# Assessing parent numbers from offspring genotypes: the importance of marker polymorphism.

**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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**ABSTRACT:**Long-distance dispersal (LDD) of seeds has a critical impact on species survival in patchy landscapes. However, relative to pollen dispersal, empirical data on how seed LDD affects genetic diversity in fragmented populations have been poorly reported. Thus, we attempted to indirectly evaluate the influence of seed LDD by estimating maternal and paternal inbreeding in the seed rain of fragmented 8 Pinus densiflora populations. In total, the sample size was 458 seeds and 306 adult trees. Inbreeding was estimated by common parentage analysis to evaluate gene flow within populations and by sibship reconstruction analysis to estimate gene flow within and among populations. In the parentage analysis, the observed probability that sampled seeds had the same parents within populations was significantly larger than the expected probability in many populations. This result suggested that gene dispersal was limited to within populations. In the sibship reconstruction, many donors both within and among populations appeared to contribute to sampled seeds. Significant differences in sibling ratios were not detected between paternity and maternity. These results suggested that seed-mediated gene flow and pollen-mediated gene flow from outside population contributed some extent to high genetic diversity of the seed rain (HE > 0.854). We emphasize that pine seeds may have excellent potential for gene exchange within and among populations.The Journal of heredity 04/2013; · 2.05 Impact Factor - SourceAvailable from: Sofia Consuegra[Show abstract] [Hide abstract]

**ABSTRACT:**Ensuring appropriate levels of genetic diversity in captive populations is essential to avoid inbreeding and loss of rare alleles by genetic drift. Pedigree reconstruction and parentage analysis in the absence of parental genotypes can be a challenging task that relies in the assignment of sibship relationships among the offspring. Here, we used eight highly variable microsatellite markers and three different assignment methods to reconstruct the most likely genotypes of a parental group of wild Seriola dumerili fish based on the genotypes of six cohorts of their offspring, to assess their relative contributions to the offspring. We found that a combination of the four most variable microsatellites was enough to identify the number of parents and their contribution to the offspring, suggesting that the variability of the markers can be more critical than the number of markers. Estimated effective population sizes were lower than the number of breeders and variable among years. The results suggest unequal parental contribution that should be accounted for breeding programs in the future.Animal Genetics 03/2013; · 2.58 Impact Factor - [Show abstract] [Hide abstract]

**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. · 3.73 Impact Factor

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Journal of Heredity 2009:100(2):197–205

doi:10.1093/jhered/esn095

Advance Access publication November 4, 2008

Assessing Parent Numbers from

Offspring Genotypes: The Importance of

Marker Polymorphism

? The American Genetic Association. 2008. All rights reserved.

For permissions, please email: journals.permissions@oxfordjournals.org.

KRISTINA M. SEFC AND STEPHAN KOBLMU¨LLER

From the Department of Zoology, University of Graz, Universita ¨tsplatz 2, 8010 Graz, Austria (Sefc); the Department of

Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyva ¨gen 18D, SE-752 36 Uppsala, Sweden

(Koblmu ¨ller).

Address correspondence to K. M. Sefc at the address above, or e-mail: kristina.sefc@uni-graz.at.

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 (He? 0.68) yielded only slow improvement of the results, but all 3 methods performed well with 5–7 markers of

He5 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.

Key words:

GERUD, monogamy, multiple mating, parentage, paternity

Studies of animal and plant mating systems, sperm and

pollen competition, parental investment in relation to ge-

netic parentage, pre- and postzygotic selection, the distri-

bution of reproductive success, and several other issues of

evolutionary and ethological interest depend on the de-

termination of the number and identity of reproducing

individuals (e.g., Bernasconi 2003; Uller and Olsson 2008).

Molecular methods contributed significantly to the field and

increased our knowledge far beyond the amount of infor-

mation that can, for example, be obtained from behavioral

observation of breeding animals and plant pollinators (e.g.,

Avise et al. 2002; Griffiths et al. 2002; Llaurens et al. 2008).

Accordingly, methods for the analysis of genetic data with

respect to relatedness and parentage inference have been de-

veloped and refined in recent years (e.g., Marshall et al.

