Browsing by Subject "TRAITS"

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  • Surendran, Praveen; Feofanova, Elena; Lahrouchi, Najim; Ntalla, Ioanna; Karthikeyan, Savita; Cook, James; Chen, Lingyan; Mifsud, Borbala; Yao, Chen; Kraja, Aldi T.; Cartwright, James H.; Hellwege, Jacklyn N.; Giri, Ayush; Tragante, Vinicius; Thorleifsson, Gudmar; Liu, Dajiang J.; Prins, Bram P.; Stewart, Isobel D.; Cabrera, Claudia P.; Eales, James M.; Akbarov, Artur; Auer, Paul L.; Bielak, Lawrence F.; Bis, Joshua C.; Braithwaite, Vickie S.; Brody, Jennifer A.; Daw, E. Warwick; Warren, Helen R.; Drenos, Fotios; Nielsen, Sune Fallgaard; Faul, Jessica D.; Fauman, Eric B.; Fava, Cristiano; Ferreira, Teresa; Foley, Christopher N.; Franceschini, Nora; Gao, He; Giannakopoulou, Olga; Giulianini, Franco; Gudbjartsson, Daniel F.; Guo, Xiuqing; Harris, Sarah E.; Havulinna, Aki S.; Helgadottir, Anna; Huffman, Jennifer E.; Hwang, Shih-Jen; Kanoni, Stavroula; Kontto, Jukka; Larson, Martin G.; Li-Gao, Ruifang; Lindström, Jaana; Lotta, Luca A.; Lu, Yingchang; Luan, Jian'an; Mahajan, Anubha; Malerba, Giovanni; Masca, Nicholas G. D.; Mei, Hao; Menni, Cristina; Mook-Kanamori, Dennis O.; Mosen-Ansorena, David; Muller-Nurasyid, Martina; Pare, Guillaume; Paul, Dirk S.; Perola, Markus; Poveda, Alaitz; Rauramaa, Rainer; Richard, Melissa; Richardson, Tom G.; Sepulveda, Nuno; Sim, Xueling; Smith, Albert; Smith, Jennifer A.; Staley, James R.; Stanakova, Alena; Sulem, Patrick; Theriault, Sebastien; Thorsteinsdottir, Unnur; Trompet, Stella; Varga, Tibor V.; Edwards, Digna R. Velez; Veronesi, Giovanni; Weiss, Stefan; Willems, Sara M.; Yao, Jie; Young, Robin; Yu, Bing; Zhang, Weihua; Zhao, Jing-Hua; Zhao, Wei; Zhao, Wei; Evangelou, Evangelos; Aeschbacher, Stefanie; Asllanaj, Eralda; Blankenberg, Stefan; Bonnycastle, Lori L.; Bork-Jensen, Jette; Brandslund, Ivan; Braund, Peter S.; Burgess, Stephen; Cho, Kelly; Christensen, Cramer; Connell, John; de Mutsert, Renee; Dominiczak, Anna F.; Dorr, Marcus; Eiriksdottir, Gudny; Farmaki, Aliki-Eleni; Gaziano, J. Michael; Grarup, Niels; Grove, Megan L.; Hallmans, Goran; Hansen, Torben; Have, Christian T.; Heiss, Gerardo; Jorgensen, Marit E.; Jousilahti, Pekka; Kajantie, Eero; Kamat, Mihir; Karajamaki, AnneMari; Karpe, Fredrik; Koistinen, Heikki A.; Kovesdy, Csaba P.; Kuulasmaa, Kari; Laatikainen, Tiina; Lannfelt, Lars; Lee, I-Te; Lee, Wen-Jane; Linneberg, Allan; Martin, Lisa W.; Moitry, Marie; Nadkarni, Girish; Neville, Matt J.; Palmer, Colin N. A.; Papanicolaou, George J.; Pedersen, Oluf; Peters, James; Poulter, Neil; Rasheed, Asif; Rasmussen, Katrine L.; Rayner, N. William; Magi, Reedik; Renstrom, Frida; Rettig, Rainer; Rossouw, Jacques; Schreiner, Pamela J.; Sever, Peter S.; Sigurdsson, Emil L.; Skaaby, Tea; Sun, Yan; Sundstrom, Johan; Thorgeirsson, Gudmundur; Esko, Tonu; Trabetti, Elisabetta; Tsao, Philip S.; Tuomi, Tiinamaija; Turner, Stephen T.; Tzoulaki, Ioanna; Vaartjes, Ilonca; Vergnaud, Anne-Claire; Willer, Cristen J.; Wilson, Peter W. F.; Witte, Daniel R.; Yonova-Doing, Ekaterina; Zhang, He; Aliya, Naheed; Almgren, Peter; Amouyel, Philippe; Asselbergs, Folkert W.; Barnes, Michael R.; Blakemore, Alexandra; Boehnke, Michael; Bots, Michiel L.; Bottinger, Erwin P.; Buring, Julie E.; Chambers, John C.; Chen, Yii-Der Ida; Chowdhury, Rajiv; Conen, David; Correa, Adolfo; Smith, George Davey; de Boer, Rudolf A.; Deary, Ian J.; Dedoussis, George; Deloukas, Panos; Di Angelantonio, Emanuele; Elliott, Paul; Felix, Stephan B.; Ferrieres, Jean; Ford, Ian; Fornage, Myriam; Franks, Paul W.; Franks, Stephen; Frossard, Philippe; Gambaro, Giovanni; Gaunt, Tom R.; Groop, Leif; Gudnason, Vilmundur; Harris, Tamara B.; Hayward, Caroline; Hennig, Branwen J.; Herzig, Karl-Heinz; Ingelsson, Erik; Tuomilehto, Jaakko; Jarvelin, Marjo-Riitta; Jukema, J. Wouter; Kardia, Sharon L. R.; Kee, Frank; Kooner, Jaspal S.; Kooperberg, Charles; Launer, Lenore J.; Lind, Lars; Loos, Ruth J. F.; Majumder, Abdulla Al Shafi; Laakso, Markku; McCarthy, Mark; Melander, Olle; Mohlke, Karen L.; Murray, Alison D.; Nordestgaard, Borge Gronne; Orho-Melander, Marju; Packard, Chris J.; Padmanabhan, Sandosh; Palmas, Walter; Polasek, Ozren; Porteous, David J.; Prentice, Andrew M.; Province, Michael A.; Relton, Caroline L.; Rice, Kenneth; Ridker, Paul M.; Rolandsson, Olov; Rosendaal, Frits R.; Rotter, Jerome; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J.; Sattar, Naveed; Sheu, Wayne H-H; Smith, Blair H.; Soranzo, Nicole; Spector, Timothy D.; Starr, John M.; Sebert, Sylvain; Taylor, Kent D.; Lakka, Timo A.; Timpson, Nicholas J.; Tobin, Martin D.; van der Harst, Pim; van der Meer, Peter; Ramachandran, Vasan S.; Verweij, Niek; Virtamo, Jarmo; Volker, Uwe; Weir, David R.; Zeggini, Eleftheria; Charchar, Fadi J.; Wareham, Nicholas J.; Langenberg, Claudia; Tomaszewski, Maciej; Butterworth, Adam S.; Caulfield, Mark J.; Danesh, John; Edwards, Todd L.; Holm, Hilma; Hung, Adriana M.; Lindgren, Cecilia M.; Liu, Chunyu; Manning, Alisa K.; Morris, Andrew P.; Morrison, Alanna C.; O'Donnell, Christopher J.; Psaty, Bruce M.; Saleheen, Danish; Stefansson, Kari; Boerwinkle, Eric; Chasman, Daniel; Levy, Daniel; Newton-Cheh, Christopher; Munroe, Patricia B.; Howson, Joanna M. M. (2020)
    Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to similar to 1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency
  • Chen, Jing; Bacelis, Jonas; Sole-Navais, Pol; Srivastava, Amit; Juodakis, Julius; Rouse, Amy; Hallman, Mikko; Teramo, Kari; Melbye, Mads; Feenstra, Bjarke; Freathy, Rachel M.; Smith, George Davey; Lawlor, Deborah A.; Murray, Jeffrey C.; Williams, Scott M.; Jacobsson, Bo; Muglia, Louis J.; Zhang, Ge (2020)
