DOI: 10.5061/dryad.0rxwdbs7c
title: Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi)

description: The composition of mammalian gut microbiomes is highly conserved within
 species, yet the mechanisms by which microbiome composition is transmitted
 and maintained within lineages of wild animals remain unclear. Mutually
 compatible hypotheses exist, including that microbiome fidelity results
 from inherited dietary habits, shared environmental exposure,
 morphophysiological filtering, and/or maternal effects. Interspecific
 hybrids are a promising system in which to interrogate the determinants of
 microbiome composition because hybrids can decouple traits and processes
 that are otherwise co-inherited in their parent species. We used a
 population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya
 to evaluate the roles of these four mechanisms in regulating microbiome
 composition. We analyzed fecal DNA for both the trnL-P6 and the 16S rRNA
 V4 region to characterize the diets and microbiomes of the hybrid zebra
 and of their parent species, plains zebra (E. quagga) and Grevy’s zebra
 (E. grevyi). We found that both diet and microbiome composition clustered
 by species, and that hybrid diets and microbiomes were largely nested
 within those of the maternal species, plains zebra. Hybrid microbiomes
 were less variable than those of either parent species where they
 co-occurred. Diet and microbiome composition were strongly correlated,
 although the strength of this correlation varied between species. These
 patterns are most consistent with the maternal-effects hypothesis,
 somewhat consistent with the diet hypothesis, and largely inconsistent
 with the environmental-sourcing and morphophysiological-filtering
 hypotheses. Maternal transmittance likely operates in conjunction with
 inherited feeding habits to conserve microbiome composition within
 species.
description: Fecal samples from free-ranging zebra were collected from
 Laikipia County in January 2020. DNA was extracted from fecal samples and
 the plant and bacterial components were sequenced to characterize diet and
 microbiome composition respectively. Diet sequence data were curated using
 the OBITOOLS v2 package, while microbiome sequence data were processed
 using the DADA2 v1.18 big data pipeline, implemented in R
 v4.0.2.
description: This 'README_file_Hybrid_zebra_microbiomes.txt' file was
 generated on 2024-01-22 by JOEL O. ABRAHAM GENERAL INFORMATION 1. Title of
 Dataset: Determinants of microbiome composition: insights from
 free-ranging hybrid zebras (Equus quagga × grevyi) 2. Author Information
 A. Principal Investigator Contact Information Name: Joel O. Abraham
 Institution: Princeton University Email: B.
 Associate or Co-investigator Contact Information Name: Daniel I.
 Rubenstein Institution: Princeton University Email:
 3. Date of data collection (approximate):
 2020-01-08 to 2020-01-17 4. Geographic location of data collection:
 Laikipia County, Kenya 5. Information about funding sources that supported
 the collection of the data: NSF DEB-2225088 and the High Meadows
 Environmental Institute at Princeton University. Joel O. Abraham is
 supported by the NSF Graduate Research Fellowship (Fellow ID: 2019256075).
 ## SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data:
 None. 2. Links to publications that cite or use the data: TBD 3. Links to
 other publicly accessible locations of the data: TBD 4.
