On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

In recent years there has been a dramatic increase in the availability of high density genetic marker data for both model and non‐model organisms. A potential application of these data is to infer relatedness in the absence of a complete pedigree. Using a marker panel of 771 SNPs genotyped in three generations of an extensive zebra finch pedigree, correlations between pedigree relatedness and seven marker‐based estimates of relatedness were examined, as was the relationship between heterozygosity and inbreeding. Although marker‐based and pedigree relatedness were highly correlated, the variance in estimated relatedness was high. Further, the correlation between heterozygosity and inbreeding was weak, even though mean inbreeding coefficient is typical of that seen in wild vertebrate pedigrees; the weak relationship was in part due to the small variance in inbreeding in the pedigree. Our data suggest that using marker information to reconstruct the pedigree, and then calculating relatedness from the pedigree, is likely to give more accurate relatedness estimates than using marker‐based estimators directly.     

Bias in studies of heterozygosity and mate choice

A key question for molecular and behavioural ecologists who study mating systems is to understand why, in many species, females choose to mate with extra-pair males. Recently a possible explanation, 'genetic compatibility', has gained increasing empirical support (for a comprehensive review, see Kempenaers 2007 ). Genetic compatibility hypotheses assume that females seek extra-pair mates with alleles that complement their own. Typically, this will be achieved by mating with a male of a different genotype than her own, in order to maximise the heterozygosity of her offspring. Because numerous studies have indicated positive associations between heterozygosity and fitness (see Coltman & Slate 2003 ), it follows that mating with 'compatible' males will result in heterozygous, and therefore fit, offspring. Most empirical support for genetic compatibility has been obtained with microsatellite markers that have first been used to assess parentage and then to estimate relatedness and/or individual heterozygosity. A problem with this approach is a possible bias that favours the detection of extra-pair paternity when the extra-pair male has a genotype different from that of the female and her social mate. This in turn could lead to the erroneous conclusion that extra-pair males are less related to the female than within-pair males. In this issue of Molecular Ecology , Wetzel & Westneat 2009 (hereafter W&W), use simulation studies to assess the extent of this bias, using parameter estimates obtained from recent empirical data. They identify two forms of bias that may affect tests of the genetic compatibility hypothesis, and provide guidelines on how these biases may be avoided.     

Decidual reaction of the cervix; a review of 27 cases

Decidual reaction of the cervix is a benign growth produced by the hormones of pregnancy. These reactions or changes in the cervix are present in about 20 per cent of normal pregnant women. They may look like cancer but are not cancer. They are benign lesions. Bleeding is a common symptom and may occur at any stage of pregnancy. The presence of decidual reaction does not predispose to spontaneous miscarriage. In most cases no treatment is required; in a few light cauterization may be needed to control bleeding. Any suspicious lesion should be biopsied to rule out malignancy. By microscopic examination any experienced pathologist can differentiate a decidual reaction from cancer. The consensus of opinion is to let the pregnant woman deliver, normally, with this benign lesion, for it disappears after the baby is born. If cancer is found during pregnancy, it should be actively treated.     

Effects of Natural Barriers and Habitat on the Western Spread of Raccoon Rabies in Alabama

Abstract: Although domestic animal transmission of rabies has largely been mitigated, the disease remains a concern in both Europe and North America where wildlife transmission has caused epizootics. Raccoon (Procyon lotor) rabies was established in Alabama, USA, in 1975, primarily in the southeastern corner of the state. However, with the exception of isolated events, rabies has not continued to spread westward across the Alabama River. We monitored movements of 100 radiocollared raccoons on 2 sites within hardwood and agriculture habitats in a rabies enzootic area east of the Alabama River, in managed pine habitat area west of the river where rabies sporadically occurs, and in a mixed pine hardwood area outside of the known rabies enzootic area to determine if raccoon movements and habitat use in certain habitat types and the presence of a river may serve as natural barriers preventing the western spread of rabies in Alabama. We also examined raccoon contact rates to determine if they influence disease transmission through static and dynamic interactions. Raccoons in mixed pine-hardwood forest habitats had smaller home ranges and less overlap of ranges compared to the other 3 habitats. However, static interactions between habitats in the use of overlap areas did not differ (F_11,129 = 1.63, P = 0.09). Rabies antibody titers were highest in the managed pine habitat (28%) even prior to oral vaccine bait distributions in spring of 2004 and 2005. Biomarker data from radiocollared and additional raccoons captured after the bait distribution west of the Alabama River demonstrated a low efficacy of the vaccine reaching the small southern raccoons. The combination of the river as a partial barrier, the high percentage of pine forested habitat west of the river, and limited spatial movements of raccoons within these forested habitats appears to have reduced the likelihood of rabies establishing west of the river. Understanding different host-habitat- disease systems is important for successful management of diseases. Based on our results, we recommend that the oral vaccine program continue to use the Alabama River as a partial barrier and baiting be concentrated in the fragmented bottomland hardwood forests and around larger bodies of water where raccoon densities are highest. Success of baiting strategies designed to take advantage of northern raccoon dynamics and habitat use may not be applicable to southern populations.     

