Estimates Of Outcrossing Rate Research Articles

Progeny array analysis to estimate outcrossing rates, inbreeding coefficients, and inbreeding depression among native, naturalized, and invasive populations of Mimulus guttatus (Phrymaceae).

The mating system of non-native plant populations plays a role in determining the colonizing success following introduction into locations outside of the native distribution. For plant species capable of mixed-mating, both selfing and outcrossing can be advantageous and promote the establishment, persistence, and spread of newly arrived populations. To investigate how mating systems may contribute to the invasion process we estimated mating system parameters in perennial populations of the model plant species, Mimulus guttatus from its native range (West coast USA), non-native populations that are established but have not become invasive (East coast USA, >50 years), and populations in invasive regions (UK >200 years). Studies that include mating system data across the continuum of the invasion process are rare, thus here we utilize molecular markers to estimate outcrossing rates (t), inbreeding coefficients (F), and inbreeding depression in native, naturalized, and invasive populations. Overall, we found support for the persistence of mixed-mating across populations, variability in the relationship between outcrossing rates and inbreeding depression across populations, and evidence for the bridgehead process, where non-native populations may be the sources for the further establishment or reinforcement of additional non-native populations. The methodology we deployed had its own assumptions and sampling design constraints, that contributed to the variation in the parameter estimates. All M. guttatus populations likely rely on selfing through both within clone, and within flower and plant mating in addition to vegetative propagation. The results underscore the importance of introduction history in determining the role of both sexual and asexual reproduction in the successful establishment of a plant species outside its native range.

Outcrossing rates in the permanent translocation heterozygote Oenothera biennis L. (Onagraceae)

In species that primarily reproduce asexually, occasional sex can have important evolutionary consequences. Many plant species in the genus Oenothera have a genetic system called permanent translocation heterozygosity (PTH), which renders plants functionally asexual when they self-fertilize. PTH results from reciprocal translocations of chromosomes that suppress recombination and a balanced lethal mortality of homozygous gametes that prevents independent assortment of alleles. When PTH plants self-fertilize, the offspring are genetically identical to the parents, but when they outcross they can create new genotypes. Here, we sought to determine the outcrossing rate of natural populations of PTH Oenothera biennis L. (Onagraceae). We genotyped 46 parents from 14 populations in Tompkins County, NY, USA, and 754 of their offspring at highly polymorphic microsatellite loci. 99.5% of offspring were genetically identical to their seed parents, whereas 4 offspring out of 754 exhibited allelic mismatches with their seed parent. The estimated outcrossing rate ranged from 0.1% to 0.4%. Our study design also permitted us to estimate mutation rate of microsatellite loci, which ranged from 1.33 × 10−3 to 3.98 × 10−3. These results show that O. biennis typically exhibits a functionally asexual genetic system, but rare outcrossing events can generate novel genotypes that may have important evolutionary consequences.

Estimation of Outcrossing Rate of Faba Bean under Natural Moroccan Conditions

Background: Faba bean is a crop of agro-ecological and socio-economic importance in Morocco. Thus, in a changing climatic context, it is important to develop varieties that are resilient to several abiotic constraints, such as synthetics. However, the reproductive system must be understood. Methods: We aimed to estimate faba beans outcrossing rate under natural Moroccan conditions, using two varieties, ‘Reina Mora’ and ‘Zina’ and two phenotypic markers, seed coat color and its size and shape, in two contrasted locations, Saïs and Gharb. Varieties were sown in six alternate rows with six seeds per row and three replicates per location. The experiment consisted in counting the number of purple seeds within ‘Zina’s beige offspring. Besides, seeds collected from ‘Reina Mora’ were counted and processed for differences in size and shape. In total, 859 seeds were measured, including their length, width, thickness, geometric diameter, area and sphericity, enabling to distinguish hybrids from parental seeds and self-seeds. Result: Results showed an average inter-crossing of 3.7% in Saïs and 7.22% in Gharb. A more reliable open-pollination could be achieved by introducing bees and bumblebees colonies as well as using varieties from same geographic gene pools.

Differences in mating system and predicted parental conflict affect post-pollination reproductive isolation in a flowering plant.

