DOI: 10.5061/dryad.2z34tmpzj
title: Data from: Cloacal microbial diversity is associated with competitive phenotypes in socially polyandrous jacanas

description: 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.
description: # Data from: Cloacal microbial diversity is associated with 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