Early inbreeding depression in the sexually polymorphic plant Dianthus sylvestris (Caryophyllaceae): Effects of selfing and biparental inbreeding among sex morphs

Predominantly outcrossing plant species are expected to accumulate recessive deleterious mutations, which can be purged when in a homozygous state following selfing. Individuals may vary in their genetic load because of different selfing histories, which could lead to differences in inbreeding depression among families. Lineage-dependent inbreeding depression can appear in gynodioecious species if obligatory outcrossed females are more likely to produce female offspring and if partially selfing hermaphrodites are more likely to produce hermaphrodites. We investigated inbreeding depression at the zygote, seed, and germination stages in the gynomonoecious-gynodioecious Dianthus sylvestris, including pure-sexed plants and a mixed morph. We performed hand-pollinations on 56 plants, belonging to the three morphs, each receiving 2-3 cross treatments (out-, sib- and self-pollination) on multiple flowers. Effects of cross treatments varied among stages and influenced seed provisioning, with sibling competition mainly occurring within outcrossed fruits. We found significant inbreeding depression for seed mass and germination and cumulative early inbreeding depression varied greatly among families. Among sex morphs, we found that females and hermaphrodites differed in biparental inbreeding depression, whereas uniparental was similar for all. Significant inbreeding depression levels may play a role in female maintenance in this species, and individual variation in association with sex-lineages proclivity is discussed.     

Little to no inbreeding depression in a tapeworm with mixed mating

Meta‐studies on hermaphrodites have found a negative relationship between primary selfing rates and levels of inbreeding depression (ID) and, thus, generally support purging in inbred systems. However, in plants, high among‐taxa variance in ID results in no difference in the mean ID between outcrossing and mixed‐mating taxa. Selective interference likely explains high ID among mixed‐mating taxa, whereas low levels of ID among mixed‐mating taxa are not as stressed. Among animal hermaphrodites, primarily molluscs, there are little data on mixed‐mating systems. To fill a taxonomic and mating system gap, we tested for ID in a mixed‐mating tapeworm, Oochoristica javaensis. We provide a direct estimate of ID across infection of an intermediate host by comparing selfing rates at two life history stages. We found little to no evidence for ID, and the level of ID falls in line with what is reported for highly selfing species even though O. javaensis has mixed mating. We discuss this result within the context of kin mating in O. javaensis. Our results emphasize that primary selfing rates alone may be insufficient to classify the inbreeding history in all species when testing for a relationship to ID. Mixed‐mating taxa, and possibly some outcrossing taxa, may exhibit low levels of ID if biparental inbreeding is also driving purging. We advocate that ID studies report estimates of inbreeding history (e.g. F_IS or identity disequilibrium) from nature‐derived adult samples to provide context rather than relying on primary selfing rates alone.     

Testing why the sex of the maternal parent affects seedling survival in a gynodioecious species

In gynodioecious plants, seed offspring from hermaphrodites often perform less well than those from females. This lower performance sometimes can be attributed to inbreeding by hermaphrodites or to relatively greater provisioning of individual seeds by females. However, these hypotheses are not explanatory when only outcrossing occurs and when individual seeds of the two morphs are equally well provisioned. Three hypotheses may explain the lower fitness of seed offspring from hermaphrodites in such cases. The morphology hypothesis states that the opportunity for gametophytic selection is lower within flowers of hermaphrodites compared to flowers on females, because the perfect flowers of hermaphrodites are relatively short-styled. The cytotype hypothesis states that the performance difference is directly caused by an individual's cytotype, whose frequency in the population may differ for the two sex morphs. The pleiotropy hypothesis states that negative pleiotropic effects of nuclear restorer alleles or alleles hitchhiking with them are expressed more often by offspring from hermaphrodites. We performed two experiments using the gynodioecious plant Silene acaulis to contrast these hypotheses. In our first experiment we contrasted the morphology and pleiotropy hypotheses by performing controlled pollinations and subsequently planting seeds in both the greenhouse and field. Hermaphrodites of S. acaulis can produce both pistillate and perfect flowers, which allowed us to determine whether flower morphology affects offspring survivorship independent of the sex of the maternal parent. We found that neither seed mass nor germination differed between seeds from females and hermaphrodites. Offspring from pistillate flowers on hermaphrodites did not differ significantly in their survival compared to offspring from perfect flowers on hermaphrodites, but had lower survivorship compared to offspring from pistillate flowers on females, refuting the morphology hypothesis. In a second experiment, we compared offspring survival of full-sibling pairs of females and hermaphrodites (who shared the same cytoplasm) to contrast the cytotype and pleiotropy hypotheses. We found that seed offspring from females and hermaphrodites that shared the same cytoplasm differed in their survival, which is counter to the prediction of the cytotype hypothesis. In both experiments, the sex of the maternal parent significantly affected offspring survival, with seed offspring from hermaphrodites surviving less well than those from females. These results support the pleiotropy hypothesis. We conclude by discussing alternative ways of thinking about negative pleiotropic effects of nuclear restorers or "the cost of restoration."     