Mating system shifts from outcrossing to selfing are frequent in plant evolution. Relative to outcrossing, selfing is associated with reduced parental conflict over seed provisioning, which may result in postzygotic, asymmetric, reproductive isolation in crosses between populations of different mating systems. To test the hypothesis that post-pollination reproductive isolation between populations increases with increasing differences in mating system and predicted parental conflict, we performed a crossing experiment involving all combinations of three self-compatible populations (with low outcrossing rates), and three self-incompatible populations (with high outcrossing rates) of the arctic-alpine herb Arabis alpina, assessing fitness-related seed and plant traits of the progeny. Predicted levels of parental conflict ("genome strength") were quantified based on strength of self-incompatibility and estimates of outcrossing rates. Crosses between self-compatible and self-incompatible populations yielded very small seeds of low viability, resulting in strong reproductive isolation. In 14 of 15 reciprocal between-population crosses, seeds were heavier when the paternal plant had the stronger genome, and seed mass differences between cross directions increased with an increased difference in parental conflict. Overall, our results suggest that, when sufficiently large, differences in mating system and hence in expected parental conflict may result in strong post-pollination reproductive barriers contributing to speciation.

Mating Systems of Single Families and Population Genetic Diversity of Endangered Ormosia hosiei in South China.

Ormosia hosiei is a tree species native to China that has been extensively used for ornamental and furniture purposes due to its valued timber. The mating system has substantial impact on genetic diversity and structure of plant natural population. Such information should be considered when planning tree planting for forest restoration. Here we used 12 microsatellite markers and described the mating system of single families and the population genetic diversity of O. hosiei. A high level of genetic diversity was observed in both adults and progenies, although slight differences existed among populations and their progenies, with the expected heterozygosity ranging from 0.763 to 0.794. Overall, O. hosiei displayed a predominantly outcrossed mating. The estimate of multi-locus outcrossing rate (tm) was high with low variations among families, ranged from 0.997 to 1.000. The value of tm-ts, ranged from 0.000 to 0.139, indicated that biparental inbreeding occurred in progenies. Therefore, to obtain a reasonable genetic representation of native tree species and prevent problems associated with inbreeding depression, we suggested effective in situ conservation by replanting seedlings, but seedling production for restoration purposes may require a much larger sampling effort than is currently used. Moreover, it is necessary to conduct further multiple population and multi-year experiments to verify our conclusions.

Mating system of a Mammillaria magnimamma (Cactaceae) population of the semi-arid central Mexican region

Knowledge on the reproductive biology of globose cacti in the genus Mammillaria is incipient, despite being one of the most diverse and threatened groups in Cactaceae. We studied a clonal population of Mammillaria magnimamma (Hawort) located in the Valle del Mezquital, Mexico in which sexual reproduction occurs, although neither seedlings nor juveniles were observed. Based on their short life cycle, globose life form, and melittophilous pollination syndrome, this species was expected to exhibit a mixed mating system and null seed recruitment. We examined the population structure, reproductive phenology, and the mating system by means of controlled-pollination experiments (autonomous self-pollination, manual self-pollination, manual outcross pollination and open pollination). We tested for differences between treatments in the number of seeds per fruit and estimated outcrossing rates. Most (88%) of the M. magnimamma population consisted of clones (10.6 stems/ind) and no juvenile plants or seedlings were recorded. Seed were produced in all the experimental treatments. The average number of seeds per fruit was significantly higher (χ2 = 29.52; d.f. = 3; P < 0.0001) in the outcross than the self-pollination treatments. Outcrossing rates estimated from fruits, te, fruits = 0.829, and seeds, te, seeds = 0.8774, showed that M. magnimamma exhibits a mixed mating system. Despite the large number of seed produced, the persistence of these populations likely depends on clonal reproduction. The null recruitment and elevated anthropogenic pressure that this species undergoes across its distribution range threaten its populations.