1998; Neff et al. 2002; Wang 2004; Jones 2005; Jones et al.

2007). One of the many applications of genetic and allozyme

data to parentage studies is the reconstruction of the

number of parents from the genotypes of animal offspring

or plant seeds and seedlings. Assuming that all offspring in

a group have one of their parents in common, which is the

case for seeds collected from inflorescences and fruits as

well as for broods of animals in which one sex mates with

several individuals of the other sex, the data analysis consists

in first deducing the genotype of the shared parent (if it has

not been sampled) and then determining the number of

additional parents contributing alleles to the offspring

group. The power to exclude unrelated individuals from par-

entage and to discriminate different parents increases with

increasing levels of polymorphism of the genetic markers, as

it becomes more likely that different parents transmit dif-

ferent alleles to their respective offspring (Neff and Pitcher

2002). Such highly polymorphic markers are not always

readily available, and likelihood methods have been de-

veloped to account for the possibility of allele sharing be-

tween different parents using population allele frequencies

and Mendelian expectations for the ratios of alleles in full-

sib groups. With these algorithms, 2 offspring sharing fre-

quent alleles are not necessarily inferred to also share the

same parent (e.g., Meagher 1986; Emery et al. 2001; Smith

197

Page 2

et al. 2001; Wang 2004; Hain and Neff 2007). Hence, the

minimum number of parents required to explain the geno-

types detected in the offspring is often smaller than the

maximum likelihood estimate of parent numbers (Campbell

1998; Ma ¨kinen et al. 2007; Portnoy et al. 2007; Sefc et al.

2008).

Highly disparate results obtained from the estimation of

parent numbers by parsimonious minimum sire number re-

constructions and maximum likelihood analyses of empirical

data (Sefc et al. 2008; Hermann C, Koblmu ¨ller S, Sefc KM,

unpublished data) and furthermore the failure to retrieve the

correct answers from simulated data with both methods,

when the markers were not sufficiently informative (Sefc

et al. 2008), prompted us to examine the performance of

different methods for paternity reconstruction in more

detail. In the present study, we investigate the effect of

marker information content (number of markers and their

diversity) on reconstructions of minimum parent number,

maximum likelihood, and Bayesian estimates (programs

COLONY and PARENTAGE) in simulated data sets

without knowledge of parental genotypes. We refer to the

simulated data as the genotypes of broods, in which off-

spring share a common mother and were sired by one or

several males, but the same type of data is encountered

when broods are sired by a single father and several mothers

or when plant inflorescences or fruits are tested for

pollination by multiple donors.

Materials and Methods

Parentage was reconstructed from 13 data sets consisting of

different numbers of loci (n 5 3, 5, 7, 9, and 11 loci) and

with 3 different levels of polymorphism per marker

(gene diversity He5 0.57, 0.68, and 0.84). The exclusion

probabilities achieved with each marker set (P1, when one

parent is known, and P0, when neither parent is known)

were calculated in GERUD vs 2.0 (Jones 2005) and are

given in Table 1. The number of alleles and allele

frequencies, which were used for the simulation of brood

genotypes and to represent the population from which

broods were sampled, were as follows: for He5 0.57, 5

alleles at frequencies of 0.54098, 0.36067, 0.06557, 0.02732,

and 0.00546; for He 5 0.68, 8 alleles at frequencies of

0.41919, 0.32576, 0.14393, 0.09091, 0.0101, 0.00505,

0.00253, and 0.00253; and for He 5 0.84, 12 alleles at

frequencies of 0.26053, 0.17105, 0.15789, 0.12368, 0.10526,

0.09737, 0.02895, 0.01842, 0.01316, 0.01053, 0.01053, and

0.00263; these are values that were observed at 3 micro-

satellite loci in a large natural population sample.

The simulation of broods assumed that all offspring

shared one parent and that 5 different individuals acted as

the second parent, for example, such as when a female

mated with 5 males, each of whom sired a proportion of the

clutch. Two brood sizes, n 5 80 and n 5 25, were simulated.