 Links/relationships to ancillary data sets: NA 5. Was data derived from
 another source? NO 6. Recommended citation for this dataset: Abraham,
 J.O., Lin, B., Miller, A.E., Henry, L.P., Demmel, M.Y., Warungu, R.,
 Mwangi, M., Lobura, P.M., Pallares, L.F., Ayroles, J.F, Pringle, R.M,
 Rubenstein, D.I. (2024). Determinants of microbiome composition: insights
 from free-ranging hybrid zebras (Equus quagga × grevyi). Dryad, Dataset,
 ## DATA & FILE OVERVIEW 1. File List:
 README_file_Hybird_zebra_microbiomes.txt: README file explaining how the
 dataset was generated and the data contained in the dataset
 Sample_metadata.text: File containing the sample metadata
 Hybrid_zebra_diet_forward_reads.fastq: Raw sequence data (forward reads
 for diet data) Hybrid_zebra_diet_reverse_reads.fastq: Raw sequence data
 (reverse reads for diet data) Hybrid_zebra_microbiome_forward_reads.fastq:
 Raw sequence data (forward reads for microbiome data)
 Hybrid_zebra_microbiome_reverse_reads.fastq: Raw sequence data (reverse
 reads for microbiome data) Diet_composition_data.txt: Relative read
 abundances of plant mOTUs in zebra fecal samples (post-filtering)
 Microbiome_composition_data.csv: Rarefied abundances of bacterial ASVs in
 zebra fecal samples (post-filtering) Bacterial_taxonomy.csv: Taxonomic
 information for all bacterial ASVs in zebra microbiomes
 Bacterial_phylogeny.nwk: Phylogenetic tree of bacterial ASVs in zebra
 microbiomes Hybrid zebra microbiome analyses.R: R script for analyzing
 data and generating visualizations. ### METHODOLOGICAL INFORMATION 1.
 Description of methods used for collection/generation of data: Fecal
 samples from free-ranging zebra were collected from Laikipia County in
 January 2020. DNA was extracted from fecal samples and the plant and
 bacterial components were sequenced to characterize diet and microbiome
 composition respectively. 2. Methods for processing the data: Diet
 sequence data were curated using the OBITOOLS v2 package, while microbiome
 sequence data were processed using the DADA2 v1.18 big data pipeline,
 implemented in R v4.0.2. 3. Instrument- or software-specific information
 needed to interpret the data: R is necessary to run the R script file. The
 R script was written in R v4.0.2. 4. Standards and calibration
 information, if appropriate: NA 5. Environmental/experimental conditions:
 NA 6. Describe any quality-assurance procedures performed on the data: NA
 7. People involved with sample collection, processing, analysis and/or
 submission: Joel O. Abraham, Bing Lin, Audrey E. Miller, Lucas P. Henry,
 Margaret Y. Demmel, Rosemary Warungu, Margaret Mwangi, Patrick M. Lobura,
 Luisa F. Pallares, Julien F. Ayroles, Robert M. Pringle, Daniel I.
 Rubenstein AEM and BL conceived of the project and designed the sampling
 approach, with input from DIR and JFA. AEM and BL led fecal sampling in
 the field, with help from RW, MM, and PML to find and identify hybrids.
 JOA, AEM, and BL performed lab work, with technical advice from LFP, LPH,
 and MYD. Lab work was conducted at the Mpala genomics facility in Kenya
 and at RMP’s laboratory at Princeton University. JOA led bioinformatics
 and data analyses, with input from LPH and MYD. #### DATA-SPECIFIC
 INFORMATION FOR: Sample\_metadata.text 1. Number of variables: 12 2.
 Number of cases/rows: 91 3. Variable List: sample_number: A unique number
 assigned to each sample for indexing purposes sample_ID: A unique ID
 assigned to each sample; corresponds to columns headers in
 'Diet_composition_data.txt' and
 'Microbiome_composition_data.csv' location: Reserve on which a
 given sample was collected; 'OLP' corresponds to Ol Pejeta (main
 area of the park); 'OLP-R' corresponds to Ol Pejeta (fenced-off
 reserve); 'MPA' corresponds to Mpala; 'OLJ'
 corresponds to Ol Jogi latitude: Latitude at which the sample was
 collected longitude: Longitude at which the sample was collected status:
 Whether the sample was collected from the same reserve where hybrid zebra
 occur ('SYM' for sympatric) or a different reserve
 ('ALL' for allopatric) species: The zebra species from which the
 sample was collected ('PL' is plains zebra, 'GR' is
