Assessing Parent Numbers from Offspring Genotypes: The Importance of Marker Polymorphism

Department of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
The Journal of heredity (Impact Factor: 1.97). 12/2008; 100(2):197-205. DOI: 10.1093/jhered/esn095
Source: PubMed

ABSTRACT Methods to infer parent numbers from offspring genotypes either determine the minimum number of parents required to explain alleles and multilocus genotypes detected in the offspring or use models to incorporate information on population allele frequencies and allele segregation. Disparate results by different approaches suggest that one or perhaps all methods are subject to bias. Here, we investigate the performance of minimum parent number estimates, maximum likelihood, and Bayesian analyses (programs COLONY and PARENTAGE) with respect to marker information content in simulated data sets without knowledge of parental genotypes. Offspring families of different sizes were assumed to share one parent and to be sired by 1 or 5 additional parents. All methods committed large errors in terms of underestimation (minimum value) and overestimation (COLONY), or both (PARENTAGE) of parent numbers, unless the data were highly informative, and their relative performances depended on full-sib group sizes and sire numbers. Increasing the number of markers with low gene diversity (H(e) < or = 0.68) yielded only slow improvement of the results, but all 3 methods performed well with 5-7 markers of H(e) = 0.84. We emphasize the importance of high marker polymorphism for inferring parent numbers and individual parent contributions, as well as for the detection of monogamous reproduction.

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Available from: Stephan Koblmüller, Sep 02, 2015
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    • "According to COLONY, this clutch was sired by at least 4 fathers. COLONY tends to overestimate the number of parents when the number of loci analyzed is low (Jones et al., 2007; Sefc and Koblmüller, 2009), while GERUD 2.0 is considered more accurate when paternity analyses can be run individually with less than 6 sires (Jones, 2005). For this reason, we chose to use COLONY results only for confirmation of our GERUD 2.0 outcomes, and excluded nest B2 from the analysis. "
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    ABSTRACT: Females of all seven living species of sea turtles are known to be polyandrous and show multiple paternity. The frequency of multiple paternity varies among species, and among populations of the same species. In the olive ridley sea turtle (Lepidochelys olivacea), multiple paternity levels correlate with the abundance of individuals in the mating system, being much higher in arribada rookeries than in solitary nesting sites. We used two highly polymorphic microsatellite markers (Cm84 and Or1) to assess the level of multiple paternity in an olive ridley solitary population nesting in the Gulf of Fonseca, Honduras. We found evidence of multiple paternity in 6 out of 8 clutches (75%), with a minimum number of two fathers in four clutches, and a minimum of three in the remaining two clutches. This high level of multiple paternity in a small solitary population suggests that some of the females nesting in Honduras may be coming from proximal Nicaraguan arribada nesting beaches. Historical evidences and recent satellite telemetry data support this hypothesis. In addition, we show that multiple paternity studies can be effectively performed in the absence of maternal samples, and that pooled DNA samples can be used with results comparable to individual hatchling sampling in multiple paternity analyses.
    Journal of Experimental Marine Biology and Ecology 11/2014; 463. DOI:10.1016/j.jembe.2014.10.023 · 2.48 Impact Factor
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    • "Although the accuracy of assignments increased with the number of loci [1], [40], Jones et al. [41] proposed to analyze no more than 3 or 4 loci in order to offset the costs associated with the genotyping of many broods. Based on analyses of simulated data, Sefc and Koblmüller [1], [40] suggested that COLONY performed well with 5 markers of He = 0.84. In fact, 3 to 5 microsatellites have generally been used to reconstruct parentage for the majority of previous studies on gastropod species [15]–[21]. "
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    ABSTRACT: Inferring of parentage in natural populations is important in understanding the mating systems of a species, which have great effects on its genetic structure and evolution. Muricidae, a large group (approximately 1,600 species) of marine gastropods, are poorly investigated in patterns of multiple paternity and sperm competition based on molecular techniques. The veined Rapa whelk, Rapana venosa, a commercially important muricid species with internal fertilization, is an ideal species to study the occurrence and frequency of multiple paternity and to facilitate understanding of their reproductive strategies. We developed five highly polymorphic microsatellites in R. venosa and applied them to identify multiple paternity in 19 broods (1381 embryos) collected from Dandong, China. Multiple paternity was detected in 17 (89.5%) of 19 broods. The number of sires per brood ranged from 1 to 7 (4.3 on average). Of the 17 multiply sired broods, 16 (94.1%) were significantly skewed from equal paternal contributions, and had a dominant sire which was also dominant in each assayed capsule. Our results indicate that a high level of multiple paternity occurs in the wild population of R. venosa. Similar patterns of multiple paternity in the 2-6 assayed capsules from each brood imply that fertilization events within the body of a female occur mostly (but not entirely) as random draws from a "well-but-not-perfectly blended sperm pool" of her several mates. Strongly skewed distributions of fertilization success among sires also suggest that sperm competition and/or cryptic female choice might be important for post-copulatory paternity biasing in this species.
    PLoS ONE 01/2014; 9(1):e86508. DOI:10.1371/journal.pone.0086508 · 3.23 Impact Factor
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    • "We employed programs COLONY (Jones & Wang 2010), GERUD 2.0 (Jones 2001, Jones 2005), and CERVUS (Marshall et al. 1998) to estimate the prevalence of multiple paternity, as it has been suggested that using multiple methods is better than relying on a single approach (Croshaw et al. 2009, Sefc & Koblmuller 2009, Walling et al. 2010). All 22 loci (Appendix 5) were included for analyses in program COLONY, which employs a full-pedigree likelihood method to simultaneously estimate full-sib, half-sib, and parent-offspring relationships. "
    05/2013, Degree: Master of Science
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