Paternity contributions were either evenly distributed among

the 5 sires, with each male siring 16 or 5 offspring in the

large and small broods, respectively, or had a skewed

distribution with the primary sire accounting for 40 (large

broods) or 13 (small broods) of the offspring and the

remaining 4 males each siring 10 (large broods) or 3 (small

broods) young. ‘‘Large’’ and ‘‘small’’ broods therefore con-

tain full-sib groups of different sizes, whereby larger full-sib

groups provide more information to reconstruct the geno-

types of their parents. Furthermore, monogamous broods

(1 mother and 1 father) with 25 and 80 offspring were

simulated.

To generate brood genotypes, parental genotypes were

first assembled according to the population allele frequen-

cies. For example, for data consisting of 5 markers, each

with He5 0.68, 10 alleles (2 per locus) were randomly

drawn for each assumed parent from the above allele dis-

tribution of the marker with Heof 0.68. An offspring’s

genotype was then created by randomly drawing 1 allele per

locus from each of its parents. For each of the investigated

combinations of brood type and data set composition, 100

replicate broods were generated and analyzed.

Because all offspring in a brood shared their mother, the

reconstructed number of full-sib groups in a brood was

taken as estimate of the number of different sires con-

tributing to the brood. For each of the multiply sired

broods, we calculated maximum likelihood estimates of sire

numbers(COLONYestimates),

(PARENTAGE estimates), and reconstructions of the

minimum number of sires required to explain offspring

genotypes (MIN estimates). For monogamous broods, only

COLONY and PARENTAGE estimates were calculated

becausetheminimumsirenumberestimatecouldnotbelower

than 1 anyway. As neither mutations nor typing errors were

included in the genotype simulations, sibship reconstruction

Bayesian estimates

Table 1.

neither parent is known (P0)

Exclusion probabilities achieved by the marker sets used in brood simulations when one parent is known (P1) and when

# Loci He

3 Loci5 Loci 7 Loci9 Loci11 Loci

0.57P15 0.6404

P05 0.4192

P15 0.8208

P05 0.6101

P15 0.9686

P05 0.8870

P15 0.8181

P05 0.5957

P15 0.9431

P05 0.7919

P15 0.9969

P05 0.9736

P15 0.9080

P05 0.7185

P15 0.9819

P05 0.8889

P15 0.9997

P05 0.9938

P15 0.9535

P05 0.8041

P15 0.9942

P05 0.9407

n/a

P15 0.9669

P05 0.8365

P15 0.9968

P05 0.9567

n/a

0.68

0.84

He, expected heterozygosity per locus; # loci, number of loci, each with the indicated He, making up the data set. n/a, not applicable.

198

Journal of Heredity 2009:100(2)

Page 3

in the program COLONY vs 1.0 (Wang 2004) was carried out

with error rates set to zero.For maximum likelihood estimates

ofthenumberofsirescontributingtoabrood,COLONYwas

run as described in the manual, using the population allele

frequencies given above. To obtain MIN estimates, the

population allele frequencies were set to 0.001 for all alleles

presentintheoffspring,andan additionalallele(notpresentin

the offspring) was given a high frequency in order to make

allele frequencies add up to 1. When alleles found in offspring

are assigned low population frequencies, it is more likely that

a shared allele represents shared paternity, and the maximum

likelihood estimate returns the minimally required number of

sire genotypes (Sefc et al. 2008). To confirm convergence

of the MIN method on the minimum sire number,

7 monogamous data sets were analyzed. The necessity to

employ this modification of COLONY, which has the

disadvantage that it may occasionally overestimate the

minimum value (see Results), was given by the need to

automate the large number of analyses. When analyses can be

run individually and no more than 6 sires contributed to the

brood, minimum sire numbers are better calculated by

the program GERUD (Jones 2005), which tests increasing

numbers of sires for compliance with the offspring genotypes

and is therefore guaranteed to arrive at the true minimum.

