Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica

Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at the HrU6 locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10^-8 and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker-pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra-pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra-pair offspring.     

Multiple paternity in the red-eyed treefrog Agalychnis callidryas (Cope)

DNA fingerprinting of tadpoles from two different ‘one female-two male’ matings of the red-eyed treefrog, Agalychnis callidryas, revealed multiple paternity of offspring. Offspring were assigned paternity based on bands shared with the putative father, but not shared between putative fathers or with the mother. Paternity was split 44/56% and 36/64% in two matings. These results do not support a hypothesis of sperm priority in access to unfertilized eggs by primary males. Multiple paternity may be commonplace in species of anurans with matings by multiple males.     

Biochemical genetic markers of squirrel monkeys and their use for pedigree validation

Family data for 14 biochemical genetic markers of squirrel monkeys (genusSaimiri) were derived from 73 pedigreed progeny and both parents of each, as well as from 16 additional progeny and one parent of each. The data for each marker and the phenotypic patterns were consistent with autosomal codominant inheritance. It was concluded from the genetic marker data that the pedigree records of seven progeny were incorrect. Retrospective investigations of colony records followed by typing of animals that might possibly have been a parent enabled five of the pedigree records to be corrected. Although five of the pedigree errors were cases of mistaken paternity, the other two apparently were the consequence of infant swapping between dams shortly after birth. Because squirrel monkeys exhibit a high degree of allomaternal behavior, infant swapping between dams may occur more frequently than in many other nonhuman primate species.This research was supported in part by NIH Grant P40 RR01254.     

A Simple Numerical Procedure for Estimating the Prior Probability in the Biomathematical Proof of Paternity

This note gives a simple procedure for finding the maximum likelihood estimate of the prior probabilities in paternity cases. The procedure is based on a fixed point principle.     

Beyond “beyond GDP indicators:” The need for reflexivity in science for governance

“Beyond GDP” initiatives flag the limits of the quantitative indicators of progress currently used for governance. Focusing on the quality assessment of quantitative information used for governance, we use some of the conceptual tools of theoretical ecology and evolutionary biology in order to identify the pre-analytical choices that determine the usefulness and pertinence of a model. Starting from the definition of a model as a formal representation of a specific and necessarily subjective observation, we show that the production of indicators is the final result of a series of decisions on what to observe and how. These choices, in turn, depend on the narrative, or set of narratives, adopted. Narratives provide causality and context to knowledge claims and are needed to select the indicators to be used for policy. Moving beyond the GDP debate requires reflexivity, that is, awareness of the key role that pre-analytical choices play in the definition of both the relevance of the chosen perceptions and narratives (determined by the normative stands of different actors – who defines wellbeing?), and the usefulness of the chosen models and data (determined by the pertinence of the resulting representation – how to measure wellbeing?). Reflexivity is essential in order to take into account the purposes for which different indicators were created and to define new purposes for the “beyond GDP” indicators.     

The messenger matters: Pollinator functional group influences mating system dynamics

The incredible diversity of plant mating systems has fuelled research in evolutionary biology for over a century. Currently, there is broad concern about the impact of rapidly changing pollinator communities on plant populations. Very few studies, however, examine patterns and mechanisms associated with multiple paternity from cross‐pollen loads. Often, foraging pollinators collect a mixed pollen load that may result in the deposition of pollen from different sires to receptive stigmas. Coincident deposition of self‐ and cross‐pollen leads to interesting mating system dynamics and has been investigated in numerous species. But, mixed pollen loads often consist of a diversity of cross‐pollen and result in multiple sires of seeds within a fruit. In this issue of Molecular Ecology, Rhodes, Fant, and Skogen ( 2017 ) examine how pollinator identity and spatial isolation influence multiple paternity within fruits of a self‐incompatible evening primrose. The authors demonstrate that pollen pool diversity varies between two pollinator types, hawkmoths and diurnal solitary bees. Further, progeny from more isolated plants were less likely to have multiple sires regardless of the pollinator type. Moving forward, studies of mating system dynamics should consider the implications of multiple paternity and move beyond the self‐ and cross‐pollination paradigm. Rhodes et al. ( 2017 ) demonstrate the importance of understanding the roles that functionally diverse pollinators play in mating system dynamics.     

Male mating success in an aquatically mating pinniped, the harbour seal (Phoca vitulina), assessed by microsatellite DNA markers

Similar to many other pinniped species, harbour seals ( Phoca vitulina ) mate exclusively at sea. Here we present the first attempt to measure male mating success in an aquatically mating pinniped. Male mating success was estimated by paternity analysis in two cohorts of pups born at Sable Island, Nova Scotia, Canada, using microsatellite DNA markers. The genotypes of 275 pups born in 1994 and 1995 were compared to those of 90 candidate males at six microsatellite loci using a likelihood approach to resolve paternity. Paternity could be assigned for two, 22, 40 and 85 pups at confidence levels of 95, 80, 65 and 50%, respectively. Most successful males were assigned the paternity of a single offspring, suggesting a low variance in male mating success relative to most pinniped species. The proportion of paternal half sibs within cohorts and between maternally related sibs estimated by maximum likelihood were not significantly different from zero. It is thus unlikely that most offspring were sired by a small number of highly successful unsampled males, and that female harbour seals do not usually exhibit fidelity to the same male in sequential breeding seasons. A low level of polygyny in Sable Island harbour seals is consistent with predictions based on their breeding ecology, as females are highly mobile and widely dispersed in the aquatic mating environment at Sable Island.     