    Author summaryWhy was this study done? Maternal height, BMI, blood glucose, and blood pressure are associated with gestational duration, birth weight, and birth length. These birth outcomes are subsequently associated with late-onset health conditions. The causal mechanisms and the relative contributions of maternal and fetal genetic effects underlying these observed associations are not clear. What did the researchers do and find? We dissected the relative contributions of maternal and fetal genetic effects using haplotype genetic score analysis in 10,734 mother-infant pairs of European ancestry. Genetically elevated maternal height is associated with longer gestational duration and larger birth size. In the fetus, alleles associated with adult height are positively associated with birth size. Alleles elevating blood pressure are associated with shorter gestational duration through a maternal effect and are associated with reduced fetal growth through a fetal genetic effect. Alleles that increase blood glucose in the mother are associated with increased birth weight, whereas risk alleles for type 2 diabetes in the fetus are associated with reduced birth weight. Alleles raising birth weight in fetus are associated with shorter gestational duration and higher maternal blood pressure during pregnancy. What do these findings mean? Maternal size and fetal growth are important factors in shaping the duration of gestation. Fetal growth is influenced by both maternal and fetal effects. Higher maternal BMI and glucose levels positively associate with birth weight through maternal effects. In the fetus, alleles associated with higher metabolic risks are negatively associated with birth weight. More rapid fetal growth is associated with shorter gestational duration and higher maternal blood pressure. These maternal and fetal genetic effects can largely explain the observed associations between maternal phenotypes and birth outcomes, as well as the life-course associations between these birth outcomes and adult phenotypes. Background Many maternal traits are associated with a neonate's gestational duration, birth weight, and birth length. These birth outcomes are subsequently associated with late-onset health conditions. The causal mechanisms and the relative contributions of maternal and fetal genetic effects behind these observed associations are unresolved. Methods and findings Based on 10,734 mother-infant duos of European ancestry from the UK, Northern Europe, Australia, and North America, we constructed haplotype genetic scores using single-nucleotide polymorphisms (SNPs) known to be associated with adult height, body mass index (BMI), blood pressure (BP), fasting plasma glucose (FPG), and type 2 diabetes (T2D). Using these scores as genetic instruments, we estimated the maternal and fetal genetic effects underlying the observed associations between maternal phenotypes and pregnancy outcomes. We also used infant-specific birth weight genetic scores as instrument and examined the effects of fetal growth on pregnancy outcomes, maternal BP, and glucose levels during pregnancy. The maternal nontransmitted haplotype score for height was significantly associated with gestational duration (p= 2.2 x 10(-4)). Both maternal and paternal transmitted height haplotype scores were highly significantly associated with birth weight and length (p<1 x 10(-17)). The maternal transmitted BMI scores were associated with birth weight with a significant maternal effect (p= 1.6 x 10(-4)). Both maternal and paternal transmitted BP scores were negatively associated with birth weight with a significant fetal effect (p= 9.4 x 10(-3)), whereas BP alleles were significantly associated with gestational duration and preterm birth through maternal effects (p= 3.3 x 10(-2)andp= 4.5 x 10(-3), respectively). The nontransmitted haplotype score for FPG was strongly associated with birth weight (p= 4.7 x 10(-6)); however, the glucose-increasing alleles in the fetus were associated with reduced birth weight through a fetal effect (p= 2.2 x 10(-3)). The haplotype scores for T2D were associated with birth weight in a similar way but with a weaker maternal effect (p= 6.4 x 10(-3)) and a stronger fetal effect (p= 1.3 x 10(-5)). The paternal transmitted birth weight score was significantly associated with reduced gestational duration (p= 1.8 x 10(-4)) and increased maternal systolic BP during pregnancy (p= 2.2 x 10(-2)). The major limitations of the study include missing and heterogenous phenotype data in some data sets and different instrumental strength of genetic scores for different phenotypic traits. Conclusions We found that both maternal height and fetal growth are important factors in shaping the duration of gestation: genetically elevated maternal height is associated with longer gestational duration, whereas alleles that increase fetal growth are associated with shorter gestational duration. Fetal growth is influenced by both maternal and fetal effects and can reciprocally influence maternal phenotypes: taller maternal stature, higher maternal BMI, and higher maternal blood glucose are associated with larger birth size through maternal effects; in the fetus, the height- and metabolic-risk-increasing alleles are associated with increased and decreased birth size, respectively; alleles raising birth weight in the fetus are associated with shorter gestational duration and higher maternal BP. These maternal and fetal genetic effects may explain the observed associations between the studied maternal phenotypes and birth outcomes, as well as the life-course associations between these birth outcomes and adult phenotypes.
