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

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.

New records of buffy-tufted-ear marmoset Callithrix aurita (É. Geoffroy, 1812), in a protected area of Teresópolis, Brazilian Atlantic Forest

Callithrix aurita, an Atlantic Forest endemic primate, is a threatened species due to habitat loss, deforestation, interspecific competition and hybridization. In 2018, it entered the list of the world's 25-most threatened primate species, therefore, new occurrence sites must help in its conservation. Transects in the Montanhas de Teresópolis Municipal Natural Park and occasional sampling on the surrounding roads, using playback, have been carried out between March 2020 and January 2021. Eleven new records were made of the occurrence of the species in and around the PNMMT, in secondary forest sites with altitudes between 711 and 1000m. These records reinforce the importance of the Park for the conservation of this primate. The presence of this species can help the planning and management of this protected area, indicating areas for preservation.

Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World's Most Threatened Primates

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.

ENRIQUECIMENTO AMBIENTAL X COMPORTAMENTO EM CATIVEIRO DE CALLITHRIX AURITA (É. Geoffroy, 1812)

Técnicas de enriquecimento ambiental foram utilizadas para avaliação dos comportamentos em cativeiro de um grupo de três indivíduos, duas fêmeas e um macho de Callithrix aurita (sagui-da-serra-escuro), cativos do Mantenedor de Fauna Silvestre da UNIVAP, São José dos Campos, SP. Foram implantados seis diferentes enriquecimentos alimentares e observações com duração de uma hora pelo método “focal sampling grupal” no período de agosto a novembro de 2015. Os comportamentos categorizados, inicialmente, eram Alimentação, Alerta, Comunicação, Social, Manutenção e Território. A categoria Cuidado Parental foi adicionada após o nascimento de dois filhotes. Percebeu-se que Alimentação e Alerta foram as categorias mais evidentes, que Cuidado Parental apareceu equilibrada entre os membros e as expressões de comportamentos típicos foram significantes para concluir que enriquecimentos ambientais melhoram o bem-estar animal de animal em cativeiro.