Inbreeding effects on mating system traits for two species of Lupinus (Leguminosae)

The consequences of inbreeding for reproductive traits were investigated for two closely related annual lupines that differ in their mating system. Lupinus bicolor (Leguminosae) is a primarily selling species while Lupinus nanus outcrosses at intermediate rates. A controlled crossing program was used for each species to produce selfed and outcrossed progeny. These progeny were then grown in a greenhouse and scored for the date of first flower, flower morphology, and autofertility. Selfed progeny of L. bicolor produced significantly smaller flowers but did not differ from outcrossed progeny for the remaining traits. Selfed progeny of L. nanus produced flowers that significantly differed in shape and had fewer ovules than the flowers of outcrossed progeny. Selfed progeny of L. nanus also had significantly lower rates of autofertility in comparison to outcrossed progeny. The significant effects of inbreeding on these mating system traits may indicate the presence of directional dominance at the loci underlying these characters. The consequences of these direct effects of inbreeding on reproductive traits for plants growing in natural populations may include nonadaptive changes in the outcrossing rate between generations.     

The role of autonomous self-pollination in floral longevity in varieties of Impatiens hypophylla (Balsaminaceae)

The floral longevity of unpollinated, hand self-, and hand cross-pollinated flowers was compared in two varieties of Impatiens hypophylla, which contrasts with their mating systems. When flowers were emasculated and hand-pollinated every day after anthesis, their longevity was reduced. In the absence of emasculation and hand pollination, the staminate phase of the flowers of both varieties was 1 d longer. After the staminate phase, flowers of the outcrossing variety dropped their androecium, exposing the stigma and initiating the pistillate phase, which lasted for ～2 d. In contrast, flowers of the mixed-mating variety self-pollinated autonomously and then terminated their flowering. Under great seasonal variation in the pollinator visitation rate, which was observed in their natural populations, the outcrossing variety should maximize expected outcross success through the phenology of floral sex phases, whereas the mixed-mating variety self-pollinated ovules that were not outcrossed within the staminate phase. Based on these results, I suggest that the autonomous self-pollination in I. hypophylla induced differences both in the selfing coefficient and in floral longevity between the varieties.     

Mating system, sex ratio, and persistence of females in the gynodioecious shrub Daphne laureola L. (Thymelaeaceae)

Although in gynodioecious populations male steriles require a fecundity advantage to compensate for their gametic disadvantage, southern Spanish populations of the long-lived shrub Daphne laureola do not show any fecundity advantage over hermaphrodites in terms of seed production and early seedling establishment. By using allozyme markers, we assess the mating system of this species in five populations differing in sex ratio, and infer levels of inbreeding depression over the whole life cycle by comparing the inbreeding coefficients at the seed and adult plant stages. Extremely low outcrossing rates (0.001相似文献   

The role of pollination level on the reproduction of females and hermaphrodites in the gynodioecious plant Gypsophila repens (Caryophyllaceae)

In gynodioecious plant species, females are expected to have more resources available for maturing seeds because pistillate flowers are smaller, do not produce pollen, and are thus less costly that perfect flowers. The potential female advantage arising from more abundant resources is, however, likely to vary depending on whether seed production is limited by resource or pollen availability. Here we experimentally investigated the influence of pollen and resource limitation on female advantage in a gynodioecious species using two levels of pollination. Total seed production of females was always greater than that of hermaphrodites: females produced more flowers and more fruits that contained similar numbers of seeds of similar mass. Under low pollination, female and hermaphrodite plants allocated resources to increased flower production rather than to increased seed size or quality. We did not detect any influence of pollen or resource limitation on female advantage, which remained similar under low (= abundant resources) and full pollination. Outcrossed fruits performed better than selfed fruits when the same plant received both selfed and outcrossed pollen on different flowers. These differences were not greater under high pollination, possibly because resources available for each fruit did not differ between our pollen intensity treatments.     