  • Belachew, Kiflemariam Yehuala; Nagel, Kerstin; Fiorani, Fabio; Stoddard, Frederick Lothrop (2018)
    Background Soil moisture deficiency causes yield reduction and instability in faba bean (Vicia faba L.) production. The extent of sensitivity to drought stress varies across accessions originating from diverse moisture regimes of the world. Hence, we conducted successive greenhouse experiments in pots and rhizotrons to explore diversity in root responses to soil water deficit. Methods A set of 89 accessions from wet and dry growing regions of the world was defined according to the Focused Identification of Germplasm Strategy and screened in a perlite-sand medium under well watered conditions in a greenhouse experiment. Stomatal conductance, canopy temperature, chlorophyll concentration, and root and shoot dry weights were recorded during the fifth week of growth. Eight accessions representing the range of responses were selected for further investigation. Starting five days after germination, they were subjected to a root phenotyping experiment using the automated phenotyping platform GROWSCREEN-Rhizo. The rhizotrons were filled with peat-soil under well watered and water limited conditions. Root architectural traits were recorded five, 12, and 19 days after the treatment (DAT) began. Results In the germplasm survey, accessions from dry regions showed significantly higher values of chlorophyll concentration, shoot and root dry weights than those from wet regions. Root and shoot dry weight as well as seed weight, and chlorophyll concentration were positively correlated with each other. Accession DS70622 combined higher values of root and shoot dry weight than the rest. The experiment in GROWSCREEN-Rhizo showed large differences in root response to water deficit. The accession by treatment interactions in taproot and second order lateral root lengths were significant at 12 and 19 DAT, and the taproot length was reduced up to 57% by drought. The longest and deepest root systems under both treatment conditions were recorded by DS70622 and DS11320, and total root length of DS70622 was three times longer than that of WS99501, the shortest rooted accession. The maximum horizontal distribution of a root system and root surface coverage were positively correlated with taproot and total root lengths and root system depth. DS70622 and WS99501 combined maximum and minimum values of these traits, respectively. Thus, roots of DS70622 and DS11320, from dry regions, showed drought-avoidance characteristics whereas those of WS99501 and Melodie/2, from wet regions, showed the opposite. Discussion The combination of the germplasm survey and use of GROWSCREEN-Rhizo allowed exploring of adaptive traits and detection of root phenotypic markers for potential drought avoidance. The greater root system depth and root surface coverage, exemplified by DS70622 and DS11320, can now be tested as new sources of drought tolerance.
  • Leikas, Sointu; Kuula, Liisa; Pesonen, Anu-Katriina (2021)
    Experience sampling studies have shown that people act out of character a lot of the time. These findings have raised the question of potential costs of counter-habitual behavior. The present experience sampling study (N = 242; measurement occasions = 4342) tested, for five behavioral dimensions derived from the Big Five theory, whether self-reported counter-habitual behavior is related to psychological costs in everyday life. The results mostly supported the view that engaging in desirable counter-habitual behaviors is beneficial, though some evidence for counter-habitual costs was found for self-control. Overall, the results suggest that the state-content significance hypothesis better accounts for everyday life behavioral, affective, and self-regulatory processes than the views highlighting the importance of acting according to one's "true self" (C) 2021 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
  • Hamberg, Leena; Velmala, Sannakajsa M.; Sievänen, Risto; Kalliokoski, Tuomo; Pennanen, Taina (2018)
    The relationship between the growth rate of aboveground parts of trees and fine root development is largely unknown. We investigated the early root development of fast-and slow-growing Norway spruce (Picea abies (L.) H. Karst.) families at a developmental stage when the difference in size is not yet observed. Seedling root architecture data, describing root branching, were collected with the WinRHIZO (TM) image analysis system, and mixed models were used to determine possible differences between the two growth phenotypes. A new approach was used to investigate the spatial extent of root properties along the whole sample root from the base of 1-year-old seedlings to the most distal part of a root. The root architecture of seedlings representing fastgrowing phenotypes showed similar to 30% higher numbers of root branches and tips, which resulted in larger root extensions and potentially a better ability to acquire nutrients. Seedlings of fast-growing phenotypes oriented and allocated root tips and bio-mass further away from the base of the seedling than those growing slowly, a possible advantage in nutrient-limited and heterogeneous boreal forest soils. We conclude that a higher long-term growth rate of the aboveground parts in Norway spruce may relate to greater allocation of resources to explorative roots that confers a competitive edge during early growth phases in forest ecosystems.
