DOI: 10.5281/zenodo.10575034
title: Linking diet switching to reproductive performance across populations of two Critically Endangered mammalian herbivores

description: Data associated with Harvey Sky, N., Britnell, J., Antwis, R. et al. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 7, 333 (2024). https://doi.org/10.1038/s42003-024-05983-3

The data deposited here includes raw metabarcoding output fasta files and some processed metabarcoding and sample data in xslx files. We include a more detailed description of each file below.

Data regarding Kenyan black rhino and Grevy’s zebra are treated as sensitive and confidential. There are therefore restrictions on the data that we can make available. Due to these confidentiality considerations, the sample data stored here does not include locations of sample collection within each reserve for either species, or the identity or breeding data for black rhino. It also only includes the final processed values for NDVI and rainfall. The remote sensing data is available from the repositories cited in the methods, but we cannot provide the shapefiles or other data used to calculate the final values for each sample. 

Raw fasta files_plants.zip

A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of dietary plants in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads. 

Raw fasta files_bacteria.zip

A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of microbiome bateria in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads. 

Sample data and processed metabarcoding data_Black rhino.xlsx

Sample data tab

The data that we are able to share that is associated with each black rhino sample.

SampleID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files. 

IndividualID - We are not able to share rhino names or other identifiers, but we have given each individual a unique number so that it can be seen which samples came from the same individuals. 

NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article. 

Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article. 

Season - Post is the post-rain sampling season June-July 2018. Pre is the pre-rain sampling season January-March 2019. 

Reserve - The reserve that the sample was collected on. 

Date - The date of sample collection. 

Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.

Poaceae, Fabaceae, Ebenaceae - The relative abundance of each of these three dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.

Bacteria numbers of reads

The number of reads assigned to each bacterial ASV found in each sample. 

Bacteria sequences and reads

The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article. 

Plant numbers of reads

The number of reads assigned to each dietary plant ASV found in each sample. 

Plant sequences and reads

The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article. 

 

Sample data and processed metabarcoding data_Grevy's zebra.xlsx

Sample data tab

The data that we are able to share that is associated with each Grevy's zebra sample.

Sample ID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files. 

NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article. 

Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article. 

Reserve - The reserve that the sample was collected on. 

Season - Post is the post-rain sampling season July-August 2018. Pre is the pre-rain sampling season January-February 2019. 

Date - The date of sample collection. 

Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. 

Poaceae, Fabaceae - The relative abundance of each of these two dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.

Indigofera - The relative abundance of each of this Fabaceae genus was included in our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding.

Bacteria numbers of reads

The number of reads assigned to each bacterial ASV found in each sample. 

Bacteria sequences and reads

The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article.  

Plant numbers of reads

The number of reads assigned to each dietary plant ASV found in each sample. 

Plant sequences and reads

The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article.