Simplification of head and neck volumetric modulated arc therapy patient-specific quality assurance,using a Delta4 PT

Background/AimIn many facilities, intensity-modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT) use intensity-modulated beams, formed by a multi-leaf collimator (MLC). In IMRT and VMAT, MLC and linear accelerator errors (both geometric and dose), can significantly affect the doses administered to patients. Therefore, IMRT and VMAT treatment plans must include the use of patient-specific quality assurance (QA) before treatment to confirm dose accuracy.Materials and methodsIn this study, we compared and analyzed the results of dose verification using a multi-dimensional dose verification system Delta4 PT, an ionization chamber dosimeter, and gafchromic film, using data from 52 patients undergoing head and neck VMAT as the test material.ResultBased on the results of the absolute dose verification for the ionization chamber dosimeter and Delta4 PT, taking an axial view, the upper limit of the 95% confidence interval was 3.13%, and the lower limit was −3.67%, indicating good agreement. These results mean that as long as absolute dose verification for the axial view does not deviate from this range, Delta4 PT can be used as an alternative to an ionization chamber dosimeter for absolute dose verification. When we then reviewed dose distribution verification, the pass rate for Delta4 PT was acceptable, and was less varied than that of gafchromic film.ConclusionThis results in that provided the pass rate result for Delta4 PT does not fall below 96%, it can be used as a substitute for gafchromic film in dose distribution verification. These results indicate that patient-specific QA could be simplified.     

Detailed evaluation of Mobius3D dose calculation accuracy for volumetric-modulated arc therapy

PurposeTo perform a detailed evaluation of dose calculation accuracy and clinical feasibility of Mobius3D. Of particular importance, multileaf collimator (MLC) modeling accuracy in the Mobius3D dose calculation algorithm was investigated.MethodsMobius3D was fully commissioned by following the vendor-suggested procedures, including dosimetric leaf gap (DLG) optimization. The DLG optimization determined an optimal DLG correction factor which minimized the average difference between calculated and measured doses for 13 patient volumetric-modulated arc therapy (VMAT) plans. Two sets of step-and-shoot plans were created to examine MLC and off-axis open fields modeling accuracy of the Mobius3D dose calculation algorithm: MLC test set and off-axis open field test set. The test plans were delivered to MapCHECK for the MLC tests and an ionization chamber for the off-axis open field test, and these measured doses were compared to Mobius3D-calculated doses.ResultsThe mean difference between the calculated and measured doses across the 13 VMAT plans was 0.6% with an optimal DLG correction factor of 1.0. The mean percentage of pixels passing gamma from a 3%/1 mm gamma analysis for the MLC test set was 43.5% across the MLC tests. For the off-axis open field tests, the Mobius3D-calculated dose for 1.5 cm square field was −4.6% lower than the chamber-measured dose.ConclusionsIt was demonstrated that Mobius3D has dose calculation uncertainties for small fields and MLC tongue-and-groove design is not adequately taken into consideration in Mobius3D. Careful consideration of DLG correction factor, which affects the resulting dose distributions, is required when commissioning Mobius3D for patient-specific QA.     

Paternity tests support a diallelic self‐incompatibility system in a wild olive (Olea europaea subsp. laperrinei,Oleaceae)

Self‐incompatibility (SI) is the main mechanism that favors outcrossing in plants. By limiting compatible matings, SI interferes in fruit production and breeding of new cultivars. In the Oleeae tribe (Oleaceae), an unusual diallelic SI system (DSI) has been proposed for three distantly related species including the olive (Olea europaea), but empirical evidence has remained controversial for this latter. The olive domestication is a complex process with multiple origins. As a consequence, the mixing of S‐alleles from two distinct taxa, the possible artificial selection of self‐compatible mutants and the large phenological variation of blooming may constitute obstacles for deciphering SI in olive. Here, we investigate cross‐genotype compatibilities in the Saharan wild olive (O. e. subsp. laperrinei). As this taxon was geographically isolated for thousands of years, SI should not be affected by human selection. A population of 37 mature individuals maintained in a collection was investigated. Several embryos per mother were genotyped with microsatellites in order to identify compatible fathers that contributed to fertilization. While the pollination was limited by distance inside the collection, our results strongly support the DSI hypothesis, and all individuals were assigned to two incompatibility groups (G1 and G2). No self‐fertilization was observed in our conditions. In contrast, crosses between full or half siblings were frequent (ca. 45%), which is likely due to a nonrandom assortment of related trees in the collection. Finally, implications of our results for orchard management and the conservation of olive genetic resources are discussed.