The Bayesian parentage reconstruction implemented in

PARENTAGE (Emery et al. 2001) evaluates probability

distributions of parent numbers and their relative contribu-

tions conditional on observed offspring genotypes and

population allele frequencies and prior assumptions. Be-

cause of long computation times (exceeding 2 h per run with

the more informative data sets), not all the generated data

sets, and only 50 replicates of each, were analyzed with

PARENTAGE. The analyzed data sets were as follows:

both large and small multiply sired broods with skewed

paternity distributions, as well as large monogamous broods,

with data for 3, 5, and 7 loci at Heof 0.57, 0.68, and 0.84

and small monogamous broods with data for 3 and 5 loci at

Heof 0.57, 0.68, and 0.84. To improve the mixing properties

of the Markov Chain, a low probability of more than 1

mother was set by using a prior distribution with a mean of

1 and a standard deviation of 0.1 (Emery et al. 2001;

PARENTAGE manual). The prior range of possible fathers

was set to 1–15. In previous studies, results were shown to

be robust to changes in priors for father number and

paternity share (Bretman and Tregenza 2005; Beveridge

et al. 2006). The simulated data contain no genotyping

errors and mutations, but because the program does not

allow a mutation rate of zero, the prior for the mutation rate

was set to the low value of 10?10. The here chosen Markov

Chain settings of 5000 iterations with a burn-in of 5000

iterations and a thinning interval of 400 are commonly

employed by users of the program (e.g., Bretman and

Tregenza 2005; Beveridge et al. 2006; Simmons et al. 2007;

Frentiu and Chenoweth 2008).

Scripts to generate brood genotypes and COLONY and

PARENTAGE input files, run the programs, and parse the

output files were written in PERL programming language.

Results

Errors in sire number estimates by the MIN and COLONY

analyses were in most cases due to under- and over-

estimation,respectively, of

PARENTAGE estimates deviated from the true value in

both directions (Figures 1 and 3; Supplementary Figure).

The allocation of the correct number of offspring to each

contributing sire is even more difficult than the estimation

of the number of sires involved in a brood. The percentage

of analyses, in which the proportions of paternal contribu-

tions to the broods were correctly reconstructed, was con-

siderably lower than the percentage of analyses with accurate

estimates of sire number, except with the most powerful

marker set (Figure 1; Supplementary Figure).

In a small number of analyses (0.8%), the MIN estimator

overestimated the true value by 1 (and once by 2) sire.

Apparently, the frequency of 0.001 assigned to each ob-

served allele, albeit very low, did not force the likelihood

algorithm to minimize the sire number estimate in all cases.

Hence, even when our MIN estimate was equal to or smaller

than the true sire number, the minimally necessary number

of sires to explain all offspring genotypes may be still

smaller, such that our analyses may underrate the degree to

which the ‘‘accurate’’ minimum numbers would underesti-

mate the true number of sires. However, 2 lines of evidence

indicate that the MIN analyses in COLONY will in most

cases arrive at the accurate minimum sire numbers. In a

previous study, the MIN estimates obtained from the modi-

fied COLONY input were identical to minimum sire

number reconstructions in GERUD (Sefc et al. 2008).

Moreover, in the present study, several data sets of

monogamous broods were analyzed with the MIN method

in COLONY in order to confirm that the method indeed

returned the minimally possible sire number (known to be 1

in monogamous broods). Seven data sets, in which the

maximum likelihood estimate of COLONY overestimated

sire number, were chosen for this check, and the MIN

method correctly estimated a single sire in all replicates

(large broods with data from 3 and 5 loci and Heof 0.57 and

0.68, and 3 loci with Heof 0.84). Although we do not

advocate our modification of the COLONY program to

obtain MIN estimates in cases, where it is possible to use the

program GERUD, one potential advantage of the MIN sire

number reconstruction in COLONY compared with

GERUD lies in the ability of the COLONY model to

account for genotyping errors and mutations in empirical

data sets, which could cause spurious assumptions of

additional sires by GERUD analyses.

thetruevalue, whereas

Paternity Reconstruction from Large Full-Sib Groups

(‘‘Large Broods’’)

In large broods, the distribution of paternity among sires

had little effect on the outcome of paternity reconstruction

with the MIN and COLONY methods, and success rates

were similar in broods with a primary sire and in broods with

equally contributing sires (Figure 1A–C and Supplementary

199

Sefc and Koblmu ¨ller?Assessing Parent Numbers from Offspring Genotypes

Page 4

Figure). Apparently, there was little difference in the amount

of information available for paternity reconstruction

between 16 offspring per sire in the even broods and 10

offspring per secondary sire in the skewed broods.