Pollen dispersal and genetic diversity of Yucca valida (Asparagaceae), a plant involved in an obligate pollination mutualism

Abstract In insect-pollinated plants, gene flow through pollen depends on the behaviour of pollinators when moving pollen, as well as the spatial distribution of the plants. For the perennial species Yucca valida, we evaluated gene flow mediated by its obligate pollinator, the yucca-moth Tegeticula baja. We also estimated genetic diversity and population structure throughout the plant’s geographical distribution. Using nuclear microsatellites, we genotyped 405 individuals, representing 105 trees and progenies from 15 plants (300 seedlings). We estimated outcrossing rate, pollen donors, dispersion distance and genetic autocorrelation index, as well as diversity and differentiation indexes. We found that Y. valida has a mostly outcrossing mating system. Gene flow through pollen occurs over short distances (42 m) within a small reproductive neighbourhood (1.4 ha) where individuals are genetically related. Each mother plant’s progeny has at least 2.8 pollen donors. Despite the inbreeding detected, interaction among yucca life-history traits may maintain high levels of genetic diversity and low differentiation among Y. valida populations. The spatial scale at which gene flow operates is essential in understanding the distribution of genetic variation within and between populations.

Outcrossing rates in an experimentally admixed population of self-compatible and self-incompatible Arabidopsis lyrata

The transition to self-compatibility from self-incompatibility is often associated with high rates of self-fertilization, which can restrict gene flow among populations and cause reproductive isolation of self-compatible (SC) lineages. Secondary contact between SC and self-incompatible (SI) lineages might re-establish gene flow if SC lineages remain capable of outcrossing. By contrast, intrinsic features of SC plants that reinforce high rates of self-fertilization could maintain evolutionary divergence between lineages. Arabidopsis lyrata subsp. lyrata is characterized by multiple origins of self-compatibility and high rates of self-fertilization in SC-dominated populations. It is unclear whether these high rates of selfing by SC plants have intrinsic or extrinsic causes. We estimated outcrossing rates and examined patterns of pollinator movement for 38 SC and 40 SI maternal parents sampled from an admixed array of 1509 plants sourced from six SC and six SI populations grown under uniform density. Although plants from SI populations had higher outcrossing rates (mean tm = 0.78 ± 0.05 SE) than plants from SC populations (mean tm = 0.56 ± 0.06 SE), outcrossing rates among SC plants were substantially higher than previous estimates from natural populations. Patterns of pollinator movement appeared to contribute to lower outcrossing rates for SC plants; we estimated that 40% of floral visits were geitonogamous (between flowers of the same plant). The relatively high rates of outcrossing for SC plants under standardized conditions indicate that selfing rates in natural SC populations of A. lyrata are facultative and driven by extrinsic features of A. lyrata, including patterns of pollinator movement.

Long pollen dispersal prevents biparental inbreeding depression in seeds in a natural population of the tropical tree Shorea laxa

The aim of this study was to detect biparental inbreeding depression in seeds in a natural population of the tropical tree Shorea laxa. Using microsatellite markers, we conducted parentage analysis and directly estimated outcrossing rate and contemporary pollen dispersal across a natural population (100 ha). We found a high outcrossing rate and frequent long pollen dispersal in S. laxa, even though the population-level flowering during the study was not intensive. We also found a significant but weak negative correlation between pairwise relatedness and spatial distance between adult trees. Structural equation modeling revealed significant decrease in seed size with increasing pairwise relatedness of seed parents, indicating biparental inbreeding depression and also indicating a positive contribution of maternal internal relatedness and a negative contribution of pollen dispersal distance to the relationships among seed size and pairwise relatedness of seed parents. These results suggest that long-distance pollen dispersal is essential to prevent biparental inbreeding depression in S. laxa. When developing conservation strategies for S. laxa, attention must be paid to the breeding structure and phenology to ensure long-distance pollen dispersal and prevent reproductive isolation and inbreeding.

How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae).

Genome‐wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of Tolpis succulenta (Asteraceae) on Graciosa island in the Azores. These two known extant populations of T. succulenta on Graciosa have recently evolved self‐compatibility. Despite the expectation that selfing would occur at an appreciable rate (self‐incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self‐incompatible colonists of T. succulenta from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self‐compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season.

Do annual and perennial populations of an insect-pollinated plant species differ in mating system?