Outcrossing and paternity in Glycine argyrea by paired fruit analysis

Glycine argyrea (Fabaceae), a perennial wild relative of soybean, has a dual flowering strategy of both self-fertilized cleistogamous flowers and chasmogamous flowers on the same plant. Using allozyme polymorphisms the frequency and pattern of outcrossing was determined. The genotypes of seeds from each of several fruit (legumes) per plant were analysed by starch gel electrophoresis, and the maternal genotype inferred. The maximum likelihood estimates of outcrossing rate for the chasmogamous flowers averaged 0.38. The observed level of heterozygosity in the adult population (h = 0.25) compared with the level expected under random mating (h = 0.32) indicated that partial outcrossing was typical of this population. To analyse the mating pattern further, the pollen genotypes of several seeds per legume for pairs of legumes from the same plant were determined. About 35% of fruit from chasmogamous flowers had no genetically detectable outcross progeny, presumably because they were not cross-pollinated effectively. The majority of the remaining fruit had seed which were of mixed origin (both self-fertilized and outcrossed), suggesting that insect pollination does not preclude self-fertilization. As might be expected from this entomophilous pollination system, the pollen of outcrossed seed within one fruit usually (85% of cross-pollinated legumes) came from one male source. Evidence of pollen carry-over was found in the other legumes. The joint distribution of male sources among the pairs of legumes (paired fruit analysis) showed that non-self sources were shared in 30% of pairs. The probability that two outcrossed seeds from the same fruit would be half-sibs was estimated as 0.15, and for two seeds from different fruit on the same plant as 0.42. There is a hierarchy of genetic identity within and among legumes on the same plant, and on different plants, providing scope for the operation of selection at different levels.     

Optimal sex allocation under pollen limitation

Most flowering plants are simultaneous hermaphrodites. Within species and even within local populations, sex allocation is usually highly plastic. Here, we link pollen sufficiency to the size of pollen-exchanging groups (i.e., pollen neighborhoods) and to pollen transfer efficiency, using an individual-based game-theoretic framework to determine the stable distribution of sex allocation that does not require the unrealistic assumption of infinitely large, panmictic populations. In the absence of selfing, we obtain the novel result that pollen limitation destabilizes hermaphroditism and favors separate sexes, whereas hermaphroditism remains stable without pollen limitation. With mixed mating, hermaphroditism is stable except when the fitness value of selfed offspring is less than half that of outcrossed offspring (i.e., strong inbreeding depression). In that case, the size of pollen neighborhoods, pollen transfer efficiencies, and the relative fitness of selfed offspring determine whether separate sexes or hermaphroditism is the stable outcome. The model thus predicts that separate sexes can derive from either of two ancestral states: obligate outcrossing under pollen limitation, or mixed mating (competing self-fertilization) under severe inbreeding depression. It also predicts conditions under which variance in sex-allocation among hermaphrodites within pollen exchanging groups along a gradient of pollen limitation can range from high (dioecy) to near zero (equal proportions of male and female investment).     

Differential outcrossing rates in dispersing and non-dispersing achenes in the heterocarpic plant Crepis sancta (Asteraceae)

The association between mating systems and dispersal in plants has been studied mostly in cleistogamous species where, generally, seeds produced by cleistogamous (selfed) flowers are less dispersed than seeds produced by chasmogamous (potentially outcrossed) flowers. In heterocarpic Asteraceae, non-dispersing fruits (achenes) are produced at the periphery of the capitulum (outer florets) whereas dispersing achenes are produced by inner florets in the same capitulum. Since all the florets are protandrous, the outer floret developing first are in female phasis when anthesis of inner florets takes place. Thus, outer florets can be potentially selfed by the inner florets of the same capitulum whereas the latter must be pollinated by flowers of other capitula. Therefore outer florets should be more inbred than inner florets. To test this hypothesis, we measured the natural outcrossing rate in outer and inner florets using allozymes in three populations of the heterocarpic Crepis sancta. The results showed that the outcrossing rate was highest for non-dispersed achenes. Moreover, among the outcrossed achenes within a capitulum it was observed that the number of paternal parents of non-dispersing achenes was higher than for dispersing achenes. The pattern observed was therefore the opposite to the pattern of cleistogamous plants and contradicts the putative pollination mechanism we proposed for Asteraceae. The results agree with the predictions of sib competition theory which considers that outcrossing may minimize competitive interactions among relatives (sibs) falling near the mother plant. Higher outcrossing rate in outer florets could also occur because pollinators are more attracted to these florets.     