  • He, Siwen; Soininen, Janne; Chen, Kai; Wang, Beixin (2020)
    Metacommunity theory provides a useful framework to describe the underlying factors (e.g., environmental and dispersal-related factors) influencing community structure. The strength of these factors may vary depending on the properties of the region studied (e.g., environmental heterogeneity and spatial location) and considered biological groups. Here, we examined environmental and dispersal-related controls of stream macroinvertebrates and diatoms in three regions in China using the distance-decay relationship analysis. We performed analyses for the whole stream network and separately for two stream network locations (headwater and downstream sites) to test the network position hypothesis (NPH), which states that the strength of environmental and dispersal-related controls varies between headwater and downstream communities. Community dissimilarities were significantly related to environmental distances, but not geographical distances. These results suggest that communities are structured strongly by environmental filtering, but weakly by dispersal-related factors such as dispersal limitation. More importantly, we found that, at the whole network scale, environmental control was the highest in the regions with highest environmental heterogeneity. Results further showed that the influence of environmental control was strong in both headwaters and downstream sites, whereas spatial control was generally weak in all sites. This suggests a lack of consistent support for the NPH in our studied stream networks. Moreover, we found that local-scale variables relative to basin-scale variables better explained community dissimilarities for diatoms than for macroinvertebrates. This indicates that diatoms and macroinvertebrates responded to environment at different scales. Collectively, these results suggest that the importance of drivers behind the metacommunity assembly varied among regions with different level of environmental heterogeneity and between organism groups, potentially indicating context dependency among stream systems and taxa.
  • Martikainen, K.; Tyrisevä, A. M.; Matilainen, K.; Pösö, J.; Uimari, P. (2017)
    Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F-PH), runs of homozygosity (F-ROH) and pedigree (F-PED). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F-PED was 0.02, F-ROH 0.06 and F-PH 0.63. A correlation of 0.71 was found between F-PED and F-ROH, 0.66 between F-PED and F-PH and 0.94 between F-ROH and F-PH. Pedigree-based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F-ROH or F-PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F-ROH was associated with 5days longer IFL0 and IFL1, 2weeks longer IFL3 and 3days longer ICF2 compared to non-inbred cows.
  • Martikainen, K.; Sironen, A.; Uimari, P. (2018)
    Inbreeding increases homozygosity, which in turn increases the frequency of harmful recessive alleles, resulting in inbreeding depression. Inbreeding depression on fertility reduces the profitability of dairy farming by decreasing the lifetime milk production of cows and by increasing insemination and veterinary costs. Continuous homozygous segments, called runs of homozygosity (ROH), are currently considered to provide an effective measure of genomic inbreeding. The aim of this study was to estimate the effect of increased intrachromosomal homozygosity for female fertility in the Finnish Ayrshire population using ROH and haplotype analysis. Genotypes were obtained from 13,712 females with the Illumina BovineLD v.2 BeadChip low-density panel (Illumina Inc., San Diego, CA) and imputed to 50K density. After quality control, 40,554 single nucleotide polymorphisms remained for the analysis. Phenotypic data consisted of records for nonreturn rate, intervals from first to last insemination (IFL), and intervals from calving to first insemination. The raw phenotypic values were preadjusted for systematic effects before statistical analyses. The ROH-based inbreeding coefficients (F-ROH) were used as covariats in the mixed model equation to estimate the association between inbreeding and inbreeding depression on female fertility. First, we estimated the effect of increased chromosomal F-ROH. We detected significant inbreeding depression on IFL. Based on our results, a 10% increase in F-ROH on chromosomes 2, 18, and 22 were associated with IFL of heifers lengthening by 1.6, 0.9, and 0.7 d, respectively. Similarly, a 10% increase in F-ROH on chromosome 15 was associated with IFL of second-parity cows increasing by 2.3 d. Next, we located the regions within the chromosomes showing inbreeding depression. Our analysis revealed regions near the beginning of chromosome 2 and toward the ends of chromosomes 15, 18, and 22 that were associated with inbreeding depression on IFL. Last, we performed a haplotype analysis for the detected regions. The most promising haplotypes of each region were associated with IFL of heifers increasing by 4.4, 3.2, and 4.1 d on chromosomes 2, 18, and 22, respectively. The haplotype on chromosome 15 associated with IFL of second-parity cows increasing by 7.6 d. Overall, the breeding program requires inbreeding control, as increased genomic inbreeding in our study was associated with reduced reproductive ability in Finnish Ayrshire cattle.
