Statistical confidence for likelihood‐based paternity inference in natural populations

Abstract

Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.

Size advantage for male function and size‐dependent sex allocation inAmbrosia artemisiifolia, a wind‐pollinated plant

“…We randomly arranged 100 potted plants before flower bud formation in a square 5 × 20 reticular pattern with a distance of 1 m between pots (4 m east–west; 19 m north–south) on a weed‐proof sheet in the experimental fields of Kyushu University in 2012 (Figure 2). These plants were selected to allow assignment of 80% seeds to their fathers under the 95% confidence level from 320 plants genotyped with 10 microsatellite markers using CERVUS v. 3.0.7 (Appendix S1, Genton et al., 2005; Abercrombie et al., 2009; Marshall, Slate, Kruuk, & Pemberton, 1998). We set this percentage of assignment to allow pollination from unknown populations that could be in the vicinity of the experimental population, although the closest known naturalized population was about 7.5 km away.…”

Paternity analysis reveals significant isolation and near neighbor pollen dispersal in small Cariniana legalis Mart. Kuntze populations in the Brazilian Atlantic Forest

“…Paternity of each seed was determined based on the ∆ statistic (Marshall et al. 1998), defined as the difference between the “LOD score” of the first most likely father candidate and the “LOD score” of the second most likely candidate. Significance was determined with the paternity tests simulated by Cervus program.…”

Postdispersal nepotism in male long‐tailed macaques (Macaca fascicularis)

“…Paternal half‐siblings were determined genetically through an independent paternity analysis using the software cervus 3.0 (Marshall et al. 1998; Kalinowski et al. 2007) (see Supporting Information and Table S5 for details).…”