PARENTAGE analyses were conducted on skewed broods

only.

Markers with low polymorphism (He5 0.57) performed

poorly in paternity reconstruction with all 3 methods even

when a high number (n 5 7–11) of such markers was used

(Figures 1A–C and 2A). Unexpectedly, the rate of correct

paternity inference by COLONY decreased, when the

number of markers was increased from 3 to 5 and 7. Only

sets of 9 and 11 markers yielded better COLONY results

than a set of 3 markers, but the proportion of analyses with

correctly inferred paternity remained low, and deviations of

sire number estimates from true values remained high

(Figures 1B and 2A). The proportion of correct sire number

estimates was higher in the PARENTAGE program but still

remained below 50% with up to 7 markers (Figure 1C). Due

to the long computation times, data sets with more than

7 loci were not analyzed with PARENTAGE. The average

deviations between PARENTAGE estimates and true

sire numbers were lower than with the other 2 methods

(Figure 2A).

With moderately polymorphic markers (He5 0.68), at

least 9 markers were required for the MIN method and 11

for the COLONY method to identify the true sire number

in .80% of replicates and minimize the deviation of the

Figure 1.

areas represent the percentage of replicate broods, for which minimum (MIN), maximum likelihood (COLONY), and Bayesian

(PARENTAGE) analyses returned the sire numbers given on the y axis. The horizontal line marks the correct estimate of 5 sires,

and bubbles representing the proportions of correct estimates are shaded gray and black. Gray areas indicate the portion of

analyses yielding correct sire numbers but erring in the number of offspring contributed by each sire; black areas correspond to the

proportion of analyses, in which both sire number and contributions were correctly inferred. Marker sets consisted of 3–11 loci

with gene diversities (He) of 0.57 and 0.68 and 3–7 loci with He5 0.84. (A–C) MIN, COLONY, and PARENTAGE analyses of

80 offspring, where the primary father sired 40 young and each of the additional 4 fathers sired 10 young. (D–F) MIN, COLONY,

and PARENTAGE analyses of 25 offspring, where the primary father sired 13 young and each of the additional 4 fathers sired 3

young.

Sire number estimation from simulated brood genotypes with skewed distribution of paternal contributions. Bubble

200

Journal of Heredity 2009:100(2)

Page 5

incorrect estimates (Figures 1A–B and 2A). The PARENT-

AGE estimates based on 3, 5, and 7 loci were correct in 40,

28, and 52% of the replicates, respectively, with only modest

improvement of estimates with increasing marker numbers

(Figures 1C and 2A). Although not optimal, the PARENT-

AGE method performed better with small data sets (3–7

markers) than the other 2 methods in terms of the pro-

portion of correct estimates of sire number and paternal con-

tribution and of the average deviation from the true sire

number. Interestingly, fewer markers with Heof 0.57 and

0.68 caused PARENTAGE to underestimate sire numbers,

whereas overestimation was more frequent with data sets

containing more markers.

With highly polymorphic markers (He5 0.84), a set of

3 markers was sufficiently informative to infer sire number

in .80% of the replicates by the MIN method, whereas 5–7

markers were needed to achieve the same success rate with

the COLONY and PARENTAGE methods (Figure 1A–C).

With the most informative marker set (7 loci with He5

0.84), both sire number and individual paternal contribution

were estimated correctly in at least 95% of the replicates by

MIN and COLONY analyses and in .80% of the replicates

by PARENTAGE.

