Data From: what mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate

The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (Mandrillus sphinx) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological c..., Further details of data analysis can be found in the publication manuscript, but in brief, samples were collected from a wild population of mandrills (Mandrillus sphinx) in Lopé National Park, Gabon. The majority of the samples are non-invasively collected feces, but samples of blood and plucked hair were also collected from anesthetized animals. Each sample was PCR-amplified for a 157-base fragment of the DRB gene of the class II major histocompatibility complex, then sequenced on Illumina Miseq. An initial Miseq run was performed in 2018, containing 192 fecal samples. In 2019, a Miseq Nano run was performed, containing the 24 samples of blood and plucked hair along with 23 replicate fecal samples from the 2018 sequencing run. In 2021, the third sequencing run was performed using standard Miseq, and this run included nine replicates of the blood and hair samples and 183 replicated fecal samples.
To quantify repeatability between runs, each Illumina run was processed separately. Pre-pro..., Most files can be opened using an open source text editor such as JEdit or Notepad++. The .csv files will be easist to view in a spreadsheet such as Excel or Google Sheets, but they can also be opened in a text editor if needed. Users may wish to open fasta files using an open source genetics software such as MEGA-X., # Data From: What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate

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Jan. 12, 2024

One aim of this study was to quantify replicability of Illumina sequencing results from fecal samples and higher-quality samples of blood and plucked hair. Samples of both types were sequenced in at least two independent Illumina runs, and an allele assignment was determined using the degree of change method(Lighten et al. 2014). We then calculated the proportion of sequence variants that replicated between runs for each sample to represent a replicability score(RA), and compared average RA scores for feces vs blood/hair. The data used for these tests are contained in the folder 'DOC_assignments_per_run'. We also tested whether replicability is related to sequence depth or the sequence's rank within the amplicon. These data are also available in this package.

A second aim of this study was to characterize functional genetic dive...