  • Prasad, Rashmi B.; Lessmark, Anna; Almgren, Peter; Kovacs, Gyorgyi; Hansson, Ola; Oskolkov, Nikolay; Vitai, Marta; Ladenvall, Claes; Kovacs, Peter; Fadista, Joao; Lachmann, Michael; Zhou, Yuedan; Sonestedt, Emily; Poon, Wenny; Wollheim, Claes B.; Orho-Melander, Marju; Stumvoll, Michael; Tuomi, Tiinamaija; Paeaebo, Svante; Koranyi, Laszlo; Groop, Leif (2016)
    Aims/hypothesis Genome-wide association studies (GWAS) have identified more than 65 genetic loci associated with risk of type 2 diabetes. However, the contribution of distorted parental transmission of alleles to risk of type 2 diabetes has been mostly unexplored. Our goal was therefore to search for parent-of-origin effects (POE) among type 2 diabetes loci in families. Methods Families from the Botnia study (n = 4,211, 1,083 families) were genotyped for 72 single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes and assessed for POE on type 2 diabetes. The family-based Hungarian Transdanubian Biobank (HTB) (n = 1,463, > 135 families) was used to replicate SNPs showing POE. Association of type 2 diabetes loci within families was also tested. Results Three loci showed nominal POE, including the previously reported variants in KCNQ1, for type 2 diabetes in families from Botnia (rs2237895: p(POE) = 0.037), which can be considered positive controls. The strongest POE was seen for rs7578597 SNP in the THADA gene, showing excess transmission of the maternal risk allele T to diabetic offspring (Botnia: p(POE) = 0.01; HTB p(POE) = 0.045). These data are consistent with previous evidence of allelic imbalance for expression in islets, suggesting that the THADA gene can be imprinted in a POE-specific fashion. Five CpG sites, including those flanking rs7578597, showed differential methylation between diabetic and non-diabetic donor islets. Conclusions/interpretation Taken together, the data emphasise the need for genetic studies to consider from which parent an offspring has inherited a susceptibility allele.
  • FinnGen Project; Locke, Adam E.; Havulinna, Aki S.; Pirinen, Matti; Eriksson, Johan G.; Ala-Korpela, Mika; Järvelin, Marjo-Riitta; Männikkö, Minna; Laivuori, Hannele; Palotie, Aarno; Salomaa, Veikko; Laakso, Markku; Ripatti, Samuli (2019)
    Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.
  • Heino, Jani; Grönroos, Mira (2017)
    It was recently suggested that beta diversity can be partitioned into contributions of single sites to overall beta diversity (LCBD) or into contributions of individual species to overall beta diversity (SCBD). We explored the relationships of LCBD and SCBD to site and species characteristics, respectively, in stream insect assemblages. We found that LCBD was mostly explained by variation in species richness, with a negative relationship being detected. SCBD was strongly related to various species characteristics, such as occupancy, abundance, niche position and niche breadth, but was only weakly related to biological traits of species. In particular, occupancy and its quadratic terms showed a very strong unimodal relationship with SCBD, suggesting that intermediate species in terms of site occupancy contribute most to beta diversity. Our findings of unravelling the contributions of sites or species to overall beta diversity are of high importance to community ecology, conservation and bioassessment using stream insect assemblages, and may bear some overall generalities to be found in other organism groups.
  • Mahajan, Anubha; Taliun, Daniel; Thurner, Matthias; Robertson, Neil R.; Torres, Jason M.; Rayner, N. William; Payne, Anthony J.; Steinthorsdottir, Valgerdur; Scott, Robert A.; Grarup, Niels; Cook, James P.; Schmidt, Ellen M.; Wuttke, Matthias; Sarnowski, Chloe; Magill, Reedik; Nano, Jana; Gieger, Christian; Trompet, Stella; Lecoeur, Cecile; Preuss, Michael H.; Prins, Bram Peter; Guo, Xiuqing; Bielak, Lawrence F.; Below, Jennifer E.; Bowden, Donald W.; Chambers, John Campbell; Kim, Young Jin; Ng, Maggie C. Y.; Petty, Lauren E.; Sim, Xueling; Zhang, Weihua; Bennett, Amanda J.; Bork-Jensen, Jette; Brummett, Chad M.; Canouil, Mickael; Kardt, Kai-Uwe Ec; Fischer, Krista; Kardia, Sharon L. R.; Kronenberg, Florian; Lall, Kristi; Liu, Ching-Ti; Locke, Adam E.; Luan, Jian'an; Ntalla, Loanna; Nylander, Vibe; Schoenherr, Sebastian; Schurmann, Claudia; Yengo, Loic; Bottinger, Erwin P.; Brandslund, Ivan; Christensen, Cramer; Dedoussis, George; Florez, Jose C.; Ford, Ian; France, Oscar H.; Frayling, Timothy M.; Giedraitis, Vilmantas; Hackinger, Sophie; Hattersley, Andrew T.; Herder, Christian; Ikram, M. Arfan; Ingelsson, Martin; Jorgensen, Marit E.; Jorgensen, Torben; Kriebel, Jennifer; Kuusisto, Johanna; Ligthart, Symen; Lindgren, Cecilia M.; Linneberg, Allan; Lyssenko, Valeriya; Mamakou, Vasiliki; Meitinger, Thomas; Mohlke, Karen L.; Morris, Andrew D.; Nadkarni, Girish; Pankow, James S.; Peters, Annette; Sattar, Naveed; Stancakova, Alena; Strauch, Konstantin; Taylor, Kent D.; Thorand, Barbara; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Tuomilehto, Jaakko; Witte, Daniel R.; Dupuis, Josee; Peyser, Patricia A.; Zeggini, Eleftheria; Loos, Ruth J. F.; Froguel, Philippe; Ingelsson, Erik; Lind, Lars; Groop, Leif; Laakso, Markku; Collins, Francis S.; Jukema, J. Wouter; Palmer, Colin N. A.; Grallert, Harald; Metspalu, Andres; Dehghan, Abbas; Koettgen, Anna; Abecasis, Goncalo R.; Meigs, James B.; Rotter, Jerome; Marchini, Jonathan; Pedersen, Oluf; Hansen, Torben; Langenberg, Claudia; Wareham, Nicholas J.; Stefansson, Kari; Gloyn, Anna L.; Morris, Andrew P.; Boehnke, Michael; McCarthy, Mark (2018)
    We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci,135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency 2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).