Except in the analyses with the most powerful marker

sets, the COLONY method overestimated sire numbers by

up to 100%, whereas the deviations of sire number

estimates from the true value were lower with the MIN

and PARENTAGE methods (Figures 1A–C and 2A). When

interested in mating frequencies (e.g., Song et al. 2007), it

may in fact be more important to minimize the total

deviation across analyses than to maximize the rate at which

the true values are recovered at the cost of large errors for

some broods. In this case, the MIN method and the

PARENTAGE model may be appropriate choices for

analyses of large broods and moderately polymorphic

markers.

Figure 2.

were averaged across the 100 replicates analyzed for each brood type and marker set with the MIN and the COLONY methods

and the 50 replicates analyzed with PARENTAGE. (A) Broods of 80 offspring sired by a primary father (40 offspring) and 4

additional sires (10 offspring each). (B) Broods of 25 offspring sired by a primary father (13 offspring) and 4 additional sires (3

offspring each). (E) Monogamous broods with 80 offspring. (F) Monogamous broods with 25 offspring.

Average deviations between true sire numbers and numbers estimated from simulated brood genotypes. Deviations

201

Sefc and Koblmu ¨ller?Assessing Parent Numbers from Offspring Genotypes

Page 6

Paternity Reconstruction from Small Full-Sib Groups

(‘‘Small Broods’’)

Given that the amount of information available for paternity

reconstruction increases with increasing numbers of off-

spring per sire, one would expect to obtain better results

from the large broods, where each of the males sired at least

10 offspring, than in the small broods, where some sires are

represented by only 3 offspring. Indeed, the MIN method

produced fewer correct inferences of sire numbers and

contributions and greater deviations of sire number esti-

mates from the true value in the small broods than in the

large broods (Figures 1A,D and 2A,B). MIN analyses with

3–11 markers of He5 0.57 completely failed to reconstruct

the correct sire number, and accurate inference of sire

number in .80% of the replicates required 5–7 markers of

He 5 0.84. Similar results were obtained with the

PARENTAGE program, which produced fewer correct

estimates from small broods except when highly informative

data sets were used (Figure 1F). Although the rates of cor-

rect sire number estimates by PARENTAGE were

comparable to those achieved by the MIN method, none

of the PARENTAGE runs returned correct estimates of

individual paternal contributions (Figure 1F).

The COLONY method generally performed better in

the small broods than it did in the large broods in terms of

the deviations between sire number estimates and true

values (Figure 2B), although not always in terms of the

proportion of correct sire number inferences (Figure 1B,E).

In particular, accurate COLONY sire number estimates

based on the less informative marker sets were obtained

more frequently in the small than in the large broods,

whereas the rates of accurate estimates based on highly

informative marker sets were generally lower in the small

than in the large broods, the latter conforming to expect-

ations on the effect of brood sample size (Wang 2007).

Moreover, the proportions of correct estimates based on the

less informative marker sets were considerably higher, and

deviations from true values were lower, by the COLONY

than by the PARENTAGE and the MIN methods (Figures

1D–F and 2B). Nonetheless, only the most informative

marker set recovered the correct sire number in .80% of

the replicates (Figure 1E).

Both the MIN and the COLONY methods performed

somewhat worse in small broods with skewed sire con-

tributions, in which secondary sires were represented by only

3 offspring each (Figure 1D–E), than in those broods, to

which each of the sires contributed 5 offspring (Supplemen-

tary Figure). A negative effect of reproductive skew on

paternity reconstruction was also observed in other simula-

tion studies (Neff et al. 2002; Myers and Zamudio 2004).

Only skewed broods were analyzed with PARENTAGE.

Monogamous Broods

An accurate reconstruction of the minimum number of sires

required to explain genotypes of ‘‘monogamous broods’’

(i.e., broods sired by a single male and a single female) will

always arrive at the correct sire number of n 5 1, but unless

the exclusion probability of the marker set is very high, this

does not prove monogamy. In fact, in the simulated broods

with 5 sires, a small proportion of the MIN and

PARENTAGE results were consistent with monogamy

(Figure 1A,D,F). The risk of falsely inferring monogamy

from multiply sired broods by the MIN method is closely

related to the exclusion probability of the data and can be

assessed, for example, in the program GERUDSIM (Jones

2005), by simulating and analyzing user-defined broods and

marker sets.