 Grevy's zebra, and 'HY' is hybrid zebra) pop: The
 subpopulation from which the sample was collected ('sym_hyb' is
 Ol Pejeta hybrids, 'sym_dad' is Ol Pejeta Grevy's,
 'sym_mom' is Ol Pejeta plains, 'all_dad' is Mpala/Ol
 Jogi Grevy's, 'all_mom' is Mpala/Ol Jogi plains) sex: The
 sex of the zebra from which the sample was collected ('M' is
 male, 'F' is female) age: The age category of the zebra from
 which the sample was collected ('AD' is adult, 'JU' is
 juvenile) group_size: Size of the group that the zebra from which the
 sample was collected was observed in date: The time each sample was
 collected 4. Missing data codes: 'NA' 5. Specialized formats or
 other abbreviations used: NA #### DATA-SPECIFIC INFORMATION FOR:
 Diet\_composition\_data.txt 1. Number of variables: 19 2. Number of
 cases/rows: 144 3. Variable List: id: Unique ID assigned to each plant
 mOTU best_identity_MRC: Percent sequence match with best match in local
 reference library best_identity_GDB: Percent sequence match with best
 match in global reference library best_match_MRC: Barcode reference ID in
 the local reference library that best matches the mOTU sequence
 best_match_GDB: Barcode reference ID in the global reference library that
 best matches the mOTU sequence kingdom_name_ok: The kingdom assigned to
 the plant mOTU by comparing to the two reference libraries (always
 Viridiplantae) phylum_name_ok: The phylum assigned to the plant mOTU by
 comparing to the two reference libraries (always Streptophyta)
 class_name_ok: The class assigned to the plant mOTU by comparing to the
 two reference libraries order_name_ok: The order assigned to the plant
 mOTU by comparing to the two reference libraries (if available)
 family_name_ok: The family assigned to the plant mOTU by comparing to the
 two reference libraries (if available) genus_name_ok: The genus assigned
 to the plant mOTU by comparing to the two reference libraries (if
 available) species_name_ok: The species name assigned to the plant mOTU by
 comparing to the two reference libraries (if available) scientific_name
 rank: The finest taxonomic rank available for each plant mOTU
 species_list_MRC: The list of species matched to each plant mOTU from the
 local reference library species_list_GDB: The list of species matched to
 each plant mOTU from the global reference library sci_name_ok: The finest
 resolution taxonomic categorization of each plant mOTU sci_name_plot: The
 taxonomic categorization of each plant mOTU used for visualization
 purposes sequence: The DNA sequence corresponding to each plant mOTU
 Occurence: The number of samples each plant mOTU occurred in (note that
 samples were sequenced in triplicate so occurence values are inflated by a
 factor of three) Note: columns 20-105 are the relative read abundances of
 each plant mOTU in each sample 4. Missing data codes: 'NA' 5.
 Specialized formats or other abbreviations used: NA #### DATA-SPECIFIC
 INFORMATION FOR: Microbiome\_composition\_data.csv 1. Number of variables:
 2892 2. Number of cases/rows: 84 3. Variable List: Each contains the read
 count (averaged across all three replicates) of a particular bacterial ASV
 in a given sample (post-rarefaction); each row is a sample, each column is
 a bacterial ASV. The taxonomic information for each bacterial ASV can be
 found in the file 'Bacterial_taxonomy.csv' 4. Missing data
 codes: 'NA' 5. Specialized formats or other abbreviations used:
 NA #### DATA-SPECIFIC INFORMATION FOR: Bacterial\_taxonomy.csv 1. Number
 of variables: 19 2. Number of cases/rows: 2892 3. Variable List: Kingdom:
 The kingdom assigned to the bacterial ASV (always Bacteria) Phylum: The
 phylum assigned to the bacterial ASV (if available) Class: The class
 assigned to the bacterial ASV (if available) Order: The order assigned to
 the bacterial ASV (if available) Family: The family assigned to the
 bacterial ASV (if available) Genus: The genus assigned to the bacterial
 ASV (if available) Species: The species name assigned to the bacterial ASV
 (if available) sequence: The DNA sequence corresponding to each bacterial
 ASV 4. Missing data codes: 'NA' 5. Specialized formats or other
 abbreviations used: NA