Data from: Cloacal microbial diversity is associated with competitive phenotypes in socially polyandrous jacanas
Data files
Aug 04, 2025 version files 837.18 KB
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jacana_micro_GitHub_R2.R
20.50 KB
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jacana.microbiome.alpha.correlations.R
6.38 KB
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manifest_jacana.txt
3.37 KB
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metadata_jacana_micro.csv
12.63 KB
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qiime2_jacana_micro_GitHub_R1.rtf
7.58 KB
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README.md
1.81 KB
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taxonomy.csv
361.88 KB
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tree.nwk
150.76 KB
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unrarefied_ASV_table.csv
272.26 KB
Abstract
The composition of host-associated microbial communities may correlate with the overall status of the host, including physiology and fitness. New bi-directional hypotheses suggest that sexual behaviors can shape, and be shaped by reproductive microbiomes, which may be particularly important for species with mating systems that feature strong sexual selection. These dynamics have been particularly understudied in female animals. Using 16S rRNA sequencing, we compared the cloacal microbiome of females and males from two socially polyandrous bird species that vary in the strength of sexual selection, Jacana spinosa (Northern Jacana) and J. jacana (Wattled Jacana). We hypothesized that the strength of sexual selection would shape cloacal microbial diversity, such that the more polyandrous J. spinosa would have a more diverse microbiome, and that microbiomes would be more diverse in females than in males. If the reproductive microbiome is indicative of competitive status, we also hypothesized that cloacal microbial diversity would be associated with competitive traits, including plasma testosterone levels, body mass, or weaponry. We found no differences in microbial alpha diversity between species or sexes, but we did find that microbial beta diversity significantly differed between species. We also found a positive relationship between microbial alpha diversity and testosterone in female J. spinosa. Future experiments are needed to explore the potential drivers of correlations between the cloacal microbiome and competitive phenotypes in socially polyandrous jacanas.
Analysis scripts for Houtz, Acosta, Berlow, Lipshutz 2025. A brief description of the purpose of each script is outlined here. Scripts were run in R v4.
jacana.microbiome.alpha.correlations.R - script to analyze and visualize correlations between competitive traits and alpha diversity
jacana_micro_GitHub_R2.R - R script to analyze and visualize microbiome data, including alpha and beta diversity
manifest_jacana.txt - link sample names with sequenced read file names
metadata_jacana_micro.csv - metadata file containing:
- sample name (NO = Northern Jacana / J. spinosa, WA = Wattled Jacana / J. jacana, F = female, M = male)
- 3 alpha diversity indices (Chao1, Shannon, Faith's PD)
- sample/control information
- date of DNA extraction (day-month-year)
- quant_reading = DNA concentration (ng/ml)
- date of PCR (day-month-year)
- sex
- species
- site in Panama
- type of collection (delayed, immediate, without aggression assay)
- breeding_notes = breeding status (bp = brood patch)
- breeding stage
- sperm length (µm)
- average testes length (mm)
- average testes width (mm)
- gonad mass (oz)
- body mass (g)
- facial shield length (mm)
- facial shield width (mm)
- wattle length (mm)
- bill length (mm)
- bill width (mm)
- bill depth (mm)
- tarsus length (mm)
- wing length (mm)
- average wing spur (mm)
- testosterone (ng/uL)
- log testosterone
- description of issues
- NA = not applicable; missing data
qiime2_jacana_micro_GitHub_R1.rtf - QIIME script
taxonomy.csv - taxonomy file, exported from QIIME2 for use in R
tree.nwk - phylogenetic tree, exported from QIIME2 for use in R
unrarefied_ASV_table.csv - ASV table, exported from QIIME2 for use in R
