Dandan; Zhang, Jinping; Guan, Panfeng; Ni, Zhongfu; Yao, Yingyin; Sun, Qixin; Peng, Huiru

2014-11-01

QTLs controlling yield-related traits were mapped using a population derived from common wheat and Tibetan semi-wild wheat and they provided valuable information for using Tibetan semi-wild wheat in future wheat molecular breeding. Tibetan semi-wild wheat (Triticum aestivum ssp tibetanum Shao) is a kind of primitive hexaploid wheat and harbors several beneficial traits, such as tolerance to biotic and abiotic stresses. And as a wild relative of common wheat, heterosis of yield of the progeny between them was significant. This study focused on mapping QTLs controlling yield-related traits using a recombined inbred lines (RILs) population derived from a hybrid between a common wheat line NongDa3331 (ND3331) and the Tibetan semi-wild wheat accession Zang 1817. In nine location-year environments, a total of 148 putative QTLs controlling nine traits were detected, distributed on 19 chromosomes except for 1A and 2D. Single QTL explained the phenotypic variation ranging from 3.12 to 49.95%. Of these QTLs, 56 were contributed by Zang 1817. Some stable QTLs contributed by Zang 1817 were also detected in more than four environments, such as QPh-3A1, QPh-4B1 and QPh-4D for plant height, QSl-7A1 for spike length, QEp-4B2 for ears per plant, QGws-4D for grain weight per spike, and QTgw-4D for thousand grain weight. Several QTL-rich Regions were also identified, especially on the homoeologous group 4. The TaANT gene involved in floral organ development was mapped on chromosome 4A between Xksm71 and Xcfd6 with 0.8 cM interval, and co-segregated with the QTLs controlling floret number per spikelet, explaining 4.96-11.84% of the phenotypic variation. The current study broadens our understanding of the genetic characterization of Tibetan semi-wild wheat, which will enlarge the genetic diversity of yield-related traits in modern wheat breeding program.

Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children

PubMed Central

Voruganti, V. Saroja; Cole, Shelley A.; Haack, Karin; Comuzzie, Anthony G.; Muzny, Donna M.; Wheeler, David A.; Chang, Kyle; Hawes, Alicia; Gibbs, Richard A.

2011-01-01

Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5′ and 3′ flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3′-UTR, and 2 in the 5′-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001–0.009) were associated with obesity-related traits (P = 0.01–0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77–0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children. PMID:21771880

Estimation of (co)variances for genomic regions of flexible sizes: application to complex infectious udder diseases in dairy cattle

PubMed Central

2012-01-01

Background Multi-trait genomic models in a Bayesian context can be used to estimate genomic (co)variances, either for a complete genome or for genomic regions (e.g. per chromosome) for the purpose of multi-trait genomic selection or to gain further insight into the genomic architecture of related traits such as mammary disease traits in dairy cattle. Methods Data on progeny means of six traits related to mastitis resistance in dairy cattle (general mastitis resistance and five pathogen-specific mastitis resistance traits) were analyzed using a bivariate Bayesian SNP-based genomic model with a common prior distribution for the marker allele substitution effects and estimation of the hyperparameters in this prior distribution from the progeny means data. From the Markov chain Monte Carlo samples of the allele substitution effects, genomic (co)variances were calculated on a whole-genome level, per chromosome, and in regions of 100 SNP on a chromosome. Results Genomic proportions of the total variance differed between traits. Genomic correlations were lower than pedigree-based genetic correlations and they were highest between general mastitis and pathogen-specific traits because of the part-whole relationship between these traits. The chromosome-wise genomic proportions of the total variance differed between traits, with some chromosomes explaining higher or lower values than expected in relation to chromosome size. Few chromosomes showed pleiotropic effects and only chromosome 19 had a clear effect on all traits, indicating the presence of QTL with a general effect on mastitis resistance. The region-wise patterns of genomic variances differed between traits. Peaks indicating QTL were identified but were not very distinctive because a common prior for the marker effects was used. There was a clear difference in the region-wise patterns of genomic correlation among combinations of traits, with distinctive peaks indicating the presence of pleiotropic QTL. Conclusions The results show that it is possible to estimate, genome-wide and region-wise genomic (co)variances of mastitis resistance traits in dairy cattle using multivariate genomic models. PMID:22640006

Human Activity Helps Prey Win the Predator-Prey Space Race

PubMed Central

Muhly, Tyler B.; Semeniuk, Christina; Massolo, Alessandro; Hickman, Laura; Musiani, Marco

2011-01-01

Predator-prey interactions, including between large mammalian wildlife species, can be represented as a “space race”, where prey try to minimize and predators maximize spatial overlap. Human activity can also influence the distribution of wildlife species. In particular, high-human disturbance can displace large carnivore predators, a trait-mediated direct effect. Predator displacement by humans could then indirectly benefit prey species by reducing predation risk, a trait-mediated indirect effect of humans that spatially decouples predators from prey. The purpose of this research was to test the hypothesis that high-human activity was displacing predators and thus indirectly creating spatial refuge for prey species, helping prey win the “space race”. We measured the occurrence of eleven large mammal species (including humans and cattle) at 43 camera traps deployed on roads and trails in southwest Alberta, Canada. We tested species co-occurrence at camera sites using hierarchical cluster and nonmetric multidimensional scaling (NMS) analyses; and tested whether human activity, food and/or habitat influenced predator and prey species counts at camera sites using regression tree analysis. Cluster and NMS analysis indicated that at camera sites humans co-occurred with prey species more than predator species and predator species had relatively low co-occurrence with prey species. Regression tree analysis indicated that prey species were three times more abundant on roads and trails with >32 humans/day. However, predators were less abundant on roads and trails that exceeded 18 humans/day. Our results support the hypothesis that high-human activity displaced predators but not prey species, creating spatial refuge from predation. High-human activity on roads and trails (i.e., >18 humans/day) has the potential to interfere with predator-prey interactions via trait-mediated direct and indirect effects. We urge scientist and managers to carefully consider and quantify the trait-mediated indirect effects of humans, in addition to direct effects, when assessing human impacts on wildlife and ecosystems. PMID:21399682

Epistasis in intra- and inter-gene pool crosses of the common bean.

PubMed

Borel, J C; Ramalho, M A P; Abreu, A F B

2016-02-26

Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses.

Mining the LIPG Allelic Spectrum Reveals the Contribution of Rare and Common Regulatory Variants to HDL Cholesterol

PubMed Central

Raghavan, Avanthi; Neeli, Hemanth; Jin, Weijun; Badellino, Karen O.; Demissie, Serkalem; Manning, Alisa K.; DerOhannessian, Stephanie L.; Wolfe, Megan L.; Cupples, L. Adrienne; Li, Mingyao; Kathiresan, Sekar; Rader, Daniel J.

2011-01-01

Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5′ UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5′ UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci. PMID:22174694

Imaging-Genetics in Dyslexia: Connecting risk genetic variants to brain neuroimaging and ultimately to reading impairments

PubMed Central

Eicher, John D.; Gruen, Jeffrey R.

2013-01-01

Dyslexia is a common pediatric disorder that affects 5-17% of schoolchildren in the United States. It is marked by unexpected difficulties in fluent reading despite adequate intelligence, opportunity, and instruction. Classically, neuropsychologists have studied dyslexia using a variety of neurocognitive batteries to gain insight into the specific deficits and impairments in affected children. Since dyslexia is a complex genetic trait with high heritability, analyses conditioned on performance on these neurocognitive batteries have been used to try to identify associated genes. This has led to some successes in identifying contributing genes, although much of the heritability remains unexplained. Additionally, the lack of relevant human brain tissue for analysis and the challenges of modeling a uniquely human trait in animals are barriers to advancing our knowledge of the underlying pathophysiology. In vivo imaging technologies, however, present new opportunities to examine dyslexia and reading skills in a clearly relevant context in human subjects. Recent investigations have started to integrate these imaging data with genetic data in attempts to gain a more complete and complex understanding of reading processes. In addition to bridging the gap from genetic risk variant to a discernible neuroimaging phenotype and ultimately to the clinical impairments in reading performance, the use of neuroimaging phenotypes will reveal novel risk genes and variants. In this article, we briefly discuss the genetic and imaging investigations and take an in-depth look at the recent imaging-genetics investigations of dyslexia. PMID:23916419

In-Silico Genomic Approaches To Understanding Lactation, Mammary Development, And Breast Cancer

USDA-ARS?s Scientific Manuscript database

Lactation-related traits are influenced by genetics. From a quantitative standpoint, these traits have been well studied in dairy species, but there has also been work on the genetics of lactation in humans and mice. In addition, there is evidence to support the notion that other mammary gland trait...

Genetic analysis of kernel traits in maize-teosinte introgression populations

USDA-ARS?s Scientific Manuscript database

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is mos...

Higher-Order Item Response Models for Hierarchical Latent Traits

ERIC Educational Resources Information Center

Huang, Hung-Yu; Wang, Wen-Chung; Chen, Po-Hsi; Su, Chi-Ming

2013-01-01

Many latent traits in the human sciences have a hierarchical structure. This study aimed to develop a new class of higher order item response theory models for hierarchical latent traits that are flexible in accommodating both dichotomous and polytomous items, to estimate both item and person parameters jointly, to allow users to specify…

Fear-Conditioning Mechanisms Associated with Trait Vulnerability to Anxiety in Humans

PubMed Central

Indovina, Iole; Robbins, Trevor W.; Núñez-Elizalde, Anwar O.; Dunn, Barnaby D.; Bishop, Sonia J.

2011-01-01

Summary Investigations of fear conditioning in rodents and humans have illuminated the neural mechanisms underlying cued and contextual fear. A critical question is how personality dimensions such as trait anxiety act through these mechanisms to confer vulnerability to anxiety disorders, and whether humans' ability to overcome acquired fears depends on regulatory skills not characterized in animal models. In a neuroimaging study of fear conditioning in humans, we found evidence for two independent dimensions of neurocognitive function associated with trait vulnerability to anxiety. The first entailed increased amygdala responsivity to phasic fear cues. The second involved impoverished ventral prefrontal cortical (vPFC) recruitment to downregulate both cued and contextual fear prior to omission (extinction) of the aversive unconditioned stimulus. These two dimensions may contribute to symptomatology differences across anxiety disorders; the amygdala mechanism affecting the development of phobic fear and the frontal mechanism influencing the maintenance of both specific fears and generalized anxiety. PMID:21315265

A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

PubMed Central

Buchanan, Carrie C; Torstenson, Eric S; Bush, William S

2012-01-01

Background Since publication of the human genome in 2003, geneticists have been interested in risk variant associations to resolve the etiology of traits and complex diseases. The International HapMap Consortium undertook an effort to catalog all common variation across the genome (variants with a minor allele frequency (MAF) of at least 5% in one or more ethnic groups). HapMap along with advances in genotyping technology led to genome-wide association studies which have identified common variants associated with many traits and diseases. In 2008 the 1000 Genomes Project aimed to sequence 2500 individuals and identify rare variants and 99% of variants with a MAF of <1%. Methods To determine whether the 1000 Genomes Project includes all the variants in HapMap, we examined the overlap between single nucleotide polymorphisms (SNPs) genotyped in the two resources using merged phase II/III HapMap data and low coverage pilot data from 1000 Genomes. Results Comparison of the two data sets showed that approximately 72% of HapMap SNPs were also found in 1000 Genomes Project pilot data. After filtering out HapMap variants with a MAF of <5% (separately for each population), 99% of HapMap SNPs were found in 1000 Genomes data. Conclusions Not all variants cataloged in HapMap are also cataloged in 1000 Genomes. This could affect decisions about which resource to use for SNP queries, rare variant validation, or imputation. Both the HapMap and 1000 Genomes Project databases are useful resources for human genetics, but it is important to understand the assumptions made and filtering strategies employed by these projects. PMID:22319179

PTSD-Related Behavioral Traits in a Rat Model of Blast-Induced mTBI Are Reversed by the mGluR2/3 Receptor Antagonist BCI-838.

PubMed

Perez-Garcia, Georgina; De Gasperi, Rita; Gama Sosa, Miguel A; Perez, Gissel M; Otero-Pagan, Alena; Tschiffely, Anna; McCarron, Richard M; Ahlers, Stephen T; Elder, Gregory A; Gandy, Sam

2018-01-01

Battlefield blast exposure related to improvised explosive devices (IEDs) has become the most common cause of traumatic brain injury (TBI) in the recent conflicts in Iraq and Afghanistan. Mental health problems are common after TBI. A striking feature in the most recent veterans has been the frequency with which mild TBI (mTBI) and posttraumatic stress disorder (PTSD) have appeared together, in contrast to the classical situations in which the presence of mTBI has excluded the diagnosis of PTSD. However, treatment of PTSD-related symptoms that follow blast injury has become a significant problem. BCI-838 (MGS0210) is a Group II metabotropic glutamate receptor (mGluR2/3) antagonist prodrug, and its active metabolite BCI-632 (MGS0039) has proneurogenic, procognitive, and antidepressant activities in animal models. In humans, BCI-838 is currently in clinical trials for refractory depression and suicidality. The aim of the current study was to determine whether BCI-838 could modify the anxiety response and reverse PTSD-related behaviors in rats exposed to a series of low-level blast exposures designed to mimic a human mTBI or subclinical blast exposure. BCI-838 treatment reversed PTSD-related behavioral traits improving anxiety and fear-related behaviors as well as long-term recognition memory. Treatment with BCI-838 also increased neurogenesis in the dentate gyrus (DG) of blast-exposed rats. The safety profile of BCI-838 together with the therapeutic activities reported here, make BCI-838 a promising drug for the treatment of former battlefield Warfighters suffering from PTSD-related symptoms following blast-induced mTBI.

PTSD-Related Behavioral Traits in a Rat Model of Blast-Induced mTBI Are Reversed by the mGluR2/3 Receptor Antagonist BCI-838

PubMed Central

Perez-Garcia, Georgina; De Gasperi, Rita; Gama Sosa, Miguel A.; Perez, Gissel M.; Otero-Pagan, Alena; Tschiffely, Anna; McCarron, Richard M.; Ahlers, Stephen T.

2018-01-01

Battlefield blast exposure related to improvised explosive devices (IEDs) has become the most common cause of traumatic brain injury (TBI) in the recent conflicts in Iraq and Afghanistan. Mental health problems are common after TBI. A striking feature in the most recent veterans has been the frequency with which mild TBI (mTBI) and posttraumatic stress disorder (PTSD) have appeared together, in contrast to the classical situations in which the presence of mTBI has excluded the diagnosis of PTSD. However, treatment of PTSD-related symptoms that follow blast injury has become a significant problem. BCI-838 (MGS0210) is a Group II metabotropic glutamate receptor (mGluR2/3) antagonist prodrug, and its active metabolite BCI-632 (MGS0039) has proneurogenic, procognitive, and antidepressant activities in animal models. In humans, BCI-838 is currently in clinical trials for refractory depression and suicidality. The aim of the current study was to determine whether BCI-838 could modify the anxiety response and reverse PTSD-related behaviors in rats exposed to a series of low-level blast exposures designed to mimic a human mTBI or subclinical blast exposure. BCI-838 treatment reversed PTSD-related behavioral traits improving anxiety and fear-related behaviors as well as long-term recognition memory. Treatment with BCI-838 also increased neurogenesis in the dentate gyrus (DG) of blast-exposed rats. The safety profile of BCI-838 together with the therapeutic activities reported here, make BCI-838 a promising drug for the treatment of former battlefield Warfighters suffering from PTSD-related symptoms following blast-induced mTBI. PMID:29387781

Neurophysiologic Methods to Measure Stress During Survival, Evasion, Resistance, and Escape Training

DTIC Science & Technology

2007-05-01

amygdala function as well as perceived stress, trait anxiety , and trait anger. Overview of current research strategy: HRV analysis represents another...expected to relate to perceived stress, trait anxiety , and trait anger. In prospective analyses, HRV is expected to pre- dict cortisol reactivity...studying brain activity linked with fear, anxiety , and other emotional states in humans, is described in this section. The ASER is elicited by an abrupt

The cooperative economy of food: Implications for human life history and physiology.

PubMed

Kramer, Karen L

2018-04-06

The human diet has undergone substantial modifications since the emergence of modern humans and varies considerably in today's traditional societies. Despite these changes and cross-cultural differences, the human diet can be characterized by several common elements. These include diverse, high quality foods, technological complexity to acquire and process food, and the establishment of home bases for storage, processing and consumption. Together these aspects of the human diet challenge any one individual to independently meet all of his or her daily caloric needs. Humans solve this challenge through food sharing, labor exchange and the division of labor. The cooperative nature of the human diet is associated with many downstream effects on our life history and physiology. This paper overviews the constellation of traits that likely led to a cooperative economy of food, and draws on ethnographic examples to illustrate its effects on human life history and physiology. Two detailed examples using body composition, time allocation and food acquisition data show how cooperation among Savanna Pumé hunter-gatherers affects activity levels, sexual dimorphism in body fat, maturational pace and age at first birth. Copyright © 2018. Published by Elsevier Inc.

A simple mathematical model of gradual Darwinian evolution: emergence of a Gaussian trait distribution in adaptation along a fitness gradient.

PubMed

Biktashev, Vadim N

2014-04-01

We consider a simple mathematical model of gradual Darwinian evolution in continuous time and continuous trait space, due to intraspecific competition for common resource in an asexually reproducing population in constant environment, while far from evolutionary stable equilibrium. The model admits exact analytical solution. In particular, Gaussian distribution of the trait emerges from generic initial conditions.

Perception of aesthetics and personality traits in orthognathic surgery patients: A comparison of still and moving images

PubMed Central

Tran, Ulrich S.; Wutzl, Arno; Seemann, Rudolf; Millesi, Gabriele; Jagsch, Reinhold

2018-01-01

It is common in practicing orthognathic surgery to evaluate faces with retruded or protruded chins (dysgnathic faces) using photographs. Because motion may alter how the face is perceived, we investigated the perception of faces presented via photographs and videos. Two hundred naïve raters (lay persons, without maxillo facial surgery background) evaluated 12 subjects with varying chin anatomy [so-called skeletal Class I (normal chin), Class II (retruded chin), and Class III (protruded chin)]. Starting from eight traits, with Factor analysis we found a two-Factor solution, i.e. an "aesthetics associated traits cluster" and a Factor "personality traits cluster" which appeared to be uncorrelated. Internal consistency of the Factors found for photographs and videos was excellent. Generally, female raters delivered better ratings than males, but the effect sizes were small. We analyzed differences and the respective effect magnitude between photograph and video perception. For each skeletal class the aesthetics associated dimensions were rated similarly between photographs and video clips. In contrast, specific personality traits were rated differently. Differences in the class-specific personality traits seen on photographs were "smoothed" in the assessment of videos, which implies that photos enhance stereotypes commonly attributed to a retruded or protruded chin. PMID:29775466

A trait-based approach to bacterial biofilms in soil.

PubMed

Lennon, Jay T; Lehmkuhl, Brent K

2016-09-01

A trait-based approach focuses on attributes of taxa that influence the structure and function of communities. Biofilm production is a common trait among microorganisms in a wide range of environmental, engineered, and host-associated ecosystems. Here, we used Pseudomonas aeruginosa to link biofilm production to moisture availability, a common stressor for microorganisms in soil. First, we demonstrate that biofilm production is a response trait that influences the desiccation phenotype by increasing survivorship, shifting the niche space, and reducing the minimum water potential needed to sustain a net-positive growth rate (Ψ*). Although the allocation of resources to biofilms is thought to be costly, we found no evidence for a trade-off between fitness and biofilm production along a soil moisture gradient. Second, we demonstrated that biofilm production is an effect trait. Specifically, biofilm production increased water retention in soils that were exposed to a series of drying and rewetting cycles. Although this form of niche construction should affect species interactions, we found no evidence that the benefits of biofilm production were extended to another co-occurring soil bacterium. Together, our results support the view that biofilm production is an important trait that may contribute to the distribution, abundance, and functioning of microorganisms in soils. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evolutionary and plastic responses of freshwater invertebrates to climate change: realized patterns and future potential

PubMed Central

Stoks, Robby; Geerts, Aurora N; De Meester, Luc

2014-01-01

We integrated the evidence for evolutionary and plastic trait changes in situ in response to climate change in freshwater invertebrates (aquatic insects and zooplankton). The synthesis on the trait changes in response to the expected reductions in hydroperiod and increases in salinity indicated little evidence for adaptive, plastic, and genetic trait changes and for local adaptation. With respect to responses to temperature, there are many studies on temporal trait changes in phenology and body size in the wild that are believed to be driven by temperature increases, but there is a general lack of rigorous demonstration whether these trait changes are genetically based, adaptive, and causally driven by climate change. Current proof for genetic trait changes under climate change in freshwater invertebrates stems from a limited set of common garden experiments replicated in time. Experimental thermal evolution experiments and common garden warming experiments associated with space-for-time substitutions along latitudinal gradients indicate that besides genetic changes, also phenotypic plasticity and evolution of plasticity are likely to contribute to the observed phenotypic changes under climate change in aquatic invertebrates. Apart from plastic and genetic thermal adjustments, also genetic photoperiod adjustments are widespread and may even dominate the observed phenological shifts. PMID:24454547

Rare and low-frequency coding variants alter human adult height

PubMed Central

Marouli, Eirini; Graff, Mariaelisa; Medina-Gomez, Carolina; Lo, Ken Sin; Wood, Andrew R; Kjaer, Troels R; Fine, Rebecca S; Lu, Yingchang; Schurmann, Claudia; Highland, Heather M; Rüeger, Sina; Thorleifsson, Gudmar; Justice, Anne E; Lamparter, David; Stirrups, Kathleen E; Turcot, Valérie; Young, Kristin L; Winkler, Thomas W; Esko, Tõnu; Karaderi, Tugce; Locke, Adam E; Masca, Nicholas GD; Ng, Maggie CY; Mudgal, Poorva; Rivas, Manuel A; Vedantam, Sailaja; Mahajan, Anubha; Guo, Xiuqing; Abecasis, Goncalo; Aben, Katja K; Adair, Linda S; Alam, Dewan S; Albrecht, Eva; Allin, Kristine H; Allison, Matthew; Amouyel, Philippe; Appel, Emil V; Arveiler, Dominique; Asselbergs, Folkert W; Auer, Paul L; Balkau, Beverley; Banas, Bernhard; Bang, Lia E; Benn, Marianne; Bergmann, Sven; Bielak, Lawrence F; Blüher, Matthias; Boeing, Heiner; Boerwinkle, Eric; Böger, Carsten A; Bonnycastle, Lori L; Bork-Jensen, Jette; Bots, Michiel L; Bottinger, Erwin P; Bowden, Donald W; Brandslund, Ivan; Breen, Gerome; Brilliant, Murray H; Broer, Linda; Burt, Amber A; Butterworth, Adam S; Carey, David J; Caulfield, Mark J; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der Ida; Chowdhury, Rajiv; Christensen, Cramer; Chu, Audrey Y; Cocca, Massimiliano; Collins, Francis S; Cook, James P; Corley, Janie; Galbany, Jordi Corominas; Cox, Amanda J; Cuellar-Partida, Gabriel; Danesh, John; Davies, Gail; de Bakker, Paul IW; de Borst, Gert J.; de Denus, Simon; de Groot, Mark CH; de Mutsert, Renée; Deary, Ian J; Dedoussis, George; Demerath, Ellen W; den Hollander, Anneke I; Dennis, Joe G; Di Angelantonio, Emanuele; Drenos, Fotios; Du, Mengmeng; Dunning, Alison M; Easton, Douglas F; Ebeling, Tapani; Edwards, Todd L; Ellinor, Patrick T; Elliott, Paul; Evangelou, Evangelos; Farmaki, Aliki-Eleni; Faul, Jessica D; Feitosa, Mary F; Feng, Shuang; Ferrannini, Ele; Ferrario, Marco M; Ferrieres, Jean; Florez, Jose C; Ford, Ian; Fornage, Myriam; Franks, Paul W; Frikke-Schmidt, Ruth; Galesloot, Tessel E; Gan, Wei; Gandin, Ilaria; Gasparini, Paolo; Giedraitis, Vilmantas; Giri, Ayush; Girotto, Giorgia; Gordon, Scott D; Gordon-Larsen, Penny; Gorski, Mathias; Grarup, Niels; Grove, Megan L.; Gudnason, Vilmundur; Gustafsson, Stefan; Hansen, Torben; Harris, Kathleen Mullan; Harris, Tamara B; Hattersley, Andrew T; Hayward, Caroline; He, Liang; Heid, Iris M; Heikkilä, Kauko; Helgeland, Øyvind; Hernesniemi, Jussi; Hewitt, Alex W; Hocking, Lynne J; Hollensted, Mette; Holmen, Oddgeir L; Hovingh, G. Kees; Howson, Joanna MM; Hoyng, Carel B; Huang, Paul L; Hveem, Kristian; Ikram, M. Arfan; Ingelsson, Erik; Jackson, Anne U; Jansson, Jan-Håkan; Jarvik, Gail P; Jensen, Gorm B; Jhun, Min A; Jia, Yucheng; Jiang, Xuejuan; Johansson, Stefan; Jørgensen, Marit E; Jørgensen, Torben; Jousilahti, Pekka; Jukema, J Wouter; Kahali, Bratati; Kahn, René S; Kähönen, Mika; Kamstrup, Pia R; Kanoni, Stavroula; Kaprio, Jaakko; Karaleftheri, Maria; Kardia, Sharon LR; Karpe, Fredrik; Kee, Frank; Keeman, Renske; Kiemeney, Lambertus A; Kitajima, Hidetoshi; Kluivers, Kirsten B; Kocher, Thomas; Komulainen, Pirjo; Kontto, Jukka; Kooner, Jaspal S; Kooperberg, Charles; Kovacs, Peter; Kriebel, Jennifer; Kuivaniemi, Helena; Küry, Sébastien; Kuusisto, Johanna; La Bianca, Martina; Laakso, Markku; Lakka, Timo A; Lange, Ethan M; Lange, Leslie A; Langefeld, Carl D; Langenberg, Claudia; Larson, Eric B; Lee, I-Te; Lehtimäki, Terho; Lewis, Cora E; Li, Huaixing; Li, Jin; Li-Gao, Ruifang; Lin, Honghuang; Lin, Li-An; Lin, Xu; Lind, Lars; Lindström, Jaana; Linneberg, Allan; Liu, Yeheng; Liu, Yongmei; Lophatananon, Artitaya; Luan, Jian'an; Lubitz, Steven A; Lyytikäinen, Leo-Pekka; Mackey, David A; Madden, Pamela AF; Manning, Alisa K; Männistö, Satu; Marenne, Gaëlle; Marten, Jonathan; Martin, Nicholas G; Mazul, Angela L; Meidtner, Karina; Metspalu, Andres; Mitchell, Paul; Mohlke, Karen L; Mook-Kanamori, Dennis O; Morgan, Anna; Morris, Andrew D; Morris, Andrew P; Müller-Nurasyid, Martina; Munroe, Patricia B; Nalls, Mike A; Nauck, Matthias; Nelson, Christopher P; Neville, Matt; Nielsen, Sune F; Nikus, Kjell; Njølstad, Pål R; Nordestgaard, Børge G; Ntalla, Ioanna; O'Connel, Jeffrey R; Oksa, Heikki; Loohuis, Loes M Olde; Ophoff, Roel A; Owen, Katharine R; Packard, Chris J; Padmanabhan, Sandosh; Palmer, Colin NA; Pasterkamp, Gerard; Patel, Aniruddh P; Pattie, Alison; Pedersen, Oluf; Peissig, Peggy L; Peloso, Gina M; Pennell, Craig E; Perola, Markus; Perry, James A; Perry, John R.B.; Person, Thomas N; Pirie, Ailith; Polasek, Ozren; Posthuma, Danielle; Raitakari, Olli T; Rasheed, Asif; Rauramaa, Rainer; Reilly, Dermot F; Reiner, Alex P; Renström, Frida; Ridker, Paul M; Rioux, John D; Robertson, Neil; Robino, Antonietta; Rolandsson, Olov; Rudan, Igor; Ruth, Katherine S; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J; Sandow, Kevin; Sapkota, Yadav; Sattar, Naveed; Schmidt, Marjanka K; Schreiner, Pamela J; Schulze, Matthias B; Scott, Robert A; Segura-Lepe, Marcelo P; Shah, Svati; Sim, Xueling; Sivapalaratnam, Suthesh; Small, Kerrin S; Smith, Albert Vernon; Smith, Jennifer A; Southam, Lorraine; Spector, Timothy D; Speliotes, Elizabeth K; Starr, John M; Steinthorsdottir, Valgerdur; Stringham, Heather M; Stumvoll, Michael; Surendran, Praveen; Hart, Leen M ‘t; Tansey, Katherine E; Tardif, Jean-Claude; Taylor, Kent D; Teumer, Alexander; Thompson, Deborah J; Thorsteinsdottir, Unnur; Thuesen, Betina H; Tönjes, Anke; Tromp, Gerard; Trompet, Stella; Tsafantakis, Emmanouil; Tuomilehto, Jaakko; Tybjaerg-Hansen, Anne; Tyrer, Jonathan P; Uher, Rudolf; Uitterlinden, André G; Ulivi, Sheila; van der Laan, Sander W; Van Der Leij, Andries R; van Duijn, Cornelia M; van Schoor, Natasja M; van Setten, Jessica; Varbo, Anette; Varga, Tibor V; Varma, Rohit; Edwards, Digna R Velez; Vermeulen, Sita H; Vestergaard, Henrik; Vitart, Veronique; Vogt, Thomas F; Vozzi, Diego; Walker, Mark; Wang, Feijie; Wang, Carol A; Wang, Shuai; Wang, Yiqin; Wareham, Nicholas J; Warren, Helen R; Wessel, Jennifer; Willems, Sara M; Wilson, James G; Witte, Daniel R; Woods, Michael O; Wu, Ying; Yaghootkar, Hanieh; Yao, Jie; Yao, Pang; Yerges-Armstrong, Laura M; Young, Robin; Zeggini, Eleftheria; Zhan, Xiaowei; Zhang, Weihua; Zhao, Jing Hua; Zhao, Wei; Zhao, Wei; Zheng, He; Zhou, Wei; Rotter, Jerome I; Boehnke, Michael; Kathiresan, Sekar; McCarthy, Mark I; Willer, Cristen J; Stefansson, Kari; Borecki, Ingrid B; Liu, Dajiang J; North, Kari E; Heard-Costa, Nancy L; Pers, Tune H; Lindgren, Cecilia M; Oxvig, Claus; Kutalik, Zoltán; Rivadeneira, Fernando; Loos, Ruth JF; Frayling, Timothy M; Hirschhorn, Joel N; Deloukas, Panos; Lettre, Guillaume

2016-01-01

Summary Height is a highly heritable, classic polygenic trait with ∼700 common associated variants identified so far through genome-wide association studies. Here, we report 83 height-associated coding variants with lower minor allele frequencies (range of 0.1-4.8%) and effects of up to 2 cm/allele (e.g. in IHH, STC2, AR and CRISPLD2), >10 times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (+1-2 cm/allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes mutated in monogenic growth disorders and highlight new biological candidates (e.g. ADAMTS3, IL11RA, NOX4) and pathways (e.g. proteoglycan/glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate to large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways. PMID:28146470

Divergence in Life History Traits between Two Populations of a Seed-Dimorphic Halophyte in Response to Soil Salinity

PubMed Central

Yang, Fan; Baskin, Jerry M.; Baskin, Carol C.; Yang, Xuejun; Cao, Dechang; Huang, Zhenying

2017-01-01

Production of heteromorphic seeds is common in halophytes growing in arid environments with strong spatial and temporal heterogeneity. However, evidence for geographic variation (reflecting local adaptation) is almost nonexistent. Our primary aims were to compare the life history traits of two desert populations of this halophytic summer annual Suaeda corniculata subsp. mongolica and to investigate the phenotypic response of its plant and heteromorphic seeds to different levels of salt stress. Dimorphic seeds (F1) of the halophyte S. corniculata collected from two distant populations (F0) that differ in soil salinity were grown in a common environment under different levels of salinity to minimize the carryover effects from the field environment and tested for variation in plant (F1) and seed (F2) traits. Compared to F1 plants grown in low soil salinity, those grown in high salinity (>0.2 mol⋅L-1) were smaller and produced fewer seeds but had a higher reproductive allocation and a higher non-dormant brown seed: dormant black seed ratio. High salinity during plant growth decreased germination percentage of F2 black seeds but had no effect on F2 brown seeds. Between population differences in life history traits in the common environment corresponded with those in the natural populations. Phenotypic differences between the two populations were retained in F1 plants and in F2 seeds in the common environment, which suggests that the traits are genetically based. Our results indicate that soil salinity plays an ecologically important role in population regeneration of S. corniculata by influencing heteromorphic seed production in the natural habitat. PMID:28670319

Genome-Wide Association Study among Four Horse Breeds Identifies a Common Haplotype Associated with In Vitro CD3+ T Cell Susceptibility/Resistance to Equine Arteritis Virus Infection ▿

PubMed Central

Go, Yun Young; Bailey, Ernest; Cook, Deborah G.; Coleman, Stephen J.; MacLeod, James N.; Chen, Kuey-Chu; Timoney, Peter J.; Balasuriya, Udeni B. R.

