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Pettie KP, Mumbach M, Lea AJ, Ayroles J, Chang HY, Kasowski M, Fraser HB. Chromatin activity identifies differential gene regulation across human ancestries. Genome Biol 2024; 25:21. [PMID: 38225662 PMCID: PMC10789071 DOI: 10.1186/s13059-024-03165-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. RESULTS To address this, we devise an approach to search for lineage-specific selection on three critical steps in transcriptional regulation: chromatin activity, transcription factor binding, and chromosomal looping. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. CONCLUSIONS Overall, our study indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.
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Affiliation(s)
- Kade P Pettie
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Maxwell Mumbach
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Julien Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maya Kasowski
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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Costa e Silva J, Potts BM, Wiehl G, Prober SM. Linking leaf economic and hydraulic traits with early-age growth performance and survival of Eucalyptus pauciflora. Front Plant Sci 2022; 13:973087. [PMID: 36426150 PMCID: PMC9679299 DOI: 10.3389/fpls.2022.973087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Selection on plant functional traits may occur through their direct effects on fitness (or a fitness component), or may be mediated by attributes of plant performance which have a direct impact on fitness. Understanding this link is particularly challenging for long-lived organisms, such as forest trees, where lifetime fitness assessments are rarely achievable, and performance features and fitness components are usually quantified from early-life history stages. Accordingly, we studied a cohort of trees from multiple populations of Eucalyptus pauciflora grown in a common-garden field trial established at the hot and dry end of the species distribution on the island of Tasmania, Australia. We related the within-population variation in leaf economic (leaf thickness, leaf area and leaf density) and hydraulic (stomatal density, stomatal length and vein density) traits, measured from two-year-old plants, to two-year growth performance (height and stem diameter) and to a fitness component (seven-year survival). When performance-trait relationships were modelled for all traits simultaneously, statistical support for direct effects on growth performance was only observed for leaf thickness and leaf density. Performance-based estimators of directional selection indicated that individuals with reduced leaf thickness and increased leaf density were favoured. Survival-performance relationships were consistent with size-dependent mortality, with fitness-based selection gradients estimated for performance measures providing evidence for directional selection favouring individuals with faster growth. There was no statistical support for an effect associated with the fitness-based quadratic selection gradient estimated for growth performance. Conditional on a performance measure, fitness-based directional selection gradients estimated for the leaf traits did not provide statistical support for direct effects of the focal traits on tree survival. This suggested that, under the environmental conditions of the trial site and time period covered in the current study, early-stage selection on the studied leaf traits may be mediated by their effects on growth performance, which in turn has a positive direct influence on later-age survival. We discuss the potential mechanistic basis of the direct effects of the focal leaf traits on tree growth, and the relevance of a putative causal pathway of trait effects on fitness through mediation by growth performance in the studied hot and dry environment.
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Affiliation(s)
- João Costa e Silva
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Brad M. Potts
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- Australian Research Council (ARC) Training Centre for Forest Value, University of Tasmania, Hobart, TAS, Australia
| | - Georg Wiehl
- CSIRO Land and Water, Private Bag 5, Wembley, WA, Australia
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Boenkost F, González Casanova A, Pokalyuk C, Wakolbinger A. Haldane's formula in Cannings models: the case of moderately strong selection. J Math Biol 2021; 83:70. [PMID: 34870765 PMCID: PMC8648686 DOI: 10.1007/s00285-021-01698-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/03/2021] [Accepted: 11/19/2021] [Indexed: 11/28/2022]
Abstract
For a class of Cannings models we prove Haldane’s formula, \documentclass[12pt]{minimal}
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\begin{document}$$\pi (s_N) \sim \frac{2s_N}{\rho ^2}$$\end{document}π(sN)∼2sNρ2, for the fixation probability of a single beneficial mutant in the limit of large population size N and in the regime of moderately strong selection, i.e. for \documentclass[12pt]{minimal}
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\begin{document}$$s_N \sim N^{-b}$$\end{document}sN∼N-b and \documentclass[12pt]{minimal}
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\begin{document}$$0< b<1/2$$\end{document}0<b<1/2. Here, \documentclass[12pt]{minimal}
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\begin{document}$$s_N$$\end{document}sN is the selective advantage of an individual carrying the beneficial type, and \documentclass[12pt]{minimal}
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\begin{document}$$\rho ^2$$\end{document}ρ2 is the (asymptotic) offspring variance. Our assumptions on the reproduction mechanism allow for a coupling of the beneficial allele’s frequency process with slightly supercritical Galton–Watson processes in the early phase of fixation.