Vice versa, monogamous broods may be erroneously

assigned multiple parents by maximum likelihood and

Bayesian models. Indeed, as in the above COLONY

analyses of multiply sired broods, sire number was greatly

overestimated in monogamous broods unless highly in-

formative marker sets were used, especially when the broods

were large (Figures 3A,C and 2C,D). At least 9 markers of

He5 0.68, or 5 markers of He5 0.84, were required for

COLONY to detect monogamy in .80% of the replicates

in both large and small broods.

In contrast, monogamy of broods was correctly inferred

by PARENTAGE in .80% of replicates with all tested data

sets (Figure 3B,D). Although this result is highly desirable, it

may be linked to the propensity of PARENTAGE to

underestimate sire numbers from small data sets (see above),

which makes results converge on a single sire, rather than

represent superior capability of sire number reconstruction.

Discussion

Most importantly, our analyses suggest that paternity

inference from brood genotypes requires highly informative

marker sets and that low levels of marker polymorphism

cannot be easily compensated for by increasing the number

of such markers. Moreover, even sophisticated methods

including allele segregation and population allele frequency

information into the estimation of sire number were unable

to arrive at correct solutions when the markers were not

sufficiently informative. Hence, it will in many circum-

stances prove more efficient to invest in the development of

highly polymorphic markers than to sufficiently increase the

number of markers with little or moderate diversity. These

findings may be of particular importance for parentage

studies in plants, where allozyme markers have long

remained the predominant tool (Bernasconi 2003) and have

only recently been superseded by the employment of highly

polymorphic microsatellite markers (Reusch 2000; Teixera

and Bernasconi 2007; Llaurens et al. 2008). However, even

with microsatellites, genetic diversity values above 0.8

(required to obtain correct results in our analyses of 5 and

more loci) may, at least in some species or populations, not

be encountered at many loci. In fact, only few microsatellite-

based paternity studies employ either highly polymorphic

markers (e.g., Adams et al. 2005; Mackiewicz et al. 2005;

Portnoy et al. 2007; Teixera and Bernasconi 2007; Wilson

and Martin-Smith 2007) or more than 7 loci (e.g., Reusch

2000; Myers and Zamudio 2004; Beveridge et al. 2006;

202

Journal of Heredity 2009:100(2)

Page 7

Herbinger et al. 2006), whereas the majority of studies are

being conducted with only 3–5 markers of oftentimes

moderate diversity. Investigators should bear in mind that,

without more informative data, estimates of parent numbers

and relative paternal contributions may be approximate

(Sefc et al. 2008).

It is also noteworthy that marker sets with higher

exclusion probabilities did not necessarily produce better

sire number estimates, depending on analysis method and

family structure. For example, although exclusion probabil-

ities increased rapidly between 3 and 7 markers of He5 0.57

(Table 1), COLONY inferences of sire numbers deterio-

rated (Figure 2). Furthermore, a set of 3 markers with He5

0.84 had lower exclusion probabilities than 7 markers with

He 5 0.64 (Table 1) but yielded more accurate MIN

estimates, particularly for small broods (Figures 1 and 2).

The positive correlation between brood size and

corresponding COLONY estimates of sire number is an

artifact of the analysis method but could be mistaken, in

a methodological context, for a failure to detect all

contributing sires in small brood samples (Hain and Neff

2007), or, in a biological context, for an indication of

increasing offspring numbers with increasing numbers of

mates (Bateman 1948; Neff et al. 2008). Generally, both the

overestimation of sire numbers and the failure to detect the

full number of extra sires may compromise conclusions on

the extent of polygamous mating, sneaking rates, and other

alternative reproductive behaviors (e.g., Chapman et al.

2004). In particular, when methods biased toward sire

number underestimation (e.g., the MIN and PARENTAGE

methods) are applied to moderately informative data sets,

inferences of monogamy could also be obtained from

broods with more than a single sire.