  • Huang, Yisong; Ollikainen, Miina; Sipilä, Pyry; Mustelin, Linda; Wang, Xin; Su, Shaoyong; Huan, Tianxiao; Levy, Daniel; Wilson, James; Snieder, Harold; Kaprio, Jaakko; Wang, Xiaoling (2018)
    Recently, 2 transcriptome-wide studies identified 40 genes that were differentially expressed in relation to blood pressure. However, to what extent these BP-related gene expression signatures and their associations with BP are driven by genetic or environmental factors has not been investigated. In this study of 391 twins (193 twin pairs and 5 singletons; age 55-69 years; 40% male; 57% monozygous) recruited from the Finnish Twin Cohort, transcriptome-wide data on peripheral leukocytes were obtained using the Illumina HT12 V4 array. Our transcriptome-wide analysis identified 1 gene (MOK [MAPK/MAK/MRK overlapping kinase], P=7.16x10(-8)) with its expression levels associated with systolic BP at the cutoff of false-discovery rate
  • Jelenkovic, Aline; Sund, Reijo; Hur, Yoon-Mi; Yokoyama, Yoshie; Hjelmborg, Jacob V. B.; Moller, Soren; Honda, Chika; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Ooki, Syuichi; Aaltonen, Sari; Stazi, Maria A.; Fagnani, Corrado; D'Ippolito, Cristina; Freitas, Duarte L.; Maia, Jose Antonio; Ji, Fuling; Ning, Feng; Pang, Zengchang; Rebato, Esther; Busjahn, Andreas; Kandler, Christian; Saudino, Kimberly J.; Jang, Kerry L.; Cozen, Wendy; Hwang, Amie E.; Mack, Thomas M.; Gao, Wenjing; Yu, Canqing; Li, Liming; Corley, Robin P.; Huibregtse, Brooke M.; Derom, Catherine A.; Vlietinck, Robert F.; Loos, Ruth J. F.; Heikkila, Kauko; Wardle, Jane; Llewellyn, Clare H.; Fisher, Abigail; McAdams, Tom A.; Eley, Thalia C.; Gregory, Alice M.; He, Mingguang; Ding, Xiaohu; Bjerregaard-Andersen, Morten; Beck-Nielsen, Henning; Sodemann, Morten; Tarnoki, Adam D.; Tarnoki, David L.; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Burt, S. Alexandra; Klump, Kelly L.; Silberg, Judy L.; Eaves, Lindon J.; Maes, Hermine H.; Krueger, Robert F.; McGue, Matt; Pahlen, Shandell; Gatz, Margaret; Butler, David A.; Bartels, Meike; van Beijsterveldt, Toos C. E. M.; Craig, Jeffrey M.; Saffery, Richard; Dubois, Lise; Boivin, Michel; Brendgen, Mara; Dionne, Ginette; Vitaro, Frank; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Swan, Gary E.; Krasnow, Ruth; Tynelius, Per; Lichtenstein, Paul; Haworth, Claire M. A.; Plomin, Robert; Bayasgalan, Gombojav; Narandalai, Danshiitsoodol; Harden, K. Paige; Tucker-Drob, Elliot M.; Spector, Timothy; Mangino, Massimo; Lachance, Genevieve; Baker, Laura A.; Tuvblad, Catherine; Duncan, Glen E.; Buchwald, Dedra; Willemsen, Gonneke; Skytthe, Axel; Kyvik, Kirsten O.; Christensen, Kaare; Oncel, Sevgi Y.; Aliev, Fazil; Rasmussen, Finn; Goldberg, Jack H.; Sorensen, Thorkild I. A.; Boomsma, Dorret I.; Kaprio, Jaakko; Silventoinen, Karri (2016)
    Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1-19 years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments.
