Gene Loss and Evolution of Surviving Paralogs Figure 2. Paralogous syntenic conservation among ALDH1A genomic neighborhoods (GN) in the human genome. (A) Composite dotplot representing the distribution of paralogs of genes (black dots) within a 10 Mb-window surrounding each member of the ALDH1A family throughout the human genome (red crosses: ALDH1A-neighbor paralogs; dark blue crosses: ALDH1A2-neighbor paralogs, and light-green crosses: ALDH1A3-neighbor paralogs. The genomes of Ciona intestinalis and Branchiostoma floridae, which represent urochordates and cephalochordates, respectively, the two closest vertebrate relatives [66,110], were used as outgroups to define paralogy groups in the human genome. Gene accession numbers and genomic information for each group of paralogy represented in the dotplot is provided in Table S1. Human chromosomes are represented in the y-axis, and drawn to scale in the x-axis with the p-terminus of each chromosome at the left and the q-terminus at the right of each white row. Chromosomal regions that appear enriched in Aldh1a-neighbor paralogs are indicated with colored boxes, highlighted in pink if ALDH1A genes are present, and in yellow if no ALDH1A genes are present. The distribution of paralogs of genes located in the yellow boxes is also represented PLoS Genetics | www.plosgenetics.org 5 May 2009 | Volume 5 | Issue 5 | e1000496