Parentage test in broad-snouted caimans (Caiman latirostris, Crocodylidae) using microsatellite DNA

In this study, microsatellite markers, developed for Alligator mississipiensis and Caiman latirostris, were used to assess parentage among individuals from the captive colony of Caiman latirostris at the University of São Paulo, in Piracicaba, São Paulo, Brazil. Many of the females in the colony were full siblings, which made maternal identification difficult due to genotypic similarity. Even so, the most likely mother could be identified unambiguously among offspring in most of the clutches studied. Two non-parental females displayed maternal behavior which would have misled managers in assigning maternity based on behavior alone. This set of variable loci demonstrates the utility of parentage testing in captive propagation programs.     

微卫星DNA在吉戎兔亲子鉴定中的应用研究

选用Sat2、Sat3、Sat4、Sat5、Sat7、Sat8、Sat12、Sat13、Sat16、Sol08、Sol28、Sol30、Sol03 等13个微卫星位点PCR扩增30只吉戎兔的基因组DNA,然后在8%聚丙烯酰胺凝胶上电泳分型,检测结果为平均等位基因数为3.46个,平均杂合度（H）为0.578,平均多态信息含量（PIC）为0.531,双亲资料未知时13个位点的累计非父排除率（PE1）为0.935226,置信度低于80%,一亲本资料已知时13个位点的累计非父排除率（PE2）为0.999329,置信度为95%。由于所鉴定兔群的母本资料已知,因此基因型的分型结果能有效确认18只仔兔子的真父。     

Hierarchical polygyny in multiparous lesser flat-headed bats

How males gain access to mates and the potential for female choice will determine whether polygyny can operate at several levels, from within litters and groups to the wider population. Female lesser flat-headed bats (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually for bats, they are multiparous, providing the opportunity to test whether multi-level polygyny differs among males depending on whether they roost with females, with males or are solitary. We genotyped 662 individuals from 54 internodes and analysed parentage of 165 litters. Our results revealed 170 sets of paternal twins/triplets, of which 96 were full-sibs and 74 were half-sibs. We found that males captured roosting with females typically sired more offspring overall than did other males and also showed a greater tendency to monopolize paternity within both litters and roosting groups. In comparison, males that sired fewer full-sibs were assigned more maternal half-sibs. These latter individuals, which included solitary males and those from all-male groups, might gain copulations either via roaming with furtive mating or during visits by females. Indeed, female lesser flat-headed bats store sperm, so could benefit from multiple mating to reduce genetic incompatibilities. At the same time, however, we found no evidence of outbreeding. Finally, relatedness and mtDNA analyses revealed that polygyny also operated within matrilineal kin, suggesting a system that might promote social cohesiveness. Future studies of individual movements will help to determine the extent to which mixed paternities in litters, matrilines and groups are driven by male or female behaviour.     

Twenty-one novel microsatellite DNA loci isolated from the Puget Sound white-crowned sparrow, Zonotrichia leucophrys pugetensis

The white‐crowned sparrow, Zonotrichia leucophrys, has served as a model species for studies of song and reproductive physiology. Here, we describe primers for 21 novel microsatellite loci isolated from the Puget Sound subspecies, Zonotrichia leucophrys pugetensis, which will be useful for parentage and population genetic analyses. Based on genotypes from seven to 22 adult birds from one population, the average number of alleles per locus was 10.9 (four to 21 alleles) and observed heterozygosity varied from 0.50 to 1.00. All loci also amplified products in at least one of three other passerine species tested.     

Probability of random sire exclusion using microsatellite markers for parentage verification

Many microsatellite sequences have been described in the bovine genome. Being highly polymorphic these have been suggested as markers for parentage verification and individual identification in cattle. We have evaluated the use of five highly polymorphic microsatellite markers for parentage verification in 14 breeds of cattle in the UK. Three of the microsatellite loci occur within introns in genes: BoLA DRB3 , steroid 21-hydroxylase, and the beta subunit of the follicle-stimulating hormone. The other two are anonymous sites ETH131 and HEL6. Results were analysed by a statistical approach that takes in to account deviations from Hardy-Wienberg equilibrium and linkage disequilibrium for multiple loci. The method of determining the probability of random sire exclusion uses observed genotype frequencies instead of allele frequencies. Independently, the markers used have a probability of between 0.72 and 0.62 of identifying a parentage error, while used together the five markers give, on average across breeds, a probability of 0.99 of excluding an incorrect sire.     

KINALYZER, a computer program for reconstructing sibling groups

A software suite KINALYZER reconstructs full-sibling groups without parental information using data from codominant marker loci such as microsatellites. KINALYZER utilizes a new algorithm for sibling reconstruction in diploid organisms based on combinatorial optimization. KINALYZER makes use of a Minimum 2-Allele Set Cover approach based on Mendelian inheritance rules and finds the smallest number of sibling groups that contain all the individuals in the sample. Also available is a 'Greedy Consensus' approach that reconstructs sibgroups using subsets of loci and finds the consensus of the partial solutions. Unlike likelihood methods for sibling reconstruction, KINALYZER does not require information about population allele frequencies and it makes no assumptions regarding the mating system of the species. KINALYZER is freely available as a web-based service.     

Kinship and social structure of bobcats (Lynx rufus) inferred from microsatellite and radio-telemetry data

Kinship analysis using 12 microsatellites was compared with radio-telemetry data to examine the social structure of bobcats Lynx rufus in southern Texas. Genetically identified kinship relationships combined with capture data were used to reconstruct pedigrees. Three family groups were constructed from parent/offspring pairs identified from shared alleles. All parents identified by genetic analysis had established home ranges. Individuals with no distinct home ranges were not genetically observed to have offspring among the bobcats sampled. This suggests that establishing a home range is necessary for bobcats to breed. Of three identified male offspring and three identified female offspring, two female offspring were philopatric. These females became a part of the breeding population in their natal area. Among sibling pairs that included nine female and four male individuals, four females and one male were residents suggesting male-biased dispersal.     

EXAMINATION OF POPULATION STRUCTURE IN RED-COCKADED WOODPECKERS USING DNA PROFILES

The degree to which DNA similarity is related to kinship and population structure in natural populations was investigated for a small population of cooperatively-breeding Red-cockaded Woodpeckers (Picoides borealis) in the western Piedmont region of South Carolina. An independent pedigree was established from records of color-banded individuals. Results of DNA profiles were then examined relative to this pedigree. DNA similarity among unrelated woodpeckers averaged 0.55 ± 0.01 (SE). The mean number of DNA bands scored and similarity did not significantly differ between founders and the current population. Examination of parentage in 10 families indicated that multiple paternity did not occur when band by band comparisons or similarity values were compared among parents, helpers, and offspring. Thus, Red-cockaded Woodpeckers were monogamous in this population. DNA similarity among all individuals ranged from 0.32-0.78. Distribution of these similarity values by kinship resulted in some overlap with other kin values. Therefore, specific similarity values could not be assigned a kinship value without knowledge of the pedigree. However, least-squares linear regression indicated that similarity was significantly related to kinship (P < 0.05). These results indicate that use of DNA profiles may be important in quantifying population structure, however, they must be used in conjunction with a known pedigree before any assessment of kinship among individuals is made. Band by band comparisons remain a viable technique for examination of parentage when all putative parents have been sampled.