2011-01-01

Previously, we have shown that horses could be divided into susceptible and resistant groups based on an in vitro assay using dual-color flow cytometric analysis of CD3+ T cells infected with equine arteritis virus (EAV). Here, we demonstrate that the differences in in vitro susceptibility of equine CD3+ T lymphocytes to EAV infection have a genetic basis. To investigate the possible hereditary basis for this trait, we conducted a genome-wide association study (GWAS) to compare susceptible and resistant phenotypes. Testing of 267 DNA samples from four horse breeds that had a susceptible or a resistant CD3+ T lymphocyte phenotype using both Illumina Equine SNP50 BeadChip and Sequenom's MassARRAY system identified a common, genetically dominant haplotype associated with the susceptible phenotype in a region of equine chromosome 11 (ECA11), positions 49572804 to 49643932. The presence of a common haplotype indicates that the trait occurred in a common ancestor of all four breeds, suggesting that it may be segregated among other modern horse breeds. Biological pathway analysis revealed several cellular genes within this region of ECA11 encoding proteins associated with virus attachment and entry, cytoskeletal organization, and NF-κB pathways that may be associated with the trait responsible for the in vitro susceptibility/resistance of CD3+ T lymphocytes to EAV infection. The data presented in this study demonstrated a strong association of genetic markers with the trait, representing de facto proof that the trait is under genetic control. To our knowledge, this is the first GWAS of an equine infectious disease and the first GWAS of equine viral arteritis. PMID:21994447

Unraveling the evolution of uniquely human cognition.

PubMed

MacLean, Evan L

2016-06-07

A satisfactory account of human cognitive evolution will explain not only the psychological mechanisms that make our species unique, but also how, when, and why these traits evolved. To date, researchers have made substantial progress toward defining uniquely human aspects of cognition, but considerably less effort has been devoted to questions about the evolutionary processes through which these traits have arisen. In this article, I aim to link these complementary aims by synthesizing recent advances in our understanding of what makes human cognition unique, with theory and data regarding the processes of cognitive evolution. I review evidence that uniquely human cognition depends on synergism between both representational and motivational factors and is unlikely to be accounted for by changes to any singular cognitive system. I argue that, whereas no nonhuman animal possesses the full constellation of traits that define the human mind, homologies and analogies of critical aspects of human psychology can be found in diverse nonhuman taxa. I suggest that phylogenetic approaches to the study of animal cognition-which can address questions about the selective pressures and proximate mechanisms driving cognitive change-have the potential to yield important insights regarding the processes through which the human cognitive phenotype evolved.

Two-trait-locus linkage analysis: A powerful strategy for mapping complex genetic traits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schork, N.J.; Boehnke, M.; Terwilliger, J.D.

1993-11-01

Nearly all diseases mapped to date follow clear Mendelian, single-locus segregation patterns. In contrast, many common familial diseases such as diabetes, psoriasis, several forms of cancer, and schizophrenia are familial and appear to have a genetic component but do not exhibit simple Mendelian transmission. More complex models are required to explain the genetics of these important diseases. In this paper, the authors explore two-trait-locus, two-marker-locus linkage analysis in which two trait loci are mapped simultaneously to separate genetic markers. The authors compare the utility of this approach to standard one-trait-locus, one-marker-locus linkage analysis with and without allowance for heterogeneity. Themore » authors also compare the utility of the two-trait-locus, two-marker-locus analysis to two-trait-locus, one-marker-locus linkage analysis. For common diseases, pedigrees are often bilineal, with disease genes entering via two or more unrelated pedigree members. Since such pedigrees often are avoided in linkage studies, the authors also investigate the relative information content of unilineal and bilineal pedigrees. For the dominant-or-recessive and threshold models that the authors consider, the authors find that two-trait-locus, two-marker-locus linkage analysis can provide substantially more linkage information, as measured by expected maximum lod score, than standard one-trait-locus, one-marker-locus methods, even allowing for heterogeneity, while, for a dominant-or-dominant generating model, one-locus models that allow for heterogeneity extract essentially as much information as the two-trait-locus methods. For these three models, the authors also find that bilineal pedigrees provide sufficient linkage information to warrant their inclusion in such studies. The authors discuss strategies for assessing the significance of the two linkages assumed in two-trait-locus, two-marker-locus models. 37 refs., 1 fig., 4 tabs.« less

Advances in Exercise, Fitness, and Performance Genomics in 2015.

PubMed

Sarzynski, Mark A; Loos, Ruth J F; Lucia, Alejandro; Pérusse, Louis; Roth, Stephen M; Wolfarth, Bernd; Rankinen, Tuomo; Bouchard, Claude

2016-10-01

This review of the exercise genomics literature encompasses the highest-quality articles published in 2015 across seven broad topics: physical activity behavior, muscular strength and power, cardiorespiratory fitness and endurance performance, body weight and adiposity, insulin and glucose metabolism, lipid and lipoprotein metabolism, and hemodynamic traits. One study used a quantitative trait locus for wheel running in mice to identify single nucleotide polymorphisms (SNPs) in humans associated with physical activity levels. Two studies examined the association of candidate gene ACTN3 R577X genotype on muscular performance. Several studies examined gene-physical activity interactions on cardiometabolic traits. One study showed that physical inactivity exacerbated the body mass index (BMI)-increasing effect of an FTO SNP but only in individuals of European ancestry, whereas another showed that high-density lipoprotein cholesterol (HDL-C) SNPs from genome-wide association studies exerted a smaller effect in active individuals. Increased levels of moderate-to-vigorous-intensity physical activity were associated with higher Matsuda insulin sensitivity index in PPARG Ala12 carriers but not Pro12 homozygotes. One study combined genome-wide and transcriptome-wide profiling to identify genes and SNPs associated with the response of triglycerides (TG) to exercise training. The genome-wide association study results showed that four SNPs accounted for all of the heritability of △TG, whereas the baseline expression of 11 genes predicted 27% of △TG. A composite SNP score based on the top eight SNPs derived from the genomic and transcriptomic analyses was the strongest predictor of ΔTG, explaining 14% of the variance. The review concludes with a discussion of a conceptual framework defining some of the critical conditions for exercise genomics studies and highlights the importance of the recently launched National Institutes of Health Common Fund program titled "Molecular Transducers of Physical Activity in Humans."

Genetic risk for attention-deficit/hyperactivity disorder contributes to neurodevelopmental traits in the general population.

PubMed

Martin, Joanna; Hamshere, Marian L; Stergiakouli, Evangelia; O'Donovan, Michael C; Thapar, Anita

2014-10-15

Attention-deficit/hyperactivity disorder (ADHD) can be viewed as the extreme end of traits in the general population. Epidemiological and twin studies suggest that ADHD frequently co-occurs with and shares genetic susceptibility with autism spectrum disorder (ASD) and ASD-related traits. The aims of this study were to determine whether a composite of common molecular genetic variants, previously found to be associated with clinically diagnosed ADHD, predicts ADHD and ASD-related traits in the general population. Polygenic risk scores were calculated in the Avon Longitudinal Study of Parents and Children (ALSPAC) population sample (N = 8229) based on a discovery case-control genome-wide association study of childhood ADHD. Regression analyses were used to assess whether polygenic scores predicted ADHD traits and ASD-related measures (pragmatic language abilities and social cognition) in the ALSPAC sample. Polygenic scores were also compared in boys and girls endorsing any (rating ≥ 1) ADHD item (n = 3623). Polygenic risk for ADHD showed a positive association with ADHD traits (hyperactive-impulsive, p = .0039; inattentive, p = .037). Polygenic risk for ADHD was also negatively associated with pragmatic language abilities (p = .037) but not with social cognition (p = .43). In children with a rating ≥ 1 for ADHD traits, girls had a higher polygenic score than boys (p = .003). These findings provide molecular genetic evidence that risk alleles for the categorical disorder of ADHD influence hyperactive-impulsive and attentional traits in the general population. The results further suggest that common genetic variation that contributes to ADHD diagnosis may also influence ASD-related traits, which at their extreme are a characteristic feature of ASD. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Evolution of social learning does not explain the origin of human cumulative culture.

PubMed

Enquist, Magnus; Ghirlanda, Stefano

2007-05-07

Because culture requires transmission of information between individuals, thinking about the origin of culture has mainly focused on the genetic evolution of abilities for social learning. Current theory considers how social learning affects the adaptiveness of a single cultural trait, yet human culture consists of the accumulation of very many traits. Here we introduce a new modeling strategy that tracks the adaptive value of many cultural traits, showing that genetic evolution favors only limited social learning owing to the accumulation of maladaptive as well as adaptive culture. We further show that culture can be adaptive, and refined social learning can evolve, if individuals can identify and discard maladaptive culture. This suggests that the evolution of such "adaptive filtering" mechanisms may have been crucial for the birth of human culture.

From cultural traditions to cumulative culture: parameterizing the differences between human and nonhuman culture.

PubMed

Kempe, Marius; Lycett, Stephen J; Mesoudi, Alex

2014-10-21

Diverse species exhibit cultural traditions, i.e. population-specific profiles of socially learned traits, from songbird dialects to primate tool-use behaviours. However, only humans appear to possess cumulative culture, in which cultural traits increase in complexity over successive generations. Theoretically, it is currently unclear what factors give rise to these phenomena, and consequently why cultural traditions are found in several species but cumulative culture in only one. Here, we address this by constructing and analysing cultural evolutionary models of both phenomena that replicate empirically attestable levels of cultural variation and complexity in chimpanzees and humans. In our model of cultural traditions (Model 1), we find that realistic cultural variation between populations can be maintained even when individuals in different populations invent the same traits and migration between populations is frequent, and under a range of levels of social learning accuracy. This lends support to claims that putative cultural traditions are indeed cultural (rather than genetic) in origin, and suggests that cultural traditions should be widespread in species capable of social learning. Our model of cumulative culture (Model 2) indicates that both the accuracy of social learning and the number of cultural demonstrators interact to determine the complexity of a trait that can be maintained in a population. Combining these models (Model 3) creates two qualitatively distinct regimes in which there are either a few, simple traits, or many, complex traits. We suggest that these regimes correspond to nonhuman and human cultures, respectively. The rarity of cumulative culture in nature may result from this interaction between social learning accuracy and number of demonstrators. Copyright © 2014 Elsevier Ltd. All rights reserved.

The End of Life, The Ends of Life: An Anthropological View

PubMed Central

Varisco, Daniel Martin

2012-01-01

All known human societies have a worldview that deserves to be called religion; all religions must explain death. Anthropologists study the diversity of religious systems, present and past, in order to understand what is common to humanity. Rather than starting from the view of a particular revelation or set of doctrines, the anthropologist tries to step outside his or her own subjective worldview and identify patterns in the evolution of human thinking about the reality of physical death. Are humans the only animals that are conscious of death, or do we share sentiments observable in our closest living relatives, the chimpanzees? At what point in history did the concept of an afterlife, life in some spiritual sense after physical death, appear? Is the religious explanation of life and death a mere reflection of a communal social fact, as the sociologist Emil Durkheim suggested, or a shared psychological trait, as more recent scholars assert? Can and should the modern scientist make a definitive statement about the finality of death and human consciousness? PMID:23610511

Constraint, natural selection, and the evolution of human body form

PubMed Central

Savell, Kristen R. R.; Auerbach, Benjamin M.; Roseman, Charles C.

2016-01-01

Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics. PMID:27482101

Constraint, natural selection, and the evolution of human body form.

PubMed

Savell, Kristen R R; Auerbach, Benjamin M; Roseman, Charles C

2016-08-23

Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics.

A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes.

PubMed

Park, Sung Hee; Lee, Ji Young; Kim, Sangsoo

2011-01-01

Current Genome-Wide Association Studies (GWAS) are performed in a single trait framework without considering genetic correlations between important disease traits. Hence, the GWAS have limitations in discovering genetic risk factors affecting pleiotropic effects. This work reports a novel data mining approach to discover patterns of multiple phenotypic associations over 52 anthropometric and biochemical traits in KARE and a new analytical scheme for GWAS of multivariate phenotypes defined by the discovered patterns. This methodology applied to the GWAS for multivariate phenotype highLDLhighTG derived from the predicted patterns of the phenotypic associations. The patterns of the phenotypic associations were informative to draw relations between plasma lipid levels with bone mineral density and a cluster of common traits (Obesity, hypertension, insulin resistance) related to Metabolic Syndrome (MS). A total of 15 SNPs in six genes (PAK7, C20orf103, NRIP1, BCL2, TRPM3, and NAV1) were identified for significant associations with highLDLhighTG. Noteworthy findings were that the significant associations included a mis-sense mutation (PAK7:R335P), a frame shift mutation (C20orf103) and SNPs in splicing sites (TRPM3). The six genes corresponded to rat and mouse quantitative trait loci (QTLs) that had shown associations with the common traits such as the well characterized MS and even tumor susceptibility. Our findings suggest that the six genes may play important roles in the pleiotropic effects on lipid metabolism and the MS, which increase the risk of Type 2 Diabetes and cardiovascular disease. The use of the multivariate phenotypes can be advantageous in identifying genetic risk factors, accounting for the pleiotropic effects when the multivariate phenotypes have a common etiological pathway.

Ecological volatility and human evolution: a novel perspective on life history and reproductive strategy.

PubMed

Wells, Jonathan C K

2012-11-01

Humans are characterized by a suite of traits that seem to differentiate them profoundly from closely related apes such as the gorilla, chimpanzee, and orang-utan. These traits include longevity, cooperative breeding, stacking of offspring, lengthy maturation, and a complex life-course profile of adiposity. When, how, and why these traits emerged during our evolutionary history is currently attracting considerable attention. Most approaches to life history emphasize dietary energy availability and the risk of mortality as the two key stresses shaping life-history variability between and within species. The high energy costs of the large Homo brain are also seen as the central axis around which other life-history traits were reorganized. I propose that ecological volatility may have been a key stress, selecting in favor of the suite of traits in order to tolerate periods of energy scarcity, and increase reproductive output during periods of good conditions. Theses life-history adaptations may have preceded and enabled the trend toward encephalization. Copyright © 2012 Wiley Periodicals, Inc.

The dark cube: dark and light character profiles.

PubMed

Garcia, Danilo; Rosenberg, Patricia

2016-01-01

Background. Research addressing distinctions and similarities between people's malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) has detected inconsistent linear associations to temperament traits. Additionally, these dark traits seem to have a common core expressed as uncooperativeness. Hence, some researchers suggest that the dark traits are best represented as one global construct (i.e., the unification argument) rather than as ternary construct (i.e., the uniqueness argument). We put forward the dark cube (cf. Cloninger's character cube) comprising eight dark profiles that can be used to compare individuals who differ in one dark character trait while holding the other two constant. Our aim was to investigate in which circumstances individuals who are high in each one of the dark character traits differ in Cloninger's "light" character traits: self-directedness, cooperativeness, and self-transcendence. We also investigated if people's dark character profiles were associated to their light character profiles. Method. A total of 997 participants recruited from Amazon's Mechanical Turk (MTurk) responded to the Short Dark Triad and the Short Character Inventory. Participants were allocated to eight different dark profiles and eight light profiles based on their scores in each of the traits and any possible combination of high and low scores. We used three-way interaction regression analyses and t-tests to investigate differences in light character traits between individuals with different dark profiles. As a second step, we compared the individuals' dark profile with her/his character profile using an exact cell-wise analysis conducted in the ROPstat software (http://www.ropstat.com). Results. Individuals who expressed high levels of Machiavellianism and those who expressed high levels of psychopathy also expressed low self-directedness and low cooperativeness. Individuals with high levels of narcissism, in contrast, scored high in self-directedness. Moreover, individuals with a profile low in the dark traits were more likely to end up with a profile high in cooperativeness. The opposite was true for those individuals with a profile high in the dark traits. The rest of the cross-comparisons revealed some of the characteristics of human personality as a non-linear complex dynamic system. Conclusions. Our study suggests that individuals who are high in Machiavellianism and psychopathy share a unified non-agentic and uncooperative character (i.e., irresponsible, low in self-control, unempathetic, unhelpful, untolerant), while individuals high in narcissism have a more unique character configuration expressed as high agency and, when the other dark traits are high, highly spiritual but uncooperative. In other words, based on differences in their associations to the light side of character, the Dark Triad seems to be a dyad rather than a triad.

The dark cube: dark and light character profiles

PubMed Central

2016-01-01

Background. Research addressing distinctions and similarities between people’s malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) has detected inconsistent linear associations to temperament traits. Additionally, these dark traits seem to have a common core expressed as uncooperativeness. Hence, some researchers suggest that the dark traits are best represented as one global construct (i.e., the unification argument) rather than as ternary construct (i.e., the uniqueness argument). We put forward the dark cube (cf. Cloninger’s character cube) comprising eight dark profiles that can be used to compare individuals who differ in one dark character trait while holding the other two constant. Our aim was to investigate in which circumstances individuals who are high in each one of the dark character traits differ in Cloninger’s “light” character traits: self-directedness, cooperativeness, and self-transcendence. We also investigated if people’s dark character profiles were associated to their light character profiles. Method. A total of 997 participants recruited from Amazon’s Mechanical Turk (MTurk) responded to the Short Dark Triad and the Short Character Inventory. Participants were allocated to eight different dark profiles and eight light profiles based on their scores in each of the traits and any possible combination of high and low scores. We used three-way interaction regression analyses and t-tests to investigate differences in light character traits between individuals with different dark profiles. As a second step, we compared the individuals’ dark profile with her/his character profile using an exact cell-wise analysis conducted in the ROPstat software (http://www.ropstat.com). Results. Individuals who expressed high levels of Machiavellianism and those who expressed high levels of psychopathy also expressed low self-directedness and low cooperativeness. Individuals with high levels of narcissism, in contrast, scored high in self-directedness. Moreover, individuals with a profile low in the dark traits were more likely to end up with a profile high in cooperativeness. The opposite was true for those individuals with a profile high in the dark traits. The rest of the cross-comparisons revealed some of the characteristics of human personality as a non-linear complex dynamic system. Conclusions. Our study suggests that individuals who are high in Machiavellianism and psychopathy share a unified non-agentic and uncooperative character (i.e., irresponsible, low in self-control, unempathetic, unhelpful, untolerant), while individuals high in narcissism have a more unique character configuration expressed as high agency and, when the other dark traits are high, highly spiritual but uncooperative. In other words, based on differences in their associations to the light side of character, the Dark Triad seems to be a dyad rather than a triad. PMID:26966650

A simple genetic architecture underlies morphological variation in dogs.

PubMed

Boyko, Adam R; Quignon, Pascale; Li, Lin; Schoenebeck, Jeffrey J; Degenhardt, Jeremiah D; Lohmueller, Kirk E; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G; vonHoldt, Bridgett M; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G; Castelhano, Marta; Mosher, Dana S; Sutter, Nathan B; Johnson, Gary S; Novembre, John; Hubisz, Melissa J; Siepel, Adam; Wayne, Robert K; Bustamante, Carlos D; Ostrander, Elaine A

2010-08-10

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (< or = 3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

PubMed Central

Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

2010-01-01

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species. PMID:20711490

Social selection is a powerful explanation for prosociality.

PubMed

Nesse, Randolph M

2016-01-01

Cultural group selection helps explain human cooperation, but social selection offers a complementary, more powerful explanation. Just as sexual selection shapes extreme traits that increase matings, social selection shapes extreme traits that make individuals preferred social partners. Self-interested partner choices create strong and possibly runaway selection for prosocial traits, without requiring group selection, kin selection, or reciprocity.

Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub

PubMed Central

Carlson, Jane E.; Adams, Christopher A.; Holsinger, Kent E.

2016-01-01

Background and Aims Trait–environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub Protea repens. Specifically, the study examines whether broad-scale patterns of trait variation are consistent with spatial differences in selection and ecophysiology in the wild. Methods In a common garden study of plants sourced from 19 populations, associations were measured between five morphological traits and three axes describing source climates. Trait–trait and trait–environment associations were analysed in a multi-response model. Within two focal populations in the wild, selection and path analyses were used to test associations between traits, fecundity and physiological performance. Key Results Across 19 populations in a common garden, stomatal density increased with the source population’s mean annual temperature and decreased with its average amount of rainfall in midsummer. Concordantly, selection analysis in two natural populations revealed positive selection on stomatal density at the hotter, drier site, while failing to detect selection at the cooler, moister site. Dry-site plants with high stomatal density also had higher stomatal conductances, cooler leaf temperatures and higher light-saturated photosynthetic rates than those with low stomatal density, but no such relationships were present among wet-site plants. Leaf area, stomatal pore index and specific leaf area in the garden also co-varied with climate, but within-population differences were not associated with fitness in either wild population. Conclusions The parallel patterns of broad-scale variation, differences in selection and differences in trait–ecophysiology relationships suggest a mechanism for adaptive differentiation in stomatal density. Densely packed stomata may improve performance by increasing transpiration and cooling, but predominately in drier, hotter climates. This study uniquely shows context-dependent benefits of stomatal density – a trait rarely linked to local adaptation in plants. PMID:26424782

Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits.

PubMed

Traglia, Michela; Bseiso, Dina; Gusev, Alexander; Adviento, Brigid; Park, Daniel S; Mefford, Joel A; Zaitlen, Noah; Weiss, Lauren A

2017-02-01

Common diseases often show sex differences in prevalence, onset, symptomology, treatment, or prognosis. Although studies have been performed to evaluate sex differences at specific SNP associations, this work aims to comprehensively survey a number of complex heritable diseases and anthropometric traits. Potential genetically encoded sex differences we investigated include differential genetic liability thresholds or distributions, gene-sex interaction at autosomal loci, major contribution of the X-chromosome, or gene-environment interactions reflected in genes responsive to androgens or estrogens. Finally, we tested the overlap between sex-differential association with anthropometric traits and disease risk. We utilized complementary approaches of assessing GWAS association enrichment and SNP-based heritability estimation to explore explicit sex differences, as well as enrichment in sex-implicated functional categories. We do not find consistent increased genetic load in the lower-prevalence sex, or a disproportionate role for the X-chromosome in disease risk, despite sex-heterogeneity on the X for several traits. We find that all anthropometric traits show less than complete correlation between the genetic contribution to males and females, and find a convincing example of autosome-wide genome-sex interaction in multiple sclerosis (P = 1 × 10 -9 ). We also find some evidence for hormone-responsive gene enrichment, and striking evidence of the contribution of sex-differential anthropometric associations to common disease risk, implying that general mechanisms of sexual dimorphism determining secondary sex characteristics have shared effects on disease risk. Copyright © 2017 by the Genetics Society of America.

Heritability estimates of the Big Five personality traits based on common genetic variants.

PubMed

Power, R A; Pluess, M

2015-07-14

According to twin studies, the Big Five personality traits have substantial heritable components explaining 40-60% of the variance, but identification of associated genetic variants has remained elusive. Consequently, knowledge regarding the molecular genetic architecture of personality and to what extent it is shared across the different personality traits is limited. Using genomic-relatedness-matrix residual maximum likelihood analysis (GREML), we here estimated the heritability of the Big Five personality factors (extraversion, agreeableness, conscientiousness, neuroticism and openness for experience) in a sample of 5011 European adults from 527,469 single-nucleotide polymorphisms across the genome. We tested for the heritability of each personality trait, as well as for the genetic overlap between the personality factors. We found significant and substantial heritability estimates for neuroticism (15%, s.e. = 0.08, P = 0.04) and openness (21%, s.e. = 0.08, P < 0.01), but not for extraversion, agreeableness and conscientiousness. The bivariate analyses showed that the variance explained by common variants entirely overlapped between neuroticism and openness (rG = 1.00, P < 0.001), despite low phenotypic correlation (r = - 0.09, P < 0.001), suggesting that the remaining unique heritability may be determined by rare or structural variants. As far as we are aware of, this is the first study estimating the shared and unique heritability of all Big Five personality traits using the GREML approach. Findings should be considered exploratory and suggest that detectable heritability estimates based on common variants is shared between neuroticism and openness to experiences.

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.).

PubMed

Fu, Qiang; Zhang, Peijiang; Tan, Lubin; Zhu, Zuofeng; Ma, Dan; Fu, Yongcai; Zhan, Xinchun; Cai, Hongwei; Sun, Chuanqing

2010-02-01

Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations (BC(4)F(2) and BC(4)F(4)), a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations. Of the 26 QTLs, the alleles of 10 (38.5%) QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future. Copyright 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits

PubMed Central

Traglia, Michela; Bseiso, Dina; Gusev, Alexander; Adviento, Brigid; Park, Daniel S.; Mefford, Joel A.; Zaitlen, Noah; Weiss, Lauren A.

2017-01-01

Common diseases often show sex differences in prevalence, onset, symptomology, treatment, or prognosis. Although studies have been performed to evaluate sex differences at specific SNP associations, this work aims to comprehensively survey a number of complex heritable diseases and anthropometric traits. Potential genetically encoded sex differences we investigated include differential genetic liability thresholds or distributions, gene–sex interaction at autosomal loci, major contribution of the X-chromosome, or gene–environment interactions reflected in genes responsive to androgens or estrogens. Finally, we tested the overlap between sex-differential association with anthropometric traits and disease risk. We utilized complementary approaches of assessing GWAS association enrichment and SNP-based heritability estimation to explore explicit sex differences, as well as enrichment in sex-implicated functional categories. We do not find consistent increased genetic load in the lower-prevalence sex, or a disproportionate role for the X-chromosome in disease risk, despite sex-heterogeneity on the X for several traits. We find that all anthropometric traits show less than complete correlation between the genetic contribution to males and females, and find a convincing example of autosome-wide genome-sex interaction in multiple sclerosis (P = 1 × 10−9). We also find some evidence for hormone-responsive gene enrichment, and striking evidence of the contribution of sex-differential anthropometric associations to common disease risk, implying that general mechanisms of sexual dimorphism determining secondary sex characteristics have shared effects on disease risk. PMID:27974502

Evaluating intra- and inter-individual variation in the human placental transcriptome.

PubMed

Hughes, David A; Kircher, Martin; He, Zhisong; Guo, Song; Fairbrother, Genevieve L; Moreno, Carlos S; Khaitovich, Philipp; Stoneking, Mark

2015-03-19

Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection. We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

Genotype by environment interactions for behavioral reactivity in sheep.

PubMed

Hazard, D; Bouix, J; Chassier, M; Delval, E; Foulquié, D; Fassier, T; Bourdillon, Y; François, D; Boissy, A

2016-04-01

In sheep, social reactivity and reactivity to humans are relevant behavioral responses that are used to investigate the behavioral adaptation of farm animals to various rearing conditions. Such traits were previously reported as heritable and associated with several QTLs. However, few behavior-related genotype by environment (G × E) interactions have been reported to date. The experiment was performed on 2,989 male and female lambs issued from 30 sires. Every sire had progeny reared under both intensive and extensive conditions. After weaning, all lambs were individually exposed to two standardized behavioral tests. A broad range of behaviors including vocalizations, locomotion, localization, vigilance, and flight distance were assessed. Two complementary statistic approaches, with and without assumptions on the biological significance of behaviors, were performed to investigate social reactivity and reactivity to humans. G × E interactions were investigated based on the genetic correlations estimated for each factor or trait between farming conditions; those significantly different from 1 indicating a G × E. Environmental effects showed that social reactivity and reactivity to humans were higher in intensively reared lambs. The heritability of factors or traits used to measure social reactivity and reactivity to humans was similar in both rearing conditions. Estimated heritabilities were high for vocalizations in response to social isolation, moderate for locomotion and vigilance in response to social isolation, and low for both flight distance to an approaching human and proximity to a motionless human. No significant G × E interaction was found for vocalizations. G × E interactions were found for locomotion, vigilance and flight distance. Genetic correlations between both environments were low to moderate for vigilance, locomotion and flight distance. Vocalization in response to social isolation with or without human presence was identified as a robust trait and could be used to improve sheep sociability, independently of the environment. A G × E interaction was observed for behavioral reactivity to humans. Although moderate, the genetic correlation for this trait between intensive and extensive conditions could be used to select sires in the same environment by taking into account the G × E and to produce in different environments progenies that are less reactive to humans.

A Comprehensive Analysis of the Correlations between Resting-State Oscillations in Multiple-Frequency Bands and Big Five Traits

PubMed Central

Ikeda, Shigeyuki; Takeuchi, Hikaru; Taki, Yasuyuki; Nouchi, Rui; Yokoyama, Ryoichi; Kotozaki, Yuka; Nakagawa, Seishu; Sekiguchi, Atsushi; Iizuka, Kunio; Yamamoto, Yuki; Hanawa, Sugiko; Araki, Tsuyoshi; Miyauchi, Carlos Makoto; Sakaki, Kohei; Nozawa, Takayuki; Yokota, Susumu; Magistro, Daniele; Kawashima, Ryuta

2017-01-01

Recently, the association between human personality traits and resting-state brain activity has gained interest in neuroimaging studies. However, it remains unclear if Big Five personality traits are represented in frequency bands (~0.25 Hz) of resting-state functional magnetic resonance imaging (fMRI) activity. Based on earlier neurophysiological studies, we investigated the correlation between the five personality traits assessed by the NEO Five-Factor Inventory (NEO-FFI), and the fractional amplitude of low-frequency fluctuation (fALFF) at four distinct frequency bands (slow-5 (0.01–0.027 Hz), slow-4 (0.027–0.073 Hz), slow-3 (0.073–0.198 Hz) and slow-2 (0.198–0.25 Hz)). We enrolled 835 young subjects and calculated the correlations of resting-state fMRI signals using a multiple regression analysis. We found a significant and consistent correlation between fALFF and the personality trait of extraversion at all frequency bands. Furthermore, significant correlations were detected in distinct brain regions for each frequency band. This finding supports the frequency-specific spatial representations of personality traits as previously suggested. In conclusion, our data highlight an association between human personality traits and fALFF at four distinct frequency bands. PMID:28680397

A Comprehensive Analysis of the Correlations between Resting-State Oscillations in Multiple-Frequency Bands and Big Five Traits.