Theory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China. The occurrence of both allopatric and sympatric populations allows us to examine the stability of mating system differences between life histories under varying ecological conditions. We estimated outcrossing rates and biparental inbreeding in 16 allopatric and five sympatric populations in which both life histories coexisted using 20 microsatellite loci. In each population we measured height, branch number, corolla size, tube length and herkogamy for ~30 individuals. In a sympatric population, we recorded daily flower number, pollinator visitation and the fruit and seed set of annual and perennial plants. As predicted, outcrossing rates (t) were considerably higher in perennial (mean = 0.76) than annual (mean = 0.09) populations. This difference in mating system was also maintained at sympatric sites where plants grew intermixed. In both allopatric and sympatric populations the degree of herkogamy was consistently larger in outcrossing than selfing plants. Perennials were more branched, with more and larger flowers than in annuals. In a sympatric population, annuals had a significantly higher fruit and seed set than perennials. Genetically based differences in herkogamy between annuals and perennials appear to play a key role in governing outcrossing rates in populations, regardless of variation in local ecological conditions. The maintenance of mating system and life history trait differentiation between perennial and annual populations of I. sinensis probably results from correlated evolution in response to local environmental conditions.

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.

Bayesian quantification of ecological determinants of outcrossing in natural plant populations: Computer simulations and the case study of biparental inbreeding in English yew.

The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires codominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterized by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.

A high-throughput amplicon-based method for estimating outcrossing rates

BackgroundThe outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCR-genotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.ResultsWe have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.ConclusionsThis novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.

Estimation of Outcrossing Rate in Napier Grass

Napier grass [Cenchrus purpureus (Schumach.) Morrone], also known as elephant grass, is an important tropical forage that has the potential to become an alternative feedstock for energy production. Knowledge about the mode of reproduction and outcrossing rate is essential to select the best strategy to apply in breeding programs to develop new cultivars for application in energy and forage production systems. The objective of this work was to evaluate the outcrossing rate in two Napier grass breeding populations. Six microsatellite markers were used to genotype 28 half‐sibling families totaling 588 individuals, and pollen viability was checked by fluorescein diacetate test (FDA) methodology. A total of 14,603 pollen grains were assessed; 7751 (53%) were considered viable, and 6852 (47%) were considered sterile. Forty‐two alleles were found among all evaluated individuals, and analysis of molecular variance results showed that 14% of variance occurred among half‐siblings and 86% occurred within half‐siblings. Comparison of molecular data among parental and half‐sibling populations found 95.3% of seeds derived from outcrossing, indicating that Napier grass is predominantly allogamous. Currently, directional crosses and hybrid formation in Napier grass depend on the inflorescence protection and pollen collection of selected individuals. Since our results suggest that the self‐fecundation rate is very low (5%), other strategies like unprotected directional crosses can be applied to implementation of large‐scale hybrid production.

The critical role of honeyeaters in the pollination of the catspaw Anigozanthos humilis (Haemodoraceae)

The pollination biology of Anigozanthos humilis (Haemodoraceae) was studied within a Banksia woodland reserve using a combination of field techniques and genetic analysis. Motion-triggered cameras were deployed on 25 flowering plants to identify visitors to flowers, quantify visitation rates and assess visitor behaviour. Entire A. humilis plants were caged to exclude potential floral visitors with six treatments: (i) bird and honey possum exclusion, allowing access by insects; (ii) bird and insect exclusion, allowing access by honey possums; (iii) total animal exclusion; (iv) open, allowing access by birds, insects and honey possums; (v) hand-pollination with cross-pollen; and (vi) hand-pollination with self-pollen. Open pollinated seed were genotyped to assess mating system parameters including outcrossing rate. From 23424 h of surveillance with camera traps, 109 visits were recorded, 106 (97%) of which were western spinebills (Acanthorhynchus superciliosus), with three visits by brown honeyeaters (Lichmera indistincta). We recorded an average of 8 (±4) visits per plant, equivalent to one visit every eleven days over the 2016 flowering season (mean = 63 days). Mean seed set per fruit was negligible (0.2–0.3 seed per fruit) for all pollination treatments except open- and hand-pollination with cross pollen. Mean seed set per fruit for hand cross-pollinated flowers (37.1 seed per fruit) was 37 times that of open pollinated flowers (1.0 seed per fruit). Outcrossing rate estimates were not significantly different to one. Our results indicate that at least for the study population and season, A. humilis was largely dependent on western spinebills for delivery of outcross pollen and resulting seed set, but visitation rates were low and pollen limitation was severe. Given the known sensitivity of western spinebills to habitat fragmentation, our results suggest flow on effects that may negatively impact on reproduction, and means that A. humilis may be particularly vulnerable to environmental changes that impact on bird pollinators.