Our results prompt no general recommendation of one

of the methods over the others because their performances,

relative to each other, depended on brood size, the true

number of sires, and the distribution of paternal contribu-

tions between sires. Overall, the 3 methods fared poorly

with fewer, and less polymorphic, markers and estimated

sire numbers similarly well when the markers were highly

informative. The COLONY method performed best in

reconstructing the individual contributions of the inferred

sires (Figure 1; Supplementary Figure). Importantly, useful

information can be drawn from comparisons between esti-

mates of the different methods, as disparate results indicate

that there may be insufficient information for accurate

paternity reconstruction. In these cases, the true sire number

will probably lie within the range of the different estimates

(see also Sefc et al. 2008). In contrast, congruency between

estimates from methods biased in opposite directions

provides strong support for the obtained estimate.

Another maximum likelihood parentage reconstruction

method,implemented in

(Herbinger 2005), yielded similar results as COLONY from

empirical data (Herbinger et al. 2006; Sefc et al. 2008) and

displayed similar biases in paternity reconstruction from

theprogramPEDIGREE

Figure 3.

which maximum likelihood (COLONY) and Bayesian (PARENTAGE) analyses returned the sire numbers given on the y axis.

Black bubbles represent correct estimates, that is, a single sire (also marked by the horizontal line). (A) COLONY and (B)

PARENTAGE analyses of 80 offspring. (C) COLONY and (D) PARENTAGE analyses of 25 offspring.

Sire number estimation from monogamous broods. Bubble areas represent the percentage of replicate broods, for

203

Sefc and Koblmu ¨ller?Assessing Parent Numbers from Offspring Genotypes

Page 8

simulated data (Sefc et al. 2008). The tendency of the

PEDIGREE algorithm to split large full-sib groups into

subgroups, which causes a positive correlation between

brood size and inferred sire number, can be compensated by

analysis of parameter settings penalizing group splitting

(Herbinger et al. 2006), such that the minimum number of

sires can be approached with higher penalties, which then

entails the risk of underestimating the true value. The set-

tings required to arrive at the true number of sires vary with

the composition of the broods (Sefc et al. 2008), which

makes the choice of the settings a critical step of the

PEDIGREE analyses.

Jones et al. (2007) compared parentage inference in

COLONY, PARENTAGE, and NEST (their own Bayesian

model, which assigns reproductive success to different

categories of candidate parent individuals based on off-

spring and candidate parent genotypes), and reconstructions

of the minimum numbers of parents per nest, in an

investigation of the reproductive success of different

categories of candidate parents. Their data comprised 23

nests, each represented by 48 offspring genotyped at 5 loci

with Hevalues between 0.57 and 0.88 (mean He5 0.74,

P05 0.92, P15 0.99; Fiumera et al. 2002). On average,

COLONY estimated twice as many mothers per nest as the

other 3 methods. Although the true number of parents per

nest was unknown, it was concluded that COLONY over-

estimated parent numbers. This agrees with our findings for

this level of marker polymorphism. Likewise, the congru-

ency between the minimum parent number and the

PARENTAGE reconstructions (Jones et al. 2007) is con-

sistent with our observation that MIN and PARENTAGE

methods perform similarly well and display a comparable

bias in small broods. Based on NEST analyses of simulated

data and weighing the effort and benefits associated with

increased sampling of loci, different nests, or offspring per

nest, Jones et al. (2007) propose to analyze no more than 3

or 4 loci in order to offset the costs associated with the

genotyping of many broods. Although this number of

markers may indeed be sufficient to reconstruct parentage

when candidate parents are included in the data set, our

analysis indicates that sire number reconstruction without

parental information requires more, or more polymorphic,

loci. Furthermore, although none of the methods tested in

our study was able to reconstruct sire numbers from

moderately and little informative data sets, the employment

of different methods appears to be a useful way to assess the

reliability of the obtained results.

Supplementary Material

Supplementary materials can be found at http://www.jhered.

oxfordjournals.org/.

Funding

Austrian Research Fund (P17380) to K.M.S.

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Received May 20, 2008; Revised September 24, 2008;

Accepted October 2, 2008

Corresponding Editor: Howard Ross

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