Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Malukiewicz J

PROVIDER: S-EPMC8390465 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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

Malukiewicz Joanna J Cartwright Reed A RA Dergam Jorge A JA Igayara Claudia S CS Nicola Patricia A PA Pereira Luiz M C LMC Ruiz-Miranda Carlos R CR Stone Anne C AC Silva Daniel L DL Silva Fernanda de Fatima Rodrigues da FFRD Varsani Arvind A Walter Lutz L Wilson Melissa A MA Zinner Dietmar D Roos Christian C

Scientific reports 20210826 1

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 ...[more]

PMID: 34446741

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Project description:IntroductionIn recent decades, Madagascar has become one of the most important plant hotspots in the world. The country's remaining forests and vegetation are disappearing at an alarming rate, while dozens of new species are discovered each year. Amongst the plant families that have long been studied, Orchidaceae appear as one of the most charismatic, diverse and of high conservation concern. Based on a reviewed, comprehensive herbarium dataset, we have compiled a curated checklist of all orchid species occurring in Madagascar. Based on this complete dataset, we then compiled sampling effort, species diversity distribution and some general statistics on their ecology and IUCN conservation status.MethodsWe compiled and standardised a global dataset using five public databases as the main data sources, supplemented by the most recent publications. The database contains ~ 10,000 geolocated records collected between 1816 and 2021. We used GIS software and rarefaction methods to examine sampling and diversity patterns.ResultsAccording to our dataset, there are currently 913 orchid species collected in Madagascar, of which 759 orchid species (83.1%) are endemic. Doubling the sampling effort could lead to the discovery of around 100 more species, bringing the total estimated number of orchid species in Madagascar to between 986 and 1048. About one-third (297 species) of all orchid species are known only by type specimens (189 species) or have not been collected in Madagascar for more than 50 years (214 species). Although the raw data show that the Andasibe-Moramanga area would have the highest orchid species concentration, our analysis of the data, adjusted for bias, shows that the centres of orchid diversity in Madagascar are in the Tsaratanàna Strict Nature Reserve and the Ranomafana National Park. Life-form statistics show that 55.0% of orchid species are strict epiphytes. The main flowering period of orchids in Madagascar is between November and March. To date, 84% of the 226 Malagasy orchid species listed in the IUCN Red List are threatened with extinction (CR, EN or VU).ConclusionDespite geographically uneven coverage, the biodiversity of Malagasy orchids appears to be already well documented. We provide maps corrected for sampling bias that indicate priority areas for future surveys. Upcoming efforts should also focus on rediscovery and conservation of rare and/or threatened species and ensure that the protected area network is well aligned with the distribution of priority species for conservation. Finally, the conservation status of 75% of the orchid species found in Madagascar is not yet known and the inclusion of these species must be a top priority in the coming years.

Project description:Background and aimsPinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex.MethodsWe address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves.Key resultsWe found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression.ConclusionsOur detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

Dataset Information

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

Publications

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

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