Reproductive biology of Echinodorus longipetalus (Alismataceae): Sexual morphs,breeding system and pollinators

The floral biology, pollinators and breeding system of Echinodorus longipetalus Micheli were studied in a marshy area of the district of Taquaritinga (State of São Paulo), southeastern Brazil. E. longipetalus is gynodioecious and as far as is known, this is the first record of unisexual flowers, besides perfect flowers, in Echinodorus. Proportion of female individuals in the studied population is 50% and produces 31% more flowers than hermaphrodites. Perfect and pistillate flowers of E. longipetalus are similar in appearance and are pollinated by several species of Hymenoptera (mainly by Xylocopa (Neoxylocopa) suspecta Moure & Camargo). Perfect flowers offer pollen as a reward. Pistillate flowers attract floral visitors by deceit with their staminodes that resemble the stamens of the perfect flowers. Visits to pistillate flowers are quick (1–2 s), while visits to perfect flowers last up to 120 s. The perfect flowers are self-compatible and produce fruits through spontaneous self-pollination (control flowers), whereas the pistillate ones only set fruits through cross-pollinations. Perfect and pistillate flowers set more fruits under natural conditions than in manual treatments, respectively. Although the pistillate and perfect flowers bear a strong similarity, the selective pollinator behavior seems to be responsible for the increase of fruit set in perfect flowers.     

BEST OF BOTH WORLDS? ASSOCIATION BETWEEN OUTCROSSING AND PARASITE LOADS IN A SELFING FISH

Mixed-mating strategies (i.e., intermediate levels of self-fertilization and outcrossing in hermaphrodites) are relatively common in plants and animals, but why self-fertilization (selfing) rates vary so much in nature has proved difficult to explain. We tested the hypothesis that parasites help maintain mixed-mating using a partially selfing fish (Kryptolebias marmoratus) as a model. We show that outcrossed progeny in the wild are genetically more diverse and less susceptible to multiple parasite infections than their selfed counterparts. Given that outcrossing in K. marmoratus can only be attained by male-hermaphrodite matings, our data provide an explanation for the coexistence of males and hermaphrodites in androdioecious species where hermaphrodites are unable to outcross among themselves. Moreover, our study provides evidence that parasites contribute to maintaining mixed-mating in a natural animal population.     

MIXED MATING SYSTEMS IN HAWAIIAN BIDENS (ASTERACEAE)

Floral features related to the breeding system were studied for 11 species of Hawaiian Bidens. Protandry and male sterility promote outcrossing, while self-compatibility and geitonogamy contribute to inbreeding. The combination of these floral mechanisms results in a mixed mating system in all species studied. Outcrossing rates of 15 populations of these species ranged from 0.43 to 0.88, averaging 0.65. Apparent selling rates of females ranged from 0 to 0.25 in seven gynodioecious populations surveyed, suggesting that there is variation in the level of biparental inbreeding among populations. The presence of females increased the level of outcrossing by an average of 9% in gynodioecious populations. This study indicates that the efficiency of gynodioecy as an outcrossing mechanism largely depends on the current outcrossing rate of hermaphrodites, the frequency of females, and the extent of genetic substructuring in populations. On average, autogamy contributed 4%, geitonogamy contributed 24%, and consanguineous mating contributed 15% to the realized selfing rate (43%) in the hermaphrodites of these species.     

Reproductive biology of Echinodorus longipetalus (Alismataceae): Sexual morphs,breeding system and pollinators

The floral biology, pollinators and breeding system of Echinodorus longipetalus Micheli were studied in a marshy area of the district of Taquaritinga (State of São Paulo), southeastern Brazil. E. longipetalus is gynodioecious and as far as is known, this is the first record of unisexual flowers, besides perfect flowers, in Echinodorus. Proportion of female individuals in the studied population is 50% and produces 31% more flowers than hermaphrodites. Perfect and pistillate flowers of E. longipetalus are similar in appearance and are pollinated by several species of Hymenoptera (mainly by Xylocopa (Neoxylocopa) suspecta Moure & Camargo). Perfect flowers offer pollen as a reward. Pistillate flowers attract floral visitors by deceit with their staminodes that resemble the stamens of the perfect flowers. Visits to pistillate flowers are quick (1–2 s), while visits to perfect flowers last up to 120 s. The perfect flowers are self-compatible and produce fruits through spontaneous self-pollination (control flowers), whereas the pistillate ones only set fruits through cross-pollinations. Perfect and pistillate flowers set more fruits under natural conditions than in manual treatments, respectively. Although the pistillate and perfect flowers bear a strong similarity, the selective pollinator behavior seems to be responsible for the increase of fruit set in perfect flowers.     