Cytologic detection of cervical cancer; four years' experience with routine smear examination in private practice

Simplified Papanicolaou smear techniques appear to be adaptable to private clinical practice when experienced cytodetection laboratory facilities are available. A private physician's office seems potentially an efficient, economical and practical place for detection of cervical cancer by use of the smear technique as a routine part of examination of patients. In a series here reported upon, examination of 11,207 cervical smears taken at the first examination of patients of all ages led to diagnosis of unsuspected malignant disease in 80 cases-in all instances at a stage when it should be easily curable. Cancer was not detected in examination of 6,060 smears taken later from women who had had a "negative" smear at the time of first examination, which seems to indicate that the first screening was reasonably accurate. In a few cases, early cancer was detected when smears were reported as "atypical" or "suspicious." Such reports demand as careful follow-up as do "positive" reports. There are dangers and limitations in wide-spread clinical application of screening by this method. Care must be observed in the development of programs for its use lest the potential benefits in early detection be outweighed by the dangers from misuse.     

A test of the efficacy of whole‐genome amplification on DNA obtained from low‐yield samples

Conservation and population genetic studies are sometimes hampered by insufficient quantities of high quality DNA. One potential way to overcome this problem is through the use of whole genome amplification (WGA) kits. We performed rolling circle WGA on DNA obtained from matched hair and tissue samples of North American red squirrels (Tamiasciurus hudsonicus). Following polymerase chain reaction (PCR) at four microsatellite loci, we compared genotyping success for DNA from different source tissues, both pre‐ and post‐WGA. Genotypes obtained with tissue were robust, whether or not DNA had been subjected to WGA. DNA extracted from hair produced results that were largely concordant with matched tissue samples, although amplification success was reduced and some allelic dropout was observed. WGA of hair samples resulted in a low genotyping success rate and an unacceptably high rate of allelic dropout and genotyping error. The problem was not rectified by conducting PCR of WGA hair samples in triplicate. Therefore, we conclude that WGA is only an effective method of enhancing template DNA quantity when the initial sample is from high‐yield material.     

Mitochondrial haplotype does not affect sperm velocity in the zebra finch Taeniopygia guttata

Mitochondrial DNA (mtDNA) variation has been suggested as a possible cause of variation in male fertility because sperm activity is tightly coupled to mitochondrial oxidative phosphorylation and ATP production, both of which are sensitive to mtDNA mutations. Since male‐specific phenotypes such as sperm have no fitness consequences for mitochondria due to maternal mitochondrial (and mtDNA) inheritance, mtDNA mutations that are deleterious in males but which have negligible or no fitness effect in females can persist in populations. How often such mutations arise and persist is virtually unknown. To test whether there were associations between mtDNA variation and sperm performance, we haplotyped 250 zebra finches Taeniopygia guttata from a large pedigreed‐population and measured sperm velocity using computer‐assisted sperm analysis. Using quantitative genetic ‘animal’ models, we found no effect of mtDNA haplotype on sperm velocity. Therefore, there is no evidence that in this system mitochondrial mutations have asymmetric fitness effects on males and females, leading to genetic variation in male fertility that is blind to natural selection.     

Isolation of 18 polymorphic microsatellite loci from the North American red squirrel,Tamiasciurus hudsonicus (Sciuridae,Rodentia), and their cross‐utility in other species

We isolated 18 polymorphic microsatellite loci to be used for pedigree analysis in a wild population of North American red squirrels, Tamiasciurus hudsonicus. Allelic diversity and observed heterozygosity ranged from six to 13 and 0.39 to 0.89, respectively, in a sample of 93 individuals. Up to 13 sets of primers also amplify in other rodent species.     

Statistical confidence for likelihood-based paternity inference in natural populations

Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic Δ for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for Δ that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer ( Cervus elaphus ) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS , described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.     

Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies

While genotyping wild red deer (Cervus elaphus) at microsatellite loci for paternity assignment, we found three loci (MAP65, BOVIRBP and CelJP23) with segregating nonamplifying alleles. Nonamplifying alleles were detected through mismatches between known mother-offspring pairs and by significant deviations from Hardy-Weinberg equilibria. In a wide range of molecular ecology applications, and especially in parentage assignment, the possible existence of undetectable alleles must be taken into account; this may be particularly important for microsatellite data.