DOI: 10.20350/digitalcsic/16640
title: Dataset information used in Characterizing bacterial communities of wild birds: Insights from three southern African Hornbill species

description: data_ASVtable.csv: this dataset was exported from QIIME2 v2020.6 and includes in the rows the ASVs ID and in the columns the samples's name. The values in the table indicate the abundance of each ASV per sample, as the number of counts. data_taxonomy.csv: contains the ASV ID in the rows and the taxonomic classification in the columns. Each ASV was taxonomically classified using the Silva 138 database and only bacterial sequences were considered. data_tree.tre: rooted phylogenetic tree of our sequences. data_Alpha_diversity.xlsx: this dataset contains metadata and values of alpha diversity indices (Chao1 index, Shannon's diversity, and Faith's phylogenetic diversity). To calculate these indices, we rarefied the ASV table 100 times to the minimum sampling depth (1,085). For each of the 100 rarefied ASV tables, we calculated the indices and then computed the mean value per sample. Description of the variables: tube: Sample names. chao1: Chao1 values for each sample. diversity_shannon: Shannon diversity index values for each sample. chao1_sd: Standard deviation of Chao1 values for each sample. diversity_shannon_sd: Standard deviation of Shannon diversity index values for each sample. PD: Faith's phylogenetic diversity values for each sample. PD_sd: Standard deviation of Faith's phylogenetic diversity values for each sample. species: Code identifying species: "YBHB" for Yellow-billed hornbills, "DH" for Damara hornbills, and "MH" for Monteiro's hornbills. nest: Nest name where each bird was breeding at the time of sampling. ring: Identification number for each bird. If the bird was not ringed, this field contains the nest name and chick identity (e.g., "C1" for the oldest chick, "C2" for the second oldest). individual: Specifies whether the sample is from a female or a chick. If more than one nestling was sampled per nest, additional information indicates whether the chick was the oldest (_1), second oldest (_2), or youngest (_3). individual_2019: Indicates female and chick samples without information on the age hierarchy of chicks when more than one was sampled per nest. sample: Body part or integument sampled. "Uropygial" refers to the uropygial gland surface, "billbase" and "billtop" refer to the base and top of the bill, "nape" refers to samples from nape feathers, "blackwing" to primary wing feathers, and "blacktail" and "whitetail" to black and white tail feathers, respectively ("white" and "black" indicate the primary color of the feathers). sample_2018: Integument sampled in 2018 without differentiation between specific bill or feather samples. Here, "bill" replaces "billtop" and "billbase," and "feathers" replaces "nape," "blackwing," "whitetail," or "blacktail." order_of_sampling: "first" indicates the bird's first sample; "second" indicates the second sample of the same bird (if sampled twice). number_samples: "one" indicates birds sampled only once; "two" indicates birds sampled twice. year: Year of sampling (2018, 2019, or 2020). date: Date of sampling. age: Age of the bird at the time of sampling. sharing_2019: "yes" if a female and yellow-billed hornbill nestlings shared a nest in 2019 or if more than one nestling was sampled per nest; "no" if only the female or only one nestling was sampled per nest. sharing_2020: "yes" if a female and yellow-billed hornbill nestlings shared a nest in 2020 or if more than one nestling was sampled per nest; "no" if only the female or only one nestling was sampled per nest. BRAYDist.xlsx: Bray-Curtis (relative abundance) distance matrix. JaccardDist.xlsx: Jaccard ((presence-absence) distance matrix. UNunifracDist.xlsx: unweighted UniFrac distance matrix. WEunifracDist.xlsx: weighted UniFrac distance matrix.