A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape

被引：69

作者：

Goossens B. ^{[1
]}

Chikhi L. ^{[2
]}

Utami S.S. ^{[3
,4
]}

De Ruiter J. ^{[5
]}

Bruford M.W. ^{[1
]}

机构：

[1] Biodiv. and Ecol. Processes Group, School of Biosciences, Cardiff University, Cardiff CF10 3TL, Cathays Park

[2] Zoological Society of London, Institute of Zoology, London NW1 4RY, Regent's Park

[3] Ethologie and Socio-Oecologie, University of Utrecht, 3508 TB Utrecht

[4] Fakultas Biologi, Universitas Nasional, Jl Sawo Manila

[5] Department of Anthropology, University of Durham, Durham DH1 3HN

来源：

Conservation Genetics | 2000年 / 1卷 / 2期

关键词：

Conservation genetics; Faeces; Microsatellites; Non-invasive methods; Pongo pygmaeus abelii;

D O I：

10.1023/A:1026535006318

中图分类号：

学科分类号：

摘要：

We investigated the effect of the number of faecal samples, of extracts per sample and of PCRs per extract on the reliability of genotypes for a microsatellite locus in free-living orang-utans. For each individual 36 PCRs were performed using DNA extractions from up to four faecal samples. We found a very large inter-individual variation in positive PCRs (P+) (36/36 for one individual and 0/36 for another). As many as 30% of the cases led to erroneous genotypes when only one P+ was obtained. It is preferable to use at least 4 P+ per extract to reduce this proportion to less than 1%. With 3 P+ results, erroneous genotypes were still observed in 26% of the cases together. These results indicate that it is necessary to do a minimum of 4 PCRs per extract. In order to have a chance to observe 4 P+, three extracts should be ideally analysed for each sample. We also recommend that when possible two or more samples should be collected in the field to increase the chance of having extracts containing DNA and to provide independent replicates. While we recognise the difficulty of working with faecal samples, we advocate the use of faecal material for genetic studies of certain wild animal populations where the advantages of avoiding disturbance, stress and injury are deemed of critical importance.

引用

页码：157 / 162

页数：5

共 20 条

[1]

Edwards A., Civitemmo A., Hammond H.A., Caskey C.T., DNA typing and genetic mapping with trimeric tandem repeats, American Journal of Human Genetics, 49, pp. 746-756, (1991)

[2]

Flagstad O., Roed K., Stacy J.E., Jakobsen K.S., Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol, Mol. Ecol., 8, pp. 879-883, (1999)

[3]

Frantzen M.A.J., Silk J.B., Ferguson J.W.H., Wayne R.K., Kohn M.H., Empirical evaluation of preservation methods for faecal DNA, Mol. Ecol., 1, pp. 1423-1428, (1998)

[4]

Gagneux P., Boesch C., Woodruff D.S., Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair, Mol. Ecol., 6, pp. 861-868, (1997)

[5]

Gerloff U., Hartung B., Fruth B., Hohmann G., Tautz D., Intracommunity relationships, dispersal pattern and paternity success in a wild living community of bonobos (Pan paniscus) determined from DNA analysis of faecal samples, Proceedings of the Royal Society of London b, 266, pp. 1189-1195, (1999)

[6]

Gerloff U., Schlotterer C., Rassmann K., Rambold I., Hohmann G., Fruth B., Tautz D., Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus), Mol. Ecol., 4, pp. 515-518, (1995)

[7]

Goossens B., Waits L.P., Taberlet P., Plucked hair samples as a source of DNA: Reliability of dinucleotide microsatellite genotyping, Mol. Ecol., 7, pp. 1237-1241, (1998)

[8]

Hoss M., Kohn M., Knauer F., Schroder W., Paabo S., Excrement analysis by PCR, Nature, 359, (1992)

[9]

Hoss M., Paabo S., DNA extraction from Pleistocene bones by a silica-based purification method, Nucleic Acids Research, 21, pp. 3913-3914, (1993)

[10]

Kohn M.H., Knauer F., Stoffella A., Schroder W., Paabo S., Conservation genetics of the European brown bear - A study using excremental PCR of nuclear and mitochondrial sequences, Mol. Ecol., 4, pp. 95-103, (1995)

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