  • Silventoinen, Karri; Jelenkovic, Aline; Sund, Reijo; Latvala, Antti; Honda, Chika; Inui, Fujio; Tomizawa, Rie; Watanabe, Mikio; Sakai, Norio; Rebato, Esther; Busjahn, Andreas; Tyler, Jessica; Hopper, John L.; Ordonana, Juan R.; Sanchez-Romera, Juan F.; Colodro-Conde, Lucia; Calais-Ferreira, Lucas; Oliveira, Vinicius C.; Ferreira, Paulo H.; Medda, Emanuela; Nistico, Lorenza; Toccaceli, Virgilia; Derom, Catherine A.; Vlietinck, Robert F.; Loos, Ruth J. F.; Siribaddana, Sisira H.; Hotopf, Matthew; Sumathipala, Athula; Rijsdijk, Fruhling; Duncan, Glen E.; Buchwald, Dedra; Tynelius, Per; Rasmussen, Finn; Tan, Qihua; Zhang, Dongfeng; Pang, Zengchang; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Aslan, Anna K. Dahl; Hwang, Amie E.; Mack, Thomas M.; Krueger, Robert F.; McGue, Matt; Pahlen, Shandell; Brandt, Ingunn; Nilsen, Thomas S.; Harris, Jennifer R.; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Willemsen, Gonneke; Bartels, Meike; van Beijsterveldt, Catharina E. M.; Franz, Carol E.; Kremen, William S.; Lyons, Michael J.; Silberg, Judy L.; Maes, Hermine H.; Kandler, Christian; Nelson, Tracy L.; Whitfield, Keith E.; Corley, Robin P.; Huibregtse, Brooke M.; Gatz, Margaret; Butler, David A.; Tarnoki, Adam D.; Tarnoki, David L.; Park, Hang A.; Lee, Jooyeon; Lee, Soo Ji; Sung, Joohon; Yokoyama, Yoshie; Sorensen, Thorkild I. A.; Boomsma, Dorret; Kaprio, Jaakko (2020)
    We investigated the heritability of educational attainment and how it differed between birth cohorts and cultural-geographic regions. A classical twin design was applied to pooled data from 28 cohorts representing 16 countries and including 193,518 twins with information on educational attainment at 25 years of age or older. Genetic factors explained the major part of individual differences in educational attainment (heritability: a(2)=0.43; 0.41-0.44), but also environmental variation shared by co-twins was substantial (c(2)=0.31; 0.30-0.33). The proportions of educational variation explained by genetic and shared environmental factors did not differ between Europe, North America and Australia, and East Asia. When restricted to twins 30 years or older to confirm finalized education, the heritability was higher in the older cohorts born in 1900-1949 (a(2)=0.44; 0.41-0.46) than in the later cohorts born in 1950-1989 (a(2)=0.38; 0.36-0.40), with a corresponding lower influence of common environmental factors (c(2)=0.31; 0.29-0.33 and c(2)=0.34; 0.32-0.36, respectively). In conclusion, both genetic and environmental factors shared by co-twins have an important influence on individual differences in educational attainment. The effect of genetic factors on educational attainment has decreased from the cohorts born before to those born after the 1950s.
  • Savage, Jeanne E.; Jansen, Philip R.; Stringer, Sven; Watanabe, Kyoko; Bryois, Julien; de Leeuw, Christiaan A.; Nagel, Mats; Awasthi, Swapnil; Barr, Peter B.; Coleman, Jonathan R. I.; Grasby, Katrina L.; Hammerschlag, Anke R.; Kaminski, Jakob A.; Karlsson, Robert; Krapohl, Eva; Lam, Max; Nygaard, Marianne; Reynolds, Chandra A.; Trampush, Joey W.; Young, Hannah; Zabaneh, Delilah; Hagg, Sara; Hansell, Narelle K.; Karlsson, Ida K.; Linnarsson, Sten; Montgomery, Grant W.; Munoz-Manchado, Ana B.; Quinlan, Erin B.; Schumann, Gunter; Skene, Nathan G.; Webb, Bradley T.; White, Tonya; Arking, Dan E.; Avramopoulos, Dimitrios; Bilder, Robert M.; Bitsios, Panos; Burdick, Katherine E.; Cannon, Tyrone D.; Chiba-Falek, Ornit; Christoforou, Andrea; Cirulli, Elizabeth T.; Congdon, Eliza; Corvin, Aiden; Davies, Gail; Deary, Ian J.; DeRosse, Pamela; Dickinson, Dwight; Djurovic, Srdjan; Donohoe, Gary; Conley, Emily Drabant; Eriksson, Johan G.; Espeseth, Thomas; Freimer, Nelson A.; Giakoumaki, Stella; Giegling, Ina; Gill, Michael; Glahn, David C.; Hariri, Ahmad R.; Hatzimanolis, Alex; Keller, Matthew C.; Knowles, Emma; Koltai, Deborah; Konte, Bettina; Lahti, Jari; Le Hellard, Stephanie; Lencz, Todd; Liewald, David C.; London, Edythe; Lundervold, Astri J.; Malhotra, Anil K.; Melle, Ingrid; Morris, Derek; Need, Anna C.; Ollier, William; Palotie, Aarno; Payton, Antony; Pendleton, Neil; Poldrack, Russell A.; Räikkönen, Katri; Reinvang, Ivar; Roussos, Panos; Rujescu, Dan; Sabb, Fred W.; Scult, Matthew A.; Smeland, Olav B.; Smyrnis, Nikolaos; Starr, John M.; Steen, Vidar M.; Stefanis, Nikos C.; Straub, Richard E.; Sundet, Kjetil; Tiemeier, Henning; Voineskos, Aristotle N.; Weinberger, Daniel R.; Widen, Elisabeth; Yu, Jin; Abecasis, Goncalo; Andreassen, Ole A.; Breen, Gerome; Christiansen, Lene; Debrabant, Birgit; Dick, Danielle M.; Heinz, Andreas; Hjerling-Leffler, Jens; Ikram, M. Arfan; Kendler, Kenneth S.; Martin, Nicholas G.; Medland, Sarah E.; Pedersen, Nancy L.; Plomin, Robert; Polderman, Tinca J. C.; Ripke, Stephan; van der Sluis, Sophie; Sullivan, Patrick F.; Vrieze, Scott I.; Wright, Margaret J.; Posthuma, Danielle (2018)
    Intelligence is highly heritable(1) and a major determinant of human health and well-being(2). Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence3-7, but much about its genetic underpinnings remains to be discovered. Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and associations with 146 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain, specifically in striatal medium spiny neurons and hippocampal pyramidal neurons. Gene set analyses implicate pathways related to nervous system development and synaptic structure. We confirm previous strong genetic correlations with multiple health-related outcomes, and Mendelian randomization analysis results suggest protective effects of intelligence for Alzheimer's disease and ADHD and bidirectional causation with pleiotropic effects for schizophrenia. These results are a major step forward in understanding the neurobiology of cognitive function as well as genetically related neurological and psychiatric disorders.
