Development and characterization of novel microsatellite loci for the Blue-fronted Amazon (Amazona aestiva, Psittaciformes, Aves) and cross-species amplification for other two threatened Amazona species.

Parrots are among the most threatened avian groups of the world, with illegal pet trade being a major threat to some Amazon (Amazona genus) and macaw (Ara and Anodorhynchus genera) species. Population genetic studies and effective control of commercial breeders are important actions for the conservation of these parrot species; however, few microsatellite loci are available for most Amazona species to date. In this study, 25 polymorphic microsatellite loci were identified in silico and characterized for the Blue-fronted Amazon [Amazona aestiva (Aa)]. Loci were tested in 24 Blue-fronted Amazons from wild population from central Brazil with cross-species amplified in two individuals of Amazona vinacea (Av) and Amazona pretrei (Ap) from northeastern Minas Gerais and Rio Grande do Sul, in southeastern and south of Brazil, respectively. The number of alleles per locus for Aa ranged from 5 to 24 with an average of 13.1. Twenty-four and 25 loci were successfully amplified for Av and Ap, respectively. The observed and expected heterozygosities for Aa ranged from 0.27 to 1.00 and from 0.35 to 0.94, with averages of 0.75 and 0.85, respectively. Nine loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction (likely due to null alleles) and no significant linkage disequilibrium between loci pairs was detected. The combined paternity exclusion probability was very high, and the probability of identity was extremely low. This new set of microsatellite loci will be useful for analyzing population genetic structure and making conservation and management decisions, as well as for parentage analysis and the control of commercial breeding of Aa and potentially other Amazona species.

[Formula Derivation and Validation of Probability of Exclusion in the Cases of Standard Triplet Parentage Testing].

OBJECTIVES: To derive and experiment validate the probability of exclusion （PE） formulas in the cases of standard triplet parentage testing. METHODS: The formulas were derived voluntarily based on the PE definition: [Formula: see text]. This formula was compared with the 5 formulas （1）-（5） reported previously, and the PE values of 19 autosomal STR loci in AGCU EX20 system were calculated. Based on 1 000 samples of single-parentage cases and 1 000 unrelated individuals, the real experiment was designed and the real experiment results of PE were calculated. Ten million pairs of simulated biological mother and son and 10 million random individuals were gained by random simulation method, and the simulated experiment was designed and the simulated values of PE were calculated. In 19 STR loci, the sum of all allele frequency （S） was calculated, and the formula values of PE were compared with the values of real and simulated experiments. RESULTS: If S=1, the calculation values of formula （1）, （2）, （5） and （6） were quite the same, which accord with the double verification of real and simulated experiments. If S≠1, there was a minor error in the calculation results of formula （1）, （2）, （5） and （6）, while which had a large error in formula （3） and （4）. CONCLUSIONS: The formula （6） derived in present study and the classical formulas （1）, （2） and （5） can be applied to the standard triplet parentage testing. The S value has a certain influence on PE calculation.

Males collectively defend their one-male units against bachelor males in a multi-level primate society.

Group-level male-male co-operation, which has been documented in several primate and non-primate societies, may be mutualistically advantageous to the participants when confronted with threats such as takeovers and cuckoldry by external males. Co-operation among members of distinct social units-while universal among humans-is extremely rare in non-human primates. We present the first observations of collective action or co-operation among males of different one-male units (OMU) in a multi-level society of Rhinopithecus roxellana. A total of 59 instances of male co-operation were recorded. Male co-operation included coordinated chasing, joint vigilance, and patrolling behavior directed at lone adult males trying to enter an OMU. Male co-operation was significantly more frequent during the mating season when the risk of incursions and extra-group paternity was higher. Paternity of infants born in the subsequent birth season and kin relationships among resident males were identified using microsatellite genotype. All infants were sired by OMU males, which we interpret as possible evidence for their success at thwarting mating attempts by satellite males. OMU males were principally unrelated suggesting that male co-operation is best understood in terms of the mutual direct benefits individuals obtain through collective action. Our findings lend support to the bachelor threat hypothesis in which the cooperative behavior of several individuals is more effective than the lone action of a single individual in providing mate defense. Our research has implications for understanding male bonding, higher-level collective action, and the evolution of social co-operation in human societies.

Paternity testing using microsatellite DNA markers in captive Adélie penguins (Pygoscelis adeliae).

We investigated the paternity of 39 Adélie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n = 26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ≥4 years old in the exhibit tank during each reproductive season; n = 9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations.

Analysis of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017.

AIM OF THE STUDY: Analysis of frequency and structure of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017. MATERIAL AND METHODS: The paper is based on paternity test reports involving alleged father-child-mother trios. In a total of reviewed 958 cases, 187 exclusions were identified. The analysis was carried out on the basis of the results of DNA tests. DNA extraction was performed using QIAamp DNA Mini Kit (Qiagen) and DNA quantitation using Quantifiler Human DNA Quantification Kit and 7500 Real-Time PCR System (Applied Biosystems). AmpFLSTR Identifiler PCR Amplification Kit and a PCR System 9700 thermal cycler (Applied Biosystems) were used for DNA amplification. RESULTS: Over the analyzed period, the number of paternity tests was nearly halved, whereas the percentage of exclusions in individual years varied significantly (33.9-13.3%), with the average of 26.3%. The highest efficiency of exclusions was observed for D18S51 (0.7166) and FGA (0.7059), and the least effective system was TPOX (0.3048). CONCLUSIONS: The applied set of markers has been demonstrated to be an efficient tool in genetic paternity tests in the context of the recommended rules of exclusion.

