Mating System Analysis Research Articles

Orchard: Paternity program for autotetraploid species.

Advances in molecular marker technology have provided new opportunities to study the population genetics of polyploid taxa. Paternity analysis using microsatellite markers can be used in detection of gene flow between individuals and populations, in mating system analysis, to identify factors that influence fecundity and fertility, to identify behaviour of parent-offspring relationships and in the analysis of the reproductive success of different ecological groups. As there is no specific program for carrying out paternity analysis in tetraploid species, specialized software was designed for the assignment of paternity for autotetraploid species. orchard is a novel implementation of exclusion and likelihood statistics for carrying out paternity analysis of autotetraploids. First, the program performs an exclusion method, and then, a likelihood statistic is used with nonexcluded candidate fathers. Optional features include estimation of allele dosage of known mother trees and the estimation of pollen flow distances. orchard was tested using a data set of microsatellite data of Dipteryx odorata, a tetraploid Amazonian tree species.

Pollen limitation affects reproductive outcome in the bird-pollinated mangrove Bruguiera gymnorrhiza (Lam.) in a highly urbanized environment

Urban mangrove systems are increasingly common in SE Asia but little is known about the potential changes in pollinator ecology in highly urbanized and fragmented landscapes. We detected pollen limitation across four Bruguiera gymnorrhiza populations in Singapore with a pollen limitation index (compromised seed production due to insufficient pollen receipt) ranging from 0.633 to 0.878. Trees in larger patches had higher pollinator visitation rates than in smaller patches, and lower pollinator visitation rates resulted in reduced fruit sets. These results suggest a cascading link between habitat patch size, pollinator visitation rate, and reproductive outcomes in B. gymnorrhiza. Mating system analysis indicated that B. gymnorrhiza may have an internal mechanism acting against inbreeding depression, leading to reduced fruit set under circumstances of reduced pollinator visitation. Our results underscore the importance of pollinator service in mangroves and highlight the need for an in-depth understanding of changing plant–pollinator relationships in urban mangroves systems.

Steller sex: infidelity and sexual selection in a social Corvid (Cyanocitta stelleri).

Genetic analysis of avian mating systems has revealed that more than 70% of monogamous species show incidence of offspring parentage that does not match the social partner. Extra-pair parentage (EPP) has been linked to a variety of factors, including size and symmetry of ornamental traits, coloration, resource availability, and local conspecific density. We examined how ornamental plumage traits of individual Steller's jays (Cyanocitta stelleri) and territory characteristics influence genetic fidelity of socially monogamous pairs. We used seven highly polymorphic microsatellite markers to assign paternity to 79 offspring, and identified 12 (15.2%) as extra-pair young (EPY). Steller's jays with extra-pair young had significantly lower values of feather brightness and hue, indicating more ultraviolet-blue shifted coloration, and nested in closer proximity to the forest edge than Steller's jays with no detected EPY. Body size, crest height, asymmetry of ornamental crest stripes, as well as vegetative composition of territories and their proximity to supplemental feeders appeared to have little relationship to EPP. These results indicate that extra-pair parentage plays a role in the evolution of secondary sexual characteristics in both sexes, and suggest local density and availability of resources may influence Steller's jay mating dynamics.

Long-distance pollen dispersal ensures genetic connectivity of the low-density tree species, Eurycorymbus cavaleriei, in a fragmented karst forest landscape

Karst forest in southwest China represents one of the world’s most spectacular examples of tropical-subtropical karst landscapes and harbours high floristic richness and endemism. Many plant species tend to occur in naturally isolated patches due to the edaphic and topographic heterogeneity and are suffering an increasing stress of habitat deterioration due to both extensive human activities and global climate change in the area. Here Eurycorymbus cavaleriei was selected as a representative insect-pollinated plant species with low density to assess the pollen dispersal and mating patterns of such limestone associated trees. Paternity analysis revealed substantial long-distance pollination events, with a high level of pollen immigration (27.9–41.9 %) from outside the study sites over distance of at least 4,000 m. Pollen dispersal best fits an exponential power model with a fat-tailed (b < 1) feature and the average pollen dispersal distance was over 2,000 m inferred by the twogener analysis. Despite the dioecious nature, a small amount of biparental inbreeding and moderate correlated paternity were detected based on the multilocus mating system analysis. Relatively few pollen donors (Nep = 3.5–7.0) and substantial variance in male reproductive success (21–24 % of males were responsible for 52–58 % of pollinations) were detected. These results have important implications for the genetic conservation and management of E. cavaleriei. Extensive pollen dispersal provides evidence for substantial intra- and/or inter-patch pollinator movement, which seems promising for E. cavaleriei and other trees with generalized pollination system in karst forest landscape.

