@article{06e7f5e540f848e6816ec4793e62d3d6,
title = "Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world{\textquoteright}s most threatened primates",
abstract = "The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world{\textquoteright}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.",
author = "Joanna Malukiewicz and Cartwright, {Reed A.} and Dergam, {Jorge A.} and Igayara, {Claudia S.} and Nicola, {Patricia A.} and Pereira, {Luiz M.C.} and Ruiz-Miranda, {Carlos R.} and Stone, {Anne C.} and Silva, {Daniel L.} and Silva, {Fernanda de Fatima Rodrigues da} and Arvind Varsani and Lutz Walter and Wilson, {Melissa A.} and Dietmar Zinner and Christian Roos",
note = "Funding Information: This work was supported by a Brazilian CNPq Jovens Talentos Postdoctoral Fellowship (302044/2014-0), a Brazilian CNPq DCR grant (300264/2018-6), an American Society of Primatologists Conservation Small Grant, a Marie-Curie Individual Fellowship (AMD-793641-4) and an International Primatological Society Research Grant for JM. This work was also supported by an Arizona State University SOLS/OKED Research Investment grant to RAC, AV, MAW, and JM, as well as an Arizona State University RTI Postdoctoral Grant to JM. Additional internal funding from the German Primate Center to LW and JM also supported this work. The funding agencies had no roles in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to thank the Golden Lion Tamarin Association, CEMAFAUNA, the Guarulhos Municipal Zoo, the Beagle Lab at UFV, and many biologists, field technicians, veterinarians, and other individuals that made this research possible. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
doi = "10.1038/s41598-021-96404-6",
language = "English (US)",
volume = "11",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",
}