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Affiliation(s)
- Florin Boenkost
- Goethe-Universität Frankfurt, FB 12, 60054, Frankfurt, Germany.
| | - Adrián González Casanova
- Instituto de Matemáticas, Universidad Nacional Autónoma de México, Área de la Investigación Científica, Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX, Mexico
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Sra SK, Sharma M, Kaur G, Sharma S, Akhatar J, Sharma A, Banga SS. Evolutionary aspects of direct or indirect selection for seed size and seed metabolites in Brassica juncea and diploid progenitor species. Mol Biol Rep 2019; 46:1227-38. [PMID: 30637624 DOI: 10.1007/s11033-019-04591-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Seed size and seed metabolites have been the targets of direct or indirect selection during domestication and subsequent crop breeding. Understanding these traits and associated genetics can prove very useful for plant translational research. Large germplasm assemblage (235) of Brassica juncea and its progenitor species (B. rapa and B. nigra) was evaluated to establish seed trait variations for seed size and seed metabolites. Seeds were smallest in B. nigra and largest in B. juncea. Australian B. juncea and Indian B. rapa var brown sarson types averaged more seed oil content. Seed size and oil content were generally higher in modern cultivars in comparison to the land races. Allelic diversity for known associated genes for seed-size and oil-content (AP2, ARF2, TTG2, GRF2, GL2, CYP78A5, CYP78A6, MINI3, IKU2, IKU1, BRI1, DGAT, GPDH, LPAAT, GPAT and DA1) was studied so as to infer the effect of domestication on seed traits. Three genes (IKU1, IKU2, AP2) in B. rapa, two (TTG2 and GL2) in B. nigra and two (IKU1 and GRF2) in natural B. juncea were identified as targets of selection on the basis of Fst outlier and/or sequence diversity tests. We report parallel divergence for seed traits between B. juncea and B. rapa. Directional selection appeared stronger for seed-size as compared to correlated seed metabolites. Positive selection on seed-size is likely to have played a significant role in structuring regional variation in the germplasm.
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Cortázar-Chinarro M, Meyer-Lucht Y, Laurila A, Höglund J. Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis). Immunogenetics 2018; 70:477-484. [PMID: 29387920 PMCID: PMC6006221 DOI: 10.1007/s00251-017-1051-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.
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Affiliation(s)
- M Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
| | - Y Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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Konorov EA, Nikitin MA, Mikhailov KV, Lysenkov SN, Belenky M, Chang PL, Nuzhdin SV, Scobeyeva VA. Genomic exaptation enables Lasius niger adaptation to urban environments. BMC Evol Biol 2017; 17:39. [PMID: 28251870 PMCID: PMC5333191 DOI: 10.1186/s12862-016-0867-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger – the most successful urban inhabitant of all ants – and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus. Results Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation. Conclusions Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0867-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgenii A Konorov
- Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Mikhail A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation.,Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Kirill V Mikhailov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation.,Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey N Lysenkov
- Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Mikhail Belenky
- Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Peter L Chang
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sergey V Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.,Department of Applied Mathematics & Mathematical Biology and Bioinformatics Laboratory, St.Petersburg State Polytechnical University, St.Petersburg, 195251, Russia
| | - Victoria A Scobeyeva
- Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation.
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Abstract
Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection. We find that the method to detect diversifying selection also detects directional selection under certain conditions. One method developed for detecting directional selection is powerful and accurate for a wide range of conditions, while the other can generate an excessive number of false positives.
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Affiliation(s)
- Grant Thiltgen
- Institute of Child Health, University College London, London, UK
| | - Mario Dos Reis
- The School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Abstract
The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables.
