Clustering with UniFrac. (A) Schematic showing how clustering is performed, adapted from (). The circles, squares, and triangles represent sequences from three different communities. The UniFrac value is calculated for all pairs of communities, and the resulting distance matrix can be used to cluster the samples using Principal Coordinates Analysis (PCoA) or hierarchical clustering. (B) The results of hierarchical clustering and jackknifing of cecal microbial communities from three mother mice (MOTHER1-3) and their offspring (M1-, M2A-, M2B-, and M3) with unweighted UniFrac (Adapted from (, )). Genotypes are *ob/ob* for homozygotes for the mutant leptin allele that confers obesity, *ob/+* for heterozygotes, and +/+ for wild-types. The percentage support for nodes supported at least 70% of the time with sequence jackknifing with a maximum of 200 sequences from each mouse for 100 replicates is indicated. The main clustering is by mother. (C) Plot of the first 2 principal coordinates axes for PCoA with unweighted UniFrac. Symbols represent individual animals. The rectangles highlight the family of Mother 2 (open symbols), and the families of Mothers 1 and 3 (grey and black symbols), who are sisters.

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