PubMed

Ikeda, Shigeyuki; Takeuchi, Hikaru; Taki, Yasuyuki; Nouchi, Rui; Yokoyama, Ryoichi; Kotozaki, Yuka; Nakagawa, Seishu; Sekiguchi, Atsushi; Iizuka, Kunio; Yamamoto, Yuki; Hanawa, Sugiko; Araki, Tsuyoshi; Miyauchi, Carlos Makoto; Sakaki, Kohei; Nozawa, Takayuki; Yokota, Susumu; Magistro, Daniele; Kawashima, Ryuta

2017-01-01

Recently, the association between human personality traits and resting-state brain activity has gained interest in neuroimaging studies. However, it remains unclear if Big Five personality traits are represented in frequency bands (~0.25 Hz) of resting-state functional magnetic resonance imaging (fMRI) activity. Based on earlier neurophysiological studies, we investigated the correlation between the five personality traits assessed by the NEO Five-Factor Inventory (NEO-FFI), and the fractional amplitude of low-frequency fluctuation (fALFF) at four distinct frequency bands (slow-5 (0.01-0.027 Hz), slow-4 (0.027-0.073 Hz), slow-3 (0.073-0.198 Hz) and slow-2 (0.198-0.25 Hz)). We enrolled 835 young subjects and calculated the correlations of resting-state fMRI signals using a multiple regression analysis. We found a significant and consistent correlation between fALFF and the personality trait of extraversion at all frequency bands. Furthermore, significant correlations were detected in distinct brain regions for each frequency band. This finding supports the frequency-specific spatial representations of personality traits as previously suggested. In conclusion, our data highlight an association between human personality traits and fALFF at four distinct frequency bands.

Job Performance: Improvement Needed

ERIC Educational Resources Information Center

Goodman, Jacob

1974-01-01

Personnel directors of 38 business firms responded to a questionnaire rating 24 employee traits related to competencies, attitudes, skills, and personality which needed improvement. Five traits were common among the rank order one to five to both retailer and commercial and service organization respondents: oral communication, initiative,…

Integrating competing dimensional models of personality: linking the SNAP, TCI, and NEO using Item Response Theory.

PubMed

Stepp, Stephanie D; Yu, Lan; Miller, Joshua D; Hallquist, Michael N; Trull, Timothy J; Pilkonis, Paul A

2012-04-01

Mounting evidence suggests that several inventories assessing both normal personality and personality disorders measure common dimensional personality traits (i.e., Antagonism, Constraint, Emotional Instability, Extraversion, and Unconventionality), albeit providing unique information along the underlying trait continuum. We used Widiger and Simonsen's (2005) pantheoretical integrative model of dimensional personality assessment as a guide to create item pools. We then used Item Response Theory (IRT) to compare the assessment of these five personality traits across three established dimensional measures of personality: the Schedule for Nonadaptive and Adaptive Personality (SNAP), the Temperament and Character Inventory (TCI), and the Revised NEO Personality Inventory (NEO PI-R). We found that items from each inventory map onto these five common personality traits in predictable ways. The IRT analyses, however, documented considerable variability in the item and test information derived from each inventory. Our findings support the notion that the integration of multiple perspectives will provide greater information about personality while minimizing the weaknesses of any single instrument.

Integrating Competing Dimensional Models of Personality: Linking the SNAP, TCI, and NEO Using Item Response Theory

PubMed Central

Stepp, Stephanie D.; Yu, Lan; Miller, Joshua D.; Hallquist, Michael N.; Trull, Timothy J.; Pilkonis, Paul A.

2013-01-01

Mounting evidence suggests that several inventories assessing both normal personality and personality disorders measure common dimensional personality traits (i.e., Antagonism, Constraint, Emotional Instability, Extraversion, and Unconventionality), albeit providing unique information along the underlying trait continuum. We used Widiger and Simonsen’s (2005) pantheoretical integrative model of dimensional personality assessment as a guide to create item pools. We then used Item Response Theory (IRT) to compare the assessment of these five personality traits across three established dimensional measures of personality: the Schedule for Nonadaptive and Adaptive Personality (SNAP), the Temperament and Character Inventory (TCI), and the Revised NEO Personality Inventory (NEO PI-R). We found that items from each inventory map onto these five common personality traits in predictable ways. The IRT analyses, however, documented considerable variability in the item and test information derived from each inventory. Our findings support the notion that the integration of multiple perspectives will provide greater information about personality while minimizing the weaknesses of any single instrument. PMID:22452759

Cultural evolution and emergent group-level traits through social heterosis.

PubMed

Nonacs, Peter; Kapheim, Karen M

2014-06-01

Smaldino proposes emergent properties of human groups, arising when individuals display both differentiation and organization, constitute a novel unit of cultural selection not addressed by current evolutionary theory. We propose existing theoretical frameworks for maintenance of genetic diversity - social heterosis and social genomes - can similarly explain the appearance and maintenance of human cultural diversity (i.e., group-level traits) and collaborative interdependence.

Common subtypes of idiopathic generalized epilepsies: Lack of linkage to D20S19 close to candidate loci (EBN1, EEGV1) on chromosome 20

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sander, T.; Schmitz, B.; Janz, D.

1996-02-16

Hereditary factors play a major role in the etiology of idiopathic generalized epilepsies (IGEs). A trait locus (EBN1) for a rare subtype of IGEs, the benign neonatal familial convulsions, and a susceptibility gene (EEGV1) for the common human low-voltage electroencephalogram have been mapped close together with D20S19 to the chromosomal region 20q13.2. Both loci are potential candidates for the susceptibility to IGE spectra with age-related onset beyond the neonatal period. The present study tested the hypothesis that a putative susceptibility locus linked to D20S19 predisposes to spectra of IGEs with age-related onset from childhood to adolescence. Linkage analyses were conductedmore » in 60 families ascertained through IGE patients with juvenile myoclonic epilepsy, juvenile absence epilepsy or childhood absence epilepsy. Our results provide evidence against linkage of a putative susceptibility gene for four hierarchically broadened IGE spectra with D20S19 assuming tentative single-locus genetic models. The extent of an {open_quotes}exclusion region{close_quotes} (lod scores below -2) varied from 0.5 cM up to 22 cM on either side of D2OSl9 depending on the trait assumed. These results are contrary to the expectation that a susceptibility gene in vicinity to D20S19 confers a common major gene effect to the expression of IGE spectra with age-related onset from childhood to adolescence. 50 refs., 1 fig., 1 tab.« less

Markers of physiological stress in juvenile bonobos (Pan paniscus): are enamel hypoplasia, skeletal development and tooth size interrelated?

PubMed

Lukacs, John R

2009-07-01

A reduction in enamel thickness due to disrupted amelogenesis is referred to as enamel hypoplasia (EH). Linear EH in permanent teeth is a widely accepted marker of systemic physiological stress. An enigmatic, nonlinear form of EH commonly manifest in great ape and human deciduous canines (dc) is known as localized hypoplasia of primary canines (LHPC). The etiology of LHPC and what it signifies-localized traumatic or systemic physiological stress-remains unclear. This report presents frequency data on LHPC, hypostotic cranial traits, and tooth size in a sample of juvenile bonobos, then tests hypotheses of intertrait association that improve knowledge of the etiology and meaning of LHPC. The fenestration hypothesis is tested using hypostotic cranial traits as a proxy for membrane bone ossification, and the relationship between tooth size, LHPC, and hypostosis is investigated. Macroscopic observations of EH, hypostotic traits, and measurements of buccolingual tooth size were conducted according to established standards. LHPC was found in 51.2% of bonobos (n = 86) and in 26% of dc teeth (n = 269). Hypostotic traits were observed in 55.2% of bonobos (n = 96). A test of the association between LHPC and hypostosis yielded nonsignificant results (chi(2) = 2.935; P = 0.0867). Primary canines were larger in specimens with LHPC than in unaffected specimens (paired samples t test; udc, P = 0.011; ldc, P = 0.018), a result consistent with the fenestration hypothesis of LHPC pathogenesis. Hypostosis was not associated with differences in tooth size (P > 0.05). LHPC may be an indirect indicator of physiological stress, resulting from large, buccally displaced primary canines.

An eco-physiological model of the impact of temperature on Aedes aegypti life history traits.

PubMed

Padmanabha, Harish; Correa, Fabio; Legros, Mathieu; Nijhout, H Fredrick; Lord, Cynthia; Lounibos, L Philip

2012-12-01

Physiological processes mediate the impact of ecological conditions on the life histories of insect vectors. For the dengue/chikungunya mosquito, Aedes aegypti, three life history traits that are critical to urban population dynamics and control are: size, development rate and starvation mortality. In this paper we make use of prior laboratory experiments on each of these traits at 2°C intervals between 20 and 30°C, in conjunction with eco-evolutionary theory and studies on A.aegypti physiology, in order to develop a conceptual and mathematical framework that can predict their thermal sensitivity. Our model of reserve dependent growth (RDG), which considers a potential tradeoff between the accumulation of reserves and structural biomass, was able to robustly predict laboratory observations, providing a qualitative improvement over the approach most commonly used in other A.aegypti models. RDG predictions of reduced size at higher temperatures, but increased reserves relative to size, are supported by the available evidence in Aedes spp. We offer the potentially general hypothesis that temperature-size patterns in mosquitoes are driven by a net benefit of finishing the growing stage with proportionally greater reserves relative to structure at warmer temperatures. By relating basic energy flows to three fundamental life history traits, we provide a mechanistic framework for A.aegypti development to which ecological complexity can be added. Ultimately, this could provide a framework for developing and field testing hypotheses on how processes such as climate variation, density dependent regulation, human behavior or control strategies may influence A.aegypti population dynamics and disease risk. Copyright © 2012 Elsevier Ltd. All rights reserved.

Relevance of genetic relationship in GWAS and genomic prediction.

PubMed

Pereira, Helcio Duarte; Soriano Viana, José Marcelo; Andrade, Andréa Carla Bastos; Fonseca E Silva, Fabyano; Paes, Geísa Pinheiro

2018-02-01

The objective of this study was to analyze the relevance of relationship information on the identification of low heritability quantitative trait loci (QTLs) from a genome-wide association study (GWAS) and on the genomic prediction of complex traits in human, animal and cross-pollinating populations. The simulation-based data sets included 50 samples of 1000 individuals of seven populations derived from a common population with linkage disequilibrium. The populations had non-inbred and inbred progeny structure (50 to 200) with varying number of members (5 to 20). The individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for a quantitative trait controlled by 10 QTLs and 90 minor genes showing dominance. The SNP density was 0.1 cM and the narrow sense heritability was 25%. The QTL heritabilities ranged from 1.1 to 2.9%. We applied mixed model approaches for both GWAS and genomic prediction using pedigree-based and genomic relationship matrices. For GWAS, the observed false discovery rate was kept below the significance level of 5%, the power of detection for the low heritability QTLs ranged from 14 to 50%, and the average bias between significant SNPs and a QTL ranged from less than 0.01 to 0.23 cM. The QTL detection power was consistently higher using genomic relationship matrix. Regardless of population and training set size, genomic prediction provided higher prediction accuracy of complex trait when compared to pedigree-based prediction. The accuracy of genomic prediction when there is relatedness between individuals in the training set and the reference population is much higher than the value for unrelated individuals.

Exploring personality traits related to dopamine D2/3 receptor availability in striatal subregions of humans.

PubMed

Caravaggio, Fernando; Fervaha, Gagan; Chung, Jun Ku; Gerretsen, Philip; Nakajima, Shinichiro; Plitman, Eric; Iwata, Yusuke; Wilson, Alan; Graff-Guerrero, Ariel

2016-04-01

While several studies have examined how particular personality traits are related to dopamine D2/3 receptor (D2/3R) availability in the striatum of humans, few studies have reported how multiple traits measured in the same persons are differentially related to D2/3R availability in different striatal sub-regions. We examined how personality traits measured with the Karolinska Scales of Personality are related to striatal D2/3R availability measured with [(11)C]-raclopride in 30 healthy humans. Based on previous the literature, five personality traits were hypothesized to be most likely related to D2/3R availability: impulsiveness, monotony avoidance, detachment, social desirability, and socialization. We found self-reported impulsiveness was negatively correlated with D2/3R availability in the ventral striatum and globus pallidus. After controlling for age and gender, monotony avoidance was also negatively correlated with D2/3R availability in the ventral striatum and globus pallidus. Socialization was positively correlated with D2/3R availability in the ventral striatum and putamen. After controlling for age and gender, the relationship between socialization and D2/3R availability in these regions survived correction for multiple comparisons (p-threshold=.003). Thus, within the same persons, different personality traits are differentially related to in vivo D2/3R availability in different striatal sub-regions. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

Dissection of complex adult traits in a mouse synthetic population.

PubMed

Burke, David T; Kozloff, Kenneth M; Chen, Shu; West, Joshua L; Wilkowski, Jodi M; Goldstein, Steven A; Miller, Richard A; Galecki, Andrzej T

2012-08-01

Finding the causative genetic variations that underlie complex adult traits is a significant experimental challenge. The unbiased search strategy of genome-wide association (GWAS) has been used extensively in recent human population studies. These efforts, however, typically find only a minor fraction of the genetic loci that are predicted to affect variation. As an experimental model for the analysis of adult polygenic traits, we measured a mouse population for multiple phenotypes and conducted a genome-wide search for effector loci. Complex adult phenotypes, related to body size and bone structure, were measured as component phenotypes, and each subphenotype was associated with a genomic spectrum of candidate effector loci. The strategy successfully detected several loci for the phenotypes, at genome-wide significance, using a single, modest-sized population (N = 505). The effector loci each explain 2%-10% of the measured trait variation and, taken together, the loci can account for over 25% of a trait's total population variation. A replicate population (N = 378) was used to confirm initially observed loci for one trait (femur length), and, when the two groups were merged, the combined population demonstrated increased power to detect loci. In contrast to human population studies, our mouse genome-wide searches find loci that individually explain a larger fraction of the observed variation. Also, the additive effects of our detected mouse loci more closely match the predicted genetic component of variation. The genetic loci discovered are logical candidates for components of the genetic networks having evolutionary conservation with human biology.

Spontaneous Trait Inferences on Social Media.

PubMed

Levordashka, Ana; Utz, Sonja

2017-01-01

The present research investigates whether spontaneous trait inferences occur under conditions characteristic of social media and networking sites: nonextreme, ostensibly self-generated content, simultaneous presentation of multiple cues, and self-paced browsing. We used an established measure of trait inferences (false recognition paradigm) and a direct assessment of impressions. Without being asked to do so, participants spontaneously formed impressions of people whose status updates they saw. Our results suggest that trait inferences occurred from nonextreme self-generated content, which is commonly found in social media updates (Experiment 1) and when nine status updates from different people were presented in parallel (Experiment 2). Although inferences did occur during free browsing, the results suggest that participants did not necessarily associate the traits with the corresponding status update authors (Experiment 3). Overall, the findings suggest that spontaneous trait inferences occur on social media. We discuss implications for online communication and research on spontaneous trait inferences.

Refining Trait Resilience: Identifying Engineering, Ecological, and Adaptive Facets from Extant Measures of Resilience

PubMed Central

Maltby, John; Day, Liz; Hall, Sophie

2015-01-01

The current paper presents a new measure of trait resilience derived from three common mechanisms identified in ecological theory: Engineering, Ecological and Adaptive (EEA) resilience. Exploratory and confirmatory factor analyses of five existing resilience scales suggest that the three trait resilience facets emerge, and can be reduced to a 12-item scale. The conceptualization and value of EEA resilience within the wider trait and well-being psychology is illustrated in terms of differing relationships with adaptive expressions of the traits of the five-factor personality model and the contribution to well-being after controlling for personality and coping, or over time. The current findings suggest that EEA resilience is a useful and parsimonious model and measure of trait resilience that can readily be placed within wider trait psychology and that is found to contribute to individual well-being. PMID:26132197

Missing heritability and strategies for finding the underlying causes of complex disease

PubMed Central

Eichler, Evan E.; Flint, Jonathan; Gibson, Greg; Kong, Augustine; Leal, Suzanne M.; Moore, Jason H.; Nadeau, Joseph H.

2010-01-01

Although recent genome-wide studies have provided valuable insights into the genetic basis of human disease, they have explained relatively little of the heritability of most complex traits, and the variants identified through these studies have small effect sizes. This has led to the important and hotly debated issue of where the ‘missing heritability’ of complex diseases might be found. Here, seven leading geneticists offer their opinion about where this heritability is likely to lie, what this could tell us about the underlying genetic architecture of common diseases and how this could inform research strategies for uncovering genetic risk factors. PMID:20479774

Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight.

PubMed

Al-Mamun, Hawlader A; Kwan, Paul; Clark, Samuel A; Ferdosi, Mohammad H; Tellam, Ross; Gondro, Cedric

2015-08-14

Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep. A total of 1781 Australian Merino sheep were genotyped using the medium-density Illumina Ovine SNP50 BeadChip. Among the 53 862 single nucleotide polymorphisms (SNPs) on this array, 48 640 were used to perform a GWAS using a linear mixed model approach. Genotypes were phased with hsphase; to estimate SNP haplotype effects, linkage disequilibrium blocks were identified in the detected QTL region. Thirty-nine SNPs were associated with BW at a Bonferroni-corrected genome-wide significance threshold of 1 %. One region on sheep (Ovis aries) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (P = 2.37 × 10(-16)) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW. The region that surrounds this association signal on OAR6 contains three genes: leucine aminopeptidase 3 (LAP3), which is involved in the processing of the oxytocin precursor; NCAPG non-SMC condensin I complex, subunit G (NCAPG), which is associated with foetal growth and carcass size in cattle; and ligand dependent nuclear receptor corepressor-like (LCORL), which is associated with height in humans and cattle. The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6. In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry. These findings should facilitate the discovery of causative variants for BW and contribute to marker-assisted selection.

Evolution of plant growth and defense in a continental introduction.

PubMed

Agrawal, Anurag A; Hastings, Amy P; Bradburd, Gideon S; Woods, Ellen C; Züst, Tobias; Harvey, Jeffrey A; Bukovinszky, Tibor

2015-07-01

Substantial research has addressed adaptation of nonnative biota to novel environments, yet surprisingly little work has integrated population genetic structure and the mechanisms underlying phenotypic differentiation in ecologically important traits. We report on studies of the common milkweed Asclepias syriaca, which was introduced from North America to Europe over the past 400 years and which lacks most of its specialized herbivores in the introduced range. Using 10 populations from each continent grown in a common environment, we identified several growth and defense traits that have diverged, despite low neutral genetic differentiation between continents. We next developed a Bayesian modeling approach to account for relationships between molecular and phenotypic differences, confirming that continental trait differentiation was greater than expected from neutral genetic differentiation. We found evidence that growth-related traits adaptively diverged within and between continents. Inducible defenses triggered by monarch butterfly herbivory were substantially reduced in European populations, and this reduction in inducibility was concordant with altered phytohormonal dynamics, reduced plant growth, and a trade-off with constitutive investment. Freedom from the community of native and specialized herbivores may have favored constitutive over induced defense. Our replicated analysis of plant growth and defense, including phenotypically plastic traits, suggests adaptive evolution following a continental introduction.

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22.

PubMed

Parsons, Claire A; Mroczkowski, H Joel; McGuigan, Fiona E A; Albagha, Omar M E; Manolagas, Stavros; Reid, David M; Ralston, Stuart H; Shmookler Reis, Robert J

2005-11-01

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

The peregrine falcon in Arizona: Habitat utilization and management recommendations

USGS Publications Warehouse

Ellis, D.H.

1982-01-01

The peregrine falcon once bred in significant numbers in Arizona. Good documentation is available for specific breeding sites and an additional 20 general locations. This report, based on the published literature, an extensive personal contact survey, an aerial habitat inventory (over 124 hours air time), and ground visits to over 300 locations, provides information on habitat preferences and management practices which can contribute to the bird's survival. In seeking to identify the habitat preferences of the falcon, many site description factors were examined. Those traits which appeared common to most recent Arizona sites (and therefore most useful in evaluating habitat) were: elevation less than 9,000 feet, cliffs tall or very tall, cliffs extensive, topographic relief high, and surface water readily available. All recent sites are in extensive canyon systems or in extensive mountain ranges. Using a habitat evaluation key derived from the traits common to known breeding sites, all cliff regions in Arizona and the Navajo Indian Reservation were flown and evaluated for suitability. Nineteen falcon eyries located in subsequent ground visits were all in areas previously ranked acceptable or better. Many management alternatives are discussed: management of information on breeding sites, habitat preservation, controlling disruptive human activities, and enhancing productivity through the creation of suitable breeding ledges, providing pesticide free prey, or direct reintroductions. Given their privacy (and an increasingly pesticide free environment) the peregrine falcon will likely exist indefinitely in suitable areas across Arizona.

Mapping the functional connectome traits of levels of consciousness.

PubMed

Amico, Enrico; Marinazzo, Daniele; Di Perri, Carol; Heine, Lizette; Annen, Jitka; Martial, Charlotte; Dzemidzic, Mario; Kirsch, Murielle; Bonhomme, Vincent; Laureys, Steven; Goñi, Joaquín

2017-03-01

Examining task-free functional connectivity (FC) in the human brain offers insights on how spontaneous integration and segregation of information relate to human cognition, and how this organization may be altered in different conditions, and neurological disorders. This is particularly relevant for patients in disorders of consciousness (DOC) following severe acquired brain damage and coma, one of the most devastating conditions in modern medical care. We present a novel data-driven methodology, connICA, which implements Independent Component Analysis (ICA) for the extraction of robust independent FC patterns (FC-traits) from a set of individual functional connectomes, without imposing any a priori data stratification into groups. We here apply connICA to investigate associations between network traits derived from task-free FC and cognitive/clinical features that define levels of consciousness. Three main independent FC-traits were identified and linked to consciousness-related clinical features. The first one represents the functional configuration of a "resting" human brain, and it is associated to a sedative (sevoflurane), the overall effect of the pathology and the level of arousal. The second FC-trait reflects the disconnection of the visual and sensory-motor connectivity patterns. It also relates to the time since the insult and to the ability of communicating with the external environment. The third FC-trait isolates the connectivity pattern encompassing the fronto-parietal and the default-mode network areas as well as the interaction between left and right hemispheres, which are also associated to the awareness of the self and its surroundings. Each FC-trait represents a distinct functional process with a role in the degradation of conscious states of functional brain networks, shedding further light on the functional sub-circuits that get disrupted in severe brain-damage. Copyright © 2017. Published by Elsevier Inc.

Functional traits determine tree growth and ecosystem productivity of a tropical montane forest: Insights from a long-term nutrient manipulation experiment.

PubMed

Báez, Selene; Homeier, Jürgen

2018-01-01

Trait-response effects are critical to forecast community structure and biomass production in highly diverse tropical forests. Ecological theory and few observation studies indicate that trees with acquisitive functional traits would respond more strongly to higher resource availability than those with conservative traits. We assessed how long-term tree growth in experimental nutrient addition plots (N, P, and N + P) varied as a function of morphological traits, tree size, and species identity. We also evaluated how trait-based responses affected stand scale biomass production considering the community structure. We found that tree growth depended on interactions between functional traits and the type or combination of nutrients added. Common species with acquisitive functional traits responded more strongly to nutrient addition, mainly to N + P. Phosphorous enhanced the growth rates of species with acquisitive and conservative traits, had mostly positive effects on common species and neutral or negative effects in rare species. Moreover, trees receiving N + P grew faster irrespective of their initial size relative to trees in control or to trees in other treatment plots. Finally, species responses were highly idiosyncratic suggesting that community processes including competition and niche dimensionality may be altered under increased resource availability. We found no statistically significant effects of nutrient additions on aboveground biomass productivity because acquisitive species had a limited potential to increase their biomass, possibly due to their generally lower wood density. In contrast, P addition increased the growth rates of species characterized by more conservative resource strategies (with higher wood density) that were poorly represented in the plant community. We provide the first long-term experimental evidence that trait-based responses, community structure, and community processes modulate the effects of increased nutrient availability on biomass productivity in a tropical forest. © 2017 John Wiley & Sons Ltd.

Traits as dimensions or categories? Developmental change in the understanding of trait terms.

PubMed

Gonzalez, Celia M; Zosuls, Kristina M; Ruble, Diane N

2010-09-01

Recent research has suggested that young children have relatively well-developed trait concepts. However, this literature overlooks potential age-related differences in children's appreciation of the fundamentally dimensional nature of traits. In Study 1, we presented 4-, 5-, and 7-year-old children and adults with sets of characters and asked them to indicate the preferences of a target character who shared appearance attributes with one character (appearance match) and shared a common trait with the other character (trait match). Traits were presented in a way that emphasized either their categorical or their dimensional nature. When the dimensional nature of trait terms was emphasized, the youngest children made fewer trait-based inferences, and the use of traits increased with age. In Study 2, we gave 4-year-old children and adults the same task except that the extent to which appearance cues could serve as a meaningful basis of judgment was varied. Results were consistent with the findings of Study 1, although children were more likely to rely on dimensional presentations of traits in the absence of strong appearance cues. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?

PubMed

Moore, Timothy E; Schlichting, Carl D; Aiello-Lammens, Matthew E; Mocko, Kerri; Jones, Cynthia S

2018-05-11

Functional traits in closely related lineages are expected to vary similarly along common environmental gradients as a result of shared evolutionary and biogeographic history, or legacy effects, and as a result of biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa. Trait-trait integration was assessed via pairwise correlations within subclades. Of 20 trait-environment associations, 17 differed among subclades. Signs of regression coefficients diverged for height, leaf area and leaf nitrogen content, but not for LMA. Subclades also differed in trait-trait relationships and these differences were modulated by rainfall seasonality. Leave-one-out cross-validation revealed that whether trait variation was better predicted by environmental predictors or trait-trait integration depended on the clade and trait in question. Legacy signals in trait-environment and trait-trait relationships were apparently lost during the earliest diversification of Pelargonium, but then retained during subsequent subclade evolution. Overall, we demonstrate that global-scale patterns are poor predictors of patterns of trait variation at finer geographic and taxonomic scales. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

The implications of Big Five standing for the distribution of trait manifestation in behavior: fifteen experience-sampling studies and a meta-analysis.

PubMed

Fleeson, William; Gallagher, Patrick

2009-12-01

One of the fundamental questions in personality psychology is whether and how strongly trait standing relates to the traits that people actually manifest in their behavior when faced with real pressures and real consequences of their actions. One reason this question is fundamental is the common belief that traits do not predict how individuals behave, which leads to the reasonable conclusion that traits are not important to study. However, this conclusion is surprising given that there is almost no data on the ability of traits to predict distributions of naturally occurring, representative behaviors of individuals (and that there are many studies showing that traits do indeed predict specific behaviors). The authors describe a meta-analysis of 15 experience-sampling studies, conducted over the course of 8 years, amassing over 20,000 reports of trait manifestation in behavior. Participants reported traits on typical self-report questionnaires, then described their current behavior multiple times per day for several days as the behavior was occurring. Results show that traits, contrary to expectations, were strongly predictive of individual differences in trait manifestation in behavior, predicting average levels with correlations between .42 and .56 (approaching .60 for stringently restricted studies). Several other ways of summarizing trait manifestation in behavior were also predicted from traits. These studies provide evidence that traits are powerful predictors of actual manifestation of traits in behavior.

Neanderthal and Denisova tooth protein variants in present-day humans

PubMed Central

Zanolli, Clément; Hourset, Mathilde; Esclassan, Rémi

2017-01-01

Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein). Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes) and one is the derived enamelin major variant, T648I (rs7671281), associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or disease susceptibility in these populations. This modern regional distribution of archaic dental polymorphisms may reflect persistence of archaic variants in some populations and may contribute in part to the geographic dental variations described in modern humans. PMID:28902892

Effects of Low-Level Blast Exposure on the Nervous System: Is There Really a Controversy?

PubMed Central

Elder, Gregory A.; Stone, James R.; Ahlers, Stephen T.

2014-01-01

High-pressure blast waves can cause extensive CNS injury in human beings. However, in combat settings, such as Iraq and Afghanistan, lower level exposures associated with mild traumatic brain injury (mTBI) or subclinical exposure have been much more common. Yet controversy exists concerning what traits can be attributed to low-level blast, in large part due to the difficulty of distinguishing blast-related mTBI from post-traumatic stress disorder (PTSD). We describe how TBI is defined in human beings and the problems posed in using current definitions to recognize blast-related mTBI. We next consider the problem of applying definitions of human mTBI to animal models, in particular that TBI severity in human beings is defined in relation to alteration of consciousness at the time of injury, which typically cannot be assessed in animals. However, based on outcome assessments, a condition of “low-level” blast exposure can be defined in animals that likely approximates human mTBI or subclinical exposure. We review blast injury modeling in animals noting that inconsistencies in experimental approach have contributed to uncertainty over the effects of low-level blast. Yet, animal studies show that low-level blast pressure waves are transmitted to the brain. In brain, low-level blast exposures cause behavioral, biochemical, pathological, and physiological effects on the nervous system including the induction of PTSD-related behavioral traits in the absence of a psychological stressor. We review the relationship of blast exposure to chronic neurodegenerative diseases noting the paradoxical lowering of Abeta by blast, which along with other observations suggest that blast-related TBI is pathophysiologically distinct from non-blast TBI. Human neuroimaging studies show that blast-related mTBI is associated with a variety of chronic effects that are unlikely to be explained by co-morbid PTSD. We conclude that abundant evidence supports low-level blast as having long-term effects on the nervous system. PMID:25566175

Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKown, Athena; Klapste, Jaroslav; Guy, Robert

2014-01-01

To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

Dispositional Affect Moderates the Stress-Buffering Effect of Social Support on Risk for Developing the Common Cold.

