Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Joanna Malukiewicz, Reed A. Cartwright, Jorge A. Dergam, Claudia S. Igayara, Patricia A. Nicola, Luiz M.C. Pereira, Carlos R. Ruiz-Miranda, Anne C. Stone, Daniel L. Silva, Fernanda de Fatima Rodrigues da Silva, Arvind Varsani, Lutz Walter, Melissa A. Wilson, Dietmar Zinner, Christian Roos

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

Original languageEnglish (US)
Article number17279
JournalScientific reports
Issue number1
StatePublished - Dec 2021

ASJC Scopus subject areas

  • General


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