Effects of fine‐scale genetic structure on male mating success in gynodioecious Beta vulgaris ssp. maritima

Plant mating systems are known to influence population genetic structure because pollen and seed dispersal are often spatially restricted. However, the reciprocal outcomes of population structure on the dynamics of polymorphic mating systems have received little attention. In gynodioecious sea beet (Beta vulgaris ssp. maritima), three sexual types co‐occur: females carrying a cytoplasmic male sterility (CMS) gene, hermaphrodites carrying a non‐CMS cytoplasm and restored hermaphrodites that carry CMS genes and nuclear restorer alleles. This study investigated the effects of fine‐scale genetic structure on male reproductive success of the two hermaphroditic forms. Our study population was strongly structured and characterized by contrasting local sex‐ratios. Pollen flow was constrained over short distances and depended on local plant density. Interestingly, restored hermaphrodites sired significantly more seedlings than non‐CMS hermaphrodites, despite the previous observation that the former produce pollen of lower quality than the latter. This result was explained by the higher frequency of females in the local vicinity of restored (CMS) hermaphrodites as compared to non‐CMS hermaphrodites. Population structure thus strongly influences individual fitness and may locally counteract the expected effects of selection, suggesting that understanding fine scale population processes is central to predicting the evolution of gender polymorphism in angiosperms.     

Eleven polymorphic microsatellite markers for paternity analysis in the pectoral sandpiper,Calidris melanotos

Eleven polymorphic microsatellite markers were isolated for the pectoral sandpiper, Calidris melanotos. The number of alleles observed in a sample of 149 presumably unrelated adults ranged from nine to 23 with an observed heterozygosity ranging from 0.79 to 0.92. The set of markers described here will prove useful for accurately determining paternity and therefore elucidate the hitherto unknown mating system of this species. We also report on cross‐species amplification of these markers in the semipalmated sandpiper, Calidris pusilla.     

Mixed parentage in Neolamprologus pulcher groups

Genetic data collected on co-operatively breeding Neolamprologus pulcher groups from Lake Tanganyika revealed mixed parentage in 80% of the groups examined. A case (1/11) of shared maternity was detected where a subordinate female bred alongside the dominant female in a social group. Extra-pair paternity was assigned to other dominant males who held their own social groups, but subordinate males were not found to father young in any group (0/9).     

Queen condition,mating frequency,queen loss,and levels of worker reproduction in the hornets Vespa affinis and V. simillima

Abstract 1. Mature queens of the hornet Vespa affinis are unusual in that they lose all their body hair and wings. This has been used as evidence for matricide in hornets. Factors favouring matricide such as low paternity and long annual lifecycle are present in most hornets. 2. We determined paternity in V. affinis and compared queen condition, levels of queen loss, and worker reproduction in 163 V. affinis and 63 V. simillima colonies. These two species have very similar lifecycles and colony sizes, but different paternities (1.3 vs 2.4). Furthermore, in queen‐right V. affinis colonies small proportions (4%) of reproductive workers were present, whereas in queen‐right V. simillima colonies no reproductive workers were detected. 3. Despite these differences, queen damage in both species was influenced predominantly by her age and in V. affinis was not influenced by presence of reproductive workers. 4. The number of queen‐less V. simillima (9/63 = 14%) and V. affinis (28/163 = 17%) colonies were also not significantly different (P = 0.8). Therefore, queen damage and proportions of queen‐less colonies were not linked making it a poor indicator of matricide. 5. It is proposed that graded control of sexual and worker production in wasps and hornets prevents a situation where kin‐selected matricide is ever favoured.     

Multiple paternity occurs with low frequency in the territorial roe deer, Capreolus capreolus

An explanation for female multiple mating when males offer no material benefits but sperm remains elusive, largely because of a lack of empirical support for the genetic benefits hypothesis. We used 21 microsatellite markers to test for multiple paternities among 88 litters of roe deer, Capreolus capreolus , and to investigate the inbreeding avoidance hypothesis as a potential mechanism for the evolution of female multiple mating. From paternity analyses, we found that 13.5% of polytocous litters were sired by more than one male. We also found that a half-sib relationship was more likely than a full-sib relationship for 20.5% of all litters. This is the first report of multiple paternities in a territorial ungulate species. In support of the inbreeding avoidance hypothesis, we found that parents who were strongly related produced offspring with lower individual heterozygosity that survived less well during their first summer than fawns with unrelated parents. In addition, fawns from multiple paternity litters survived their first summer better than fawns from single paternity litters. However, it remains unclear whether all female multiple paternity events in this species are provoked by an initial consanguineous mating.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97 , 128–139.     

PEDIGREE ERROR DUE TO EXTRA‐PAIR REPRODUCTION SUBSTANTIALLY BIASES ESTIMATES OF INBREEDING DEPRESSION

Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete “apparent” pedigree data compiled from observed parental behavior and analogous “actual” pedigree data comprising genetic parentage to quantify effects of paternity error stemming from extra‐pair reproduction on estimates of f, reproductive success, and inbreeding depression in free‐living song sparrows (Melospiza melodia). Paternity error caused widespread error in estimates of f and male reproductive success, causing inbreeding depression in male and female annual and lifetime reproductive success and juvenile male survival to be substantially underestimated. Conversely, inbreeding depression in adult male survival tended to be overestimated when paternity error was ignored. Pedigree error stemming from extra‐pair reproduction therefore caused substantial and divergent bias in estimates of inbreeding depression that could bias tests of evolutionary theories regarding inbreeding and inbreeding depression and their links to variation in mating system.     

Thank you for not flowering: conservation genetics and gene flow analysis of native and non-native populations of Fraxinus (Oleaceae) in Ireland

The risks of gene flow between interfertile native and introduced plant populations are greatest when there is no spatial isolation of pollen clouds and phenological patterns overlap completely. Moreover, invasion probabilities are further increased if introduced populations are capable of producing seeds by selfing. Here we investigated the mating system and patterns of pollen-mediated gene flow among populations of native ash (Fraxinus excelsior) and mixed plantations of non-native ash (F. angustifolia and F. excelsior) as well as hybrid ash (F. excelsior × F. angustifolia) in Ireland. We analysed the flowering phenology of the mother trees and genotyped with six microsatellite loci in progeny arrays from 132 native and plantation trees (1493 seeds) and 444 potential parents. Paternity analyses suggested that plantation and native trees were pollinated by both native and introduced trees. No signs of significant selfing in the introduced trees were observed and no evidence of higher male reproductive success was found for introduced trees compared with native ones either. A small but significant genetic structure was found (φ_ft=0.05) and did not correspond to an isolation-by-distance pattern. However, we observed a significant temporal genetic structure related to the different phenological groups, especially with early and late flowering native trees; each phenological group was pollinated with distinctive pollen sources. Implications of these results are discussed in relation to the conservation and invasiveness of ash and the spread of resistance genes against pathogens such as the fungus Chalara fraxinea that is destroying common ash forests in Europe.     

Comparing parentage inference software: reanalysis of a red deer pedigree

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent–offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent–offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent–offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a ‘known pedigree’ estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population‐ rather than individual‐level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual‐ rather than population‐level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.     

Assessing age,breeding stage,and mating activity as drivers of variation in the reproductive microbiome of female tree swallows

Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first requires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free‐living, female tree swallows (Tachycineta bicolor). Using microsatellite‐based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß‐estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual''s lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith''s phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within‐individual changes and age‐related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping the cloacal microbiomes of wild birds.     

COLONY: a program for parentage and sibship inference from multilocus genotype data

Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.