Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major)

Eighteen microsatellite loci were isolated from great tinamous (Tinamus major), which are large terrestrial birds found in the Neotropics. These are the first primers developed for the Order Tinamiformes. Paternity analyses are possible because the levels of heterozygosity are sufficiently high (0.29-0.90).     

Genetic variation in infestation with a directly transmitted ectoparasite

Genetic variation in levels of parasitism of hosts is an underlying assumption of studies of coevolution, but few such estimates are available from the field. We studied genetic variation in the abundance of the chewing louse Hirundoecus malleus on its barn swallow host Hirundo rustica. These parasites are directly transmitted and a test of genetic variation of parasite abundance would thus provide a particularly strong test. The prevalence and the abundance of the chewing lice did not differ significantly between adult male and female hosts. The resemblance in parasite intensity of H. malleus of offspring and their parents was positive and highly significant, and an analysis of extra-pair paternity in the host allowed partitioning of this resemblance between genetic and common environment effects. There was no significant resemblance in parasite intensity between extra-pair offspring and their foster parents, although the resemblance remained for within-pair offspring. This provides evidence for the abundance of directly transmitted parasites having an additive genetic component. We found no evidence of common environment effects as parents did not resemble each other with respect to lice abundance.     

Development and characterization of eight new microsatellite markers for the haremic sandperch,Parapercis cylindrica (family Pinguipedidae)

Eight di‐, tri‐ and tetranucleotide microsatellite markers were developed for the haremic sandperch Parapercis cylindrica using a linker‐ligated, magnetic bead enrichment protocol. Screening of at least 17 individuals showed these markers to be polymorphic with observed heterozygosity ranging from 0.381 to 1.000 (mean = 0.742) and the numbers of alleles ranging from three to 18. The average polymorphic information content for these eight loci was 0.723. These markers may be used for parentage studies aimed at exploring the complex mating strategies employed by this haremic coral reef fish and will be valuable for population genetic studies.     

A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level

Abstract Microsatellites are powerful molecular markers, used commonly to estimate intraspecific genetic distances. With the exception of band sharing similarity index, available distance measures were developed specifically for diploid organisms and are unsuited for comparisons of polyploids. Here, we present a simple method for calculation of microsatellite genotype distances, which takes into account mutation processes and permits comparison of individuals with different ploidy levels. This method should provide a valuable tool for intraspecific analyses of polyploid organisms, which are widespread among plants and some animal taxa. An illustration is given using data from the planarian flatworm Schmidtea polychroa (Platyhelminthes).     

Parental investment with a superior alien in the brood

When a parent's parentage differs across breeding attempts, established theory predicts that the parent should invest more in a brood when perceived parentage is high. We present a model of parental investment in which offspring unrelated to the parent have a competitive advantage over the parent's own offspring and take a larger share of investment. We show that this can weaken or, if the competitive advantage is great, reverse the predicted relationship between perceived parentage and parental investment. A moderate competitive advantage of extra-pair young over within-pair young could partly explain the lack of any clear relationship between paternal care and paternity in many studies, and could easily arise if females choose extra-pair partners for good genes. Our results are also relevant to interspecific avian brood parasitism. As parasites reared together with host offspring are often superior competitors, their hosts could benefit from increasing investment in response to suspected parasitism.     

Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

Comparisons of three probability formulae for parentage exclusion

Three general formulae calibrate the average capability of marker systems to dispute falsely reported pedigree records in uniparous species. The most familiar exclusion formula applies to paternity, although the same formula applies equally to maternity. Another formula faults the relationship of a single offspring with its putative parent; for example, where the genotype of the other parent is not available. The remaining formula excludes both of the falsely recorded parents of a substituted offspring. Simplified forms of the three general formulae facilitate the calculation of maximal average exclusion values over a range of hypothetical markers. Allele frequency data on eight marker systems in horses provide practical examples. The exclusion values of the three formulae are compared.     

Efficient resolution of parentage in dogs by amplification of microsatellites

Parentage control has been performed for 15 litters from 12 different dog breeds by amplification of microsatellites. As it was possible to include all putative parents in all cases, they were solved by exclusion. Discrimination between parents/non-parents was made after genotyping of 6–9 microsatellite loci. In 12 of the cases all but one of the alleged fathers were excluded while in three cases it was unambiguously shown that superfecundation had taken place. Furthermore, one inclusion case concerning disputed maternity has been investigated. Maternity indices were calculated for 12 loci and probability of maternity was estimated to be 99-99%. These results testify that microsatellites can be applied very efficiently for resolution of parentage in dogs.     

Genetic similarity, breeding distribution range and sexual selection

Large populations with extensive breeding distributions may sustain greater genetic variability, thus producing a positive relationship between genetic variation and population size. Levels of genetic variability may also be affected by sexual selection, which could either reduce levels because a small fraction of males contribute to the following generation, or augment them by generating genetic variability through elevated rates of mutations. We investigated to what extent genetic variability, as estimated from band sharing coefficients for minisatellite markers, could be predicted by breeding distribution range, population size and intensity of sexual selection (as reflected by degree of polygyny and extra-pair paternity). Across a sample of 62 species of birds in the Western Palearctic, we found extensive interspecific variation in band sharing coefficients. High band sharing coefficients (implying low local genetic variability among individuals) were associated with restricted breeding distributions, a conclusion confirmed by analysis of statistically independent linear contrasts. Independently, species with large population sizes had small band sharing coefficients. Furthermore, bird species with a high richness of subspecies for their breeding distribution range had higher band sharing coefficients. Finally, bird species with high levels of polygyny and extra-pair paternity had small band sharing coefficients. These results suggest that breeding distribution range, population size and intensity of sexual selection are important predictors of levels of genetic variability in extant populations.     

Development and characterization of microsatellite loci in the eastern chipmunk (Tamias striatus)

We isolated and characterized 16 microsatellite loci in the eastern chipmunk, Tamias striatus. The loci were screened across 25 individuals from one population and shown to be polymorphic with the number of alleles per locus ranging from two to 17. Polymorphic information content ranged from 0.212 to 0.887 and observed heterozygosity ranged from 0.200 to 0.960. Only two loci (Chip 10 and Chip 25) deviated from Hardy–Weinberg equilibrium.