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CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.

Publication ,  Journal Article
Barbian, HJ; Connell, AJ; Avitto, AN; Russell, RM; Smith, AG; Gundlapally, MS; Shazad, AL; Li, Y; Bibollet-Ruche, F; Wroblewski, EE; Mjungu, D ...
Published in: Ecology and evolution
August 2018

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

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Published In

Ecology and evolution

DOI

EISSN

2045-7758

ISSN

2045-7758

Publication Date

August 2018

Volume

8

Issue

16

Start / End Page

7946 / 7963

Related Subject Headings

  • 4102 Ecological applications
  • 3104 Evolutionary biology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology
 

Citation

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Barbian, H. J., Connell, A. J., Avitto, A. N., Russell, R. M., Smith, A. G., Gundlapally, M. S., … Hahn, B. H. (2018). CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecology and Evolution, 8(16), 7946–7963. https://doi.org/10.1002/ece3.4302
Barbian, Hannah J., Andrew Jesse Connell, Alexa N. Avitto, Ronnie M. Russell, Andrew G. Smith, Madhurima S. Gundlapally, Alexander L. Shazad, et al. “CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.Ecology and Evolution 8, no. 16 (August 2018): 7946–63. https://doi.org/10.1002/ece3.4302.
Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, et al. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecology and evolution. 2018 Aug;8(16):7946–63.
Barbian, Hannah J., et al. “CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.Ecology and Evolution, vol. 8, no. 16, Aug. 2018, pp. 7946–63. Epmc, doi:10.1002/ece3.4302.
Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet-Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecology and evolution. 2018 Aug;8(16):7946–7963.
Journal cover image

Published In

Ecology and evolution

DOI

EISSN

2045-7758

ISSN

2045-7758

Publication Date

August 2018

Volume

8

Issue

16

Start / End Page

7946 / 7963

Related Subject Headings

  • 4102 Ecological applications
  • 3104 Evolutionary biology
  • 3103 Ecology
  • 0603 Evolutionary Biology
  • 0602 Ecology