Morphological variation in the flowers of Jacaratia mexicana A. DC. (Caricaceae), a subdioecious tree

The Caricaceae is a small family of tropical trees and herbs in which most species are dioecious. In the present study, we extend our previous work on dioecy in the Caricaceae, characterising the morphological variation in sexual expression in flowers of the dioecious tree Jacaratia mexicana . We found that, in J. mexicana , female plants produce only pistillate flowers, while male plants are sexually variable and can bear three different types of flowers: staminate, pistillate and perfect. To characterise the distinct types of flowers, we measured 26 morphological variables. Our results indicate that: (i) pistillate flowers from male trees carry healthy-looking ovules and are morphologically similar, although smaller than, pistillate flowers on female plants; (ii) staminate flowers have a rudimentary, non-functional pistil and are the only flowers capable of producing nectar; and (iii) perfect flowers produce healthy-looking ovules and pollen, but have smaller ovaries than pistillate flowers and fewer anthers than staminate flowers, and do not produce nectar. The restriction of sexual variation to male trees is consistent with the evolutionary path of dioecy from hermaphrodite ancestors through the initial invasion of male-sterile plants and a subsequent gradual reduction in female fertility in cosexual individuals (gynodioecy pathway), but further work is needed to confirm this hypothesis.     

The interactive effects of herbivory and mixed mating for the population dynamics of Impatiens capensis

In this study, we examine the demographic consequences of mixed mating and explore the interactive effects of vegetative herbivory and mating system for population dynamics of Impatiens capensis, a species with an obligate mixed mating system (i.e., individuals produce both obligately selfing cleistogamous and facultatively outcrossing chasmogamous flowers). In two natural populations, we followed seeds derived from cleistogamous and chasmogamous flowers subject to different herbivory levels throughout their life cycle. Using a mating system-explicit projection matrix model, we found that mating system types differed in important vital rates. Cleistogamous individuals had higher rates of germination than did chasmogamous individuals, whereas chasmogamous individuals expressed a fecundity advantage over cleistogamous individuals. In addition, population growth was most sensitive to changes in vital rates of cleistogamous individuals, indicating the demographic importance of selfing for these populations. Herbivory also had demographic consequences; a 33%-49% reduction in herbivory caused the population growth rates to increase by 104%-132%, primarily because of effects on vital rates of selfed individuals. Our results not only uncover a novel consequence of mating system expression, that is, mating system influences population dynamics, but also shed light on the role of herbivores in maintaining mixed mating.     

Mirror image flowers and their effect on outcrossing rate in Chamaecrista fasciculata (Leguminosae)

The influence of enantiostyly (reciprocal segregation of anthers and stigmas to different sides of the flower) on outcrossing rate was examined in Chamaecrista fasciculata (Leguminosae). I hypothesized that enantiostyly has not evolved to increase the female component of outcrossing and actually acts to increase the selling rate through geitonogamy. To quantify the role of enantiostyly to outcrossing, plants of known isozyme genotype were manipulated to be either completely left- or right-styled (nonenantiostylous) or to have equal numbers of left- and right-styled flowers (enantiostylous). Flower number was varied to quantify any interaction between floral display size and enantiostyly on outcrossing rate. These “target” plants were surrounded by unmanipulated plants homozygous for the alternative allele. Outcrossing rates of the target plants were determined by scoring the presence or absence of heterozygotes. The contribution of enantiostyly to geitonogamy may be reduced if pollinators discriminate among the floral types. Thus, observations of pollinator movement between flowers on the same plant were made to determine if pollinators discriminate between the floral types. Although pollinators moved randomly between flower types, outcrossing rate was only marginally effected by the presence of enantiostyly. Enantiostylous plants outcrossed at a slightly lower rate than nonenantiostylous plants only when the opportunity for geitonogamy was great. These results suggest that the contribution of enantiostyly to selling is minimal.     

