Evaluating Mixture Solution™- rapid and non-MCMC probabilistic mixture analysis.

We compare DNA mixture analysis via DNAˑVIEW® Mixture Solution™ and the current combined probability of inclusion (CPI) method of the South African Police Service (SAPS). South Africa has a high incidence of property-related crimes and sexual offences and consequently a great deal of low-template (LT-DNA) forensic DNA mixture casework and a perpetual backlog. A range of casework and laboratory-prepared sexual assault mixtures with initial male DNA amounts varying from about 2 to 200 cells were analysed to evaluate the benefits of a continuous model program. Unfortunately CPI methods are nearly useless for LT-DNA cases because of dropout-common from a mixture contribution of fewer than 20 or 30 cells. We further argue that proposed CPI elaborations to circumvent dropout lack supporting research or even explanation. Mixture Solution models mixture data as continuous rather than binary, with a mathematically coherent ("probabilistic") model which incorporates dropout and other phenomena realistically. Much more information is thereby utilised resulting in applicability to more cases (7 or fewer contributor cells suffice), stronger evidence against a suspect who is a mixture contributor and stronger evidence to absolve a non-contributor. Mixture Solution incidentally provides information which, along with rfu data, allows estimating contributions in terms of number of cells, which is a useful perspective. The method of calculation is explained.

Quantitative evaluation of hybridization and the impact on biodiversity conservation.

Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near-threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species-wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two-thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q-value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.

Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations.

The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations.

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.

Inhibition of monoamine oxidase by selected phenylalkylcaffeine analogues.

OBJECTIVES: Caffeine represents a useful scaffold for the design of monoamine oxidase (MAO) type B inhibitors. Specifically, substitution on the C8 position yields structures which are high-potency MAO-B inhibitors. To explore the structure-activity relationships of MAO-B inhibition by caffeine-derived compounds, this study examines the MAO inhibitory properties of a series of phenylalkylcaffeine analogues. METHODS: Employing the recombinant human enzymes, the potencies (IC50 values) by which the caffeine analogues inhibit MAO-A and MAO-B were measured. The reversibility of inhibition of a selected inhibitor was determined by measuring the recovery of enzyme activity after dilution and dialysis of enzyme-inhibitor mixtures. KEY FINDINGS: The results document that the phenylalkylcaffeine analogues are reversible and selective MAO-B inhibitors with a competitive mode of inhibition. The most potent analogue, 8-(7-phenylheptyl)caffeine, exhibits IC50 values for the inhibition of MAO-A and MAO-B of 3.01 µm and 0.086 µm, respectively. Increasing the length of the alkyl side chain leads to enhanced MAO-A and MAO-B inhibitory potency while introduction of a carbonyl group reduces MAO-B inhibitory potency. CONCLUSIONS: Phenylalkylcaffeines represent a new class of high-potency MAO-B inhibitors with the longer alkyl side chains yielding enhanced inhibitory activity. Such compounds may represent useful leads for the development of anti-parkinsonian therapies.

Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa.

Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus™ PCR amplification kit. There was little evidence of departures from Hardy-Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3 × 10(17) (White) to 1/1.88 × 10(18) (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).

Variation in scrotal color among widely distributed vervet monkey populations (Chlorocebus aethiops pygerythrus and Chlorocebus aethiops sabaeus).

Vervet monkeys (Chlorocebus aethiops) exhibit bright blue scrotal skin which may function to mediate social interactions by acting as a socio-sexual signal. Previous research on scrotal coloration among vervet monkeys was limited to experimental work on captive Ch. a. sabaeus, the least colorful vervet subspecies, and two field studies of the more colorful Ch. a. pygerythrus. In a study of free-ranging and captive vervet monkeys in South Africa (Ch. pygerythrus), West Africa (Ch. a. sabaeus) and the Caribbean (Ch. a. sabaeus), we examined scrotal color variation across geographically distant subspecies. We provide an exploration of how digital photographs may be used to quantify and analyze blue and green skin coloration by examining the blue-yellow opponency channel and luminance channel as color measures. We found that that at all ages the scrotal color of Ch. a. pygerythrus males was always bluer and darker than that of Ch. a. sabaeus males. Among Ch. a. pygerythrus scrotal color becomes bluer and lightens with increasing age, while the color of Ch. a. sabaeus males also lightens, but becomes less blue with increasing age. We suggest that color variation is related to maturation and may function as an age-related signal among Ch. a. pygerythrus and Ch. a. sabaeus. We also found color was related to three morphological features among adults. For Ch. a. pygerythrus, higher body weight is associated with more blue color and longer canine length is associated with lighter color. Lighter color was associated with longer body lengths among Ch. a. sabaeus. Future studies focused on color variation within age classes are needed to examine the potential signal content of color in this species.