PubMed

Janicki Deverts, Denise; Cohen, Sheldon; Doyle, William J

2017-10-01

The aim was to examine whether trait positive and negative affect (PA, NA) moderate the stress-buffering effect of perceived social support on risk for developing a cold subsequent to being exposed to a virus that causes mild upper respiratory illness. Analyses were based on archival data from 694 healthy adults (M age  = 31.0 years, SD = 10.7 years; 49.0% female; 64.6% Caucasian). Perceived social support and perceived stress were assessed by self-report questionnaire and trait affect by aggregating responses to daily mood items administered by telephone interview across several days. Subsequently, participants were exposed to a virus that causes the common cold and monitored for 5 days for clinical illness (infection + objective signs of illness). Two 3-way interactions emerged-Support × Stress × PA and Support × Stress × NA. The nature of these effects was such that among persons with high trait PA or low trait NA, greater social support attenuated the risk of developing a cold when under high but not low perceived stress; this stress-buffering effect did not emerge among persons with low trait PA or high trait NA. Dispositional affect might be used to identify individuals who may be most responsive to social support and support-based interventions. © 2016 Wiley Periodicals, Inc.

The relationship between cavum septum pellucidum and psychopathic traits in female offenders.

PubMed

Crooks, Dana; Anderson, Nathaniel E; Widdows, Matthew; Petseva, Nia; Decety, Jean; Pluto, Charles; Kiehl, Kent A

2018-06-22

Cavum Septum Pellucidum (CSP) is a common anatomical variant of the septum pellucidum. CSP is considered a marker for abnormal limbic brain development, but its functional consequences are non-specific. In a recent report [1], CSP size was significantly positively correlated with the affective/interpersonal traits of psychopathy in male offenders (N = 1742). Here we test the hypothesis that CSP is related to psychopathic traits in incarcerated females (N = 355). We examine continuous relationships as well as categorical assignments for CSP size corresponding to a number of prior reports. We also compare female offenders to healthy female controls (N = 385). Consistent with our reported findings in males, a positive association was observed between the interpersonal psychopathic traits and CSP size. In contrast to findings among males, an association between CSP and antisocial psychopathic traits was apparent in females. There was no significant difference in CSP size (in mm) or CSP presence/absence between incarcerated and non-incarcarated groups. However, categorical rates of medium and large CSP were more common in female inmates than in controls. This is the first systematic investigation of these variables in a female inmate sample. In combination with our prior study, these findings demonstrate that limbic abnormalities, as indexed by CSP, are related to psychopathic traits in both female and male inmates. Copyright © 2018. Published by Elsevier B.V.

Direct Conversion Provides Old Neurons from Aged Donor's Skin.

PubMed

Koch, Philipp

2015-12-03

Modeling human neuronal aging at a cellular level remains challenging. Human neurons are accessible from iPSCs, but during reprogramming age-associated traits of somatic cells get lost. In this issue of Cell Stem Cell, Mertens et al. (2015) demonstrate that neurons obtained by direct cell conversion retain age-associated transcriptional traits and functional deficits of the donor cell population. Copyright © 2015 Elsevier Inc. All rights reserved.

Multidimensional assessment of severe asthma: A systematic review and meta-analysis.

PubMed

Clark, Vanessa L; Gibson, Peter G; Genn, Grayson; Hiles, Sarah A; Pavord, Ian D; McDonald, Vanessa M

2017-10-01

The management of severe asthma is complex. Multidimensional assessment (MDA) of specific traits has been proposed as an effective strategy to manage severe asthma, although it is supported by few prospective studies. We aimed to systematically review the literature published on MDA in severe asthma, to identify the traits included in MDA and to determine the effect of MDA on asthma-related outcomes. We identified 26 studies and classified these based on study type (cohort/cross-sectional studies; experimental/outcome studies; and severe asthma disease registries). Study type determined the comprehensiveness of the assessment. Assessed traits were classified into three domains (airways, co-morbidities and risk factors). The airway domain had the largest number of traits assessed (mean ± SD = 4.2 ± 1.7) compared with co-morbidities (3.6 ± 2.2) and risk factors (3.9 ± 2.1). Bronchodilator reversibility and airflow limitation were assessed in 92% of studies, whereas airway inflammation was only assessed in 50%. Commonly assessed co-morbidities were psychological dysfunction, sinusitis (both 73%) and gastro-oesophageal reflux disease (GORD; 69%). Atopic and smoking statuses were the most commonly assessed risk factors (85% and 86%, respectively). There were six outcome studies, of which five concluded that MDA is effective at improving asthma-related outcomes. Among these studies, significantly more traits were assessed than treated. MDA studies have assessed a variety of different traits and have shown evidence of improved outcomes. This promising model of care requires more research to inform which traits should be assessed, which traits should be treated and what effect MDA has on patient outcomes. © 2017 Asian Pacific Society of Respirology.

Variation in life-history traits and their plasticities to elevational transplantation among seed families suggests potential for adaptative evolution of 15 tropical plant species to climate change.

PubMed

Ensslin, Andreas; Fischer, Markus

2015-08-01

• Because not all plant species will be able to move in response to global warming, adaptive evolution matters largely for plant persistence. As prerequisites for adaptive evolution, genetic variation in and selection on phenotypic traits are needed, but these aspects have not been studied in tropical species. We studied how plants respond to transplantation to different elevations on Mt. Kilimanjaro, Tanzania, and whether there is quantitative genetic (among-seed family) variation in and selection on life-history traits and their phenotypic plasticity to the different environments.• We reciprocally transplanted seed families of 15 common tropical, herbaceous species of the montane and savanna vegetation zone at Mt. Kilimanjaro to a watered experimental garden in the montane (1450 m) and in the savanna (880 m) zone at the mountain's slope and measured performance, reproductive, and phenological traits.• Plants generally performed worse in the savanna garden, indicating that the savanna climate was more stressful and thus that plants may suffer from future climate warming. We found significant quantitative genetic variation in all measured performance and reproductive traits in both gardens and for several measures of phenotypic plasticity in response to elevational transplantation. Moreover, we found positive selection on traits at low and intermediate trait values levelling to neutral or negative selection at high values.• We conclude that common plants at Mt. Kilimanjaro express quantitative genetic variation in fitness-relevant traits and in their plasticities, suggesting potential to adapt evolutionarily to future climate warming and increased temperature variability. © 2015 Botanical Society of America, Inc.

Fear-conditioning mechanisms associated with trait vulnerability to anxiety in humans.

PubMed

Indovina, Iole; Robbins, Trevor W; Núñez-Elizalde, Anwar O; Dunn, Barnaby D; Bishop, Sonia J

2011-02-10

Investigations of fear conditioning in rodents and humans have illuminated the neural mechanisms underlying cued and contextual fear. A critical question is how personality dimensions such as trait anxiety act through these mechanisms to confer vulnerability to anxiety disorders, and whether humans' ability to overcome acquired fears depends on regulatory skills not characterized in animal models. In a neuroimaging study of fear conditioning in humans, we found evidence for two independent dimensions of neurocognitive function associated with trait vulnerability to anxiety. The first entailed increased amygdala responsivity to phasic fear cues. The second involved impoverished ventral prefrontal cortical (vPFC) recruitment to downregulate both cued and contextual fear prior to omission (extinction) of the aversive unconditioned stimulus. These two dimensions may contribute to symptomatology differences across anxiety disorders; the amygdala mechanism affecting the development of phobic fear and the frontal mechanism influencing the maintenance of both specific fears and generalized anxiety. Copyright © 2011 Elsevier Inc. All rights reserved.

sPlot - the new global vegetation-plot database for addressing trait-environment relationships across the world's biomes

NASA Astrophysics Data System (ADS)

Purschke, Oliver; Dengler, Jürgen; Bruelheide, Helge; Chytrý, Milan; Jansen, Florian; Hennekens, Stephan; Jandt, Ute; Jiménez-Alfaro, Borja; Kattge, Jens; De Patta Pillar, Valério; Sandel, Brody; Winter, Marten

2015-04-01

The trait composition of plant communities is determined by abiotic, biotic and historical factors, but the importance of macro-climatic factors in explaining trait-environment relationships at the local scale remains unclear. Such knowledge is crucial for biogeographical and ecological theory but also relevant to devise management measures to mitigate the negative effects of climate change. To address these questions, an iDiv Working Group has established the first global vegetation-plot database (sPlot). sPlot currently contains ~700,000 plots from over 50 countries and all biomes, and is steadily growing. Approx. 70% of the most frequent species are represented by at least one trait in the global trait database TRY and gap-filled data will become available for the most common traits. We will give an overview about the structure and present content of sPlot in terms of spatial distribution, data properties and trait coverage. We will explain next steps and perspectives, present first cross-biome analyses of community-weighted mean traits and trait variability, and highlight some ecological questions that can be addressed with sPlot.

Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

PubMed Central

Brown, Patrick J.; Upadyayula, Narasimham; Mahone, Gregory S.; Tian, Feng; Bradbury, Peter J.; Myles, Sean; Holland, James B.; Flint-Garcia, Sherry; McMullen, Michael D.; Buckler, Edward S.; Rocheford, Torbert R.

2011-01-01

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects. PMID:22125498

Phenotype traits of bermudagrass ecotypes from pastures stocked at different intensities during a 40-year period

USDA-ARS?s Scientific Manuscript database

Stocking intensities can affect persistence of bermudagrass pastures. The objectives of this study were to compare phenotype traits of bermudagrass [Cynodon dactylon (L) Pers] (BG) ecotypes (ECOT) selected from both ‘Coastal’ (COS) and common (COM) BG pastures stocked at different, controlled intens...

Implementing meta-analysis from genome-wide association studies for pork quality traits

USDA-ARS?s Scientific Manuscript database

Pork quality plays an important role in the meat processing industry, thus different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. Howe...

Environment dominates over host genetics in shaping human gut microbiota.

PubMed

Rothschild, Daphna; Weissbrod, Omer; Barkan, Elad; Kurilshikov, Alexander; Korem, Tal; Zeevi, David; Costea, Paul I; Godneva, Anastasia; Kalka, Iris N; Bar, Noam; Shilo, Smadar; Lador, Dar; Vila, Arnau Vich; Zmora, Niv; Pevsner-Fischer, Meirav; Israeli, David; Kosower, Noa; Malka, Gal; Wolf, Bat Chen; Avnit-Sagi, Tali; Lotan-Pompan, Maya; Weinberger, Adina; Halpern, Zamir; Carmi, Shai; Fu, Jingyuan; Wijmenga, Cisca; Zhernakova, Alexandra; Elinav, Eran; Segal, Eran

2018-03-08

Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.

ANIMAL ANALOGIES IN FIRST IMPRESSIONS OF FACES.

PubMed

Zebrowitz, Leslie A; Wadlinger, Heather A; Luevano, Victor X; White, Benjamin M; Xing, Cai; Zhang, Yi

2011-08-01

Analogies between humans and animals based on facial resemblance have a long history. We report evidence for reverse anthropomorphism and the extension of facial stereotypes to lions, foxes, and dogs. In the stereotype extension, more positive traits were attributed to animals judged more attractive than con-specifics; more childlike traits were attributed to those judged more babyfaced. In the reverse anthropomorphism, human faces with more resemblance to lions, ascertained by connectionist modeling of facial metrics, were judged more dominant, cold, and shrewd, controlling attractiveness, babyfaceness, and sex. Faces with more resemblance to Labradors were judged warmer and less shrewd. Resemblance to foxes did not predict impressions. Results for lions and dogs were consistent with trait impressions of these animals and support the species overgeneralization hypothesis that evolutionarily adaptive reactions to particular animals are overgeneralized, with people perceived to have traits associated with animals their faces resemble. Other possible explanations are discussed.

ANIMAL ANALOGIES IN FIRST IMPRESSIONS OF FACES

PubMed Central

Zebrowitz, Leslie A.; Wadlinger, Heather A.; Luevano, Victor X.; White, Benjamin M.; Xing, Cai; Zhang, Yi

2013-01-01

Analogies between humans and animals based on facial resemblance have a long history. We report evidence for reverse anthropomorphism and the extension of facial stereotypes to lions, foxes, and dogs. In the stereotype extension, more positive traits were attributed to animals judged more attractive than con-specifics; more childlike traits were attributed to those judged more babyfaced. In the reverse anthropomorphism, human faces with more resemblance to lions, ascertained by connectionist modeling of facial metrics, were judged more dominant, cold, and shrewd, controlling attractiveness, babyfaceness, and sex. Faces with more resemblance to Labradors were judged warmer and less shrewd. Resemblance to foxes did not predict impressions. Results for lions and dogs were consistent with trait impressions of these animals and support the species overgeneralization hypothesis that evolutionarily adaptive reactions to particular animals are overgeneralized, with people perceived to have traits associated with animals their faces resemble. Other possible explanations are discussed. PMID:25339791

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

PubMed

Ward, Lucas D; Kellis, Manolis

2016-01-04

More than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed HaploReg (http://compbio.mit.edu/HaploReg) to aid the functional dissection of genome-wide association study (GWAS) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. Since first launching the website in 2011, we have greatly expanded HaploReg, increasing the number of chromatin state maps to 127 reference epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eQTL) variants and their tissue-specific target genes from GTEx, Geuvadis, and other recent studies. We present these updates as HaploReg v4, and illustrate a use case of HaploReg for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Heritability, covariation and natural selection on 24 traits of common evening primrose (Oenothera biennis) from a field experiment.

PubMed

Johnson, M T J; Agrawal, A A; Maron, J L; Salminen, J-P

2009-06-01

This study explored genetic variation and co-variation in multiple functional plant traits. Our goal was to characterize selection, heritabilities and genetic correlations among different types of traits to gain insight into the evolutionary ecology of plant populations and their interactions with insect herbivores. In a field experiment, we detected significant heritable variation for each of 24 traits of Oenothera biennis and extensive genetic covariance among traits. Traits with diverse functions formed several distinct groups that exhibited positive genetic covariation with each other. Genetic variation in life-history traits and secondary chemistry together explained a large proportion of variation in herbivory (r(2) = 0.73). At the same time, selection acted on lifetime biomass, life-history traits and two secondary compounds of O. biennis, explaining over 95% of the variation in relative fitness among genotypes. The combination of genetic covariances and directional selection acting on multiple traits suggests that adaptive evolution of particular traits is constrained, and that correlated evolution of groups of traits will occur, which is expected to drive the evolution of increased herbivore susceptibility. As a whole, our study indicates that an examination of genetic variation and covariation among many different types of traits can provide greater insight into the evolutionary ecology of plant populations and plant-herbivore interactions.

Genetics and Genomics of Single-Gene Cardiovascular Diseases: Common Hereditary Cardiomyopathies as Prototypes of Single-Gene Disorders

PubMed Central

Marian, Ali J.; van Rooij, Eva; Roberts, Robert

2016-01-01

This is the first of 2 review papers on genetics and genomics appearing as part of the series on “omics.” Genomics pertains to all components of an organism’s genes, whereas genetics involves analysis of a specific gene(s) in the context of heredity. The paper provides introductory comments, describes the basis of human genetic diversity, and addresses the phenotypic consequences of genetic variants. Rare variants with large effect sizes are responsible for single-gene disorders, whereas complex polygenic diseases are typically due to multiple genetic variants, each exerting a modest effect size. To illustrate the clinical implications of genetic variants with large effect sizes, 3 common forms of hereditary cardiomyopathies are discussed as prototypic examples of single-gene disorders, including their genetics, clinical manifestations, pathogenesis, and treatment. The genetic basis of complex traits is discussed in a separate paper. PMID:28007145

Parent-of-origin specific allelic associations among 106 genomic loci for age at menarche

PubMed Central

Thompson, Deborah J; Ferreira, Teresa; He, Chunyan; Chasman, Daniel I; Esko, Tõnu; Thorleifsson, Gudmar; Albrecht, Eva; Ang, Wei Q; Corre, Tanguy; Cousminer, Diana L; Feenstra, Bjarke; Franceschini, Nora; Ganna, Andrea; Johnson, Andrew D; Kjellqvist, Sanela; Lunetta, Kathryn L; McMahon, George; Nolte, Ilja M; Paternoster, Lavinia; Porcu, Eleonora; Smith, Albert V; Stolk, Lisette; Teumer, Alexander; Tšernikova, Natalia; Tikkanen, Emmi; Ulivi, Sheila; Wagner, Erin K; Amin, Najaf; Bierut, Laura J; Byrne, Enda M; Hottenga, Jouke-Jan; Koller, Daniel L; Mangino, Massimo; Pers, Tune H; Yerges-Armstrong, Laura M; Zhao, Jing Hua; Andrulis, Irene L; Anton-Culver, Hoda; Atsma, Femke; Bandinelli, Stefania; Beckmann, Matthias W; Benitez, Javier; Blomqvist, Carl; Bojesen, Stig E; Bolla, Manjeet K; Bonanni, Bernardo; Brauch, Hiltrud; Brenner, Hermann; Buring, Julie E; Chang-Claude, Jenny; Chanock, Stephen; Chen, Jinhui; Chenevix-Trench, Georgia; Collée, J. Margriet; Couch, Fergus J; Couper, David; Coveillo, Andrea D; Cox, Angela; Czene, Kamila; D’adamo, Adamo Pio; Smith, George Davey; De Vivo, Immaculata; Demerath, Ellen W; Dennis, Joe; Devilee, Peter; Dieffenbach, Aida K; Dunning, Alison M; Eiriksdottir, Gudny; Eriksson, Johan G; Fasching, Peter A; Ferrucci, Luigi; Flesch-Janys, Dieter; Flyger, Henrik; Foroud, Tatiana; Franke, Lude; Garcia, Melissa E; García-Closas, Montserrat; Geller, Frank; de Geus, Eco EJ; Giles, Graham G; Gudbjartsson, Daniel F; Gudnason, Vilmundur; Guénel, Pascal; Guo, Suiqun; Hall, Per; Hamann, Ute; Haring, Robin; Hartman, Catharina A; Heath, Andrew C; Hofman, Albert; Hooning, Maartje J; Hopper, John L; Hu, Frank B; Hunter, David J; Karasik, David; Kiel, Douglas P; Knight, Julia A; Kosma, Veli-Matti; Kutalik, Zoltan; Lai, Sandra; Lambrechts, Diether; Lindblom, Annika; Mägi, Reedik; Magnusson, Patrik K; Mannermaa, Arto; Martin, Nicholas G; Masson, Gisli; McArdle, Patrick F; McArdle, Wendy L; Melbye, Mads; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L; Nevanlinna, Heli; Neven, Patrick; Nohr, Ellen A; Oldehinkel, Albertine J; Oostra, Ben A; Palotie, Aarno; Peacock, Munro; Pedersen, Nancy L; Peterlongo, Paolo; Peto, Julian; Pharoah, Paul DP; Postma, Dirkje S; Pouta, Anneli; Pylkäs, Katri; Radice, Paolo; Ring, Susan; Rivadeneira, Fernando; Robino, Antonietta; Rose, Lynda M; Rudolph, Anja; Salomaa, Veikko; Sanna, Serena; Schlessinger, David; Schmidt, Marjanka K; Southey, Mellissa C; Sovio, Ulla; Stampfer, Meir J; Stöckl, Doris; Storniolo, Anna M; Timpson, Nicholas J; Tyrer, Jonathan; Visser, Jenny A; Vollenweider, Peter; Völzke, Henry; Waeber, Gerard; Waldenberger, Melanie; Wallaschofski, Henri; Wang, Qin; Willemsen, Gonneke; Winqvist, Robert; Wolffenbuttel, Bruce HR; Wright, Margaret J; Boomsma, Dorret I; Econs, Michael J; Khaw, Kay-Tee; Loos, Ruth JF; McCarthy, Mark I; Montgomery, Grant W; Rice, John P; Streeten, Elizabeth A; Thorsteinsdottir, Unnur; van Duijn, Cornelia M; Alizadeh, Behrooz Z; Bergmann, Sven; Boerwinkle, Eric; Boyd, Heather A; Crisponi, Laura; Gasparini, Paolo; Gieger, Christian; Harris, Tamara B; Ingelsson, Erik; Järvelin, Marjo-Riitta; Kraft, Peter; Lawlor, Debbie; Metspalu, Andres; Pennell, Craig E; Ridker, Paul M; Snieder, Harold; Sørensen, Thorkild IA; Spector, Tim D; Strachan, David P; Uitterlinden, André G; Wareham, Nicholas J; Widen, Elisabeth; Zygmunt, Marek; Murray, Anna; Easton, Douglas F

2014-01-01

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality1. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation2,3, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P<5×10−8) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1/WDR25, MKRN3/MAGEL2 and KCNK9) demonstrating parent-of-origin specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and gamma-aminobutyric acid-B2 receptor signaling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition. PMID:25231870

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

PubMed

Perry, John Rb; Day, Felix; Elks, Cathy E; Sulem, Patrick; Thompson, Deborah J; Ferreira, Teresa; He, Chunyan; Chasman, Daniel I; Esko, Tõnu; Thorleifsson, Gudmar; Albrecht, Eva; Ang, Wei Q; Corre, Tanguy; Cousminer, Diana L; Feenstra, Bjarke; Franceschini, Nora; Ganna, Andrea; Johnson, Andrew D; Kjellqvist, Sanela; Lunetta, Kathryn L; McMahon, George; Nolte, Ilja M; Paternoster, Lavinia; Porcu, Eleonora; Smith, Albert V; Stolk, Lisette; Teumer, Alexander; Tšernikova, Natalia; Tikkanen, Emmi; Ulivi, Sheila; Wagner, Erin K; Amin, Najaf; Bierut, Laura J; Byrne, Enda M; Hottenga, Jouke-Jan; Koller, Daniel L; Mangino, Massimo; Pers, Tune H; Yerges-Armstrong, Laura M; Zhao, Jing Hua; Andrulis, Irene L; Anton-Culver, Hoda; Atsma, Femke; Bandinelli, Stefania; Beckmann, Matthias W; Benitez, Javier; Blomqvist, Carl; Bojesen, Stig E; Bolla, Manjeet K; Bonanni, Bernardo; Brauch, Hiltrud; Brenner, Hermann; Buring, Julie E; Chang-Claude, Jenny; Chanock, Stephen; Chen, Jinhui; Chenevix-Trench, Georgia; Collée, J Margriet; Couch, Fergus J; Couper, David; Coveillo, Andrea D; Cox, Angela; Czene, Kamila; D'adamo, Adamo Pio; Smith, George Davey; De Vivo, Immaculata; Demerath, Ellen W; Dennis, Joe; Devilee, Peter; Dieffenbach, Aida K; Dunning, Alison M; Eiriksdottir, Gudny; Eriksson, Johan G; Fasching, Peter A; Ferrucci, Luigi; Flesch-Janys, Dieter; Flyger, Henrik; Foroud, Tatiana; Franke, Lude; Garcia, Melissa E; García-Closas, Montserrat; Geller, Frank; de Geus, Eco Ej; Giles, Graham G; Gudbjartsson, Daniel F; Gudnason, Vilmundur; Guénel, Pascal; Guo, Suiqun; Hall, Per; Hamann, Ute; Haring, Robin; Hartman, Catharina A; Heath, Andrew C; Hofman, Albert; Hooning, Maartje J; Hopper, John L; Hu, Frank B; Hunter, David J; Karasik, David; Kiel, Douglas P; Knight, Julia A; Kosma, Veli-Matti; Kutalik, Zoltan; Lai, Sandra; Lambrechts, Diether; Lindblom, Annika; Mägi, Reedik; Magnusson, Patrik K; Mannermaa, Arto; Martin, Nicholas G; Masson, Gisli; McArdle, Patrick F; McArdle, Wendy L; Melbye, Mads; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L; Nevanlinna, Heli; Neven, Patrick; Nohr, Ellen A; Oldehinkel, Albertine J; Oostra, Ben A; Palotie, Aarno; Peacock, Munro; Pedersen, Nancy L; Peterlongo, Paolo; Peto, Julian; Pharoah, Paul Dp; Postma, Dirkje S; Pouta, Anneli; Pylkäs, Katri; Radice, Paolo; Ring, Susan; Rivadeneira, Fernando; Robino, Antonietta; Rose, Lynda M; Rudolph, Anja; Salomaa, Veikko; Sanna, Serena; Schlessinger, David; Schmidt, Marjanka K; Southey, Mellissa C; Sovio, Ulla; Stampfer, Meir J; Stöckl, Doris; Storniolo, Anna M; Timpson, Nicholas J; Tyrer, Jonathan; Visser, Jenny A; Vollenweider, Peter; Völzke, Henry; Waeber, Gerard; Waldenberger, Melanie; Wallaschofski, Henri; Wang, Qin; Willemsen, Gonneke; Winqvist, Robert; Wolffenbuttel, Bruce Hr; Wright, Margaret J; Boomsma, Dorret I; Econs, Michael J; Khaw, Kay-Tee; Loos, Ruth Jf; McCarthy, Mark I; Montgomery, Grant W; Rice, John P; Streeten, Elizabeth A; Thorsteinsdottir, Unnur; van Duijn, Cornelia M; Alizadeh, Behrooz Z; Bergmann, Sven; Boerwinkle, Eric; Boyd, Heather A; Crisponi, Laura; Gasparini, Paolo; Gieger, Christian; Harris, Tamara B; Ingelsson, Erik; Järvelin, Marjo-Riitta; Kraft, Peter; Lawlor, Debbie; Metspalu, Andres; Pennell, Craig E; Ridker, Paul M; Snieder, Harold; Sørensen, Thorkild Ia; Spector, Tim D; Strachan, David P; Uitterlinden, André G; Wareham, Nicholas J; Widen, Elisabeth; Zygmunt, Marek; Murray, Anna; Easton, Douglas F; Stefansson, Kari; Murabito, Joanne M; Ong, Ken K

2014-10-02

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.

The TRPM8 protein is a testosterone receptor: II. Functional evidence for an ionotropic effect of testosterone on TRPM8.

PubMed

Asuthkar, Swapna; Demirkhanyan, Lusine; Sun, Xiaohui; Elustondo, Pia A; Krishnan, Vivek; Baskaran, Padmamalini; Velpula, Kiran Kumar; Thyagarajan, Baskaran; Pavlov, Evgeny V; Zakharian, Eleonora

2015-01-30

Testosterone is a key steroid hormone in the development of male reproductive tissues and the regulation of the central nervous system. The rapid signaling mechanism induced by testosterone affects numerous behavioral traits, including sexual drive, aggressiveness, and fear conditioning. However, the currently identified testosterone receptor(s) is not believed to underlie the fast signaling, suggesting an orphan pathway. Here we report that an ion channel from the transient receptor potential family, TRPM8, commonly known as the cold and menthol receptor is the major component of testosterone-induced rapid actions. Using cultured and primary cell lines along with the purified TRPM8 protein, we demonstrate that testosterone directly activates TRPM8 channel at low picomolar range. Specifically, testosterone induced TRPM8 responses in primary human prostate cells, PC3 prostate cancer cells, dorsal root ganglion neurons, and hippocampal neurons. Picomolar concentrations of testosterone resulted in full openings of the purified TRPM8 channel in planar lipid bilayers. Furthermore, acute applications of testosterone on human skin elicited a cooling sensation. Our data conclusively demonstrate that testosterone is an endogenous and highly potent agonist of TRPM8, suggesting a role of TRPM8 channels well beyond their well established function in somatosensory neurons. This discovery may further imply TRPM8 channel function in testosterone-dependent behavioral traits. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Is Homo heidelbergensis a distinct species? New insight on the Mauer mandible.

PubMed

Mounier, Aurélien; Marchal, François; Condemi, Silvana

2009-03-01

The discovery of new fossils in Africa, Asia, and Europe, and the recognition of a greater diversity in the middle Pleistocene fossil record, has led to a reconsideration of the species Homo heidelbergensis. This nomen, formulated by Schoetensack in 1908 to describe the Mauer jaw (Germany), was almost forgotten during most of the past century. Numerous fossils have been attributed to it but no consensus has arisen concerning their classification. The holotype anatomical traits are still poorly understood, and numerous fossils with no mandibular remains have been placed in the taxon. Some researchers propose H. heidelbergensis as an Afro-European taxon that is ancestral to both modern humans and Neandertals whereas others think it is a strictly European species that is part of the Neandertal lineage. We focus on the validity of H. heidelbergensis, using the traditional basis of species recognition: anatomical description. We provide a comparative morphological analysis using 47 anatomical traits of 36 Pleistocene fossils from Africa, Asia, and Europe and 35 extant human mandibles. We re-examine the mandibular features of Mauer and discuss the specimen's inclusion in H. heidelbergensis, as well as alternative evolutionary theories. To lend objectivity to specimen grouping, we use multiple correspondence analysis associated with hierarchical classification that creates clusters corresponding to phenetic similarities between jaws. Our phenetic and comparative morphological analyses support the validity of H. heidelbergensis as a taxon. A set of morphological features can be statistically identified for the definition of the species. Some traits can be used to delimit H. heidelbergensis in an evolutionary framework (e.g., foramina mentale posteriorly positioned, horizontal retromolar surface). Those traits are also present on African (e.g., Tighenif) and European (e.g., Sima de los Huesos) specimens that show a close relationship with the Mauer mandible. Therefore, the definition of H. heidelbergensis is more precise and mainly supports the theory of an Afro-European taxon, which is the last common ancestor of H. neanderthalensis and H. sapiens. However, the results of this study fail to entirely discount the hypothesis that considers H. heidelbergensis as a chronospecies leading to the Neandertals.

Personality Disorders and Psychological Functioning Among Latina Women with Eating Disorders.

PubMed

Minnick, Alyssa M; Cachelin, Fary M; Durvasula, Ramani S

2017-01-01

Little is known about personality disorders (PD) and comorbidities among Latinas with eating disorders (ED). The dysregulation and chronicity of PDs can complicate and augment the symptomatology of EDs. This set of analyses provides a preliminary examination of PD and psychopathology in a sample of Latina women with ED. Participants (N = 34) were administered the Structured Clinical Interview for the Diagnostic and Statistical Manual, Eating Disorders Examination, and Millon Clinical Multiaxial Inventory-III to assess personality pathology, and questionnaires (Beck Depression Inventory-II and Brief Symptom Inventory) to assess psychological functioning. Results indicated the most common clinically significant trait in the sample was depressive personality (50% of the sample had a score of 75 or higher on this trait). For Bulimia Nervosa (BN) and Binge Eating Disorder (BED), avoidant (41%) and depressive (65%) personalities, respectively, were the most common clinically significant traits. Anxiety disorders were the most common psychiatric diagnoses, and 52.9% of the sample reported both clinically significant PD traits and other major psychopathology. There were no significant differences between the BED and BN groups on prevalence of PD traits and psychopathology. This pilot study highlights the need for further examination of PD and psychopathology in Latinas with ED. Unlike previous research with White women, we found no differences on PD and psychopathology between BED and BN, and the most prevalent PDs among Latinas were different than White women. Personality and psychological functioning should be assessed in all patients with ED, with ongoing research focused on identifying patterns in understudied groups such as Latinas, a practice that may improve treatment for this underserved population.

Personality Traits Are Associated with Academic Achievement in Medical School: A Nationally Representative Study.

