DOI: 10.5061/dryad.qrfj6q5k2
title: Phylogenies related to: Codiversification of gut microbiota with humans

description: The gut microbiomes of human populations worldwide have many core
 microbial species in common. However, within a species, some strains can
 show remarkable population specificity. The question is whether such
 specificity arises from a shared evolutionary history (codiversification)
 between humans and their microbes. To test for codiversification of host
 and microbiota, we analyzed paired gut metagenomes and human genomes for
 1225 individuals in Europe, Asia, and Africa, including mothers and their
 children.  Between and within countries, signals of
 codiversification were evident for humans and their gut microbes.
 Moreover, species displaying the strongest codiversification independently
 evolved traits characteristic of host dependency, including reduced
 genomes, and oxygen and temperature sensitivity. These findings all point
 to the importance of understanding the potential role of
 population-specific microbial strains in microbiome-mediated disease
 phenotypes.
description: <strong>Microbial phylogenies</strong>: We created
 microbial phylogenies from adult and child metagenomes using StrainPhlAn
 v3.0. First, we picked the top 100 prevalent taxa in metagenomic samples
 of adults (n=839) and children (n=386) using MetaPhlAn3 (v3.0.1) using the
 following parameters (--tax_lev a --min_cu_len 2000). The taxonomy is
 based on NCBI. Next, we used StrainPhlan3 to generate microbial
 phylogenies using the following parameters: samples2markers.py
 (--breadth_threshold 80) and strainphlan.py (--phylophlan_mode accurate
 --marker_in_n_samples 10 --sample_with_n_markers 10). To allow for
 between-population comparisons, we selected taxa in adults that represent
 a total of ≥ 100 individuals, ≥ 10 individuals each from major human
 grouping; Africa (Cameroon and Gabon), Asia (Korea and Vietnam), and
 Europe (Germany and UK) and ≥ 1 individual per country, which resulted in
 59 taxa. For child samples, we picked the top 20 taxa that had the largest
 trees due to the smaller sample size. See paper for more
 details. <strong>Human host
 phylogeny</strong>: We created 100 maximum likelihood trees in SNPhylo (version 20180901) including 839 individuals using 20,506 SNPs, which were further filtered to remove uninformative SNPs based on the following parameters (ld_threshold = 0.1, maf_threshold = 0.05, and missing_rate = 0.1). This resulted in around 9,000 SNPs to create the host phylogeny (each bootstrapped tree uses a slightly different number of SNPs). We picked the best tree out of the 100 trees based on the maximum likelihood score and plotted the bootstrap value. <strong>Association file: </strong>Associating IDs in each file.  <strong>Description of files</strong>: - Maximum likelihood phylogenies of 59 microbial taxa in adults with bootstrap support: .tre file names start with "Adult_RAxML_bipartitions." followed by taxa name.  - Alignment files for 20 microbial taxa in adults: .aln file names start with "Adult_alignment_" followed by taxa name. - Maximum likelihood phylogenies of 20 microbial taxa in children with bootstrap support: .tre file names start with "Child_RAxML_bipartitions." followed by taxa name.  - Alignment files for 20 microbial taxa in children: .aln file names start with "Child_alignment_" followed by taxa name. - Maximum likelihood phylogenies of human hosts with bootstrap support: HostTree.tre - Alignment file for the human host phylogeny: HostTree_alignment.fasta - Association file: ID_table_n839.txt
description: Any tree-viewing software (iTOL, FigTree, etc.) would be able to
 open and view the tree files (.tre). Any text-viewing
 software (BBEdit, etc.) would be able to open and view the alignment files
 (.aln and .fasta).