Consequences of inbreeding for offspring fitness and gender in Silene vulgaris,a gynodioecious plant

Abstract In gynodioecious plants, hermaphrodite and female plants co‐occur in the same population. In these systems gender typically depends on whether a maternally inherited cytoplasmic male sterility factor (CMS) is counteracted by nuclear restorer alleles. These restorer alleles are often genetically dominant. Although plants of the female morph are obligatorily outcrossing, hermaphrodites may self. This selfing increases homozygosity and may thus have two effects: (1) it may decrease fitness (i.e. result in inbreeding depression) and (ii) it may increase homozygosity of the nuclear restorer alleles and therefore increase the production of females. This, in turn, enhances outcrossing in the following generation. In order to test the latter hypothesis, experimental crosses were conducted using individuals derived from four natural populations of Silene vulgaris, a gynodioecious plant. Treatments included self‐fertilization of hermaphrodites, outcrossing of hermaphrodites and females using pollen derived from the same source population as the pollen recipients, and outcrossing hermaphrodites and females using pollen derived from different source populations. Offspring were scored for seed germination, survivorship to flowering and gender. The products of self‐fertilization had reduced survivorship at both life stages when compared with the offspring of outcrossed hermaphrodites or females. In one population the fitness of offspring produced by within‐population outcrossing of females was significantly less than the fitness of offspring produced by crossing females with hermaphrodites from other populations. Self‐fertilization of hermaphrodites produced a smaller proportion of hermaphroditic offspring than did outcrossing hermaphrodites. Outcrossing females within populations produced a smaller proportion of hermaphrodite offspring than did crossing females with hermaphrodites from other populations. These results are consistent with a cytonuclear system of sex determination with dominant nuclear restorers, and are discussed with regard to how the mating system and the genetics of sex determination interact to influence the evolution of inbreeding depression.     

Herkogamy and mate diversity in the wild daffodil Narcissus longispathus: beyond the selfing–outcrossing paradigm in the evolution of mixed mating

Spatial separation of male and female reproductive structures (herkogamy) is a widespread floral trait that has traditionally been viewed as an adaptation that reduces the likelihood of self‐pollination. Here we propose that increased herkogamy may also influence another important aspect of plant mating: the diversity of pollen donors siring seeds within fruits. We test this hypothesis in Narcissus longispathus, a wild daffodil species with extensive variation in anther–stigma separation. To study the morphological basis of variation in herkogamy, floral measurements were undertaken in 16 populations of N. longispathus. We then quantified multilocus outcrossing rates and the correlation of outcrossed paternity in three of these populations sampled over several years. Mating system estimates were calculated for each population and year, and also separately for groups of plants that differed markedly in herkogamy within each population and year. In N. longispathus herkogamy was much more variable than other floral traits, and was more closely related to style length than to anther position. Averaged across populations and years, plants with high herkogamy had similar outcrossing rates (0.683) to plants with intermediate (0.648) or low herkogamy (0.590). However, a significant linear trend was found for correlation of outcrossed paternity, which increased monotonically from high herkogamy (0.221), through intermediate herkogamy (0.303) to low herkogamy (0.463) plants. The diversity of pollen donors siring seeds of high herkogamy Narcissus flowers was thus consistently greater than the diversity of pollen donors siring seeds of low herkogamy flowers. Results of this study contribute to the emerging consensus that floral traits can simultaneously influence several aspects of plant mating system in complex ways, thus extending the traditional focus centred exclusively on patterns and relative importance of self‐ and cross‐fertilisation.     

Individualized mating system estimation using genomic data

The estimation of outcrossing rates in hermaphroditic species has been a major focus in the evolutionary study of reproductive strategies, and is also essential for plant breeding and conservation. Surprisingly, genomics has thus far minimally influenced outcrossing rate studies. In this article, we generalize a Bayesian inference method (BORICE) to accommodate genomic data from multiple subpopulations of a species. As an empirical demonstration, BORICE is applied to 115 maternal families of Mimulus guttatus. The analysis shows that low‐level whole genome sequencing of parents and offspring is sufficient for individualized mating system estimation: 208 offspring (88.5%) were definitively called as outcrossed, 23 (9.8%) as selfed. After mating system parameters are established (each offspring as outcrossed or selfed and the inbreeding level of maternal plants), BORICE outputs posterior genotype probabilities for each SNP genomewide. Individual SNP calls are often burdened with considerable uncertainty and distilling information from closely linked sites (within genomic windows) can be a useful strategy. For the Mimulus data, principal components based on window statistics were sufficient to diagnose inversion polymorphisms and estimate their effects on spatial structure, phenotypic and fitness measures. More generally, mating system estimation with BORICE can set the stage for population and quantitative genomic analyses, particularly researchers collect phenotypic or fitness data from maternal individuals.