Effects of forest management on mating patterns, pollen flow and intergenerational transfer of genetic diversity in wild Arabica coffee (Coffea arabica L.) from Afromontane rainforests

Coffea arabica, the wild ancestor of all commercial Arabica coffee cultivars worldwide, is endemic to the montane rainforests of Ethiopia. These forests, which harbour the most important C. arabica gene pool, are threatened by increasing anthropogenic disturbance, potentially altering the mating patterns, pollen dispersal and maintenance of genetic diversity in C. arabica understorey populations. We genotyped 376 adult coffee shrubs and 418 progenies from three natural unmanaged, and three highly managed coffee populations, using 24 microsatellite markers. Mating system analysis of C. arabica yielded an overall multilocus outcrossing rate of 76%, which contrasts with the common knowledge that C. arabica is a predominantly selfing species. In highly managed coffee populations, paternity could be assigned to 78% of the progenies, whereas in the unmanaged natural coffee populations, only 57% of the progenies could be assigned to a father, indicating reduced long-distance pollen dispersal in managed forests. Furthermore, the fraction of selfed progenies was significantly higher in managed (23%) than unmanaged (10%) coffee forests. Finally, the lack of spatial genetic structure in all studied populations suggests high seed dispersal in unmanaged populations, and intense berry harvesting and coffee planting in the managed populations. Our results imply that in situ conservation of the wild gene pool of C. arabica must focus on limiting intensification of coffee forest management, as decreased pollen dispersal and increased selfing in C. arabica in intensively managed populations may increase the risk of genetic erosion. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 76–88.

Patterns of pollen dispersal in a small population of the Canarian endemic palm (Phoenix canariensis)

The genetic diversity of small populations is greatly influenced by local dispersal patterns and genetic connectivity among populations, with pollen dispersal being the major component of gene flow in many plants species. Patterns of pollen dispersal, mating system parameters and spatial genetic structure were investigated in a small isolated population of the emblematic palm Phoenix canariensis in Gran Canaria island (Canary Islands). All adult palms present in the study population (n=182), as well as 616 seeds collected from 22 female palms, were mapped and genotyped at 8 microsatellite loci. Mating system analysis revealed an average of 5.8 effective pollen donors (Nep) per female. There was strong variation in correlated paternity rates across maternal progenies (ranging from null to 0.9) that could not be explained by the location and density of local males around focal females. Paternity analysis revealed a mean effective pollen dispersal distance of ∼71 m, with ∼70% of effective pollen originating from a distance of <75 m, and 90% from <200 m. A spatially explicit mating model indicated a leptokurtic pollen dispersal kernel, significant pollen immigration (12%) from external palm groves and a directional pollen dispersal pattern that seems consistent with local altitudinal air movement. No evidence of inbreeding or genetic diversity erosion was found, but spatial genetic structure was detected in the small palm population. Overall, the results suggest substantial pollen dispersal over the studied population, genetic connectivity among different palm groves and some resilience to neutral genetic erosion and subsequently to fragmentation.

Genetic diversity assessment for Eugenia uniflora L., E. pyriformis Cambess., E. brasiliensis Lam. and E. francavilleana O. Berg neotropical tree species (Myrtaceae) with heterologous SSR markers

In this study, a set of nuclear microsatellite markers were transferred and characterized from two Myrtaceae sub-families to four neotropical Eugenia fruit tree species (E. uniflora L., E. pyriformis Cambess., E. brasiliensis Lam. and E. francavilleana O. Berg), which are neglected and underutilized foods of great ecological and potential economic value found in the Atlantic forest regions of South America. Leaf samples of mature E. uniflora, E. pyriformis, E. brasiliensis and E. francavilleana trees, which are popularly termed “pitanga”, “uvaia”, “grumixama” and “guamirim”, respectively, were collected from two areas greatly impacted by the agricultural practices of the sugar cane industry in the state of Sao Paulo in the southeastern region of Brazil. A total of 19 simple sequence repeat (SSR) markers from the Myrtaceae sub-families Leptospermoideae and Myrtoideae were tested, and 15 polymorphic heterologous SSR markers were identified. The expected heterozygosities for E. uniflora, E. pyriformis, E. brasiliensis and E. francavilleana were 0.64, 0.75, 0.54 and 0.71, respectively. These results suggest that these SSR markers may be useful for population genetic studies. A total of 4, 9, 11 and 4 heterologous SSR polymorphic markers for E. uniflora, E. pyriformis, E. brasiliensis and E. francavilleana, respectively, are now available for genetic diversity, gene flow and mating system analyses in these species.