PubMed

Sobowale, Kunmi; Ham, Sandra A; Curlin, Farr A; Yoon, John D

2018-06-01

This nationally representative study sought to identify personality traits that are associated with academic achievement in medical school. Third-year medical students, who completed an initial questionnaire in January 2011, were mailed a second questionnaire several months later during their fourth year. Controlling for sociodemographic characteristics and burnout, the authors used multivariate logistic regressions to determine whether Big Five personality traits were associated with receiving honors/highest grade in clinical clerkships, failing a course or rotation, and being selected for the Alpha Omega Alpha or Gold Humanism Honor Society. The adjusted response rates for the two surveys were 61 (n = 564/919) and 84% (n = 474/564). The personality trait conscientiousness predicted obtaining honors/highest grade in all clinical clerkships. In contrast, students high in neuroticism were less likely to do well in most specialties. Students with higher conscientiousness were more likely to be inducted into the Alpha Omega Alpha Honor Society, while students high in openness or agreeableness traits were more likely to be inducted into the Gold Humanism Honor Society. Burnout was not associated with any clinical performance measures. This study suggests the importance of personality traits, particularly conscientiousness, in predicting success during the clinical years of medical school. Medical educators should consider a nuanced examination of personality traits and other non-cognitive factors, particularly for psychiatry.

Using avian functional traits to assess the impact of land-cover change on ecosystem processes linked to resilience in tropical forests.

PubMed

Bregman, Tom P; Lees, Alexander C; MacGregor, Hannah E A; Darski, Bianca; de Moura, Nárgila G; Aleixo, Alexandre; Barlow, Jos; Tobias, Joseph A

2016-12-14

Vertebrates perform key roles in ecosystem processes via trophic interactions with plants and insects, but the response of these interactions to environmental change is difficult to quantify in complex systems, such as tropical forests. Here, we use the functional trait structure of Amazonian forest bird assemblages to explore the impacts of land-cover change on two ecosystem processes: seed dispersal and insect predation. We show that trait structure in assemblages of frugivorous and insectivorous birds remained stable after primary forests were subjected to logging and fire events, but that further intensification of human land use substantially reduced the functional diversity and dispersion of traits, and resulted in communities that occupied a different region of trait space. These effects were only partially reversed in regenerating secondary forests. Our findings suggest that local extinctions caused by the loss and degradation of tropical forest are non-random with respect to functional traits, thus disrupting the network of trophic interactions regulating seed dispersal by forest birds and herbivory by insects, with important implications for the structure and resilience of human-modified tropical forests. Furthermore, our results illustrate how quantitative functional traits for specific guilds can provide a range of metrics for estimating the contribution of biodiversity to ecosystem processes, and the response of such processes to land-cover change. © 2016 The Author(s).

Using avian functional traits to assess the impact of land-cover change on ecosystem processes linked to resilience in tropical forests

PubMed Central

Bregman, Tom P.; Lees, Alexander C.; MacGregor, Hannah E. A.; Darski, Bianca; de Moura, Nárgila G.; Aleixo, Alexandre; Barlow, Jos

2016-01-01

Vertebrates perform key roles in ecosystem processes via trophic interactions with plants and insects, but the response of these interactions to environmental change is difficult to quantify in complex systems, such as tropical forests. Here, we use the functional trait structure of Amazonian forest bird assemblages to explore the impacts of land-cover change on two ecosystem processes: seed dispersal and insect predation. We show that trait structure in assemblages of frugivorous and insectivorous birds remained stable after primary forests were subjected to logging and fire events, but that further intensification of human land use substantially reduced the functional diversity and dispersion of traits, and resulted in communities that occupied a different region of trait space. These effects were only partially reversed in regenerating secondary forests. Our findings suggest that local extinctions caused by the loss and degradation of tropical forest are non-random with respect to functional traits, thus disrupting the network of trophic interactions regulating seed dispersal by forest birds and herbivory by insects, with important implications for the structure and resilience of human-modified tropical forests. Furthermore, our results illustrate how quantitative functional traits for specific guilds can provide a range of metrics for estimating the contribution of biodiversity to ecosystem processes, and the response of such processes to land-cover change. PMID:27928045

Are obsessive-compulsive personality traits associated with a poor outcome in anorexia nervosa? A systematic review of randomized controlled trials and naturalistic outcome studies.

PubMed

Crane, Anna M; Roberts, Marion E; Treasure, Janet

2007-11-01

Obsessive-compulsive personality disorder (OCPD) traits are commonly associated with anorexia nervosa (AN). The aim of this review was to systematically search the literature to examine whether OCPD traits have an impact on the outcome of AN. A systematic electronic search of the literature (using Medline, PsycINFO, and the Cochrane Central Register of Controlled Trials) was undertaken to identify relevant publications (randomized controlled trials (RCT's) and naturalistic studies), until February 2006. Eleven prospective longitudinal studies and 12 RCT's met criteria for inclusion. A meta-analysis was not feasible as the studies were too heterogeneous. Just over half of published longitudinal studies found that OCPD traits were associated with a negative outcome in AN. Additionally, results from three RCTs suggested that these traits may moderate outcome. OCPD traits were reduced after treatment in five RCTs. There is tentative support to suggest that individuals with AN and concomitant OCPD traits have a poorer prognosis, and that these traits moderate outcome. A reduction in these traits may mediate this change. An individualized case formulation with treatment tailored to OCPD traits may improve the outcome of AN. (c) 2007 by Wiley Periodicals, Inc.

Personality and morphological traits affect pigeon survival from raptor attacks.

PubMed

Santos, Carlos D; Cramer, Julia F; Pârâu, Liviu G; Miranda, Ana C; Wikelski, Martin; Dechmann, Dina K N

2015-10-22

Personality traits have recently been shown to impact fitness in different animal species, potentially making them similarly relevant drivers as morphological and life history traits along the evolutionary pathways of organisms. Predation is a major force of natural selection through its deterministic effects on individual survival, but how predation pressure has helped to shape personality trait selection, especially in free-ranging animals, remains poorly understood. We used high-precision GPS tracking to follow whole flocks of homing pigeons (Columba livia) with known personalities and morphology during homing flights where they were severely predated by raptors. This allowed us to determine how the personality and morphology traits of pigeons may affect their risk of being predated by raptors. Our survival model showed that individual pigeons, which were more tolerant to human approach, slower to escape from a confined environment, more resistant to human handling, with larger tarsi, and with lighter plumage, were more likely to be predated by raptors. We provide rare empirical evidence that the personality of prey influences their risk of being predated under free-ranging circumstances.

Personality and morphological traits affect pigeon survival from raptor attacks

PubMed Central

Santos, Carlos D.; Cramer, Julia F.; Pârâu, Liviu G.; Miranda, Ana C.; Wikelski, Martin; Dechmann, Dina K. N.

2015-01-01

Personality traits have recently been shown to impact fitness in different animal species, potentially making them similarly relevant drivers as morphological and life history traits along the evolutionary pathways of organisms. Predation is a major force of natural selection through its deterministic effects on individual survival, but how predation pressure has helped to shape personality trait selection, especially in free-ranging animals, remains poorly understood. We used high-precision GPS tracking to follow whole flocks of homing pigeons (Columba livia) with known personalities and morphology during homing flights where they were severely predated by raptors. This allowed us to determine how the personality and morphology traits of pigeons may affect their risk of being predated by raptors. Our survival model showed that individual pigeons, which were more tolerant to human approach, slower to escape from a confined environment, more resistant to human handling, with larger tarsi, and with lighter plumage, were more likely to be predated by raptors. We provide rare empirical evidence that the personality of prey influences their risk of being predated under free-ranging circumstances. PMID:26489437

Effects of Plant Traits on Ecosystem and Regional Processes: a Conceptual Framework for Predicting the Consequences of Global Change

PubMed Central

CHAPIN, F. STUART

2003-01-01

Human activities are causing widespread changes in the species composition of natural and managed ecosystems, but the consequences of these changes are poorly understood. This paper presents a conceptual framework for predicting the ecosystem and regional consequences of changes in plant species composition. Changes in species composition have greatest ecological effects when they modify the ecological factors that directly control (and respond to) ecosystem processes. These interactive controls include: functional types of organisms present in the ecosystem; soil resources used by organisms to grow and reproduce; modulators such as microclimate that influence the activity of organisms; disturbance regime; and human activities. Plant traits related to size and growth rate are particularly important because they determine the productive capacity of vegetation and the rates of decomposition and nitrogen mineralization. Because the same plant traits affect most key processes in the cycling of carbon and nutrients, changes in plant traits tend to affect most biogeochemical cycling processes in parallel. Plant traits also have landscape and regional effects through their effects on water and energy exchange and disturbance regime. PMID:12588725

The ethics of impossible and possible changes to human nature.

PubMed

Murphy, Timothy F

2012-05-01

Some commentators speak freely about genetics being poised to change human nature. Contrary to such rhetoric, Norman Daniels believes no such thing is plausible since 'nature' describes characteristic traits of human beings as a whole. Genetic interventions that do their work one individual at a time are unlikely to change the traits of human beings as a class. Even so, one can speculate about ways in which human beings as a whole could be genetically altered, and there is nothing about that venture that could not be deliberated in the way other high-impact questions can be evaluated. There might well come a time when it would be defensible to use genetics to change human beings as a class, in order to protect people in the face of changed environmental circumstances or to enhance existing capacities. Moreover, if one understands human nature not in an empirically descriptive way but in a metaphysical way having implications about human behavior, it can make sense to talk about de-naturing individuals through genetic changes. Even under a metaphysical conception of human nature, however, one can still imagine that people in the future might want to alter their traits in pursuit of another normative idea of a good and valuable life, and genetic modifications might function as a pathway to that change. © 2010 Blackwell Publishing Ltd.

Cultural stereotypes and personal beliefs about individuals with dwarfism.

PubMed

Heider, Jeremy D; Scherer, Cory R; Edlund, John E

2013-01-01

Three studies assessed the content of cultural stereotypes and personal beliefs regarding individuals with dwarfism among "average height" (i.e., non-dwarf) individuals. In Studies 1 and 2, undergraduates from three separate institutions selected adjectives to reflect traits constituting both the cultural stereotype about dwarves and their own personal beliefs about dwarves (cf. Devine & Elliot, 1995). The most commonly endorsed traits for the cultural stereotype tended to be negative (e.g., weird, incapable, childlike); the most commonly endorsed traits for personal beliefs were largely positive (e.g., capable, intelligent, kind). In Study 3, undergraduates from two separate institutions used an open-ended method to indicate their personal beliefs about dwarves (cf. Eagly, Mladinic, & Otto, 1994). Responses contained a mixture of positive and negative characteristics, suggesting a greater willingness to admit to negative personal beliefs using the open-ended method.

The Implications of Big-Five Standing for the Distribution of Trait Manifestation in Behavior: Fifteen Experience-Sampling Studies and a Meta-Analysis

PubMed Central

Fleeson, William; Gallagher, M. Patrick

2009-01-01

One of the fundamental questions in personality psychology is whether and how strongly trait standing relates to the traits that people actually manifest in their behavior, when faced with real pressures and real consequences of their actions. One reason this question is fundamental is the common belief that traits do not predict how individuals behave, which leads to the reasonable conclusion that traits are not important to study. However, this conclusion is surprising given that there is almost no data on the ability of traits to predict distributions of naturally occurring, representative behaviors of individuals (and that there are many studies showing that traits do indeed predict specific behaviors). This paper describes a meta-analysis of 15 experience-sampling studies, conducted over the course of eight years, amassing over 20,000 reports of trait manifestation in behavior. Participants reported traits on typical self-report questionnaires, then described their current behavior multiple times per day for several days, as the behavior was occurring. Results showed that traits, contrary to expectations, were strongly predictive of individual differences in trait manifestation in behavior, predicting average levels with correlations between .42 and .56 (approaching .60 for stringently restricted studies). Several other ways of summarizing trait manifestation in behavior were also predicted from traits. These studies provide evidence that traits are powerful predictors of actual manifestation of traits in behavior. PMID:19968421

Pervasive genetic integration directs the evolution of human skull shape.

PubMed

Martínez-Abadías, Neus; Esparza, Mireia; Sjøvold, Torstein; González-José, Rolando; Santos, Mauro; Hernández, Miquel; Klingenberg, Christian Peter

2012-04-01

It has long been unclear whether the different derived cranial traits of modern humans evolved independently in response to separate selection pressures or whether they resulted from the inherent morphological integration throughout the skull. In a novel approach to this issue, we combine evolutionary quantitative genetics and geometric morphometrics to analyze genetic and phenotypic integration in human skull shape. We measured human skulls in the ossuary of Hallstatt (Austria), which offer a unique opportunity because they are associated with genealogical data. Our results indicate pronounced covariation of traits throughout the skull. Separate simulations of selection for localized shape changes corresponding to some of the principal derived characters of modern human skulls produced outcomes that were similar to each other and involved a joint response in all of these traits. The data for both genetic and phenotypic shape variation were not consistent with the hypothesis that the face, cranial base, and cranial vault are completely independent modules but relatively strongly integrated structures. These results indicate pervasive integration in the human skull and suggest a reinterpretation of the selective scenario for human evolution where the origin of any one of the derived characters may have facilitated the evolution of the others. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Covariation of learning and "reasoning" abilities in mice: evolutionary conservation of the operations of intelligence.

PubMed

Wass, Christopher; Denman-Brice, Alexander; Rios, Chris; Light, Kenneth R; Kolata, Stefan; Smith, Andrew M; Matzel, Louis D

2012-04-01

Contemporary descriptions of human intelligence hold that this trait influences a broad range of cognitive abilities, including learning, attention, and reasoning. Like humans, individual genetically heterogeneous mice express a "general" cognitive trait that influences performance across a diverse array of learning and attentional tasks, and it has been suggested that this trait is qualitatively and structurally analogous to general intelligence in humans. However, the hallmark of human intelligence is the ability to use various forms of "reasoning" to support solutions to novel problems. Here, we find that genetically heterogeneous mice are capable of solving problems that are nominally indicative of inductive and deductive forms of reasoning, and that individuals' capacity for reasoning covaries with more general learning abilities. Mice were characterized for their general learning ability as determined by their aggregate performance (derived from principal component analysis) across a battery of five diverse learning tasks. These animals were then assessed on prototypic tests indicative of deductive reasoning (inferring the meaning of a novel item by exclusion, i.e., "fast mapping") and inductive reasoning (execution of an efficient search strategy in a binary decision tree). The animals exhibited systematic abilities on each of these nominal reasoning tasks that were predicted by their aggregate performance on the battery of learning tasks. These results suggest that the coregulation of reasoning and general learning performance in genetically heterogeneous mice form a core cognitive trait that is analogous to human intelligence. (c) 2012 APA, all rights reserved.

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years.

PubMed

Berlin, Sofia; Hallingbäck, Henrik R; Beyer, Friderike; Nordh, Nils-Erik; Weih, Martin; Rönnberg-Wästljung, Ann-Christin

2017-07-01

Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. A hybrid Salix viminalis  × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company.

Genetic Architecture of Micro-Environmental Plasticity in Drosophila melanogaster.

PubMed

Morgante, Fabio; Sørensen, Peter; Sorensen, Daniel A; Maltecca, Christian; Mackay, Trudy F C

2015-05-06

Individuals of the same genotype do not have the same phenotype for quantitative traits when reared under common macro-environmental conditions, a phenomenon called micro-environmental plasticity. Genetic variation in micro-environmental plasticity is assumed in models of the evolution of phenotypic variance, and is important in applied breeding and personalized medicine. Here, we quantified genetic variation for micro-environmental plasticity for three quantitative traits in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel. We found substantial genetic variation for micro-environmental plasticity for all traits, with broad sense heritabilities of the same magnitude or greater than those of trait means. Micro-environmental plasticity is not correlated with residual segregating variation, is trait-specific, and has genetic correlations with trait means ranging from zero to near unity. We identified several candidate genes associated with micro-environmental plasticity of startle response, including Drosophila Hsp90, setting the stage for future genetic dissection of this phenomenon.

Evaluative judgments are based on evaluative information: Evidence against meaning change in evaluative context effects.

PubMed

Kaplan, M F

1975-07-01

Trait adjectives commonly employed in person perception studies have both evaluative and denotative meanings. Evaluative ratings of single traits shift with variations in the context of other traits ascribed to the stimulus person; the extent to which denotative changes underlie these evaluative context effects has been a theoretical controversy. In the first experiment, it was shown that context effects on quantitative ratings of denotation can be largely accounted for by evaluative halo effects. In the second experiment, increasing the denotative relatedness of context traits to the test trait didnot increase the effect of the context. Only the evaluative meaning of the context affected evaluation of the rated test trait. These studies suggest that the denotative relationship between a test adjective and its context has little influence on context effects in person perception, and that denotative meaning changes do not mediate context effects. Instead, evaluative judgments appear to be based on evaluative meaning.

How Do Different Ways of Measuring Individual Differences in Zero-Acquaintance Personality Judgment Accuracy Correlate With Each Other?

PubMed

Hall, Judith A; Back, Mitja D; Nestler, Steffen; Frauendorfer, Denise; Schmid Mast, Marianne; Ruben, Mollie A

2018-04-01

This research compares two different approaches that are commonly used to measure accuracy of personality judgment: the trait accuracy approach wherein participants discriminate among targets on a given trait, thus making intertarget comparisons, and the profile accuracy approach wherein participants discriminate between traits for a given target, thus making intratarget comparisons. We examined correlations between these methods as well as correlations among accuracies for judging specific traits. The present article documents relations among these approaches based on meta-analysis of five studies of zero-acquaintance impressions of the Big Five traits. Trait accuracies correlated only weakly with overall and normative profile accuracy. Substantial convergence between the trait and profile accuracy methods was only found when an aggregate of all five trait accuracies was correlated with distinctive profile accuracy. Importantly, however, correlations between the trait and profile accuracy approaches were reduced to negligibility when statistical overlap was corrected by removing the respective trait from the profile correlations. Moreover, correlations of the separate trait accuracies with each other were very weak. Different ways of measuring individual differences in personality judgment accuracy are not conceptually and empirically the same, but rather represent distinct abilities that rely on different judgment processes. © 2017 Wiley Periodicals, Inc.

The "common good" phenomenon: Why similarities are positive and differences are negative.

PubMed

Alves, Hans; Koch, Alex; Unkelbach, Christian

2017-04-01

Positive attributes are more prevalent than negative attributes in the social environment. From this basic assumption, 2 implications that have been overlooked thus far: Positive compared with negative attributes are more likely to be shared by individuals, and people's shared attributes (similarities) are more positive than their unshared attributes (differences). Consequently, similarity-based comparisons should lead to more positive evaluations than difference-based comparisons. We formalized our probabilistic reasoning in a model and tested its predictions in a simulation and 8 experiments (N = 1,181). When participants generated traits about 2 target persons, positive compared with negative traits were more likely to be shared by the targets (Experiment 1a) and by other participants' targets (Experiment 1b). Conversely, searching for targets' shared traits resulted in more positive traits than searching for unshared traits (Experiments 2, 4a, and 4b). In addition, positive traits were more accessible than negative traits among shared traits but not among unshared traits (Experiment 3). Finally, shared traits were only more positive when positive traits were indeed prevalent (Experiments 5 and 6). The current framework has a number of implications for comparison processes and provides a new interpretation of well-known evaluative asymmetries such as intergroup bias and self-superiority effects. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Bayesian Poisson-lognormal Model for Count Data for Multiple-Trait Multiple-Environment Genomic-Enabled Prediction

PubMed Central

Montesinos-López, Osval A.; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H.; Montesinos-López, José C.; Singh, Pawan; Juliana, Philomin; Salinas-Ruiz, Josafhat

2017-01-01

When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype × environment interaction (G × E), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G × E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data. The proposed model was developed under the Bayesian paradigm for which we developed a Markov Chain Monte Carlo (MCMC) with noninformative priors. This allows obtaining all required full conditional distributions of the parameters leading to an exact Gibbs sampler for the posterior distribution. Our model was tested with simulated data and a real data set. Results show that the proposed multi-trait, multi-environment model is an attractive alternative for modeling multiple count traits measured in multiple environments. PMID:28364037

Vulnerability to xylem embolism as a major correlate of the environmental distribution of rain forest species on a tropical island.

PubMed

Trueba, Santiago; Pouteau, Robin; Lens, Frederic; Feild, Taylor S; Isnard, Sandrine; Olson, Mark E; Delzon, Sylvain

2017-02-01

Increases in drought-induced tree mortality are being observed in tropical rain forests worldwide and are also likely to affect the geographical distribution of tropical vegetation. However, the mechanisms underlying the drought vulnerability and environmental distribution of tropical species have been little studied. We measured vulnerability to xylem embolism (P 50 ) of 13 woody species endemic to New Caledonia and with different xylem conduit morphologies. We examined the relation between P 50 , along with other leaf and xylem functional traits, and a range of habitat variables. Selected species had P 50 values ranging between -4.03 and -2.00 MPa with most species falling in a narrow range of resistance to embolism above -2.7 MPa. Embolism vulnerability was significantly correlated with elevation, mean annual temperature and percentage of species occurrences located in rain forest habitats. Xylem conduit type did not explain variation in P 50 . Commonly used functional traits such as wood density and leaf traits were not related to embolism vulnerability. Xylem embolism vulnerability stands out among other commonly used functional traits as a major driver of species environmental distribution. Drought-induced xylem embolism vulnerability behaves as a physiological trait closely associated with the habitat occupation of rain forest woody species. © 2016 John Wiley & Sons Ltd.

Vertical transmission of learned signatures in a wild parrot

PubMed Central

Berg, Karl S.; Delgado, Soraya; Cortopassi, Kathryn A.; Beissinger, Steven R.; Bradbury, Jack W.

2012-01-01

Learned birdsong is a widely used animal model for understanding the acquisition of human speech. Male songbirds often learn songs from adult males during sensitive periods early in life, and sing to attract mates and defend territories. In presumably all of the 350+ parrot species, individuals of both sexes commonly learn vocal signals throughout life to satisfy a wide variety of social functions. Despite intriguing parallels with humans, there have been no experimental studies demonstrating learned vocal production in wild parrots. We studied contact call learning in video-rigged nests of a well-known marked population of green-rumped parrotlets (Forpus passerinus) in Venezuela. Both sexes of naive nestlings developed individually unique contact calls in the nest, and we demonstrate experimentally that signature attributes are learned from both primary care-givers. This represents the first experimental evidence for the mechanisms underlying the transmission of a socially acquired trait in a wild parrot population. PMID:21752824

Coagulase-negative staphylococci as reservoirs of genes facilitating MRSA infection

PubMed Central

Otto, Michael

2013-01-01

Recent research has suggested that Staphylococcus epidermidis is a reservoir of genes that, after horizontal transfer, facilitate the potential of Staphylococcus aureus to colonize, survive during infection, or resist antibiotic treatment, traits that are notably manifest in methicillin-resistant S. aureus (MRSA). S. aureus is a dangerous human pathogen and notorious for acquiring antibiotic resistance. MRSA in particular is one of the most frequent causes of morbidity and death in hospitalized patients. S. aureus is an extremely versatile pathogen with a multitude of mechanisms to cause disease and circumvent immune defenses. In contrast, most other staphylococci, such as S. epidermidis, are commonly benign commensals and only occasionally cause disease. Recent findings highlight the key importance of efforts to better understand how genes of staphylococci other than S. aureus contribute to survival in the human host, how they are transferred to S. aureus, and why this exchange appears to be uni-directional. PMID:23165978

Shared characteristics between Mycobacterium tuberculosis and fungi contribute to virulence.

PubMed

Willcocks, Sam; Wren, Brendan W

2014-01-01

Mycobacterium tuberculosis, an etiologic agent of tuberculosis, exacts a heavy toll in terms of human morbidity and mortality. Although an ancient disease, new strains are emerging as human population density increases. The emergent virulent strains appear adept at steering the host immune response from a protective Th1 type response towards a Th2 bias, a feature shared with some pathogenic fungi. Other common characteristics include infection site, metabolic features, the composition and display of cell surface molecules, the range of innate immune receptors engaged during infection, and the ability to form granulomas. Literature from these two distinct fields of research are reviewed to propose that the emergent virulent strains of M. tuberculosis are in the process of convergent evolution with pathogenic fungi, and are increasing the prominence of conserved traits from environmental phylogenetic ancestors that facilitate their evasion of host defenses and dissemination.

Strategic management of five deciduous forest invaders using Microstegium vimineum as a model species

Treesearch

Cynthia D. Huebner

2007-01-01

This paper links key plant invasive traits with key landscape traits to define strategic management for five common forest invaders, using empirical data of Microstegium vimineum dispersal into forests as a preliminary model. Microstegium vimineum exhibits an Allee effect that may allow management to focus on treating its source...

Multi-ethnic meta-analysis identifies RAI1 as a possible obstructive sleep apnea related quantitative trait locus in men

USDA-ARS?s Scientific Manuscript database

Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single et...

Darwin's Difficulties and Students' Struggles with Trait Loss: Cognitive-Historical Parallelisms in Evolutionary Explanation

ERIC Educational Resources Information Center

Ha, Minsu; Nehm, Ross H.

2014-01-01

Although historical changes in scientific ideas sometimes display striking similarities with students' conceptual progressions, some scholars have cautioned that such similarities lack meaningful commonalities. In the history of evolution, while Darwin and his contemporaries often used natural selection to explain evolutionary trait gain or…

Genotype and environmental interaction for fruit quality traits in vintage tomato varieties

USDA-ARS?s Scientific Manuscript database

Tomato (Solanum lycopersicum L.) is the second most commonly consumed vegetable after in the world, after potato. There is a growing demand for quality tomato in the market place. Traits such as lycopene, total soluble solids (TSS), vitamin C and titratable acid (TA) content contribute to the overal...

Positive and Negative Experiences of Career Technical Secondary Students in Online Courses

ERIC Educational Resources Information Center

Harms, David Mathew

2016-01-01

Research indicates that secondary students who are successful in online classes share common traits. However, many secondary career technical education (CTE) students taking online courses do not demonstrate the traits identified for success. CTE students may not benefit from online classes unless they are designed with their needs in mind. The…

Assessment of long-term peach evaluation data reveals fruit trait distribution and selection tendencies

USDA-ARS?s Scientific Manuscript database

Conventional plant breeding has a long history of success. Although it is often a daunting job, it is still the most common approach used in today’s variety improvement programs. Efficient production of hybrids with potential for release as new varieties with desired traits relies on optimal selecti...

Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services

PubMed Central

Lamarque, Pénélope; Lavorel, Sandra; Mouchet, Maud; Quétier, Fabien

2014-01-01

Land use and climate change are primary causes of changes in the supply of ecosystem services (ESs). Although the consequences of climate change on ecosystem properties and associated services are well documented, the cascading impacts of climate change on ESs through changes in land use are largely overlooked. We present a trait-based framework based on an empirical model to elucidate how climate change affects tradeoffs among ESs. Using alternative scenarios for mountain grasslands, we predicted how direct effects of climate change on ecosystems and indirect effects through farmers’ adaptations are likely to affect ES bundles through changes in plant functional properties. ES supply was overall more sensitive to climate than to induced management change, and ES bundles remained stable across scenarios. These responses largely reflected the restricted extent of management change in this constrained system, which was incorporated when scaling up plot level climate and management effects on ecosystem properties to the entire landscape. The trait-based approach revealed how the combination of common driving traits and common responses to changed fertility determined interactions and tradeoffs among ESs. PMID:25225382

Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services.

PubMed

Lamarque, Pénélope; Lavorel, Sandra; Mouchet, Maud; Quétier, Fabien

2014-09-23

Land use and climate change are primary causes of changes in the supply of ecosystem services (ESs). Although the consequences of climate change on ecosystem properties and associated services are well documented, the cascading impacts of climate change on ESs through changes in land use are largely overlooked. We present a trait-based framework based on an empirical model to elucidate how climate change affects tradeoffs among ESs. Using alternative scenarios for mountain grasslands, we predicted how direct effects of climate change on ecosystems and indirect effects through farmers' adaptations are likely to affect ES bundles through changes in plant functional properties. ES supply was overall more sensitive to climate than to induced management change, and ES bundles remained stable across scenarios. These responses largely reflected the restricted extent of management change in this constrained system, which was incorporated when scaling up plot level climate and management effects on ecosystem properties to the entire landscape. The trait-based approach revealed how the combination of common driving traits and common responses to changed fertility determined interactions and tradeoffs among ESs.

Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions

PubMed Central

Dillmann, Christine; Bely, Marina; la Guerche, Stéphane; Giraud, Christophe; Huet, Sylvie; Sicard, Delphine; Masneuf-Pomarede, Isabelle; de Vienne, Dominique; Marullo, Philippe

2015-01-01

Despite its biotechnological interest, hybridization, which can result in hybrid vigor, has not commonly been studied or exploited in the yeast genus. From a diallel design including 55 intra- and interspecific hybrids between Saccharomyces cerevisiae and S. uvarum grown at two temperatures in enological conditions, we analyzed as many as 35 fermentation traits with original statistical and modeling tools. We first showed that, depending on the types of trait – kinetics parameters, life-history traits, enological parameters and aromas –, the sources of variation (strain, temperature and strain * temperature effects) differed in a large extent. Then we compared globally three groups of hybrids and their parents at two growth temperatures: intraspecific hybrids S. cerevisiae * S. cerevisiae, intraspecific hybrids S. uvarum * S. uvarum and interspecific hybrids S. cerevisiae * S. uvarum. We found that hybridization could generate multi-trait phenotypes with improved oenological performances and better homeostasis with respect to temperature. These results could explain why interspecific hybridization is so common in natural and domesticated yeast, and open the way to applications for wine-making. PMID:25946464

Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues.

PubMed

Wheeler, Heather E; Shah, Kaanan P; Brenner, Jonathon; Garcia, Tzintzuni; Aquino-Michaels, Keston; Cox, Nancy J; Nicolae, Dan L; Im, Hae Kyung

2016-11-01

Understanding the genetic architecture of gene expression traits is key to elucidating the underlying mechanisms of complex traits. Here, for the first time, we perform a systematic survey of the heritability and the distribution of effect sizes across all representative tissues in the human body. We find that local h2 can be relatively well characterized with 59% of expressed genes showing significant h2 (FDR < 0.1) in the DGN whole blood cohort. However, current sample sizes (n ≤ 922) do not allow us to compute distal h2. Bayesian Sparse Linear Mixed Model (BSLMM) analysis provides strong evidence that the genetic contribution to local expression traits is dominated by a handful of genetic variants rather than by the collective contribution of a large number of variants each of modest size. In other words, the local architecture of gene expression traits is sparse rather than polygenic across all 40 tissues (from DGN and GTEx) examined. This result is confirmed by the sparsity of optimal performing gene expression predictors via elastic net modeling. To further explore the tissue context specificity, we decompose the expression traits into cross-tissue and tissue-specific components using a novel Orthogonal Tissue Decomposition (OTD) approach. Through a series of simulations we show that the cross-tissue and tissue-specific components are identifiable via OTD. Heritability and sparsity estimates of these derived expression phenotypes show similar characteristics to the original traits. Consistent properties relative to prior GTEx multi-tissue analysis results suggest that these traits reflect the expected biology. Finally, we apply this knowledge to develop prediction models of gene expression traits for all tissues. The prediction models, heritability, and prediction performance R2 for original and decomposed expression phenotypes are made publicly available (https://github.com/hakyimlab/PrediXcan).

Dissociable relations between amygdala subregional networks and psychopathy trait dimensions in conduct-disordered juvenile offenders.

