Cloacal microbial diversity is associated with competitive phenotypes in socially polyandrous jacanas

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 hypothesize..., , # 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
* t...,