DifferInt: compositional differentiation among populations at three levels of genetic integration

In many fields of study, it is important to know how different populations are genetically. Commonly used measures such as FST and its derivatives based on gene identity probabilities do not reliably reflect difference, as they can be maximal when almost all populations are identical and very small when populations are completely distinct. Compositional differentiation, in contrast, is maximal only for completely distinct populations. Moreover, underlying forces of fragmentation that act on single- and multilocus genotypes may be missed if only the allelic level is viewed. For these reasons, descriptive measures of compositional differentiation based on untransformed distributions of genetic types at different levels of genetic integration (alleles, single- and multilocus genotypes) were derived. Here, two measures of complementary differentiation and two new measures of dispersive differentiation are described. One of each considers genic differences between individuals, ensuring their consistency across integration levels. An increase from one level to the next indicates differences among the populations in their forms of gene association. The computer program DifferInt calculates these measures for one or more codominantly expressed gene loci at the gene-pool, single-locus and multilocus levels. Effects of gene pools and gene association on differentiation are compared by permutation analysis. Snail diagrams depict the contribution of each population to differentiation. Results are demonstrated using a numerical example. The applicability of the measures calculated by this program in conservation, phylogeography, mating system analysis and adaptation studies is discussed.

Highly expressed genes in gonads of the bat star Patiria miniata: gene ontology, expression differences, and gamete recognition loci

AbstractEvolutionary analysis of mating systems in broadcast‐spawning marine animals and plants has focused on sperm‐ and egg‐surface proteins and glycopeptides that mediate reproductive interactions at different stages of gamete recognition. Improved understanding of the ecology and evolution of such interactions depends on extending our knowledge to multiple genes expressed in both sperm and eggs of diverse taxonomic groups with different modes of fertilization. Here, we use readily accessible next‐generation sequencing methods and desktop bioinformatics to characterize the repertoire of highly expressed genes in testes and ovaries of the asterinid sea star Patiria miniata, including gene ontology annotations for male‐ and female‐expressed molecules, and descriptions of two genes that encode egg‐surface molecules involved in fertilization that have not previously been studied in sea stars. The results are used to contrast expression differences between the testis and ovary, and to develop hypotheses of gamete‐specific expression. We also explore differences in ovary gene expression among multiple females from northern and southern populations that show nucleotide differentiation at many non‐expressed loci and at a gamete recognition locus.

Mendelian inheritance, genetic linkage, and genotypic disequilibrium at nine microsatellite loci of Cariniana legalis (Mart.) O. Kuntze

Cariniana legalis is one of the largest tropical trees with a wide distribution in the Brazilian Atlantic rainforest. We investigated the Mendelian inheritance, genetic linkage, and genotypic disequilibrium at seven microsatellite loci specifically isolated for C. legalis, and at two previously developed heterologous microsatellite loci. Forty to 100 open-pollinated seeds were collected from 22 seed-trees in two populations. Using the Bonferroni correction, no remarkable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected in the nine loci studied. Only 3.7% of the tests were significant for investigations of the Mendelian proportions. On the other hand, only 2.8% of tests for linkage detection showed significance. In addition, among all pairwise tests used for investigating linkage disequilibrium, significance was found in 9.7% of the locus pairs. Our results show clear evidence that the nine simple sequence repeat loci can be used without restriction in genetic diversity, mating system, and parentage analyses.

Development of microsatellite markers for the endangered medicinal plant Launaea arborescens (Asteraceae)

Microsatellite loci were developed in Launaea arborescens, an endangered and medicinal Asteraceae species in North Africa, for further investigation of its conservation genetics. • We isolated and characterized 10 polymorphic and nine monomorphic microsatellite loci from L. arborescens using the protocol of Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO). For the 10 polymorphic loci, the number of alleles detected per locus varied from two to six, and the observed and expected heterozygosities ranged from 0.000 to 0.833 and 0.059 to 0.713, respectively. • The polymorphic markers provide a useful tool for conservation genetics studies of L. arborescens, including analysis of mating system, estimating gene flow, and identifying discrete genetic units within the species.

