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

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Title: CHIIMP: An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.
Authors: Barbian, Hannah J.1, Connell, Andrew Jesse1, Avitto, Alexa N.1, Russell, Ronnie M.1, Smith, Andrew G.1, Gundlapally, Madhurima S.1, Shazad, Alexander L.1, Li, Yingying1, Bibollet‐Ruche, Frederic1, Wroblewski, Emily E.2, Mjungu, Deus3, Lonsdorf, Elizabeth V.4, Stewart, Fiona A.5, Piel, Alexander K.5, Pusey, Anne E.6, Sharp, Paul M.7, Hahn, Beatrice H.1 bhahn@pennmedicine.upenn.edu
Source: Ecology & Evolution (20457758). Aug2018, Vol. 8 Issue 16, p7946-7963. 18p.
Subject Terms: *Species diversity, Chimpanzees, Microsatellite repeats, Alleles, Genotypes, Short tandem repeat analysis
Abstract: Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: CHIIMP: An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.
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  Data: <searchLink fieldCode="AR" term="%22Barbian%2C+Hannah+J%2E%22">Barbian, Hannah J.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Connell%2C+Andrew+Jesse%22">Connell, Andrew Jesse</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Avitto%2C+Alexa+N%2E%22">Avitto, Alexa N.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Russell%2C+Ronnie+M%2E%22">Russell, Ronnie M.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Smith%2C+Andrew+G%2E%22">Smith, Andrew G.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Gundlapally%2C+Madhurima+S%2E%22">Gundlapally, Madhurima S.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Shazad%2C+Alexander+L%2E%22">Shazad, Alexander L.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Li%2C+Yingying%22">Li, Yingying</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Bibollet‐Ruche%2C+Frederic%22">Bibollet‐Ruche, Frederic</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Wroblewski%2C+Emily+E%2E%22">Wroblewski, Emily E.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Mjungu%2C+Deus%22">Mjungu, Deus</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Lonsdorf%2C+Elizabeth+V%2E%22">Lonsdorf, Elizabeth V.</searchLink><relatesTo>4</relatesTo><br /><searchLink fieldCode="AR" term="%22Stewart%2C+Fiona+A%2E%22">Stewart, Fiona A.</searchLink><relatesTo>5</relatesTo><br /><searchLink fieldCode="AR" term="%22Piel%2C+Alexander+K%2E%22">Piel, Alexander K.</searchLink><relatesTo>5</relatesTo><br /><searchLink fieldCode="AR" term="%22Pusey%2C+Anne+E%2E%22">Pusey, Anne E.</searchLink><relatesTo>6</relatesTo><br /><searchLink fieldCode="AR" term="%22Sharp%2C+Paul+M%2E%22">Sharp, Paul M.</searchLink><relatesTo>7</relatesTo><br /><searchLink fieldCode="AR" term="%22Hahn%2C+Beatrice+H%2E%22">Hahn, Beatrice H.</searchLink><relatesTo>1</relatesTo><i> bhahn@pennmedicine.upenn.edu</i>
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  Data: <searchLink fieldCode="JN" term="%22Ecology+%26+Evolution+%2820457758%29%22">Ecology & Evolution (20457758)</searchLink>. Aug2018, Vol. 8 Issue 16, p7946-7963. 18p.
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  Data: *<searchLink fieldCode="DE" term="%22Species+diversity%22">Species diversity</searchLink><br /><searchLink fieldCode="DE" term="%22Chimpanzees%22">Chimpanzees</searchLink><br /><searchLink fieldCode="DE" term="%22Microsatellite+repeats%22">Microsatellite repeats</searchLink><br /><searchLink fieldCode="DE" term="%22Alleles%22">Alleles</searchLink><br /><searchLink fieldCode="DE" term="%22Genotypes%22">Genotypes</searchLink><br /><searchLink fieldCode="DE" term="%22Short+tandem+repeat+analysis%22">Short tandem repeat analysis</searchLink>
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  Data: Abstract: 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. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=8gh&AN=131862070
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      – SubjectFull: Microsatellite repeats
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