PubMed

Aghajani, Moji; Colins, Olivier F; Klapwijk, Eduard T; Veer, Ilya M; Andershed, Henrik; Popma, Arne; van der Wee, Nic J; Vermeiren, Robert R J M

2016-11-01

Psychopathy is a serious psychiatric phenomenon characterized by a pathological constellation of affective (e.g., callous, unemotional), interpersonal (e.g., manipulative, egocentric), and behavioral (e.g., impulsive, irresponsible) personality traits. Though amygdala subregional defects are suggested in psychopathy, the functionality and connectivity of different amygdala subnuclei is typically disregarded in neurocircuit-level analyses of psychopathic personality. Hence, little is known of how amygdala subregional networks may contribute to psychopathy and its underlying trait assemblies in severely antisocial people. We addressed this important issue by uniquely examining the intrinsic functional connectivity of basolateral (BLA) and centromedial (CMA) amygdala networks in relation to affective, interpersonal, and behavioral traits of psychopathy, in conduct-disordered juveniles with a history of serious delinquency (N = 50, mean age = 16.83 ± 1.32). As predicted, amygdalar connectivity profiles exhibited dissociable relations with different traits of psychopathy. Interpersonal psychopathic traits not only related to increased connectivity of BLA and CMA with a corticostriatal network formation accommodating reward processing, but also predicted stronger CMA connectivity with a network of cortical midline structures supporting sociocognitive processes. In contrast, affective psychopathic traits related to diminished CMA connectivity with a frontolimbic network serving salience processing and affective responding. Finally, behavioral psychopathic traits related to heightened BLA connectivity with a frontoparietal cluster implicated in regulatory executive functioning. We suggest that these trait-specific shifts in amygdalar connectivity could be particularly relevant to the psychopathic phenotype, as they may fuel a self-centered, emotionally cold, and behaviorally disinhibited profile. Hum Brain Mapp 37:4017-4033, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Repeatability and degree of territorial aggression differs among urban and rural great tits (Parus major).

PubMed

Hardman, Samuel I; Dalesman, Sarah

2018-03-22

Animals in urban habitats face many novel selection pressures such as increased human population densities and human disturbance. This is predicted to favour bolder and more aggressive individuals together with greater flexibility in behaviour. Previous work has focussed primarily on studying these traits in captive birds and has shown increased aggression and reduced consistency between traits (behavioural syndromes) in birds from urban populations. However, personality (consistency within a behavioural trait) has not been well studied in the wild. Here we tested whether urban free-living male great tits show greater territorial aggression than rural counterparts. We also tested predictions that both behavioural syndromes and personality would show lower consistency in urban populations. We found that urban populations were more aggressive than rural populations and urban birds appeared to show lower levels of individual behavioural repeatability (personality) as predicted. However, we found no effect of urbanisation on behavioural syndromes (correlations between multiple behavioural traits). Our results indicate that urban environments may favour individuals which exhibit increased territorial aggression and greater within-trait flexibility which may be essential to success in holding urban territories. Determining how urban environments impact key fitness traits will be important in predicting how animals cope with ongoing urbanisation.

[The point-digital interpretation and the choice of the dermatoglyphic patterns on human fingers for diagnostics of consanguineous relationship].

PubMed

Zvyagin, V N; Rakitin, V A; Fomina, E E

The objective of the present study was the development of the point-digital model for the scaless interpretation of the dermatoglyphic papillary patterns on human fingers that would allow to comprehensively describe, in digital terms, the main characteristics of the traits and perform the quantitative assessment of the frequency of their inheritance. A specially developed computer program, D.glyphic. 7-14 was used to mark the dermatoglyphic patterns on the fingerprints obtained from 30 familial triplets (father + mother + child).The values of all the studied traits for kinship diagnostics were found by calculating the ratios of the sums of differences between the traits in the parent-parent pairs to those in the respective parent-child pairs. The algorithms for the point marking of the traits and reading out the digital information about them have been developed. The traditional dermatoglyphic patterns were selected and the novel ones applied for the use in the framework of the point-digital model for the interpretation of the for diagnostics of consanguineous relationship. The present experimental study has demonstrated the high level of inheritance of the selected traits and the possibility to develop the algorithms and computation techniques for the calculation of consanguineous relationship coefficients based on these traits.

Assortative social learning and its implications for human (and animal?) societies.

PubMed

Katsnelson, Edith; Lotem, Arnon; Feldman, Marcus W

2014-07-01

Choosing from whom to learn is an important element of social learning. It affects learner success and the profile of behaviors in the population. Because individuals often differ in their traits and capabilities, their benefits from different behaviors may also vary. Homophily, or assortment, the tendency of individuals to interact with other individuals with similar traits, is known to affect the spread of behaviors in humans. We introduce models to study the evolution of assortative social learning (ASL), where assorting on a trait acts as an individual-specific mechanism for filtering relevant models from which to learn when that trait varies. We show that when the trait is polymorphic, ASL may maintain a stable behavioral polymorphism within a population (independently of coexistence with individual learning in a population). We explore the evolution of ASL when assortment is based on a nonheritable or partially heritable trait, and when ASL competes with different non-ASL strategies: oblique (learning from the parental generation) and vertical (learning from the parent). We suggest that the tendency to assort may be advantageous in the context of social learning, and that ASL might be an important concept for the evolutionary theory of social learning. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Analysis of Natural Allelic Variation of Arabidopsis Seed Germination and Seed Longevity Traits between the Accessions Landsberg erecta and Shakdara, Using a New Recombinant Inbred Line Population1

PubMed Central

Clerkx, Emile J.M.; El-Lithy, Mohamed E.; Vierling, Elizabeth; Ruys, Gerda J.; Vries, Hetty Blankestijn-De; Groot, Steven P.C.; Vreugdenhil, Dick; Koornneef, Maarten

2004-01-01

Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new recombinant inbred line population derived from a cross between the accessions Landsberg erecta (Ler) and Shakdara (Sha). A set of 114 F9 recombinant inbred lines was genotyped with 65 polymerase chain reaction-based markers and the phenotypic marker erecta. The traits analyzed were dormancy, speed of germination, seed sugar content, seed germination after a controlled deterioration test, hydrogen peroxide (H2O2) treatment, and on abscisic acid. Furthermore, the effects of heat stress, salt (NaCl) stress, osmotic (mannitol) stress, and natural aging were analyzed. For all traits one or more QTLs were identified, with some QTLs for different traits colocating. The relevance of colocation for mechanisms underlying the various traits is discussed. PMID:15122038

Polygenic influences on dyslipidemias.

PubMed

Dron, Jacqueline S; Hegele, Robert A

2018-04-01

Rare large-effect genetic variants underlie monogenic dyslipidemias, whereas common small-effect genetic variants - single nucleotide polymorphisms (SNPs) - have modest influences on lipid traits. Over the past decade, these small-effect SNPs have been shown to cumulatively exert consistent effects on lipid phenotypes under a polygenic framework, which is the focus of this review. Several groups have reported polygenic risk scores assembled from lipid-associated SNPs, and have applied them to their respective phenotypes. For lipid traits in the normal population distribution, polygenic effects quantified by a score that integrates several common polymorphisms account for about 20-30% of genetic variation. Among individuals at the extremes of the distribution, that is, those with clinical dyslipidemia, the polygenic component includes both rare variants with large effects and common polymorphisms: depending on the trait, 20-50% of susceptibility can be accounted for by this assortment of genetic variants. Accounting for polygenic effects increases the numbers of dyslipidemic individuals who can be explained genetically, but a substantial proportion of susceptibility remains unexplained. Whether documenting the polygenic basis of dyslipidemia will affect outcomes in clinical trials or prospective observational studies remains to be determined.

Identification of Metabolic Modifiers That Underlie Phenotypic Variations in Energy-Balance Regulation

PubMed Central

Chang, Chia Lin; Cai, James J.; Cheng, Po Jen; Chueh, Ho Yen; Hsu, Sheau Yu Teddy

2011-01-01

OBJECTIVE Although recent studies have shown that human genomes contain hundreds of loci that exhibit signatures of positive selection, variants that are associated with adaptation in energy-balance regulation remain elusive. We reasoned that the difficulty in identifying such variants could be due to heterogeneity in selection pressure and that an integrative approach that incorporated experiment-based evidence and population genetics-based statistical judgments would be needed to reveal important metabolic modifiers in humans. RESEARCH DESIGN AND METHODS To identify common metabolic modifiers that underlie phenotypic variation in diabetes-associated or obesity-associated traits in humans, or both, we screened 207 candidate loci for regulatory single nucleotide polymorphisms (SNPs) that exhibited evidence of gene–environmental interactions. RESULTS Three SNPs (rs3895874, rs3848460, and rs937301) at the 5′ gene region of human GIP were identified as prime metabolic-modifier candidates at the enteroinsular axis. Functional studies have shown that GIP promoter reporters carrying derived alleles of these three SNPs (haplotype GIP−1920A) have significantly lower transcriptional activities than those with ancestral alleles at corresponding positions (haplotype GIP−1920G). Consistently, studies of pregnant women who have undergone a screening test for gestational diabetes have shown that patients with a homozygous GIP−1920A/A genotype have significantly lower serum concentrations of glucose-dependent insulinotropic polypeptide (GIP) than those carrying an ancestral GIP−1920G haplotype. After controlling for a GIPR variation, we showed that serum glucose concentrations of patients carrying GIP−1920A/A homozygotes are significantly higher than that of those carrying an ancestral GIP−1920G haplotype (odds ratio 3.53). CONCLUSIONS Our proof-of-concept study indicates that common regulatory GIP variants impart a difference in GIP and glucose metabolism. The study also provides a rare example that identified the common variant-common phenotypic variation pattern based on evidence of moderate gene–environmental interactions. PMID:21300845

Clinical and personality traits in emotional disorders: Evidence of a common framework.

PubMed

Mahaffey, Brittain L; Watson, David; Clark, Lee Anna; Kotov, Roman

2016-08-01

Certain clinical traits (e.g., ruminative response style, self-criticism, perfectionism, anxiety sensitivity, fear of negative evaluation, and thought suppression) increase the risk for and chronicity of emotional disorders. Similar to traditional personality traits, they are considered dispositional and typically show high temporal stability. Because the personality and clinical-traits literatures evolved largely independently, connections between them are not fully understood. We sought to map the interface between a widely studied set of clinical and personality traits. Two samples (N = 385 undergraduates; N = 188 psychiatric outpatients) completed measures of personality traits, clinical traits, and an interview-based assessment of emotional-disorder symptoms. First, the joint factor structure of these traits was examined in each sample. Second, structural equation modeling was used to clarify the effects of clinical traits in the prediction of clinical symptoms beyond negative temperament. Third, the incremental validity of clinical traits beyond a more comprehensive set of higher-order and lower-order personality traits was examined using hierarchical regression. Clinical and personality traits were highly correlated and jointly defined a 3-factor structure-Negative Temperament, Positive Temperament, and Disinhibition-in both samples, with all clinical traits loading on the Negative Temperament factor. Clinical traits showed modest but significant incremental validity in explaining symptoms after accounting for personality traits. These data indicate that clinical traits relevant to emotional disorders fit well within the traditional personality framework and offer some unique contributions to the prediction of psychopathology, but it is important to distinguish their effects from negative temperament/neuroticism. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis.

PubMed

Aschard, Hugues; Kang, Jae H; Iglesias, Adriana I; Hysi, Pirro; Cooke Bailey, Jessica N; Khawaja, Anthony P; Allingham, R Rand; Ashley-Koch, Allison; Lee, Richard K; Moroi, Sayoko E; Brilliant, Murray H; Wollstein, Gadi; Schuman, Joel S; Fingert, John H; Budenz, Donald L; Realini, Tony; Gaasterland, Terry; Scott, William K; Singh, Kuldev; Sit, Arthur J; Igo, Robert P; Song, Yeunjoo E; Hark, Lisa; Ritch, Robert; Rhee, Douglas J; Gulati, Vikas; Haven, Shane; Vollrath, Douglas; Zack, Donald J; Medeiros, Felipe; Weinreb, Robert N; Cheng, Ching-Yu; Chasman, Daniel I; Christen, William G; Pericak-Vance, Margaret A; Liu, Yutao; Kraft, Peter; Richards, Julia E; Rosner, Bernard A; Hauser, Michael A; Klaver, Caroline C W; vanDuijn, Cornelia M; Haines, Jonathan; Wiggs, Janey L; Pasquale, Louis R

2017-11-01

Primary open-angle glaucoma (POAG) is the most common chronic optic neuropathy worldwide. Epidemiological studies show a robust positive relation between intraocular pressure (IOP) and POAG and modest positive association between IOP and blood pressure (BP), while the relation between BP and POAG is controversial. The International Glaucoma Genetics Consortium (n=27 558), the International Consortium on Blood Pressure (n=69 395), and the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (n=37 333), represent genome-wide data sets for IOP, BP traits and POAG, respectively. We formed genome-wide significant variant panels for IOP and diastolic BP and found a strong relation with POAG (odds ratio and 95% confidence interval: 1.18 (1.14-1.21), P=1.8 × 10 -27 ) for the former trait but no association for the latter (P=0.93). Next, we used linkage disequilibrium (LD) score regression, to provide genome-wide estimates of correlation between traits without the need for additional phenotyping. We also compared our genome-wide estimate of heritability between IOP and BP to an estimate based solely on direct measures of these traits in the Erasmus Rucphen Family (ERF; n=2519) study using Sequential Oligogenic Linkage Analysis Routines (SOLAR). LD score regression revealed high genetic correlation between IOP and POAG (48.5%, P=2.1 × 10 -5 ); however, genetic correlation between IOP and diastolic BP (P=0.86) and between diastolic BP and POAG (P=0.42) were negligible. Using SOLAR in the ERF study, we confirmed the minimal heritability between IOP and diastolic BP (P=0.63). Overall, IOP shares genetic basis with POAG, whereas BP has limited shared genetic correlation with IOP or POAG.

Antibiotics impact plant traits, even at small concentrations

PubMed Central

Deloy, Andrea; Volkert, Anna Martina; Leonhardt, Sara Diana; Pufal, Gesine

2017-01-01

Abstract Antibiotics of veterinary origin are released to agricultural fields via grazing animals or manure. Possible effects on human health through the consumption of antibiotic exposed crop plants have been intensively investigated. However, information is still lacking on the effects of antibiotics on plants themselves, particularly on non-crop species, although evidence suggests adverse effects of antibiotics on growth and performance of plants. This study evaluated the effects of three major antibiotics, penicillin, sulfadiazine and tetracycline, on the germination rates and post-germinative traits of four plant species during ontogenesis and at the time of full development. Antibiotic concentrations were chosen as to reflect in vivo situations, i.e. concentrations similar to those detected in soils. Plant species included two herb species and two grass species, and represent two crop-species and two non-crop species commonly found in field margins, respectively. Germination tests were performed in climate chambers and effects on the remaining plant traits were determined in greenhouse experiments. Results show that antibiotics, even in small concentrations, significantly affect plant traits. These effects include delayed germination and post-germinative development. Effects were species and functional group dependent, with herbs being more sensitive to antibiotics then grasses. Responses were either negative or positive, depending on plant species and antibiotic. Effects were generally stronger for penicillin and sulfadiazine than for tetracycline. Our study shows that cropland species respond to the use of different antibiotics in livestock industry, for example, with delayed germination and lower biomass allocation, indicating possible effects on yield in farmland fertilized with manure containing antibiotics. Also, antibiotics can alter the composition of plant species in natural field margins, due to different species-specific responses, with unknown consequences for higher trophic levels. PMID:28439396

Separating method factors and higher order traits of the Big Five: a meta-analytic multitrait-multimethod approach.

PubMed

Chang, Luye; Connelly, Brian S; Geeza, Alexis A

2012-02-01

Though most personality researchers now recognize that ratings of the Big Five are not orthogonal, the field has been divided about whether these trait intercorrelations are substantive (i.e., driven by higher order factors) or artifactual (i.e., driven by correlated measurement error). We used a meta-analytic multitrait-multirater study to estimate trait correlations after common method variance was controlled. Our results indicated that common method variance substantially inflates trait correlations, and, once controlled, correlations among the Big Five became relatively modest. We then evaluated whether two different theories of higher order factors could account for the pattern of Big Five trait correlations. Our results did not support Rushton and colleagues' (Rushton & Irwing, 2008; Rushton et al., 2009) proposed general factor of personality, but Digman's (1997) α and β metatraits (relabeled by DeYoung, Peterson, and Higgins (2002) as Stability and Plasticity, respectively) produced viable fit. However, our models showed considerable overlap between Stability and Emotional Stability and between Plasticity and Extraversion, raising the question of whether these metatraits are redundant with their dominant Big Five traits. This pattern of findings was robust when we included only studies whose observers were intimately acquainted with targets. Our results underscore the importance of using a multirater approach to studying personality and the need to separate the causes and outcomes of higher order metatraits from those of the Big Five. We discussed the implications of these findings for the array of research fields in which personality is studied.

Genetic and maternal effect influences on viability of common frog tadpoles under different environmental conditions.

PubMed

Pakkasmaa, S; Merilä, J; O'Hara, R B

2003-08-01

The influence of environmental stress on the expression of genetic and maternal effects on the viability traits has seldom been assessed in wild vertebrates. We have estimated genetic and maternal effects on the viability (viz probability of survival, probability of being deformed, and body size and shape) of common frog, Rana temporaria, tadpoles under stressful (low pH) and nonstressful (neutral pH) environmental conditions. A Bayesian analysis using generalized linear mixed models was applied to data from a factorial laboratory experiment. The expression of additive genetic variance was independent of pH treatments, and all traits were significantly heritable (survival: h2 approximately 0.08; deformities: h2 approximately 0.26; body size: h2 approximately 0.12; body shape: h2 approximately 0.14). Likewise, nonadditive genetic contributions to variation in all traits were significant, independent of pH treatments and typically of magnitude similar to the additive genetic effects. Maternal effects were large for all traits, especially for viability itself, and their expression was partly dependent on the environment. In the case of body size, the maternal effects were mediated largely through egg size. In general, the results give little evidence for the conjecture that environmental stress created by low pH would impact strongly on the genetic architecture of fitness-related traits in frogs, and hamper adaptation to stress caused by acidification. The low heritabilities and high dominance contributions conform to the pattern typical for traits subject to relatively strong directional selection.

Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

PubMed Central

Allard, Alix; Bink, Marco C.A.M.; Martinez, Sébastien; Kelner, Jean-Jacques; Legave, Jean-Michel; di Guardo, Mario; Di Pierro, Erica A.; Laurens, François; van de Weg, Eric W.; Costes, Evelyne

2016-01-01

In temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase. PMID:27034326

Intraspecific variation shapes community-level behavioral responses to urbanization in spiders.

PubMed

Dahirel, Maxime; Dierick, Jasper; De Cock, Maarten; Bonte, Dries

2017-09-01

Urban areas are an extreme example of human-changed environments, exposing organisms to multiple and strong selection pressures. Adaptive behavioral responses are thought to play a major role in animals' success or failure in such new environments. Approaches based on functional traits have proven especially valuable to understand how species communities respond to environmental gradients. Until recently, they have, however, often ignored the potential consequences of intraspecific trait variation (ITV). When ITV is prevalent, it may highly impact ecological processes and resilience against stressors. This may be especially relevant in animals, in which behavioral traits can be altered very flexibly at the individual level to track environmental changes. We investigated how species turnover and ITV influenced community-level behavioral responses in a set of 62 sites of varying levels of urbanization, using orb web spiders and their webs as models of foraging behavior. ITV alone explained around one-third of the total trait variation observed among communities. Spider web structure changed according to urbanization, in ways that increase the capture efficiency of webs in a context of smaller urban prey. These trait shifts were partly mediated by species turnover, but ITV increased their magnitude, potentially helping to buffer the effects of environmental changes on communities. The importance of ITV varied depending on traits and on the spatial scale at which urbanization was considered. Despite being neglected from community-level analyses in animals, our results highlight the importance of accounting for intraspecific trait variation to fully understand trait responses to (human-induced) environmental changes and their impact on ecosystem functioning. © 2017 by the Ecological Society of America.

Behavioral Variation in Gorillas: Evidence of Potential Cultural Traits

PubMed Central

Robbins, Martha M.; Ando, Chieko; Fawcett, Katherine A.; Grueter, Cyril C.; Hedwig, Daniela; Iwata, Yuji; Lodwick, Jessica L.; Masi, Shelly; Salmi, Roberta; Stoinski, Tara S.; Todd, Angelique; Vercellio, Veronica; Yamagiwa, Juichi

2016-01-01

The question of whether any species except humans exhibits culture has generated much debate, partially due to the difficulty of providing conclusive evidence from observational studies in the wild. A starting point for demonstrating the existence of culture that has been used for many species including chimpanzees and orangutans is to show that there is geographic variation in the occurrence of particular behavioral traits inferred to be a result of social learning and not ecological or genetic influences. Gorillas live in a wide variety of habitats across Africa and they exhibit flexibility in diet, behavior, and social structure. Here we apply the ‘method of exclusion’ to look for the presence/absence of behaviors that could be considered potential cultural traits in well-habituated groups from five study sites of the two species of gorillas. Of the 41 behaviors considered, 23 met the criteria of potential cultural traits, of which one was foraging related, nine were environment related, seven involved social interactions, five were gestures, and one was communication related. There was a strong positive correlation between behavioral dissimilarity and geographic distance among gorilla study sites. Roughly half of all variation in potential cultural traits was intraspecific differences (i.e. variability among sites within a species) and the other 50% of potential cultural traits were differences between western and eastern gorillas. Further research is needed to investigate if the occurrence of these traits is influenced by social learning. These findings emphasize the importance of investigating cultural traits in African apes and other species to shed light on the origin of human culture. PMID:27603668

Behavioral Variation in Gorillas: Evidence of Potential Cultural Traits.

PubMed

Robbins, Martha M; Ando, Chieko; Fawcett, Katherine A; Grueter, Cyril C; Hedwig, Daniela; Iwata, Yuji; Lodwick, Jessica L; Masi, Shelly; Salmi, Roberta; Stoinski, Tara S; Todd, Angelique; Vercellio, Veronica; Yamagiwa, Juichi

2016-01-01

The question of whether any species except humans exhibits culture has generated much debate, partially due to the difficulty of providing conclusive evidence from observational studies in the wild. A starting point for demonstrating the existence of culture that has been used for many species including chimpanzees and orangutans is to show that there is geographic variation in the occurrence of particular behavioral traits inferred to be a result of social learning and not ecological or genetic influences. Gorillas live in a wide variety of habitats across Africa and they exhibit flexibility in diet, behavior, and social structure. Here we apply the 'method of exclusion' to look for the presence/absence of behaviors that could be considered potential cultural traits in well-habituated groups from five study sites of the two species of gorillas. Of the 41 behaviors considered, 23 met the criteria of potential cultural traits, of which one was foraging related, nine were environment related, seven involved social interactions, five were gestures, and one was communication related. There was a strong positive correlation between behavioral dissimilarity and geographic distance among gorilla study sites. Roughly half of all variation in potential cultural traits was intraspecific differences (i.e. variability among sites within a species) and the other 50% of potential cultural traits were differences between western and eastern gorillas. Further research is needed to investigate if the occurrence of these traits is influenced by social learning. These findings emphasize the importance of investigating cultural traits in African apes and other species to shed light on the origin of human culture.

Rare and low-frequency coding variants alter human adult height.

PubMed

Marouli, Eirini; Graff, Mariaelisa; Medina-Gomez, Carolina; Lo, Ken Sin; Wood, Andrew R; Kjaer, Troels R; Fine, Rebecca S; Lu, Yingchang; Schurmann, Claudia; Highland, Heather M; Rüeger, Sina; Thorleifsson, Gudmar; Justice, Anne E; Lamparter, David; Stirrups, Kathleen E; Turcot, Valérie; Young, Kristin L; Winkler, Thomas W; Esko, Tõnu; Karaderi, Tugce; Locke, Adam E; Masca, Nicholas G D; Ng, Maggie C Y; Mudgal, Poorva; Rivas, Manuel A; Vedantam, Sailaja; Mahajan, Anubha; Guo, Xiuqing; Abecasis, Goncalo; Aben, Katja K; Adair, Linda S; Alam, Dewan S; Albrecht, Eva; Allin, Kristine H; Allison, Matthew; Amouyel, Philippe; Appel, Emil V; Arveiler, Dominique; Asselbergs, Folkert W; Auer, Paul L; Balkau, Beverley; Banas, Bernhard; Bang, Lia E; Benn, Marianne; Bergmann, Sven; Bielak, Lawrence F; Blüher, Matthias; Boeing, Heiner; Boerwinkle, Eric; Böger, Carsten A; Bonnycastle, Lori L; Bork-Jensen, Jette; Bots, Michiel L; Bottinger, Erwin P; Bowden, Donald W; Brandslund, Ivan; Breen, Gerome; Brilliant, Murray H; Broer, Linda; Burt, Amber A; Butterworth, Adam S; Carey, David J; Caulfield, Mark J; Chambers, John C; Chasman, Daniel I; Chen, Yii-Der Ida; Chowdhury, Rajiv; Christensen, Cramer; Chu, Audrey Y; Cocca, Massimiliano; Collins, Francis S; Cook, James P; Corley, Janie; Galbany, Jordi Corominas; Cox, Amanda J; Cuellar-Partida, Gabriel; Danesh, John; Davies, Gail; de Bakker, Paul I W; de Borst, Gert J; de Denus, Simon; de Groot, Mark C H; de Mutsert, Renée; Deary, Ian J; Dedoussis, George; Demerath, Ellen W; den Hollander, Anneke I; Dennis, Joe G; Di Angelantonio, Emanuele; Drenos, Fotios; Du, Mengmeng; Dunning, Alison M; Easton, Douglas F; Ebeling, Tapani; Edwards, Todd L; Ellinor, Patrick T; Elliott, Paul; Evangelou, Evangelos; Farmaki, Aliki-Eleni; Faul, Jessica D; Feitosa, Mary F; Feng, Shuang; Ferrannini, Ele; Ferrario, Marco M; Ferrieres, Jean; Florez, Jose C; Ford, Ian; Fornage, Myriam; Franks, Paul W; Frikke-Schmidt, Ruth; Galesloot, Tessel E; Gan, Wei; Gandin, Ilaria; Gasparini, Paolo; Giedraitis, Vilmantas; Giri, Ayush; Girotto, Giorgia; Gordon, Scott D; Gordon-Larsen, Penny; Gorski, Mathias; Grarup, Niels; Grove, Megan L; Gudnason, Vilmundur; Gustafsson, Stefan; Hansen, Torben; Harris, Kathleen Mullan; Harris, Tamara B; Hattersley, Andrew T; Hayward, Caroline; He, Liang; Heid, Iris M; Heikkilä, Kauko; Helgeland, Øyvind; Hernesniemi, Jussi; Hewitt, Alex W; Hocking, Lynne J; Hollensted, Mette; Holmen, Oddgeir L; Hovingh, G Kees; Howson, Joanna M M; Hoyng, Carel B; Huang, Paul L; Hveem, Kristian; Ikram, M Arfan; Ingelsson, Erik; Jackson, Anne U; Jansson, Jan-Håkan; Jarvik, Gail P; Jensen, Gorm B; Jhun, Min A; Jia, Yucheng; Jiang, Xuejuan; Johansson, Stefan; Jørgensen, Marit E; Jørgensen, Torben; Jousilahti, Pekka; Jukema, J Wouter; Kahali, Bratati; Kahn, René S; Kähönen, Mika; Kamstrup, Pia R; Kanoni, Stavroula; Kaprio, Jaakko; Karaleftheri, Maria; Kardia, Sharon L R; Karpe, Fredrik; Kee, Frank; Keeman, Renske; Kiemeney, Lambertus A; Kitajima, Hidetoshi; Kluivers, Kirsten B; Kocher, Thomas; Komulainen, Pirjo; Kontto, Jukka; Kooner, Jaspal S; Kooperberg, Charles; Kovacs, Peter; Kriebel, Jennifer; Kuivaniemi, Helena; Küry, Sébastien; Kuusisto, Johanna; La Bianca, Martina; Laakso, Markku; Lakka, Timo A; Lange, Ethan M; Lange, Leslie A; Langefeld, Carl D; Langenberg, Claudia; Larson, Eric B; Lee, I-Te; Lehtimäki, Terho; Lewis, Cora E; Li, Huaixing; Li, Jin; Li-Gao, Ruifang; Lin, Honghuang; Lin, Li-An; Lin, Xu; Lind, Lars; Lindström, Jaana; Linneberg, Allan; Liu, Yeheng; Liu, Yongmei; Lophatananon, Artitaya; Luan, Jian'an; Lubitz, Steven A; Lyytikäinen, Leo-Pekka; Mackey, David A; Madden, Pamela A F; Manning, Alisa K; Männistö, Satu; Marenne, Gaëlle; Marten, Jonathan; Martin, Nicholas G; Mazul, Angela L; Meidtner, Karina; Metspalu, Andres; Mitchell, Paul; Mohlke, Karen L; Mook-Kanamori, Dennis O; Morgan, Anna; Morris, Andrew D; Morris, Andrew P; Müller-Nurasyid, Martina; Munroe, Patricia B; Nalls, Mike A; Nauck, Matthias; Nelson, Christopher P; Neville, Matt; Nielsen, Sune F; Nikus, Kjell; Njølstad, Pål R; Nordestgaard, Børge G; Ntalla, Ioanna; O'Connel, Jeffrey R; Oksa, Heikki; Loohuis, Loes M Olde; Ophoff, Roel A; Owen, Katharine R; Packard, Chris J; Padmanabhan, Sandosh; Palmer, Colin N A; Pasterkamp, Gerard; Patel, Aniruddh P; Pattie, Alison; Pedersen, Oluf; Peissig, Peggy L; Peloso, Gina M; Pennell, Craig E; Perola, Markus; Perry, James A; Perry, John R B; Person, Thomas N; Pirie, Ailith; Polasek, Ozren; Posthuma, Danielle; Raitakari, Olli T; Rasheed, Asif; Rauramaa, Rainer; Reilly, Dermot F; Reiner, Alex P; Renström, Frida; Ridker, Paul M; Rioux, John D; Robertson, Neil; Robino, Antonietta; Rolandsson, Olov; Rudan, Igor; Ruth, Katherine S; Saleheen, Danish; Salomaa, Veikko; Samani, Nilesh J; Sandow, Kevin; Sapkota, Yadav; Sattar, Naveed; Schmidt, Marjanka K; Schreiner, Pamela J; Schulze, Matthias B; Scott, Robert A; Segura-Lepe, Marcelo P; Shah, Svati; Sim, Xueling; Sivapalaratnam, Suthesh; Small, Kerrin S; Smith, Albert Vernon; Smith, Jennifer A; Southam, Lorraine; Spector, Timothy D; Speliotes, Elizabeth K; Starr, John M; Steinthorsdottir, Valgerdur; Stringham, Heather M; Stumvoll, Michael; Surendran, Praveen; 't Hart, Leen M; Tansey, Katherine E; Tardif, Jean-Claude; Taylor, Kent D; Teumer, Alexander; Thompson, Deborah J; Thorsteinsdottir, Unnur; Thuesen, Betina H; Tönjes, Anke; Tromp, Gerard; Trompet, Stella; Tsafantakis, Emmanouil; Tuomilehto, Jaakko; Tybjaerg-Hansen, Anne; Tyrer, Jonathan P; Uher, Rudolf; Uitterlinden, André G; Ulivi, Sheila; van der Laan, Sander W; Van Der Leij, Andries R; van Duijn, Cornelia M; van Schoor, Natasja M; van Setten, Jessica; Varbo, Anette; Varga, Tibor V; Varma, Rohit; Edwards, Digna R Velez; Vermeulen, Sita H; Vestergaard, Henrik; Vitart, Veronique; Vogt, Thomas F; Vozzi, Diego; Walker, Mark; Wang, Feijie; Wang, Carol A; Wang, Shuai; Wang, Yiqin; Wareham, Nicholas J; Warren, Helen R; Wessel, Jennifer; Willems, Sara M; Wilson, James G; Witte, Daniel R; Woods, Michael O; Wu, Ying; Yaghootkar, Hanieh; Yao, Jie; Yao, Pang; Yerges-Armstrong, Laura M; Young, Robin; Zeggini, Eleftheria; Zhan, Xiaowei; Zhang, Weihua; Zhao, Jing Hua; Zhao, Wei; Zhao, Wei; Zheng, He; Zhou, Wei; Rotter, Jerome I; Boehnke, Michael; Kathiresan, Sekar; McCarthy, Mark I; Willer, Cristen J; Stefansson, Kari; Borecki, Ingrid B; Liu, Dajiang J; North, Kari E; Heard-Costa, Nancy L; Pers, Tune H; Lindgren, Cecilia M; Oxvig, Claus; Kutalik, Zoltán; Rivadeneira, Fernando; Loos, Ruth J F; Frayling, Timothy M; Hirschhorn, Joel N; Deloukas, Panos; Lettre, Guillaume

2017-02-09

Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

PubMed Central

De La Vega, Francisco M.; Isaac, Hadar; Collins, Andrew; Scafe, Charles R.; Halldórsson, Bjarni V.; Su, Xiaoping; Lippert, Ross A.; Wang, Yu; Laig-Webster, Marion; Koehler, Ryan T.; Ziegle, Janet S.; Wogan, Lewis T.; Stevens, Junko F.; Leinen, Kyle M.; Olson, Sheri J.; Guegler, Karl J.; You, Xiaoqing; Xu, Lily H.; Hemken, Heinz G.; Kalush, Francis; Itakura, Mitsuo; Zheng, Yi; de Thé, Guy; O'Brien, Stephen J.; Clark, Andrew G.; Istrail, Sorin; Hunkapiller, Michael W.; Spier, Eugene G.; Gilbert, Dennis A.

