Dataset Information

Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

ABSTRACT: Quantitative genetic parameters are nowadays more frequently estimated with restricted maximum likelihood using the 'animal model' than with traditional methods such as parent-offspring regressions. These methods have however rarely been evaluated using equivalent data sets. We compare heritabilities and genetic correlations from animal model and parent-offspring analyses, respectively, using data on eight morphological traits in the great reed warbler (Acrocephalus arundinaceus). Animal models were run using either mean trait values or individual repeated measurements to be able to separate between effects of including more extended pedigree information and effects of replicated sampling from the same individuals. We show that the inclusion of more pedigree information by the use of mean traits animal models had limited effect on the standard error and magnitude of heritabilities. In contrast, the use of repeated measures animal model generally had a positive effect on the sampling accuracy and resulted in lower heritabilities; the latter due to lower additive variance and higher phenotypic variance. For most trait combinations, both animal model methods gave genetic correlations that were lower than the parent-offspring estimates, whereas the standard errors were lower only for the mean traits animal model. We conclude that differences in heritabilities between the animal model and parent-offspring regressions were mostly due to the inclusion of individual replicates to the animal model rather than the inclusion of more extended pedigree information. Genetic correlations were, on the other hand, primarily affected by the inclusion of more pedigree information. This study is to our knowledge the most comprehensive empirical evaluation of the performance of the animal model in relation to parent-offspring regressions in a wild population. Our conclusions should be valuable for reconciliation of data obtained in earlier studies as well as for future meta-analyses utilizing estimates from both traditional methods and the animal model.

SUBMITTER: Akesson M

PROVIDER: S-EPMC2254494 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature

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Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

Akesson Mikael M Bensch Staffan S Hasselquist Dennis D Tarka Maja M Hansson Bengt B

PloS one 20080305 3

Quantitative genetic parameters are nowadays more frequently estimated with restricted maximum likelihood using the 'animal model' than with traditional methods such as parent-offspring regressions. These methods have however rarely been evaluated using equivalent data sets. We compare heritabilities and genetic correlations from animal model and parent-offspring analyses, respectively, using data on eight morphological traits in the great reed warbler (Acrocephalus arundinaceus). Animal models ...[more]

PMID: 18320057

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Project description:Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).

Project description:BackgroundParent-offspring (PO) regression is a central tool to determine the heritability of phenotypic traits; i.e., the relative extent to which those traits are controlled by genetic factors. The applicability of PO regression to viral traits is unclear because the direction of viral transmission-who is the donor (parent) and who is the recipient (offspring)-is typically unknown and viral phylogenies are sparsely sampled.MethodsWe assessed the applicability of PO regression in a realistic setting using Ornstein-Uhlenbeck simulated data on phylogenies built from 11,442 Swiss HIV Cohort Study (SHCS) partial pol sequences and set-point viral load (SPVL) data from 3293 patients.ResultsWe found that the misidentification of donor and recipient plays a minor role in estimating heritability and showed that sparse sampling does not influence the mean heritability estimated by PO regression. A mixed-effect model approach yielded the same heritability as PO regression but could be extended to clusters of size greater than 2 and allowed for the correction of confounding effects. Finally, we used both methods to estimate SPVL heritability in the SHCS. We employed a wide range of transmission pair criteria to measure heritability and found a strong dependence of the heritability estimates to these criteria. For the most conservative genetic distance criteria, for which heritability estimates are conceptually expected to be closest to true heritability, we found estimates ranging from 32 to 46% across different bootstrap criteria. For less conservative distance criteria, we found estimates ranging down to 8%. All estimates did not change substantially after adjusting for host-demographic factors in the mixed-effect model (±2%).ConclusionsFor conservative transmission pair criteria, both PO regression and mixed-effect models are flexible and robust tools to estimate the contribution of viral genetic effects to viral traits under real-world settings. Overall, we find a strong effect of viral genetics on SPVL that is not confounded by host demographics.

Project description:Importance:Previous studies have shown an inverse association between offspring religiosity and suicidal ideation/attempts, but the association of parent religiosity on offspring suicidal ideation/attempts has not been examined. Objective:To examine associations of parent and offspring religiosity with suicide ideation and attempts in offspring. Design, Setting, and Participants:The study is based on offspring (generation 3) from a 3-generation family study at New York State Psychiatric Institute and Columbia University, in which generations 2 and 3 were defined as being at high risk or low risk for major depressive disorder because of the presence or absence of major depressive disorder in generation 1. The association between suicidal behaviors (ideation/attempts) and parent and offspring religiosity in generation 3 offspring aged 6 to 18 years (214 offspring from 112 nuclear families) was examined. Main Outcomes and Measures:Parents' psychiatric diagnoses and suicidal behaviors were assessed with the Schedule for Affective Disorders and Schizophrenia, and offspring were independently assessed using the child version. Two measures of religiosity were assessed: religious importance and religious attendance. Logistic regressions in the framework of generalized estimation equations were performed to analyze offspring suicidal behaviors while adjusting for sibling correlation and offspring age, sex, and familial depression risk status. Results:Of 214 offspring, 112 (52.3%) were girls. Offspring religious importance was associated with a lower risk for suicidal behavior in girls (odds ratio [OR], 0.48; 95% CI, 0.33-0.70) but not in boys (OR, 1.15; 95% CI, 0.74-1.80) (religiosity by sex interaction, P = .05). Religious attendance was associated with a lower risk for suicidal behavior in girls (OR, 0.64; 95% CI, 0.49-0.84) but not boys (OR, 0.94; 95% CI, 0.69-1.27) (religiosity by sex interaction, P = .17). Parent religious importance was associated with a lower risk for offspring suicidal behavior (OR, 0.61; 95% CI, 0.41-0.91) but not parent religious attendance. When parent and offspring religious importance were considered simultaneously, we found a lower risk associated with parental religious importance (OR, 0.61; 95% CI, 0.39-0.96) independent of offspring importance. These associations were independent of parental depression, marital status, and parental suicide ideation. Conclusions and Relevance:In this study, parental belief in religious importance was associated with lower risk for suicidal behavior in offspring independent of an offspring's own belief about religious importance and other known parental factors, such as parental depression, suicidal behavior, and divorce.

Dataset Information

Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

Publications

Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

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