Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes Cristian Can˜ estro, Julian M. Catchen, Adriana Rodrı´guez-Mar´ı, Hayato Yokoi, John H. Postlethwait* Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America Abstract Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage- specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss. Citation: Can˜ estro C, Catchen JM, Rodr´ıguez-Mar´ı A, Yokoi H, Postlethwait JH (2009) Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes. PLoS Genet 5(5): e1000496. doi:10.1371/journal.pgen.1000496 Editor: Takashi Gojobori, National Institute of Genetics, Japan Received March 2, 2009; Accepted April 27, 2009; Published May 29, 2009 Copyright: 2009 Ca n˜estro et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by grant IOB-0719577 from the National Science Foundation (NSF) and grant R01RR020833 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: jpostle@uoneuro.uoregon.edu Introduction Understanding the evolution of gene functions during verte- brate evolution is important for the proper interpretation of comparative analyses, especially when using model organisms to understand human gene functions. Gene duplication has been proposed to facilitate the evolution of gene functions [1], and the mechanisms of neofunctionalization and subfunctionalization may play a role [1–3] (reviewed in [4]). Human gene families show the signatures of two rounds of whole genome duplication (R1 and R2) that occurred during early vertebrate evolution [1,5–14] (but see [15]). Mutations in gene copies that arose in these R1 and R2 events often cause related diseases (for example, osteogenesis imperfecta (COL1A1) and spondyloepiphyseal dysplasia (COL2A1), bullous erythroderma ichthyosiformis (KRT1) and epidermolysis bullosa (KRT5), and syndactyly type II (HOXD13) and hand-foot- uterus syndrome (HOXA13)). Comparative analysis shows that fish genomes have two co-orthologs for many human genes as a result of a third round of genome duplication (R3) that occurred at the base of the teleost radiation [16–28]. Early on, S. Ohno [1] recognized the relevance of increased genetic diversity after genome duplication, and in his honor, gene duplicates originated by genome duplication are called ‘‘ohnologs’’ [29]. This term is useful because of the special properties that ohnologs possess at their birth compared to duplications that arise by other mechanisms such as unequal crossing-over, tandem gene duplica- tion, or retrotransposition. While many studies focus on how gene duplications can facilitate the acquisition of evolutionary innovations during vertebrate evolution, less attention has been focused on the evolutionary impact of lineage-specific gene losses. Differential ohnolog loss is important because it decreases genetic diversity within a species but increases genetic diversity between species. Loss of one copy of a pair of fully redundant gene duplicates should not usually have significant impact, but duplicate loss after functional divergence can have evolutionary consequences. Reciprocal paralog loss in different lineages can affect a species’ biology, decrease evolvability, and diminish adaptability to changing environments [30–34]. In other cases, gene loss can be adaptive, and thus relevant for a species’ evolution, perhaps even PLoS Genetics | www.plosgenetics.org 1 May 2009 | Volume 5 | Issue 5 | e1000496