Browsing by Subject "QUANTITATIVE TRAITS"

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  • Kemppainen, Petri; Husby, Arild (2018)
    A fundamental assumption in quantitative genetics is that traits are controlled by many loci of small effect. Using genomic data, this assumption can be tested using chromosome partitioning analyses, where the proportion of genetic variance for a trait explained by each chromosome (h(c)(2)), is regressed on its size. However, as h(c)(2)-estimates are necessarily positive (censoring) and the variance increases with chromosome size (heteroscedasticity), two fundamental assumptions of ordinary least squares (OLS) regression are violated. Using simulated and empirical data we demonstrate that these violations lead to incorrect inference of genetic architecture. The degree of bias depends mainly on the number of chromosomes and their size distribution and is therefore specific to the species; using published data across many different species we estimate that not accounting for this effect overall resulted in 28% false positives. We introduce a new and computationally efficient resampling method that corrects for inflation caused by heteroscedasticity and censoring and that works under a large range of dataset sizes and genetic architectures in empirical datasets. Our new method substantially improves the robustness of inferences from chromosome partitioning analyses.
  • Inouye, Michael; Silander, Kaisa; Hämäläinen, Eija; Salomaa, Veikko; Harald, Kennet; Jousilahti, Pekka; Mannisto, Satu; Eriksson, Johan G.; Saarela, Janna; Ripatti, Samuli; Perola, Markus; van Ommen, Gert-Jan B.; Taskinen, Marja-Riitta; Palotie, Aarno; Dermitzakis, Emmanouil T.; Peltonen, Leena (2010)
  • Chan, Yingleong; Holmen, Oddgeir L.; Dauber, Andrew; Vatten, Lars; Havulinna, Aki S.; Skorpen, Frank; Kvaloy, Kirsti; Silander, Kaisa; Nguyen, Thutrang T.; Willer, Cristen; Boehnke, Michael; Perola, Markus; Palotie, Aarno; Salomaa, Veikko; Hveem, Kristian; Frayling, Timothy M.; Hirschhorn, Joel N.; Weedon, Michael N. (2011)
  • McQuillan, Ruth; Eklund, Niina; Pirastu, Nicola; Kuningas, Maris; McEvoy, Brian P.; Esko, Tonu; Corre, Tanguy; Davies, Gail; Kaakinen, Marika; Lyytikainen, Leo-Pekka; Kristiansson, Kati; Havulinna, Aki S.; Gogele, Martin; Vitart, Veronique; Tenesa, Albert; Aulchenko, Yurii; Hayward, Caroline; Johansson, Asa; Boban, Mladen; Ulivi, Sheila; Robino, Antonietta; Boraska, Vesna; Igl, Wilmar; Wild, Sarah H.; Zgaga, Lina; Amin, Najaf; Theodoratou, Evropi; Polasek, Ozren; Girotto, Giorgia; Lopez, Lorna M.; Sala, Cinzia; Lahti, Jari; Laatikainen, Tiina; Prokopenko, Inga; Kals, Mart; Viikari, Jorma; Yang, Jian; Pouta, Anneli; Estrada, Karol; Hofman, Albert; Freimer, Nelson; Martin, Nicholas G.; Kahonen, Mika; Milani, Lili; Heliovaara, Markku; Räikkönen, Katri; Widen, Elisabeth; Koskinen, Seppo; Eriksson, Johan G.; Perola, Markus; ROHgen Consortium (2012)
  • Korhonen, Tellervo; Loukola, Anu; Wedenoja, Juho; Nyman, Emma; Latvala, Antti; Broms, Ulla; Happola, Anja; Paunio, Tiina; Schrage, Andrew J.; Vink, Jaqueline M.; Mbarek, Hamdi; Boomsma, Dorret I.; Penninx, Brenda W. J. H.; Pergadia, Michele L.; Madden, Pamela A. F.; Kaprio, Jaakko (2014)
  • Morozov, Sergey; Leinonen, Tuomas; Merilä, Juha; McCairns, R. J. Scott (2018)
    Conspecifics inhabiting divergent environments frequently differ in morphology, physiology, and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate, and swimming performance in three-spined sticklebacks (Gasterosteus aculeatus L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the typical low-plated morph, and a unique small-plated morph. We test the hypothesis that similar to plate loss in other freshwater populations, reduction in lateral plate size also evolved in response to selection. Additionally, we test how morphology, physiology, and performance have evolved in concert as a response to differences in selection between marine and freshwater environments. We raised pure-bred second-generation fish originating from three populations and quantified their lateral plate coverage, burst- and critical swimming speeds, as well as standard and active metabolic rates. Using a multivariate Q(ST)-F-ST framework, we detected signals of directional selection on metabolic physiology and lateral plate coverage, notably demonstrating that selection is responsible for the reduction in lateral plate coverage in a small-plated stickleback population. We also uncovered signals of multivariate selection amongst all bivariate trait combinations except the two metrics of swimming performance. Divergence between the freshwater and marine populations exceeded neutral expectation in morphology and in most physiological and performance traits, indicating that adaptation to freshwater habitats has occurred, but through different combinations of traits in different populations. These results highlight both the complex interplay between morphology, physiology and performance in local adaptation, and a framework for their investigation.