The pollen dispersal kernel and mating system of an insect-pollinated tropical palm, Oenocarpus bataua

Pollen dispersal shapes the local genetic structure of plant populations and determines the opportunity for local selection and genetic drift, but has been well studied in few animal-pollinated plants in tropical rainforests. Here, we characterise pollen movement for an insect-pollinated Neotropical canopy palm, Oenocarpus bataua, and relate these data to adult mating system and population genetic structure. The study covers a 130-ha parcel in which all adult trees (n=185) were mapped and genotyped at 12 microsatellite loci, allowing us to positively identify the source tree for 90% of pollination events (n=287 of 318 events). Mating system analysis showed O. bataua was effectively outcrossed (t(m)=1.02) with little biparental inbreeding (t(m)-t(s)=-0.005) and an average of 5.4 effective pollen donors (N(ep)) per female. Dispersal distances were relatively large for an insect-pollinated species (mean=303 m, max=1263 m), and far exceeded nearest-neighbour distances. Dispersal kernel modelling indicated a thin-tailed Weibull distribution offered the best fit to the genetic data, which contrasts with the fat-tailed kernels typically reported for pollen dispersal in trees. Preliminary analyses suggest that our findings may be explained, at least in part, by a relatively diffuse spatial and temporal distribution of flowering trees. Comparison with previously reported estimates of seed movement for O. bataua suggests that pollen and seed dispersal distances may be similar. These findings add to the growing body of information on dispersal in insect-pollinated trees, but underscore the need for continued research on tropical systems in general, and palms in particular.

Microsatellite markers for Duperrea pavettifolia (Rubiaceae)

The development of microsatellite primers for Duperrea pavettifolia will be the foundation for mating system analysis and conservation research. Nineteen microsatellite markers were developed and characterized in two wild populations by using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Polymorphisms were evaluated in 24 individuals from two natural populations. Eleven of these primers generated polymorphic loci. These microsatellite markers will be useful in future investigations into the population genetics and mating system of D. pavettifolia.

A microsatellite panel for mating system analysis and broodstock management of captive long-snouted seahorse Hippocampus guttulatus

We characterized a microsatellite-based panel for parentage analysis in Hippocampus guttulatus using families obtained under captive conditions. Offspring obtained by natural breeding from 49 founder breeders in different aquaria were genotyped for six selected loci. A theoretical exclusion power for parentage inference close to one was obtained from the broodstock, which enabled us to trace back all offspring to a single parental pair with high confidence, under the simple mating scenario managed. The family analysis revealed a very low percentage of false exclusions due to genotyping errors or null alleles (0.9%) and conformance to Mendelian segregation for all loci. Their potential for parentage analysis was confirmed in a more complex scenario, using all breeders as parental candidates, with over 95% of offspring being assigned to the same single pair. Parentage data revealed a monogamous mating system for H. guttulatus in captivity. These loci constitute a useful panel for genealogical traceability and also for investigating relatedness among founders to assist with captive breeding for H. guttulatus.

Development of microsatellite markers for Anadenanthera colubrina (Leguminosae), a neotropical tree species

We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirão Preto in São Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Flowering asynchrony and mating system effects on reproductive assurance and mutualism persistence in fragmented fig–fig wasp populations

Plants and animals may experience reproductive Allee effects in fragmented populations, and obligate pollination mutualisms may be especially sensitive to extinction risk via this density-dependent process. In this study we examine how a shift from within-crown reproductive synchrony to asynchrony influences reproductive assurance through contributions to selfing and outcrossing in small, spatially isolated populations of Ficus. The research focuses on the monoecious fig F. petiolaris and consists of phenological analyses and genetic assessments of selfing and outcrossing for populations located in Baja California's Sonoran Desert. Phenological censuses of eight populations revealed within-crown asynchrony in 44% of reproducing trees, with 16% having sufficient overlap of male and female flowering phases to permit selfing via the cycling of pollinating fig wasps within natal trees. In mating system analyses of two of these populations, however, multilocus outcrossing rates (t(m)) were indistinguishable from 1. This result, combined with low levels of inbreeding, indicates selfing to be absent or at best a minor contributor to reproductive assurance. The results indicate that the fitness benefits of within-crown asynchrony lie not with selfing, as commonly asserted, but with increased opportunities for outcross pollen transmission and receipt, changing our understanding of the mechanisms by which reproduction is facilitated and extinction risk minimized in naturally fragmented Ficus populations. Given the role of fig fruit as a keystone food resource in many tropical environments, trait variation leading to reproductive assurance in figs, such as within-crown asynchrony, has broader ecosystem-level implications.