Avoidance of close consanguineous inbreeding in captive groups of rhesus macaques.

In three captive groups of rhesus macaques (Macaca mulatto) the intensity of inbreeding avoidance was directly correlated with the closeness of kinship. The incidence of inbreeding between matrilineal relatives was lower than expected were mating to occur randomly with regard to matrilineal affiliation. The avoidance of mating between sons and their mothers and between matrilineal sibs contributed about squally to this outcome. The incidence of mating between more remote matrilineal relatives was lower than, but could not be shown to differ significantly from, that expected at the 0.05 level of probability. Familiarity fostered by interactions among matriline members probably provides a focus for avoidance of matrilineal inbreeding, and might influence male dispersal. Results of this study are consistent with reports of female rhesus macaques' avoidance of sexual activity with matrilineal male relatives as predicted by parental investment theory The observed incidence of inbreeding between patrilineal relatives was not different from that expected, but significantly fewer of the patrilineally inbred matings involved father/daughter matings than expected were mating random. Recognition of phenotypic similarities might provide a focus for avoidance of inbreeding between fathers and their daughters, but is loss reliable than strategies for avoiding matrilineal inbreeding. Adaptations for avoiding matrilineal inbreeding that are more effective than those for avoiding patrilineal inbreeding might have evolved because the risk of patrilineal inbreeding, and hence the resulting loss in fitness, is marginal compared to that for matrilineal inbreeding in free-ranging groups. © 1995 Wiley-Liss, Inc.

DNA "fingerprinting" and the genetic management of a captive chimpanzee population (Pan troglodytes).

DNA fingerprinting probes are cloned sequences which simultaneously detect a large number of similar hypervariable loci in the target DNA. The resulting highly polymorphic pattern visualized on an autoradiograph allows resolution of questions concerning individual identification and parentage. M13 bacteriophage has been used as a DNA fingerprinting probe for paternity ascertainment among captive chimpanzees housed in multi-male groups as part of the National Chimpanzee Breeding and Research Program. In 31 cases of unknown paternity where DNA samples for mother, offspring, and all potential sires were available, DNA fingerprinting with M13 resulted in the unambiguous assignment of paternity for all 31 infants. Knowledge of pedigrees among the captive-born animals is used to address several issues important in the genetic management of captive breeding colonies, including estimation of effective population size and of the rate of decline in genetic variability, variance in male and female reproduction, and the effect of social dominance on male reproductive success. Our analysis demonstrates the beneficial effects of genetic management by comparing the managed dedicated cohort to the Bastrop colony as a whole.

Formula Derivation and Validation of Probability of Exclusion in the Cases of Standard Triplet Parentage Testing / 法医学杂志

Objective To derive and experiment validate the probability of exclusion (PE) formulas in the cases of standard triplet parentage testing.Methods The formulas were derived voluntarily based on the PE definition:PE=∑Pi2（1-Pi）2+∑PiPj(1-Pi)3+ ∑PiPj（1-Pj）3+∑PiPj（Pi+Pj）(1-Pi-Pj)2.This formula was compared with the 5 formulas (1)-(5) reported previously,and the PE values of 19 autosomal STR loci in AGCU EX20 system were calculated.Based on 1 000 samples of single-parentage cases and 1 000 unrelated individuals,the real experiment was designed and the real experiment results of PE were calculated.Ten million pairs of simulated biological mother and son and 10 million random individuals were gained by random simulation method,and the simulated experiment was designed and the simulated values of PE were calculated.In 19 STR loci,the sum of all allele frequency (S) was calculated,and the formula values of PE were compared with the values of real and simulated experiments.Results If S=I,the calculation values of formula (1),(2),(5) and (6) were quite the same,which accord with the double verification of real and simulated experiments.If S≠ 1,there was a minor error in the calculation results of formula (1),(2),(5) and (6),while which had a large error in formula (3) and (4).Conclusion The formula (6) derived in present study and the classical formulas (1),(2) and (5) can be applied to the standard triplet parentage testing.The S value has a certain influence on PE calculation.

UNDERSTANDING THE POPULATION GENETIC STRUCTURE OF GLEDITSIA TRIACANTHOS L.: THE SCALE AND PATTERN OF POLLEN GENE FLOW.

Spatial and temporal patterns of gene flow determine the extent to which populations can differentiate from one another as a result of natural selection or genetic drift. In this study, we investigated pollen-mediated gene flow in two eastern Kansas populations of the subdioecious tree species, Gleditsia triacanthos L. (Leguminosae), or honeylocust. In 2 yr at each site, we used paternity-exclusion analysis to estimate the proportion of seeds sired by immigrant pollen. We also used a single-parent and parent-pair exclusion analysis on naturally established seedlings and saplings to estimate gene flow into one site over a 12-yr period and into the second site over a 22-yr period. Results of both analyses showed high minimum estimates of pollen gene flow into each site (17%-30%). In each population, we found significantly less gene flow in years of high fruit production than in years of low fruit production, but in one population, we observed little variation in gene-flow rates among age classes of seedlings and saplings. The level of pollen gene flow showed weak negative dependence on the relative isolation distances of the maternal trees sampled (140-240 m at one site vs. 85-120 m at the second site), and gene-flow estimates from naturally established juveniles were very similar at the two sites. Within populations, a multiple regression model showed that maximum-likelihood estimates of male fertility were negatively associated with distances between mates and positively associated with male size as measured by stem diameter. In neither population, however, did the regression explain more than 16% of the total variation in male fertilities.