Mating system analysis of Açaí-do-Amazonas (Euterpe precatoria Mart.) using molecular markers

Abstract Euterpe precatoria (Acai-do-Amazonas) produces fruits of which the fresh pulp is consumed. It is almost exclusively collected by extractivist farmers, because no selected genotypes are available for the establishment of plantations. For the domestication and breeding of the species, mating system studies are needed for strategy formulation. This study evaluated the mating system of a natural population of E. precatoria. Thirteen progenies were genotyped with 13 microsatellite loci by capillary electrophoresis in an automated DNA sequencer. Estimates of single-locus and multilocus outcrossing rates were 1.0, and paternity correlation was low (r^p(m)>= 0.293). Euterpe precatoria families consist mainly of half-sibs and the reproductive strategy of the species is allogamy.

Outcrossing Rates and Gene Flow in Natural Population of the Endangered Endemic Aquatic Lycophyte Isoetes yunguiensis as Revealed by ISSR Markers

In this study, mating system, genetic diversity, and genetic structure of the endangered endemic aquatic Isoetes yunguiensis in China was investigated using ISSR markers. The results of ISSR analyses showed that the estimate of multilocus outcrossing rate (tm) was high at species level (tm = 0.955), indicating that diploid I. yunguiensis is a predominant outcrossing species. Nine selected ISSR primers used in the study amplified 66 reproducible bands, 41 of which were polymorphic among 37 individuals. High level of genetic diversity was detected at the species level (PPB = 62.12%), whereas, relatively low genetic diversity existed within populations (PPB = 39.39%). Analysis of molecular variance (AMOVA) revealed that 31.99% of the genetic variation was attributable to differences between populations and the rest (68.01%) to variability within populationsof I. yunguiensis. Value of Fst (0.320) indicated that genetic differentiation between populations also was significant. These results showed that I. yunguiensis predominantly favors crossing, and has a high level of genetic diversity and highly significant genetic variation between and within populations. Gene flow (Nm) among populations is equal to 1.177. High outcrossing rates may be responsible for the high levels of genetic diversity observed in the I. yunguiensis population. To maintain the current level of genetic diversity for this species, we recommend increasing in situ conservation sites.

Implementation of directional simulation to estimate outcrossing rates in time‐variant reliability analysis of structures

AbstractTime‐dependent reliability analysis of structures by the use of an outcrossing approach normally requires the so‐called outcrossing rate to be estimated. A variety of methods has been recorded in the literature to evaluate this rate both for continues and discrete processes. Despite the availability of these methods, still more general and at the same time less sophisticated approaches are desired. In this paper, attempt is made to use the basic idea of “parallel system reliability formulation” to calculate the outcrossing rate for circumstances where the processes are continuous. These calculations are carried out by directional simulation. It is shown that this approach is simple to implement and may be used for the cases where the problem involves nonstationary processes and also for the cases where several limit state functions may have to be considered.

Effects of wildfire on floral display size and pollinator community reduce outcrossing rate in a plant with a mixed mating system.

Wildfire changes the demography, morphology, and behavior of plants, and may alter the pollinator community. Such trait changes may drastically alter the outcome of pollination mutualisms on plants; however, the direct role of fire on these mutualisms is poorly known. Following a pair of fires in the northern California coast range chaparral, we censused floral visitor communities of Trichostema laxum (Lamiaceae), quantified visiting bee behavior, and estimated outcrossing rates using a widespread Mendelian recessive floral polymorphism across a matrix of populations in burned and unburned sites. We also compared pre- and postfire floral visitation in two populations. Outcrossing rates were significantly lower in burned areas; however, our data suggest that the much larger size of plants in burned areas, not burn status itself, drove this pattern. Large-bodied bees dominated floral visitor communities after fire, likely recruiting to the abundant postfire floral resources. These bees visited more flowers per plant than did the smaller bees prevalent before fire and in unburned areas, likely increasing selfing through geitonogamy (within-plant pollination), an effect made possible by the far larger size of plants in burned areas. Outcrossing rates dropped substantially after wildfires because of changes in the pollinators, plant display size, and their interactions. Reductions in outcrossing following fire may have important implications for population resilience and evolution in a changing climate with more frequent fires.