DNA 표지를 이용한 채종원내 소나무의 교배양식 분석

To assess parameters of mating system in seed orchard, such as outcrossing rates, number of potential pollen contributors, and degree of pollen contamination, seeds, produced in '77 plot of the Japanese red pine (Pinus densiflora S et Z) seed orchard at Anmyeon island, were collected in 2007 and analysed by nSSR and cpSSR markers. Estimates of outcrossing rates ranged from 91.2 to 100% (mean 97.7%) on the basis of the analysis of cpSSR haplotypes and from 81.6 to 100% (mean 95.3%) on the basis of the analysis of nSSR genotypes. By cross checking of both DNA markers, seeds, presumed to be products of self pollination on the basis of single marker, were confirmed as outcrossed seeds, which resulted in cumulative outcrossing rates of 98.9%. On the basis of pooled cpSSR haplotype of each seed, the number of pollen contributors and paternal contribution rates were estimated as 14.8 and 0.512, respectively. In conclusion, considering pretty high level of outcrossing rates observed in a seed orchard, good genetic potential of the seeds, produced in '77 plot of the seed orchard of Japanese red pines at Anmyeon island, may be guaranteed. Investigated results from the analysis of mating system of Japanese red pines in a '77 plot of the seed orchard may also be expected to provide useful information for the management and establishment of the seed orchard of the progressive generation.

Linking Phenology to Mating System: Exploring the Reproductive Biology of the Threatened Palm Species Butia eriospatha

The reproductive biology of the vulnerable palm species Butia eriospatha was studied to provide important information that contributes to our understanding and conservation of the species. In order to determine when and how B. erisopatha reproduces, we combined data from 7 nuclear microsatellite loci with ecological data on flowering and fruiting phenology collected between 2009 and 2011 from a population (N = 515) in the Atlantic Rainforest, Southern Brazil. Periods of flowering and fruit production were seasonal and variable across reproductive events. Mating system analyses indicate that B. eriospatha is a predominantly outcrossing species, ((m) = 0.961), since a certain degree of biparental inbreeding does occur. The species is self-compatible and reproduction may also occur by geitonogamy, indicating the ability of isolated populations to survive and persist. Open-pollinated seeds varied in relatedness, including mainly half-sibs and full-sibs. The effective population size was lower than that expected for panmictic populations. Hence, seeds for conservation programs must be collected from a large number of seed-trees to ensure an adequate effective population in the sample. The collection of germplasm is a high-priority strategy that should be employed to maintain the genetic variability that remains.

Brief Note Mendelian inheritance, linkage and genotypic disequilibrium in microsatellite loci isolated from Hymenaea courbaril (Leguminosae)

The Neotropical tree Hymenaea courbaril, locally known as Jatobá, is a valuable source of lumber and also produces comestible and medicinal fruit. We characterized Mendelian inheritance, linkage and genotypic disequilibrium at nine microsatellite loci isolated from H. courbaril, in order to determine if they would provide accurate estimates of population genetic parameters of this important Amazon species. The study was made on 250 open-pollinated offspring originated from 14 seed trees. Only one of nine loci presented significant deviation from the expected Mendelian segregation (1:1). Genotypic disequilibrium between pairwise loci was investigated based on samples from 55 adult and 56 juvenile trees. No genetic linkage between any paired loci was observed. After Bonferroni's corrections for multiple tests, we found no evidence of genotypic disequilibrium between pairs of loci. We conclude that this set of loci can be used for genetic diversity/ structure, mating system, gene flow, and parentage analyses in H. courbaril populations.

Mating system parameters at hierarchical levels of fruits, individuals and populations in the Brazilian insect-pollinated tropical tree, Tabebuia roseo-alba (Bignoniaceae)

For many tree species, mating system analyses have indicated potential variations in the selfing rate and paternity correlation among fruits within individuals, among individuals within populations, among populations, and from one flowering event to another. In this study, we used eight microsatellite markers to investigate mating systems at two hierarchical levels (fruits within individuals and individuals within populations) for the insect pollinated Neotropical tree Tabebuia roseo-alba. We found that T. roseo-alba has a mixed mating system with predominantly outcrossed mating. The outcrossing rates at the population level were similar across two T. roseo-alba populations; however, the rates varied considerably among individuals within populations. The correlated paternity results at different hierarchical levels showed that there is a high probability of shared paternal parentage when comparing seeds within fruits and among fruits within plants and full-sibs occur in much higher proportion within fruits than among fruits. Significant levels of fixation index were found in both populations and biparental inbreeding is believed to be the main cause of the observed inbreeding. The number of pollen donors contributing to mating was low. Furthermore, open-pollinated seeds varied according to relatedness, including half-sibs, full-sibs, self-sibs and self-half-sibs. In both populations, the effective population size within a family (seed-tree and its offspring) was lower than expected for panmictic populations. Thus, seeds for ex situ conservation genetics, progeny tests and reforestation must be collected from a large number of seed-trees to guarantee an adequate effective population in the sample.