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Affiliation(s)
- Andrey Rudoy
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) , Barcelona , Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) , Barcelona , Spain
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Abstract
Fungicides are widely used in developed agricultural systems to control disease and safeguard crop yield and quality. Over time, however, resistance to many of the most effective fungicides has emerged and spread in pathogen populations, compromising disease control. This review describes the development of resistance using case histories based on four important diseases of temperate cereal crops: eyespot (Oculimacula yallundae and Oculimacula acuformis), Septoria tritici blotch (Zymoseptoria tritici), powdery mildew (Blumeria graminis), and Fusarium ear blight (a complex of Fusarium and Microdochium spp). The sequential emergence of variant genotypes of these pathogens with reduced sensitivity to the most active single-site fungicides, methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, and succinate dehydrogenase inhibitors illustrates an ongoing evolutionary process in response to the introduction and use of different chemical classes. Analysis of the molecular mechanisms and genetic basis of resistance has provided more rapid and precise methods for detecting and monitoring the incidence of resistance in field populations, but when or where resistance will occur remains difficult to predict. The extent to which the predictability of resistance evolution can be improved by laboratory mutagenesis studies and fitness measurements, comparison between pathogens, and reconstruction of evolutionary pathways is discussed. Risk models based on fungal life cycles, fungicide properties, and exposure to the fungicide are now being refined to take account of additional traits associated with the rate of pathogen evolution. Experimental data on the selection of specific mutations or resistant genotypes in pathogen populations in response to fungicide treatments can be used in models evaluating the most effective strategies for reducing or preventing resistance. Resistance management based on robust scientific evidence is vital to prolong the effective life of fungicides and safeguard their future use in crop protection.
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Affiliation(s)
- John A Lucas
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Nichola J Hawkins
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Bart A Fraaije
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
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Tosto M, Petrill S, Halberda J, Trzaskowski M, Tikhomirova T, Bogdanova O, Ly R, Wilmer J, Naiman D, Germine L, Plomin R, Kovas Y. Why do we differ in number sense? Evidence from a genetically sensitive investigation. Intelligence 2014; 43:35-46. [PMID: 24696527 PMCID: PMC3969293 DOI: 10.1016/j.intell.2013.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 12/10/2013] [Accepted: 12/21/2013] [Indexed: 01/29/2023]
Abstract
Basic intellectual abilities of quantity and numerosity estimation have been detected across animal species. Such abilities are referred to as 'number sense'. For human species, individual differences in number sense are detectable early in life, persist in later development, and relate to general intelligence. The origins of these individual differences are unknown. To address this question, we conducted the first large-scale genetically sensitive investigation of number sense, assessing numerosity discrimination abilities in 837 pairs of monozygotic and 1422 pairs of dizygotic 16-year-old twin pairs. Univariate genetic analysis of the twin data revealed that number sense is modestly heritable (32%), with individual differences being largely explained by non-shared environmental influences (68%) and no contribution from shared environmental factors. Sex-Limitation model fitting revealed no differences between males and females in the etiology of individual differences in number sense abilities. We also carried out Genome-wide Complex Trait Analysis (GCTA) that estimates the population variance explained by additive effects of DNA differences among unrelated individuals. For 1118 unrelated individuals in our sample with genotyping information on 1.7 million DNA markers, GCTA estimated zero heritability for number sense, unlike other cognitive abilities in the same twin study where the GCTA heritability estimates were about 25%. The low heritability of number sense, observed in this study, is consistent with the directional selection explanation whereby additive genetic variance for evolutionary important traits is reduced.
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Affiliation(s)
- M.G. Tosto
- Department of Psychology, University of York, Heslington, York YO10 5DD, United Kingdom
- Department of Psychology, Tomsk State University, 36 Lenin Prospekt, 634050, Tomsk, Russia
| | - S.A. Petrill
- The Ohio State University, Columbus, OH 43210, United States
| | - J. Halberda
- Department of Psychological and Brain Sciences, The Johns Hopkins University, Baltimore, MD 21218-268, United States
| | - M. Trzaskowski
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - T.N. Tikhomirova
- Department of Psychology, Tomsk State University, 36 Lenin Prospekt, 634050, Tomsk, Russia
| | - O.Y. Bogdanova
- Department of Psychology, Tomsk State University, 36 Lenin Prospekt, 634050, Tomsk, Russia
| | - R. Ly
- Department of Psychological and Brain Sciences, The Johns Hopkins University, Baltimore, MD 21218-268, United States
| | - J.B. Wilmer
- Department of Psychology, Wellesley College, Central Street, Wellesley, MA 02481, United States
| | - D.Q. Naiman
- Department of Psychological and Brain Sciences, The Johns Hopkins University, Baltimore, MD 21218-268, United States
| | - L. Germine
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - R. Plomin
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Y. Kovas
- Department of Psychology, Tomsk State University, 36 Lenin Prospekt, 634050, Tomsk, Russia
- King's College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
- Goldsmiths, University of London, London SE14 6NW, United Kingdom
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