2005-01-01

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies. PMID:15781572

Genetic parameters for androstenone, skatole, indole, and human nose scores as measures of boar taint and their relationship with finishing traits.

PubMed

Windig, J J; Mulder, H A; Ten Napel, J; Knol, E F; Mathur, P K; Crump, R E

2012-07-01

The purpose of this study was to evaluate measures of boar (Sus scrofa) taint as potential selection criteria to reduce boar taint so that castration of piglets will become unnecessary. Therefore, genetic parameters of boar taint measures and their genetic correlations with finishing traits were estimated. In particular, the usefulness of a human panel assessing boar taint (human nose score) was compared with chemical assessment of boar taint compounds, androstenone, skatole, and indole. Heritability estimates for androstenone, skatole, and indole were 0.54, 0.41, and 0.33, respectively. The heritability for the human nose score using multiple panelists was 0.12, and ranged from 0.12 to 0.19 for individual panelists. Genetic correlations between scores of panelists were generally high up to unity. The genetic correlations between human nose scores and the boar taint compounds ranged from 0.64 to 0.999. The boar taint compounds and human nose scores had low or favorable genetic correlations with finishing traits. Selection index estimates indicated that the effectiveness of a breeding program based on human nose scores can be comparable to a breeding program based on the boar taint compounds themselves. Human nose scores can thus be used as a cheap and fast alternative for the costly determination of boar taint compounds, needed in breeding pigs without boar taint.

Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species.

PubMed

Voss, J D; Goodson, M S; Leon, J C

2018-05-01

We propose the idea of "phenotype diffusion," which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and "obesogens"), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so identification of phenotype diffusion is highly relevant for practitioners (public health officials, physicians and veterinarians) in this field. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Integrative analysis of 111 reference human epigenomes

PubMed Central

Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Kheradpour, Pouya; Zhang, Zhizhuo; Heravi-Moussavi, Alireza; Liu, Yaping; Amin, Viren; Ziller, Michael J; Whitaker, John W; Schultz, Matthew D; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Wang, Jianrong; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Pfenning, Andreas; Wang, Xinchen; Claussnitzer, Melina; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven; Li, Wei; Marra, Marco; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis

2015-01-01

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection to-date of human epigenomes for primary cells and tissues. Here, we describe the integrative analysis of 111 reference human epigenomes generated as part of the program, profiled for histone modification patterns, DNA accessibility, DNA methylation, and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically-relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation, and human disease. PMID:25693563

Integrative analysis of 111 reference human epigenomes.

PubMed

Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J; Amin, Viren; Whitaker, John W; Schultz, Matthew D; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Pfenning, Andreas R; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas A; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip L; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven J M; Li, Wei; Marra, Marco A; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael Q; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis

2015-02-19

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Aberrant Gene Expression in Humans

PubMed Central

Yang, Ence; Ji, Guoli; Brinkmeyer-Langford, Candice L.; Cai, James J.

2015-01-01

Gene expression as an intermediate molecular phenotype has been a focus of research interest. In particular, studies of expression quantitative trait loci (eQTL) have offered promise for understanding gene regulation through the discovery of genetic variants that explain variation in gene expression levels. Existing eQTL methods are designed for assessing the effects of common variants, but not rare variants. Here, we address the problem by establishing a novel analytical framework for evaluating the effects of rare or private variants on gene expression. Our method starts from the identification of outlier individuals that show markedly different gene expression from the majority of a population, and then reveals the contributions of private SNPs to the aberrant gene expression in these outliers. Using population-scale mRNA sequencing data, we identify outlier individuals using a multivariate approach. We find that outlier individuals are more readily detected with respect to gene sets that include genes involved in cellular regulation and signal transduction, and less likely to be detected with respect to the gene sets with genes involved in metabolic pathways and other fundamental molecular functions. Analysis of polymorphic data suggests that private SNPs of outlier individuals are enriched in the enhancer and promoter regions of corresponding aberrantly-expressed genes, suggesting a specific regulatory role of private SNPs, while the commonly-occurring regulatory genetic variants (i.e., eQTL SNPs) show little evidence of involvement. Additional data suggest that non-genetic factors may also underlie aberrant gene expression. Taken together, our findings advance a novel viewpoint relevant to situations wherein common eQTLs fail to predict gene expression when heritable, rare inter-individual variation exists. The analytical framework we describe, taking into consideration the reality of differential phenotypic robustness, may be valuable for investigating complex traits and conditions. PMID:25617623

Genome-wide association analysis in dogs implicates 99 loci as risk variants for anterior cruciate ligament rupture

PubMed Central

Baker, Lauren A.; Kirkpatrick, Brian; Rosa, Guilherme J. M.; Gianola, Daniel; Valente, Bruno; Sumner, Julia P.; Baltzer, Wendy; Hao, Zhengling; Binversie, Emily E.; Volstad, Nicola; Piazza, Alexander; Sample, Susannah J.

2017-01-01

Anterior cruciate ligament (ACL) rupture is a common condition that can be devastating and life changing, particularly in young adults. A non-contact mechanism is typical. Second ACL ruptures through rupture of the contralateral ACL or rupture of a graft repair is also common. Risk of rupture is increased in females. ACL rupture is also common in dogs. Disease prevalence exceeds 5% in several dog breeds, ~100 fold higher than human beings. We provide insight into the genetic etiology of ACL rupture by genome-wide association study (GWAS) in a high-risk breed using 98 case and 139 control Labrador Retrievers. We identified 129 single nucleotide polymorphisms (SNPs) within 99 risk loci. Associated loci (P<5E-04) explained approximately half of phenotypic variance in the ACL rupture trait. Two of these loci were located in uncharacterized or non-coding regions of the genome. A chromosome 24 locus containing nine genes with diverse functions met genome-wide significance (P = 3.63E-0.6). GWAS pathways were enriched for c-type lectins, a gene set that includes aggrecan, a gene set encoding antimicrobial proteins, and a gene set encoding membrane transport proteins with a variety of physiological functions. Genotypic risk estimated for each dog based on the risk contributed by each GWAS locus showed clear separation of ACL rupture cases and controls. Power analysis of the GWAS data set estimated that ~172 loci explain the genetic contribution to ACL rupture in the Labrador Retriever. Heritability was estimated at 0.48. We conclude ACL rupture is a moderately heritable highly polygenic complex trait. Our results implicate c-type lectin pathways in ACL homeostasis. PMID:28379989

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

A Contribution of Beef to Human Health: A Review of the Role of the Animal Production Systems

PubMed Central

Pighin, Dario; Pazos, Adriana; Chamorro, Verónica; Paschetta, Fernanda; Cunzolo, Sebastián; Godoy, Fernanda; Messina, Valeria; Pordomingo, Anibal; Grigioni, Gabriela

2016-01-01

Meat and meat products constitute important source of protein, fat, and several functional compounds. Although beef consumption may implicate possible negative impacts on human health, its consumption can also contribute to human health. Quality traits of beef, as well as its nutritional properties, depend on animal genetics, feeding, livestock practices, and post mortem procedures. Available data show that emerging beef production systems are able to improve both, quality and nutritional traits of beef in a sustainable way. In this context, Argentina's actions are aimed at maximising beef beneficial effects and minimising its negative impact on human health, in a way of contributing to global food security. PMID:26989765

Desert Scrublands

USGS Publications Warehouse

Jones, L.L.C.; Halama, K.J.; Lovich, R.E.

2016-01-01

Desert scrublands comprise the lower to mid-elevation portions of four different ecosystems including the Chihuahuan, Great Basin, Mojave and Sonoran Deserts. Together the area inside their outer boundaries includes over 8% of the surface area of the United States. Despite significant differences in the flora and fauna of these bioregions they all share the common trait of being arid shrub-steppe ecosystems, receiving, on average, less than 254 mm of rain per year. The austere nature of these landscapes belies their significant biodiversity, the amazing behavioral and physiological adaptations of the biota, and the fragility of the ecosystems to human disturbances. For example, the Mojave Desert alone has at least 250 species of ephemeral plants, mostly winter annuals, and up to 90% are endemic.

Cat-Map: putting cataract on the map

PubMed Central

Bennett, Thomas M.; Hejtmancik, J. Fielding

2010-01-01

Lens opacities, or cataract(s), may be inherited as a classic Mendelian disorder usually with early-onset or, more commonly, acquired with age as a multi-factorial or complex trait. Many genetic forms of cataract have been described in mice and other animal models. Considerable progress has been made in mapping and identifying the genes and mutations responsible for inherited forms of cataract, and genetic determinants of age-related cataract are beginning to be discovered. To provide a convenient and accurate summary of current information focused on the increasing genetic complexity of Mendelian and age-related cataract we have created an online chromosome map and reference database for cataract in humans and mice (Cat-Map). PMID:21042563

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farahani, Poupak; Chiu, Sally; Bowlus, Christopher L.

Obesity is a complex disease. To date, over 100 chromosomal loci for body weight, body fat, regional white adipose tissue weight, and other obesity-related traits have been identified in humans and in animal models. For most loci, the underlying genes are not yet identified; some of these chromosomal loci will be alleles of known obesity genes, whereas many will represent alleles of unknown genes. Microarray analysis allows simultaneous multiple gene and pathway discovery. cDNA and oligonucleotide arrays are commonly used to identify differentially expressed genes by surveys of large numbers of known and unnamed genes. Two papers previously identified genesmore » differentially expressed in adipose tissue of mouse models of obesity and diabetes by analysis of hybridization to Affymetrix oligonucleotide chips.« less

Phenotypic plasticity to light and nutrient availability alters functional trait ranking across eight perennial grassland species.

PubMed

Siebenkäs, Alrun; Schumacher, Jens; Roscher, Christiane

2015-03-27

Functional traits are often used as species-specific mean trait values in comparative plant ecology or trait-based predictions of ecosystem processes, assuming that interspecific differences are greater than intraspecific trait variation and that trait-based ranking of species is consistent across environments. Although this assumption is increasingly challenged, there is a lack of knowledge regarding to what degree the extent of intraspecific trait variation in response to varying environmental conditions depends on the considered traits and the characteristics of the studied species to evaluate the consequences for trait-based species ranking. We studied functional traits of eight perennial grassland species classified into different functional groups (forbs vs. grasses) and varying in their inherent growth stature (tall vs. small) in a common garden experiment with different environments crossing three levels of nutrient availability and three levels of light availability over 4 months of treatment applications. Grasses and forbs differed in almost all above- and belowground traits, while trait differences related to growth stature were generally small. The traits showing the strongest responses to resource availability were similarly for grasses and forbs those associated with allocation and resource uptake. The strength of trait variation in response to varying resource availability differed among functional groups (grasses > forbs) and species of varying growth stature (small-statured > tall-statured species) in many aboveground traits, but only to a lower extent in belowground traits. These differential responses altered trait-based species ranking in many aboveground traits, such as specific leaf area, tissue nitrogen and carbon concentrations and above-belowground allocation (leaf area ratio and root : shoot ratio) at varying resource supply, while trait-based species ranking was more consistent in belowground traits. Our study shows that species grouping according to functional traits is valid, but trait-based species ranking depends on environmental conditions, thus limiting the applicability of species-specific mean trait values in ecological studies. Published by Oxford University Press on behalf of the Annals of Botany Company.

Sewage reflects the microbiomes of human populations.

PubMed

Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2015-02-24

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics. Copyright © 2015 Newton et al.

Runaway cultural niche construction

PubMed Central

Rendell, Luke; Fogarty, Laurel; Laland, Kevin N.

2011-01-01

Cultural niche construction is a uniquely potent source of selection on human populations, and a major cause of recent human evolution. Previous theoretical analyses have not, however, explored the local effects of cultural niche construction. Here, we use spatially explicit coevolutionary models to investigate how cultural processes could drive selection on human genes by modifying local resources. We show that cultural learning, expressed in local niche construction, can trigger a process with dynamics that resemble runaway sexual selection. Under a broad range of conditions, cultural niche-constructing practices generate selection for gene-based traits and hitchhike to fixation through the build up of statistical associations between practice and trait. This process can occur even when the cultural practice is costly, or is subject to counteracting transmission biases, or the genetic trait is selected against. Under some conditions a secondary hitchhiking occurs, through which genetic variants that enhance the capability for cultural learning are also favoured by similar dynamics. We suggest that runaway cultural niche construction could have played an important role in human evolution, helping to explain why humans are simultaneously the species with the largest relative brain size, the most potent capacity for niche construction and the greatest reliance on culture. PMID:21320897

Common Genetic Variation in the Human FNDC5 Locus, Encoding the Novel Muscle-Derived ‘Browning’ Factor Irisin, Determines Insulin Sensitivity

PubMed Central

Staiger, Harald; Böhm, Anja; Scheler, Mika; Berti, Lucia; Machann, Jürgen; Schick, Fritz; Machicao, Fausto; Fritsche, Andreas; Stefan, Norbert; Weigert, Cora; Krook, Anna; Häring, Hans-Ulrich; de Angelis, Martin Hrabě

2013-01-01

Aims/hypothesis Recently, the novel myokine irisin was described to drive adipose tissue ‘browning’, to increase energy expenditure, and to improve obesity and insulin resistance in high fat-fed mice. Here, we assessed whether common single nucleotide polymorphisms (SNPs) in the FNDC5 locus, encoding the irisin precursor, contribute to human prediabetic phenotypes (overweight, glucose intolerance, insulin resistance, impaired insulin release). Methods A population of 1,976 individuals was characterized by oral glucose tolerance tests and genotyped for FNDC5 tagging SNPs. Subgroups underwent hyperinsulinaemic-euglycaemic clamps, magnetic resonance imaging/spectroscopy, and intravenous glucose tolerance tests. From 37 young and 14 elderly participants recruited in two different centres, muscle biopsies were obtained for the preparation of human myotube cultures. Results After appropriate adjustment and Bonferroni correction for the number of tested variants, SNPs rs16835198 and rs726344 were associated with in vivo measures of insulin sensitivity. Via interrogation of publicly available data from the Meta-Analyses of Glucose and Insulin-related traits Consortium, rs726344’s effect on insulin sensitivity was replicated. Moreover, novel data from human myotubes revealed a negative association between FNDC5 expression and appropriately adjusted in vivo measures of insulin sensitivity in young donors. This finding was replicated in myotubes from elderly men. Conclusions/interpretation This study provides evidence that the FNDC5 gene, encoding the novel myokine irisin, determines insulin sensitivity in humans. Our gene expression data point to an unexpected insulin-desensitizing effect of irisin. PMID:23637927

The genetic and environmental structure of the character sub-scales of the temperament and character inventory in adolescence.

PubMed

Lester, Nigel; Garcia, Danilo; Lundström, Sebastian; Brändström, Sven; Råstam, Maria; Kerekes, Nóra; Nilsson, Thomas; Cloninger, C Robert; Anckarsäter, Henrik

2016-01-01

The character higher order scales (self-directedness, cooperativeness, and self-transcendence) in the temperament and character inventory are important general measures of health and well-being [Mens Sana Monograph 11:16-24 (2013)]. Recent research has found suggestive evidence of common environmental influence on the development of these character traits during adolescence. The present article expands earlier research by focusing on the internal consistency and the etiology of traits measured by the lower order sub-scales of the character traits in adolescence. The twin modeling analysis of 423 monozygotic pairs and 408 same sex dizygotic pairs estimated additive genetics (A), common environmental (C), and non-shared environmental (E) influences on twin resemblance. All twins were part of the on-going longitudinal Child and Adolescent Twin Study in Sweden (CATSS). The twin modeling analysis suggested a common environmental contribution for two out of five self-directedness sub-scales (0.14 and 0.23), for three out of five cooperativeness sub-scales (0.07-0.17), and for all three self-transcendence sub-scales (0.10-0.12). The genetic structure at the level of the character lower order sub-scales in adolescents shows that the proportion of the shared environmental component varies in the trait of self-directedness and in the trait of cooperativeness, while it is relatively stable across the components of self-transcendence. The presence of this unique shared environmental effect in adolescence has implications for understanding the relative importance of interventions and treatment strategies aimed at promoting overall maturation of character, mental health, and well-being during this period of the life span.

Evaluation of seven common lipid associated loci in a large Indian sib pair study.

PubMed

Rafiq, Sajjad; Venkata, Kranthi Kumar M; Gupta, Vipin; Vinay, D G; Spurgeon, Charles J; Parameshwaran, Smitha; Madana, Sandeep N; Kinra, Sanjay; Bowen, Liza; Timpson, Nicholas J; Smith, George Davey; Dudbridge, Frank; Prabhakaran, Dorairaj; Ben-Shlomo, Yoav; Reddy, K Srinath; Ebrahim, Shah; Chandak, Giriraj R

2012-11-14

Genome wide association studies (GWAS), mostly in Europeans have identified several common variants as associated with key lipid traits. Replication of these genetic effects in South Asian populations is important since it would suggest wider relevance for these findings. Given the rising prevalence of metabolic disorders and heart disease in the Indian sub-continent, these studies could be of future clinical relevance. We studied seven common variants associated with a variety of lipid traits in previous GWASs. The study sample comprised of 3178 sib-pairs recruited as participants for the Indian Migration Study (IMS). Associations with various lipid parameters and quantitative traits were analyzed using the Fulker genetic association model. We replicated five of the 7 main effect associations with p-values ranging from 0.03 to 1.97x10(-7). We identified particularly strong association signals at rs662799 in APOA5 (beta=0.18 s.d, p=1.97 x 10(-7)), rs10503669 in LPL (beta =-0.18 s.d, p=1.0 x 10(-4)) and rs780094 in GCKR (beta=0.11 s.d, p=0.001) loci in relation to triglycerides. In addition, the GCKR variant was also associated with total cholesterol (beta=0.11 s.d, p=3.9x10(-4)). We also replicated the association of rs562338 in APOB (p=0.03) and rs4775041 in LIPC (p=0.007) with LDL-cholesterol and HDL-cholesterol respectively. We report associations of five loci with various lipid traits with the effect size consistent with the same reported in Europeans. These results indicate an overlap of genetic effects pertaining to lipid traits across the European and Indian populations.

Evaluation of seven common lipid associated loci in a large Indian sib pair study

PubMed Central

2012-01-01

Background Genome wide association studies (GWAS), mostly in Europeans have identified several common variants as associated with key lipid traits. Replication of these genetic effects in South Asian populations is important since it would suggest wider relevance for these findings. Given the rising prevalence of metabolic disorders and heart disease in the Indian sub-continent, these studies could be of future clinical relevance. Methods We studied seven common variants associated with a variety of lipid traits in previous GWASs. The study sample comprised of 3178 sib-pairs recruited as participants for the Indian Migration Study (IMS). Associations with various lipid parameters and quantitative traits were analyzed using the Fulker genetic association model. Results We replicated five of the 7 main effect associations with p-values ranging from 0.03 to 1.97x10-7. We identified particularly strong association signals at rs662799 in APOA5 (beta=0.18 s.d, p=1.97 x 10-7), rs10503669 in LPL (beta =−0.18 s.d, p=1.0 x 10-4) and rs780094 in GCKR (beta=0.11 s.d, p=0.001) loci in relation to triglycerides. In addition, the GCKR variant was also associated with total cholesterol (beta=0.11 s.d, p=3.9x10-4). We also replicated the association of rs562338 in APOB (p=0.03) and rs4775041 in LIPC (p=0.007) with LDL-cholesterol and HDL-cholesterol respectively. Conclusions We report associations of five loci with various lipid traits with the effect size consistent with the same reported in Europeans. These results indicate an overlap of genetic effects pertaining to lipid traits across the European and Indian populations. PMID:23150898

Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

PubMed

Arya, Rector; Lehman, Donna; Hunt, Kelly J; Schneider, Jennifer; Almasy, Laura; Blangero, John; Stern, Michael P; Duggirala, Ravindranath

2003-12-31

Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecting obesity and dyslipidemia is very limited. To address this issue, we first conducted univariate multipoint linkage analysis for body mass index (BMI) and HDL-C to identify loci influencing variation in these phenotypes using Framingham Heart Study data relating to 1702 subjects distributed across 330 pedigrees. Subsequently, we performed bivariate multipoint linkage analysis to detect common loci influencing covariation between these two traits. We scanned the genome and identified a major locus near marker D6S1009 influencing variation in BMI (LOD = 3.9) using the program SOLAR. We also identified a major locus for HDL-C near marker D2S1334 on chromosome 2 (LOD = 3.5) and another region near marker D6S1009 on chromosome 6 with suggestive evidence for linkage (LOD = 2.7). Since these two phenotypes have been independently mapped to the same region on chromosome 6q, we used the bivariate multipoint linkage approach using SOLAR. The bivariate linkage analysis of BMI and HDL-C implicated the genetic region near marker D6S1009 as harboring a major gene commonly influencing these phenotypes (bivariate LOD = 6.2; LODeq = 5.5) and appears to improve power to map the correlated traits to a region, precisely. We found substantial evidence for a quantitative trait locus with pleiotropic effects, which appears to influence both BMI and HDL-C phenotypes in the Framingham data.

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers.

PubMed

Briñez, Boris; Perseguini, Juliana Morini Küpper Cardoso; Rosa, Juliana Santa; Bassi, Denis; Gonçalves, João Guilherme Ribeiro; Almeida, Caléo; Paulino, Jean Fausto de Carvalho; Blair, Matthew Ward; Chioratto, Alisson Fernando; Carbonell, Sérgio Augusto Morais; Valdisser, Paula Arielle Mendes Ribeiro; Vianello, Rosana Pereira; Benchimol-Reis, Luciana Lasry

2017-01-01

The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

Genetic fatalism and social policy: the implications of behavior genetics research.

PubMed Central

Alper, J. S.; Beckwith, J.

1993-01-01

Recent advances in molecular genetics methods have provided new means of determining the genetic bases of human behavioral traits. The impetus for the use of these approaches for specific behaviors depends, in large part, on previous familial studies on inheritance of such traits. In the past, a finding of a genetic basis for a trait was often accompanied with the idea that that trait is unchangeable. We discuss the definition of "genetic trait" and heritability and examine the relationship between these concepts and the malleability of traits for both molecular and nonmolecular approaches to behavioral genetics. We argue that the malleability of traits is as much a social and political question as it is a biological one and that whether or not a trait is genetic has little relevance to questions concerning determinism, free will, and individual responsibility for actions. We conclude by noting that "scientific objectivity" should not be used to conceal the social perspectives that underlie proposals regarding social change. PMID:7716971

Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data

PubMed Central

Lopes, Marcos S.; Bastiaansen, John W. M.; Janss, Luc; Knol, Egbert F.; Bovenhuis, Henk

2015-01-01

Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases. PMID:26438289

Do autistic traits play a role in the bullying of obsessive-compulsive disorder and social phobia sufferers?

PubMed

Bejerot, S; Mörtberg, E

2009-01-01

Social phobia and obsessive-compulsive disorder (OCD) share several similarities: both are categorized as anxiety disorders, avoidant personality disorder and depression are common in both, they have a similar age of onset and course, and both disorders respond to treatments with serotonin reuptake inhibitors and cognitive behavioural therapy. However, OCD and social phobia differ in respect to their relation to autism spectrum disorders (ASD; i.e. Asperger's syndrome, autism, pervasive disorder not otherwise specified). Findings that suggest a link between OCD and ASD have no parallel in social phobia. Moreover, obsessive-compulsive, paranoid and schizotypal personality disorders are prevalent in OCD and in ASD, but not in social phobia. Individuals with ASD are known to be frequent targets of bullying. We hypothesised that individuals with autistic traits would have been frequent targets for bullies during their childhood, as opposed to people without such traits. Adult patients with social phobia (n = 63) or OCD (n = 65) were assessed regarding autistic traits, and interviewed about being bullied at school. A reference group (n = 551) responded to questions about being bullied. There was a significant difference in the prevalence of being bullied between OCD (50%), social phobia patients (20%) and the reference group (27%). Autistic traits were more common in OCD than in social phobia. A history of being bullied was related to autistic traits among patients. Falling victim to bullying is not a random event. Autistic traits, i.e. low social skills, may be a predictor of being bullied in school. The high rate of bullying victims in persons who later develop OCD is suggested to be related to the overlap between OCD and ASD. Copyright 2009 S. Karger AG, Basel.

Association between DRD2, 5-HTTLPR, and ALDH2 genes and specific personality traits in alcohol- and opiate-dependent patients.

PubMed

Wang, Tzu-Yun; Lee, Sheng-Yu; Chen, Shiou-Lan; Huang, San-Yuan; Chang, Yun-Hsuan; Tzeng, Nian-Sheng; Wang, Chen-Lin; Hui Lee, I; Yeh, Tzung Lieh; Yang, Yen Kuang; Lu, Ru-Band

2013-08-01

The vulnerability of developing addictions is associated with genetic factors and personality traits. The predisposing genetic variants and personality traits may be common to all addictions or specific to a particular class of addiction. To investigate the relationship between genetic variances, personality traits, and their interactions in addiction are important. We recruited 175 opiate-dependent patients, 102 alcohol-dependent patients, and 111 healthy controls. All participants were diagnosed using DSM-IV criteria and assessed with Tridimensional Personality Questionnaire (TPQ). The dopamine D2 receptor (DRD2), 5-HTT-linked promoter region (5-HTTLPR), and aldehyde dehydrogenase 2 (ALDH2) genes were genotyped using PCR. The genotype frequency of the 5-HTTLPR and ALDH2 was significantly different between the patients and controls (P=0.013, P<0.001, respectively), and borderline significant (P=0.05) for DRD2 polymorphism. Both Novelty Seeking (NS) and Harm Avoidance (HA) scores were higher for patients (P<0.001). After stratification by candidate genes, addicts with ALDH2 *1/*1 interacting with the low-functional group of DRD2 and 5-HTTLPR genes have higher HA traits, whereas addicts with ALDH2 *1/*2 or *2/*2 and low-functional group of DRD2 and 5-HTTLPR genes have higher NS traits. We concluded that addicts, both alcohol- and opiate-dependent patients, have common genetic variants in DRD2 and 5-HTTLPR but specific for ALDH2. Higher NS and HA traits were found in both patient groups with the interaction with DRD2, 5-HTTLPR, and ALDH2 genes. The ALDH2 gene variants had different effect in the NS and HA dimension while the DRD2 and 5-HTTLPR genes did not. Copyright © 2013 Elsevier B.V. All rights reserved.

Trait differences in responses to arbuscular mycorrhizal fungi are stronger and more consistent than fixed differences among populations of Asclepias speciosa.

PubMed

Waller, Lauren P; Hahn, Philip G; Maron, John L; Lekberg, Ylva

2018-02-01

Arbuscular mycorrhizal (AM) fungi can promote plant growth and reproduction, but other plant physiological traits or traits that provide defense against herbivores can also be affected by AM fungi. However, whether responses of different traits to AM fungi are correlated and whether these relationships vary among plants from different populations are unresolved. In a common garden experiment, we grew Asclepias speciosa plants from seed collected from populations found along an environmental gradient with and without AM fungi to assess whether the responses of six growth and defense traits to AM fungi are correlated. Although there was strong genetic differentiation in mean trait values among populations, AM fungi consistently increased expression of most growth and defense traits across all populations. Responses of biomass and root to shoot ratio to AM fungi were positively correlated, suggesting that plants that are more responsive to AM fungi allocated more biomass belowground. Responses of biomass and trichome density to AM fungi were negatively correlated, indicating a trade-off in responsiveness between a growth and defensive trait. Our results suggest that while there is substantial population differentiation in many traits of A. speciosa, populations respond similarly to AM fungi, and both positive and negative correlations among trait responses occur. © 2018 Botanical Society of America.

Seasonality and phenology alter functional leaf traits.

PubMed

McKown, Athena D; Guy, Robert D; Azam, M Shofiul; Drewes, Eric C; Quamme, Linda K

2013-07-01

In plant ecophysiology, functional leaf traits are generally not assessed in relation to phenological phase of the canopy. Leaf traits measured in deciduous perennial species are known to vary between spring and summer seasons, but there is a knowledge gap relating to the late-summer phase marked by growth cessation and bud set occurring well before fall leaf senescence. The effects of phenology on canopy physiology were tested using a common garden of over 2,000 black cottonwood (Populus trichocarpa) individuals originating from a wide geographical range (44-60ºN). Annual phenological events and 12 leaf-based functional trait measurements were collected spanning the entire summer season prior to, and following, bud set. Patterns of seasonal trait change emerged by synchronizing trees using their date of bud set. In particular, photosynthetic, mass, and N-based traits increased substantially following bud set. Most traits were significantly different between pre-bud set and post-bud set phase trees, with many traits showing at least 25% alteration in mean value. Post-bud set, both the significance and direction of trait-trait relationships could be modified, with many relating directly to changes in leaf mass. In Populus, these dynamics in leaf traits throughout the summer season reflected a shift in whole plant physiology, but occurred long before the onset of leaf senescence. The marked shifts in measured trait values following bud set underscores the necessity to include phenology in trait-based ecological studies or large-scale phenotyping efforts, both at the local level and larger geographical scale.

