STRs PCR+application DNA+fingerprinting PDF

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1 NAMES ___Grayson Garcia_______________________________________________________ Group # __4___

STR DNA fingerprinting activity Objectives  Connect the use of PCR to the application of DNA profiling/paternity testing.  Explain how short tandem repeats (STRs) provide enough variation to be used a unique personal identifier.  Interpret DNA fingerprinting data related to paternity testing in animals and humans. The jaguar, along with the snow leopard, tiger, lion, and leopard, make up the five big cats that belong to the Panthera genus. In Brazil, the jaguar is listed by IBAMA (The Brazilian Institute of Environment and Renewable Natural Resources) as threatened with extinction. The conversion of habitat into farmland is the principal cause of the 50% reduction in the jaguar’s original range. The jaguar is extinct in two (Uruguay and El Salvador) of the 21 countries where it historically occurred. The jaguar is legally protected in the majority of countries where it is found. Only in Bolivia is hunting still permitted, and the jaguar does not have any legal protection in Ecuador and Guyana. T.N Soares et al. Paternity testing and behavioral ecology: A case study of jaguars (Panthera onca) in Emas National Park, Central Brazil. Genetics and Molecular Biology, 29, 4, 735-740 (2006)

In Emas National Park (Central Brazil) in November 2001 two jaguar (Panthera onca) cubs, presumably nine months old, were killed and partially eaten by a 90 kg adult male jaguar, estimated to be eight years old. The two cubs were also radio-tracked since they were three months old and were definitely brother and sister. The identity of the killer was also conclusively identified through its radio-telemetry monitoring and scientist observations. This large male (M01) was being radio-tracked and his home range overlapped by 85% for a long time with the home-range of the cubs’ mother and showed similar movements in time and space. During several days before the infanticide, the killer tracked movements of the female and the two cubs, which had been shifting their home ranges. Because of the large overlap of home ranges in space and time, this male was presumably the sire of the two cubs. However, in a subsequent capture event within the female’s (mother) home range area, a previously unrecorded 105 kg adult male (M02) was caught and radio-collared. According to preliminary capturerecapture data, the population of Panthera onca in Ema National Park is estimated as comprising about 15 specimens (Silveira, 2004). Finding another male overlapping the female’s home range suggests that the observed infanticide could involve more complex sociobiological issues and introduce some uncertain in the paternity of the two killed cubs. Since another male was found in the female’s home range, the basic question becomes: who was the sire of the two cubs killed by the first captured male? We used paternity

2 testing of the two P. onca males involved in the scenario. To our knowledge, this is the first application of molecular data to address a behavioral ecology question in jaguars. Experiment: Seven short tandem repeats (STRs) were amplified with PCR. Each locus has at least three possible alleles in this small jaguar population.

Results: The seven loci are named. The alleles for each sibling cub (C01 and C02) are shown beside the two males (M01 and M02).

Can M01 be the father? Can M02 be the father? Explain/support your answers by specifically stating which loci tell you definitive information. Jaguar M01 could be the father because he is a match at all 7 loci and gives either of his two alleles to each cub. Matching at all 7 means that there is a high probability M01 is the father. Jaguar M02 could not be the father because he is a match at two loci (FCA 126 and FCA220), but not at the other 5 loci. If even one loci doesn’t match, he is ruled out, so he is definitely not the father because he had 5 mismatches. What is the relevance of the finding? Choose which explanation is likely based on your answers above: Explanation 2 Explanation 1: If the male that had not killed the cubs (M02) was the true father of the two killed cubs, the scenario would be, in principle, a classical sociobiological event in which another male (in this case, the M01 male) entering the area would try to kill the two cubs in order to release their mother for mating. However, it is likely, based on the age of the cubs and female jaguar biology, that she had been available for mating for at least 4 months prior to the infanticide. Explanation 2: If the male that killed the cubs (M01) was the true father. Why did he track the mother and cubs for several days prior? Since the two cubs were not very young

3 when they were killed, this could represent a competition issue, in that the adult male (M01) did not recognize the cubs as his offspring and killed them for simple territorial reasons when under ecological stress.

A paternity case. Paternity cases are often in Hollywood news. Consider Justin Bieber who was accused in 2011 of being the father of some woman’s child that he had never met. A DNA paternity test can give a definitive answer if there is any real question (Bieber’s accuser was scamming and there was other evidence that demonstrated he was not the father.) https://www.youtube.com/watch?v=driWVwHMSRI Case: A woman accuses a man of not financially supporting his child. The man says the child is not his. The woman is quite certain of it. The LOCUS FATHER CHILD man suggests he does a paternity DNA test. D8S1179 12/14 12/14 She agrees. He submitted his sample to a private company that routinely performs DNA D21S11 27/32 30/30 profiling/paternity tests using PCR and 13 D7S820 8/10 8/8 STR loci. The results have just come in from CSF1PO 11/12 9/12 the company. He sends them to her through email…but the bottom of the email is cut off D3S1358 15/7 15/14 at the results. You can look at these and determine the results for her. TH01 7/9 6/6 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51

12/13 9/13 17/24 12/13 15/18 10/11 16/22

12/13 11/13 20/22 11/15 18/19 4/11 15/22

Should the man accused of being the father have to pay child support? Explain why or why not, using specific loci to defend your answer. No, the man shouldn’t have to pay for child support because there were only 3 loci that matched (D2S1338, D19S433, and TH01). This means that he is most likely not the father because even though the end of the results page was cut off, there were not enough loci that matched to prove that he is the father of the child. If a woman is absolutely certain whom the father is, but the genetic test from a paternity-testing company does not match, what could be a reason? A reason for the paternity test not matching could be that the sample was contaminated, due to a lab error, due to a point mutation in the man’s DNA, or the man could have submitted someone else’s DNA.

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