  • Nolte, Dorothea; Boutaud, Esteve; Kotze, D. Johan; Schuldt, Andreas; Assmann, Thorsten (2019)
    The worldwide biodiversity crisis is ongoing. To slow down, or even halt future species loss it is important to identify potential drivers of extinction risk. Species traits can help to understand the underlying process of extinction risk. In a comprehensive study on 464 carabid beetle species, we used ordinal logistic regression to analyze the relationship of species traits to extinction risk in Central Europe, taking phylogenetic relatedness into account. To consider varying trait responses in different habitat types, we also tested models for species groups associated with different habitat types (forest, open, riparian and wetland). Our results identified three traits of particular importance as predictors for high extinction risk: (1) high habitat specialization, (2) small distribution range size (which is not considered in the categorization of the German Red List), and (3) large body size. Furthermore, large macropterous species showed high extinction risk. Overall, species associated with mountainous, coastal and open habitats generally revealed a high risk of extinction, while most forest species showed a low extinction risk. However, forest species with predatory feeding behavior were threatened, as were wetland species that reproduce in autumn. Phylogenetic relatedness had no influence on how species traits predict carabid beetle extinction risk. In the light of these results, management and recovery plans for species which exhibit characteristic traits strongly associated with extinction risks, as well as the conservation and restoration of mountain, coastal and open habitats, have to be prioritized.
  • Laakasuo, Michael; Rotkirch, Anna; van Duijn, Max; Berg, Venla; Jokela, Markus; David-Barrett, Tamas; Miettinen, Anneli; Pearce, Eiluned; Dunbar, Robin (2020)
    Personality affects dyadic relations and teamwork, yet its role among groups of friends has been little explored. We examine for the first time whether similarity in personality enhances the effectiveness of real-life friendship groups. Using data from a longitudinal study of a European fraternity (10 male and 15 female groups), we investigate how individual Big Five personality traits were associated with group formation and whether personality homophily related to how successful the groups were over 1 year (N = 147–196). Group success was measured as group performance/identification (adoption of group markers) and as group bonding (using the inclusion-of-other-in-self scale). Results show that individuals’ similarity in neuroticism and conscientiousness predicted group formation. Furthermore, personality similarity was associated with group success, even after controlling for individual’s own personality. Especially higher group-level similarity in conscientiousness was associated with group performance, and with bonding in male groups.
  • Penteriani, Vincenzo; del Mar Delgado, Maria; Pinchera, Francesco; Naves, Javier; Fernandez-Gil, Alberto; Kojola, Ilpo; Härkönen, Sauli; Norberg, Harri; Frank, Jens; Maria Fedriani, Jose; Sahlen, Veronica; Stoen, Ole-Gunnar; Swenson, Jon E.; Wabakken, Petter; Pellegrini, Mario; Herrero, Stephen; Vicente Lopez-Bao, Jose (2016)
    The media and scientific literature are increasingly reporting an escalation of large carnivore attacks on humans in North America and Europe. Although rare compared to human fatalities by other wildlife, the media often overplay large carnivore attacks on humans, causing increased fear and negative attitudes towards coexisting with and conserving these species. Although large carnivore populations are generally increasing in developed countries, increased numbers are not solely responsible for the observed rise in the number of attacks by large carnivores. Here we show that an increasing number of people are involved in outdoor activities and, when doing so, some people engage in risk-enhancing behaviour that can increase the probability of a risky encounter and a potential attack. About half of the well-documented reported attacks have involved risk-enhancing human behaviours, the most common of which is leaving children unattended. Our study provides unique insight into the causes, and as a result the prevention, of large carnivore attacks on people. Prevention and information that can encourage appropriate human behaviour when sharing the landscape with large carnivores are of paramount importance to reduce both potentially fatal human-carnivore encounters and their consequences to large carnivores.
  • Gladstone-Gallagher, Rebecca V.; Hewitt, Judi E.; Thrush, Simon F.; Brustolin, Marco C.; Villnäs, Anna; Valanko, Sebastian; Norkko, Alf (2021)
    Despite a long history of disturbance–recovery research, we still lack a generalizable understanding of the attributes that drive community recovery potential in seafloor ecosystems. Marine soft‐sediment ecosystems encompass a range of heterogeneity from simple low‐diversity habitats with limited biogenic structure, to species‐rich systems with complex biogenic habitat structure. These differences in biological heterogeneity are a product of natural conditions and disturbance regimes. To search for unifying attributes, we explore whether a set of simple traits can characterize community disturbance–recovery potential using seafloor patch‐disturbance experiments conducted in two different soft‐sediment landscapes. The two landscapes represent two ends of a spectrum of landscape biotic heterogeneity in order to consider multi‐scale disturbance–recovery processes. We consider traits at different levels of biological organization, from the biological traits of individual species, to the traits of species at the landscape scale associated with their occurrence across the landscape and their ability to be dominant. We show that in a biotically heterogeneous landscape (Kawau Bay, New Zealand), seafloor community recovery is stochastic, there is high species turnover, and the landscape‐scale traits are good predictors of recovery. In contrast, in a biotically homogeneous landscape (Baltic Sea), the options for recovery are constrained, the recovery pathway is thus more deterministic and the scale of recovery traits important for determining recovery switches to the individual species biological traits within the disturbed patch. Our results imply that these simple, yet sophisticated, traits can be effectively used to characterize community recovery potential and highlight the role of landscapes in providing resilience to patch‐scale disturbances.