Tradeoffs limit the evolution of male traits that are attractive to females

PubMed Central

Wagner, William E.; Beckers, Oliver M.; Tolle, Amanda E.; Basolo, Alexandra L.

2012-01-01

Tradeoffs occur between a variety of traits in a diversity of organisms, and these tradeoffs can have major effects on ecological and evolutionary processes. Far less is known, however, about tradeoffs between male traits that affect mate attraction than about tradeoffs between other types of traits. Previous results indicate that females of the variable field cricket, Gryllus lineaticeps, prefer male songs with higher chirp rates and longer chirp durations. In the current study, we tested the hypothesis that a tradeoff between these traits affects the evolution of male song. The two traits were negatively correlated among full-sibling families, consistent with a genetically based tradeoff, and the tradeoff was stronger when nutrients were limiting. In addition, for males from 12 populations reared in a common environment, the traits were negatively correlated within populations, the strength of the tradeoff was largely invariant across populations, and the within-population tradeoff predicted how the traits have evolved among populations. A widespread tradeoff thus affects male trait evolution. Finally, for males from four populations assayed in the field, the traits were negatively correlated within and among populations. The tradeoff is thus robust to the presence of environmental factors that might mask its effects. Together, our results indicate there is a fundamental tradeoff between male traits that: (i) limits the ability of males to produce multiple attractive traits; (ii) limits how male traits evolve; and (iii) might favour plasticity in female mating preferences. PMID:22456890

The Human Microbiome and the Missing Heritability Problem

PubMed Central

Sandoval-Motta, Santiago; Aldana, Maximino; Martínez-Romero, Esperanza; Frank, Alejandro

2017-01-01

The “missing heritability” problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this “missing heritability” have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies. PMID:28659968

Examining the Enigmatic Einstein

ERIC Educational Resources Information Center

Khoon, Koh Aik

2007-01-01

Albert Einstein is the icon of scientific genius. His is one the most recognizable faces in the history of mankind. This paper takes a cursory look at the man who is commonly perceived to be the epitome of eccentricity. We manage to sum up his salient traits which are associated with his name. The traits are based on anecdotal evidence. This…

Development of genomic evaluations for direct measures of health in U.S. Holsteins and their correlations with fitness traits

USDA-ARS?s Scientific Manuscript database

The objectives of this research were to estimate variance components for 6 common health events recorded by producers on U.S. dairy farms, as well as investigate correlations with fitness traits currently used for selection. Producer-recorded health event data were available from Dairy Records Manag...

Identification and selection for tuber calcium, internal quality and pitted scab in segregating ‘Atlantic’ x ‘Superior’ reciprocal tetraploid populations

USDA-ARS?s Scientific Manuscript database

Tuber quality traits are a major interest for breeders and the potato chip industry. This research intended to generate populations that can be suitable for the genetic study of tuber calcium, internal quality, common scab, and other commercially important traits such as yield, specific gravity and ...

A population genetic interpretation of GWAS findings for human quantitative traits

PubMed Central

Bullaughey, Kevin; Hudson, Richard R.; Sella, Guy

2018-01-01

Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes—notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space. We solve the model for the phenotypic distribution and allelic dynamics at steady state and derive robust, closed-form solutions for summary statistics of the genetic architecture. Our results provide a simple interpretation for missing heritability and why it varies among traits. They predict that the distribution of variances contributed by loci identified in GWASs is well approximated by a simple functional form that depends on a single parameter: the expected contribution to genetic variance of a strongly selected site affecting the trait. We test this prediction against the results of GWASs for height and body mass index (BMI) and find that it fits the data well, allowing us to make inferences about the degree of pleiotropy and mutational target size for these traits. Our findings help to explain why the GWAS for height explains more of the heritable variance than the similarly sized GWAS for BMI and to predict the increase in explained heritability with study sample size. Considering the demographic history of European populations, in which these GWASs were performed, we further find that most of the associations they identified likely involve mutations that arose shortly before or during the Out-of-Africa bottleneck at sites with selection coefficients around s = 10−3. PMID:29547617

Human land use promotes the abundance and diversity of exotic species on caribbean islands.

PubMed

Jesse, Wendy A M; Behm, Jocelyn E; Helmus, Matthew R; Ellers, Jacintha

2018-05-31

Human land use causes major changes in species abundance and composition, yet native and exotic species can exhibit different responses to land use change. Native populations generally decline in human-impacted habitats while exotic species often benefit. In this study, we assessed the effects of human land use on exotic and native reptile diversity, including functional diversity, which relates to the range of habitat use strategies in biotic communities. We surveyed 114 reptile communities from localities that varied in habitat structure and human impact level on two Caribbean islands, and calculated species richness, overall abundance and evenness for every plot. Functional diversity indices were calculated using published trait data, which enabled us to detect signs of trait filtering associated with impacted habitats. Our results show that environmental variation among sampling plots was explained by two PCA ordination axes related to habitat structure (i.e. forest or non-forest) and human impact level (i.e. addition of man-made constructions such as roads and buildings). Several diversity indices were significantly correlated with the two PCA axes, but exotic and native species showed opposing responses. Native species reached the highest abundance in forests, while exotic species were absent in this habitat. Human impact was associated with an increase in exotic abundance and species richness, while native species showed no significant associations. Functional diversity was highest in non-forested environments on both islands, and further increased on St. Martin with the establishment of functionally unique exotic species in non-forested habitat. Habitat structure, rather than human impact, proved to be an important agent for environmental filtering of traits, causing divergent functional trait values across forested and non-forested environments. Our results illustrate the importance of considering various elements of land use when studying its impact on species diversity and the establishment and spread of exotic species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Spontaneous trait transference to familiar communicators: is a little knowledge a dangerous thing?

PubMed

Mae, L; Carlston, D E; Skowronski, J J

1999-08-01

In most social cognition research participants are presented with unattributed information about unfamiliar stimulus persons. However, in the real world it is more common for people to learn about others through social communication and to know something about those with whom they communicate. Such issues are explored in relation to spontaneous trait transference, a phenomenon in which communicators are perceived as having traits that they merely describe in others. Three studies show that even familiar communicators became associated with, and attributed, the traits implied by their remarks. Surprisingly, these effects occurred even when the implied traits were incongruent with participants' prior knowledge about these communicators. The results are discussed in terms of (a) the generalizability of social cognition research, (b) the automaticity of simple associative phenomena, and (c) the interplay of simple associative and higher level processes.

Effects of optimism on gambling in the rat slot machine task.

PubMed

Rafa, Dominik; Kregiel, Jakub; Popik, Piotr; Rygula, Rafal

2016-03-01

Although gambling disorder is a serious social problem in modern societies, information about the behavioral traits that could determine vulnerability to this psychopathology is still scarce. In this study, we used a recently developed ambiguous-cue interpretation ​(ACI)​ paradigm to investigate whether 'optimism' and 'pessimism' as behavioral traits may determine the gambling-like behavior of rodents. In a series of ACI tests (cognitive bias screening), we identified rats that displayed 'pessimistic' and 'optimistic' traits. Subsequently, using the rat slot machine task (rSMT), we investigated if the 'optimistic'/'pessimistic' traits could determine the crucial feature of gambling-like behavior that has been investigated in rats and humans: the ​interpretation of 'near-miss' outcomes as a positive (i.e., win) situation. We found that 'optimists' did not interpret 'near-miss', 'near loss', or 'clear win' as win trials more often than ​their 'pessimistic' ​conspecifics; however, the 'optimists' were statistically more likely to reach for a reward in the hopeless 'clear loss' situation. This agrees with human studies and provides a platform for modeling interactions between behavioral traits and gambling in animals. Copyright © 2015 Elsevier B.V. All rights reserved.

Functional traits and ecological affinities of riparian plants along the Colorado River in Grand Canyon

USGS Publications Warehouse

Palmquist, Emily C.; Ralston, Barbara E.; Sarr. Daniel,; Merritt, David; Shafroth, Patrick B; Scott, Julian

2017-01-01

Trait-based approaches to vegetation analyses are becoming more prevalent in studies of riparian vegetation dynamics, including responses to flow regulation, groundwater pumping, and climate change. These analyses require species trait data compiled from the literature and floras or original field measurements. Gathering such data makes trait-based research time intensive at best and impracticable in some cases. To support trait-based analysis of vegetation along the Colorado River through Grand Canyon, a data set of 20 biological traits and ecological affinities for 179 species occurring in that study area was compiled. This diverse flora shares species with many riparian areas in the western USA and includes species that occur across a wide moisture gradient. Data were compiled from published scientific papers, unpublished reports, plant fact sheets, existing trait databases, regional floras, and plant guides. Data for ordinal environmental tolerances were more readily available than were quantitative traits. More publicly available data are needed for traits of both common and rare southwestern U.S. plant species to facilitate comprehensive, trait-based research. The trait data set is free to use and can be downloaded from ScienceBase: https://www.sciencebase.gov/catalog/item/58af41dee4b01ccd54f9f2ff and https://dx.doi.org/10.5066/F7QV3JN1

TRY – a global database of plant traits

PubMed Central

Kattge, J; Díaz, S; Lavorel, S; Prentice, I C; Leadley, P; Bönisch, G; Garnier, E; Westoby, M; Reich, P B; Wright, I J; Cornelissen, J H C; Violle, C; Harrison, S P; Van Bodegom, P M; Reichstein, M; Enquist, B J; Soudzilovskaia, N A; Ackerly, D D; Anand, M; Atkin, O; Bahn, M; Baker, T R; Baldocchi, D; Bekker, R; Blanco, C C; Blonder, B; Bond, W J; Bradstock, R; Bunker, D E; Casanoves, F; Cavender-Bares, J; Chambers, J Q; Chapin, F S; Chave, J; Coomes, D; Cornwell, W K; Craine, J M; Dobrin, B H; Duarte, L; Durka, W; Elser, J; Esser, G; Estiarte, M; Fagan, W F; Fang, J; Fernández-Méndez, F; Fidelis, A; Finegan, B; Flores, O; Ford, H; Frank, D; Freschet, G T; Fyllas, N M; Gallagher, R V; Green, W A; Gutierrez, A G; Hickler, T; Higgins, S I; Hodgson, J G; Jalili, A; Jansen, S; Joly, C A; Kerkhoff, A J; Kirkup, D; Kitajima, K; Kleyer, M; Klotz, S; Knops, J M H; Kramer, K; Kühn, I; Kurokawa, H; Laughlin, D; Lee, T D; Leishman, M; Lens, F; Lenz, T; Lewis, S L; Lloyd, J; Llusià, J; Louault, F; Ma, S; Mahecha, M D; Manning, P; Massad, T; Medlyn, B E; Messier, J; Moles, A T; Müller, S C; Nadrowski, K; Naeem, S; Niinemets, Ü; Nöllert, S; Nüske, A; Ogaya, R; Oleksyn, J; Onipchenko, V G; Onoda, Y; Ordoñez, J; Overbeck, G; Ozinga, W A; Patiño, S; Paula, S; Pausas, J G; Peñuelas, J; Phillips, O L; Pillar, V; Poorter, H; Poorter, L; Poschlod, P; Prinzing, A; Proulx, R; Rammig, A; Reinsch, S; Reu, B; Sack, L; Salgado-Negret, B; Sardans, J; Shiodera, S; Shipley, B; Siefert, A; Sosinski, E; Soussana, J-F; Swaine, E; Swenson, N; Thompson, K; Thornton, P; Waldram, M; Weiher, E; White, M; White, S; Wright, S J; Yguel, B; Zaehle, S; Zanne, A E; Wirth, C

2011-01-01

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Sickle Trait in African-American Hemodialysis Patients and Higher Erythropoiesis-Stimulating Agent Dose

PubMed Central

Lacson, Eduardo K.; Kshirsagar, Abhijit V.; Key, Nigel S.; Hogan, Susan L.; Hakim, Raymond M.; Mooney, Ann; Jani, Chinu M.; Johnson, Curtis; Hu, Yichun; Falk, Ronald J.; Lazarus, J. Michael

2014-01-01

African Americans require higher doses of erythropoiesis-stimulating agents (ESAs) during dialysis to manage anemia, but the influence of sickle cell trait and other hemoglobinopathy traits on anemia in dialysis patients has not been adequately evaluated. We performed a cross-sectional study of a large cohort of adult African-American hemodialysis patients in the United States to determine the prevalence of hemoglobinopathy traits and quantify their influence on ESA dosing. Laboratory and clinical data were obtained over 6 months in 2011. Among 5319 African-American patients, 542 (10.2%) patients had sickle cell trait, and 129 (2.4%) patients had hemoglobin C trait; no other hemoglobinopathy traits were present. Sickle cell trait was more common in this cohort than the general African-American population (10.2% versus 6.5%–8.7%, respectively, P<0.05). Among 5002 patients (10.3% sickle cell trait and 2.4% hemoglobin C trait) receiving ESAs, demographic and clinical variables were similar across groups, with achieved hemoglobin levels being nearly identical. Patients with hemoglobinopathy traits received higher median doses of ESA than patients with normal hemoglobin (4737.4 versus 4364.1 units/treatment, respectively, P=0.02). In multivariable analyses, hemoglobinopathy traits associated with 13.2% more ESA per treatment (P=0.001). Within subgroups, sickle cell trait patients received 13.2% (P=0.003) higher dose and hemoglobin C trait patients exhibited a similar difference (12.9%, P=0.12). Sensitivity analyses using weight-based dosing definitions and separate logistic regression models showed comparable associations. Our findings suggest that the presence of sickle cell trait and hemoglobin C trait may explain, at least in part, prior observations of greater ESA doses administered to African-American dialysis patients relative to Caucasian patients. PMID:24459231

Comparison of statistical tests for association between rare variants and binary traits.

PubMed

Bacanu, Silviu-Alin; Nelson, Matthew R; Whittaker, John C

2012-01-01

Genome-wide association studies have found thousands of common genetic variants associated with a wide variety of diseases and other complex traits. However, a large portion of the predicted genetic contribution to many traits remains unknown. One plausible explanation is that some of the missing variation is due to the effects of rare variants. Nonetheless, the statistical analysis of rare variants is challenging. A commonly used method is to contrast, within the same region (gene), the frequency of minor alleles at rare variants between cases and controls. However, this strategy is most useful under the assumption that the tested variants have similar effects. We previously proposed a method that can accommodate heterogeneous effects in the analysis of quantitative traits. Here we extend this method to include binary traits that can accommodate covariates. We use simulations for a variety of causal and covariate impact scenarios to compare the performance of the proposed method to standard logistic regression, C-alpha, SKAT, and EREC. We found that i) logistic regression methods perform well when the heterogeneity of the effects is not extreme and ii) SKAT and EREC have good performance under all tested scenarios but they can be computationally intensive. Consequently, it would be more computationally desirable to use a two-step strategy by (i) selecting promising genes by faster methods and ii) analyzing selected genes using SKAT/EREC. To select promising genes one can use (1) regression methods when effect heterogeneity is assumed to be low and the covariates explain a non-negligible part of trait variability, (2) C-alpha when heterogeneity is assumed to be large and covariates explain a small fraction of trait's variability and (3) the proposed trend and heterogeneity test when the heterogeneity is assumed to be non-trivial and the covariates explain a large fraction of trait variability.

Intraspecific functional diversity of common species enhances community stability

USGS Publications Warehouse

Wood, Connor M.; McKinney, Shawn T.; Loftin, Cynthia S.

2017-01-01

Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles (Myodes gapperi) had greater iFD than deer mice (Peromyscus maniculatus), both among habitats, and within the plant community in which they were most abundant (their “primary habitat”). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperidiet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

Genetic analysis of motor milestones attainment in early childhood.

PubMed

Peter, I; Vainder, M; Livshits, G

1999-03-01

The age of attainment for four motor developmental traits, such as turning over, sitting up without support, pulling up to a standing position and walking without support, was examined in 822 children, including 626 siblings from families with 2 to 6 children, 68 pairs of dizygotic twins and 30 pairs of monozygotic twins. Correlation analysis, carried out separately for each type of sibship, showed the highest pairwise correlations in monozygotic twins and the lowest correlation in non-twin siblings for all motor milestones. Variance component analysis was used to decompose the different independent components forming the variation of the studied trait, such as genetic effect, common twin environment, common sib environment and residual factors. The results revealed that the major proportion of the total variance after adjustment for gestation age for the attainment of each motor skill, except pulling up to standing position, is explained by the common twin environment (50.5 to 66.6%), whilst a moderate proportion is explained by additive genetic factors (22.2 to 33.5%). Gestational age was found to be an important predictor of appearance of all motor milestones, affecting delay of 4.5 to 8.6 days for the attainment of the motor abilities for each week of earlier gestation. The age of attainment of the standing position was affected only by shared sibs environment (33.3% of the total variance) and showed no influence of either genetic or common twin environment. Phenotypic between trait correlations were high and significant for all studied traits (range between 0.40 and 0.67, P < 0.01 in all instances). Genetic cross correlations, however, were not easily interpreted and did not show clear variance trends among the different groups of children.

Use of a quality trait index to increase the reliability of phenotypic evaluations in broccoli

USDA-ARS?s Scientific Manuscript database

Selection of superior broccoli hybrids involves multiple considerations, including optimization of head quality traits. Quality assessment of broccoli heads is often confounded by relatively subjective human preferences for optimal appearance of heads. To assist the selection process, we assessed fi...

An Evaluation of the Navy’s Health Promotion Videotapes

DTIC Science & Technology

1990-04-30

1263. Fisher, L., Rowley, P. T., & Lipkin. M. (1981). Genetic counseling for beta- thalassemia trait following health screening in a health maintenence...counseling for x, ta- thalassemia trait in a population unselected for interest: Effects on knowledge and m ,ood. American Journal of Human Genetics

Prevalence of sexual dimorphism in mammalian phenotypic traits.

PubMed

Karp, Natasha A; Mason, Jeremy; Beaudet, Arthur L; Benjamini, Yoav; Bower, Lynette; Braun, Robert E; Brown, Steve D M; Chesler, Elissa J; Dickinson, Mary E; Flenniken, Ann M; Fuchs, Helmut; Angelis, Martin Hrabe de; Gao, Xiang; Guo, Shiying; Greenaway, Simon; Heller, Ruth; Herault, Yann; Justice, Monica J; Kurbatova, Natalja; Lelliott, Christopher J; Lloyd, K C Kent; Mallon, Ann-Marie; Mank, Judith E; Masuya, Hiroshi; McKerlie, Colin; Meehan, Terrence F; Mott, Richard F; Murray, Stephen A; Parkinson, Helen; Ramirez-Solis, Ramiro; Santos, Luis; Seavitt, John R; Smedley, Damian; Sorg, Tania; Speak, Anneliese O; Steel, Karen P; Svenson, Karen L; Wakana, Shigeharu; West, David; Wells, Sara; Westerberg, Henrik; Yaacoby, Shay; White, Jacqueline K

2017-06-26

The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans.

Can soft biometric traits assist user recognition?

NASA Astrophysics Data System (ADS)

Jain, Anil K.; Dass, Sarat C.; Nandakumar, Karthik

2004-08-01

Biometrics is rapidly gaining acceptance as the technology that can meet the ever increasing need for security in critical applications. Biometric systems automatically recognize individuals based on their physiological and behavioral characteristics. Hence, the fundamental requirement of any biometric recognition system is a human trait having several desirable properties like universality, distinctiveness, permanence, collectability, acceptability, and resistance to circumvention. However, a human characteristic that possesses all these properties has not yet been identified. As a result, none of the existing biometric systems provide perfect recognition and there is a scope for improving the performance of these systems. Although characteristics like gender, ethnicity, age, height, weight and eye color are not unique and reliable, they provide some information about the user. We refer to these characteristics as "soft" biometric traits and argue that these traits can complement the identity information provided by the primary biometric identifiers like fingerprint and face. This paper presents the motivation for utilizing soft biometric information and analyzes how the soft biometric traits can be automatically extracted and incorporated in the decision making process of the primary biometric system. Preliminary experiments were conducted on a fingerprint database of 160 users by synthetically generating soft biometric traits like gender, ethnicity, and height based on known statistics. The results show that the use of additional soft biometric user information significantly improves (approximately 6%) the recognition performance of the fingerprint biometric system.

Confirmatory factor analytic structure and measurement invariance of quantitative autistic traits measured by the social responsiveness scale-2.

PubMed

Frazier, Thomas W; Ratliff, Kristin R; Gruber, Chris; Zhang, Yi; Law, Paul A; Constantino, John N

2014-01-01

Understanding the factor structure of autistic symptomatology is critical to the discovery and interpretation of causal mechanisms in autism spectrum disorder. We applied confirmatory factor analysis and assessment of measurement invariance to a large (N = 9635) accumulated collection of reports on quantitative autistic traits using the Social Responsiveness Scale, representing a broad diversity of age, severity, and reporter type. A two-factor structure (corresponding to social communication impairment and restricted, repetitive behavior) as elaborated in the updated Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) criteria for autism spectrum disorder exhibited acceptable model fit in confirmatory factor analysis. Measurement invariance was appreciable across age, sex, and reporter (self vs other), but somewhat less apparent between clinical and nonclinical populations in this sample comprised of both familial and sporadic autism spectrum disorders. The statistical power afforded by this large sample allowed relative differentiation of three factors among items encompassing social communication impairment (emotion recognition, social avoidance, and interpersonal relatedness) and two factors among items encompassing restricted, repetitive behavior (insistence on sameness and repetitive mannerisms). Cross-trait correlations remained extremely high, that is, on the order of 0.66-0.92. These data clarify domains of statistically significant factoral separation that may relate to partially-but not completely-overlapping biological mechanisms, contributing to variation in human social competency. Given such robust intercorrelations among symptom domains, understanding their co-emergence remains a high priority in conceptualizing common neural mechanisms underlying autistic syndromes.

Evaluation of non-additive genetic variation in feed-related traits of broiler chickens.

PubMed

Li, Y; Hawken, R; Sapp, R; George, A; Lehnert, S A; Henshall, J M; Reverter, A

2017-03-01

Genome-wide association mapping and genomic predictions of phenotype of individuals in livestock are predominately based on the detection and estimation of additive genetic effects. Non-additive genetic effects are largely ignored. Studies in animals, plants, and humans to assess the impact of non-additive genetic effects in genetic analyses have led to differing conclusions. In this paper, we examined the consequences of including non-additive genetic effects in genome-wide association mapping and genomic prediction of total genetic values in a commercial population of 5,658 broiler chickens genotyped for 45,176 single nucleotide polymorphism (SNP) markers. We employed mixed-model equations and restricted maximum likelihood to analyze 7 feed related traits (TRT1 - TRT7). Dominance variance accounted for a significant proportion of the total genetic variance in all 7 traits, ranging from 29.5% for TRT1 to 58.4% for TRT7. Using a 5-fold cross-validation schema, we found that in spite of the large dominance component, including the estimated dominance effects in the prediction of total genetic values did not improve the accuracy of the predictions for any of the phenotypes. We offer some possible explanations for this counter-intuitive result including the possible confounding of dominance deviations with common environmental effects such as hatch, different directional effects of SNP additive and dominance variations, and the gene-gene interactions' failure to contribute to the level of variance. © 2016 Poultry Science Association Inc.

Relationship between psychological factors and symptoms of TMD in university undergraduate students.

PubMed

Pesqueira, Aldiéris A; Zuim, Paulo R J; Monteiro, Douglas R; Ribeiro, Paula Do Prado; Garcia, Alicio R

2010-01-01

Temporomandibular disorders is a collective term used to describe a number of related disorders involving the temporomandibular joints, masticatory muscles and occlusion with common symptoms such as pain, restricted movement, muscle tenderness and intermittent joint sounds. The multifactorial TMD etiology is related to emotional tension, occlusal interferences, tooth loss, postural deviation, masticatory muscular dysfunction, internal and external changes in TMJ structure and the various associations of these factors. The aim of this study was to evaluate the prevalence of the relationship between signs of psychological distress and temporomandibular disorder in university students. A total 150 volunteers participated in this study. They attended different courses in the field of human science at one public university and four private universities. TMD was assessed by the Research Diagnostic Criteria (RDC) questionnaire. Anxiety was measured by means of a self-evaluative questionnaire, Spielberger's Trait-State anxiety inventory, to evaluate students'state and trait anxiety. The results of the two questionnaires were compared to determine the relationship between anxiety levels and severity degrees of chronic TMD pain by means of the chi-square test. The significance level was set at 5%. The statistical analysis showed that the TMD degree has a positive association with state-anxiety (p = 0.008; p < 0.05) and negative with trait-anxiety (p = 0.619; p < 0.05). Moreover a high TMD rate was observed among the students (40%). This study concluded that there is a positive association between TMD and anxiety.

Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci

PubMed Central

Liu, Fan; Wollstein, Andreas; Hysi, Pirro G.; Ankra-Badu, Georgina A.; Spector, Timothy D.; Park, Daniel; Zhu, Gu; Larsson, Mats; Duffy, David L.; Montgomery, Grant W.; Mackey, David A.; Walsh, Susan; Lao, Oscar; Hofman, Albert; Rivadeneira, Fernando; Vingerling, Johannes R.; Uitterlinden, André G.; Martin, Nicholas G.; Hammond, Christopher J.; Kayser, Manfred

2010-01-01

Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits. PMID:20463881

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

PubMed Central

Zaitlen, Noah A.; Ye, Chun Jimmie; Witte, John S.

2016-01-01

The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature. PMID:27197206

Genome-wide genetic homogeneity between sexes and populations for human height and body mass index.

PubMed

Yang, Jian; Bakshi, Andrew; Zhu, Zhihong; Hemani, Gibran; Vinkhuyzen, Anna A E; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hamsten, Anders; Magnusson, Patrik K E; Pedersen, Nancy L; Ingelsson, Erik; Visscher, Peter M

2015-12-20

Sex-specific genetic effects have been proposed to be an important source of variation for human complex traits. Here we use two distinct genome-wide methods to estimate the autosomal genetic correlation (rg) between men and women for human height and body mass index (BMI), using individual-level (n = ∼44 000) and summary-level (n = ∼133 000) data from genome-wide association studies. Results are consistent and show that the between-sex genetic correlation is not significantly different from unity for both traits. In contrast, we find evidence of genetic heterogeneity between sexes for waist-hip ratio (rg = ∼0.7) and between populations for BMI (rg = ∼0.9 between Europe and the USA) but not for height. The lack of evidence for substantial genetic heterogeneity for body size is consistent with empirical findings across traits and species. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Radioimmunoassay of human Hageman factor (factor XII). [/sup 125/I tracer technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saito, H.; Ratnoff, O.D.; Pensky, J.

A specific, sensitive, and reproducible radioimmunoassay for human Hageman factor (HF, factor XII) has been developed with purified human HF and monospecific rabbit antibody. Precise measurements of HF antigen were possible for concentrations as low as 0.1 percent of that in normal pooled plasma. A good correlation (correlation coefficient = 0.82) existed between the titers of HF measured by clot-promoting assays and radioimmunoassays among 42 normal adults. Confirming earlier studies, HF antigen was absent in Hageman trait plasma, but other congenital deficient plasmas, including those of individuals with Fletcher trait and Fitzgerald trait, contained normal amounts of HF antigen. HFmore » antigen was reduced in the plasmas of patients with disseminated intravascular coagulation or advanced liver cirrhosis, but it was normal in those of patients with chronic renal failure or patients under treatment with warfarin. HF antigen was detected by this assay in plasmas of primates, but not detectable in plasmas of 11 nonprimate mammalian and one avian species.« less

Tests of a Direct Effect of Childhood Abuse on Adult Borderline Personality Disorder Traits: A Longitudinal Discordant Twin Design

PubMed Central

Bornovalova, Marina A.; Huibregtse, Brooke M.; Hicks, Brian M.; Keyes, Margaret; McGue, Matt; Iacono, William

2012-01-01

We used a longitudinal twin design to examine the causal association between sexual, emotional, and physical abuse in childhood (before age 18) and borderline personality disorder (BPD) traits at age 24 using a discordant twin design and biometric modeling. Additionally, we examined the mediating and moderating effects of symptoms of childhood externalizing and internalizing disorders on the link between childhood abuse and BPD traits. Although childhood abuse, BPD traits, and internalizing and externalizing symptoms were all correlated, the discordant twin analyses and biometric modeling showed little to no evidence that consistent with a causal effect of childhood abuse on BPD traits. Instead, our results indicate that the association between childhood abuse and BPD traits stems from common genetic influences that, in some cases, also overlap with internalizing and externalizing disorders. These findings are inconsistent with the widely held assumption that childhood abuse causes BPD, and suggests that BPD traits in adulthood are better accounted for by heritable vulnerabilities to internalizing and externalizing disorders. PMID:22686871

A Bayesian Poisson-lognormal Model for Count Data for Multiple-Trait Multiple-Environment Genomic-Enabled Prediction.

PubMed

Montesinos-López, Osval A; Montesinos-López, Abelardo; Crossa, José; Toledo, Fernando H; Montesinos-López, José C; Singh, Pawan; Juliana, Philomin; Salinas-Ruiz, Josafhat

2017-05-05

When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype × environment interaction (G × E), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G × E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data. The proposed model was developed under the Bayesian paradigm for which we developed a Markov Chain Monte Carlo (MCMC) with noninformative priors. This allows obtaining all required full conditional distributions of the parameters leading to an exact Gibbs sampler for the posterior distribution. Our model was tested with simulated data and a real data set. Results show that the proposed multi-trait, multi-environment model is an attractive alternative for modeling multiple count traits measured in multiple environments. Copyright © 2017 Montesinos-López et al.

Genetic Changes Accompanying the Domestication of Pisum sativum: Is there a Common Genetic Basis to the ‘Domestication Syndrome’ for Legumes?

PubMed Central

Weeden, Norman F.

2007-01-01

Background and Aims The changes that occur during the domestication of crops such as maize and common bean appear to be controlled by relatively few genes. This study investigates the genetic basis of domestication in pea (Pisum sativum) and compares the genes involved with those determined to be important in common bean domestication. Methods Quantitative trait loci and classical genetic analysis are used to investigate and identify the genes modified at three stages of the domestication process. Five recombinant inbred populations involving crosses between different lines representing different stages are examined. Key Results A minimum of 15 known genes, in addition to a relatively few major quantitative trait loci, are identified as being critical to the domestication process. These genes control traits such as pod dehiscence, seed dormancy, seed size and other seed quality characters, stem height, root mass, and harvest index. Several of the genes have pleiotropic effects that in species possessing a more rudimentary genetic characterization might have been interpreted as clusters of genes. Very little evidence for gene clustering was found in pea. When compared with common bean, pea has used a different set of genes to produce the same or similar phenotypic changes. Conclusions Similar to results for common bean, relatively few genes appear to have been modified during the domestication of pea. However, the genes involved are different, and there does not appear to be a common genetic basis to ‘domestication syndrome’ in the Fabaceae. PMID:17660515