The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional evolution or speciation are still incompletely characterized. Fish genomes provide an ideal context in which to examine the consequences of WGD, because the teleost lineage experienced an additional WGD soon after divergence from tetrapods and because five teleost genomes are available for comparative analysis. Here we present an integrated approach to characterize these post-duplication genomes based on genome-scale synteny, phylogenetic, temporal, and spatial gene expression and on protein sequence data. A minimum of 3%–4% of protein-coding loci have been retained in two copies in each of the five fish genomes, and many of these duplicates are key developmental genes that function as transcription factors or signaling molecules. Almost all duplicate gene pairs we examined have diverged in spatial and/or temporal expression during embryogenesis. A quarter of duplicate pairs have diverged in function via the acquisition of novel protein domains or via changes in the subcellular localization of their encoded proteins. We compared the spatial expression and protein domain architecture of zebrafish WGD-duplicates to those of their single mouse ortholog and found many examples supporting a model of neofunctionalization. WGD-duplicates have acquired novel protein domains more often than have single-copy genes. Post-WGD changes at the gene regulatory level were more common than changes at the protein level. We conclude that the most significant consequence of WGD for vertebrate evolution has been to enable more-specialized regulatory control of development via the acquisition of novel spatiotemporal expression domains. We find limited evidence that reciprocal gene loss led to reproductive isolation and speciation in this lineage.

The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α2β2). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.

Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest lineage of teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and teleostean fish species, including spotted gar, zebrafish and medaka (the PhyloFish project), offered a unique opportunity to study the evolution of gene expression following TGD in teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e. prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two ‘similar’ copies occurred not only before, but also after the radiation of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.

The adaptive immune system (AIS) mediated by T cells and B cells arose ~450 million years ago in a common ancestor of jawed vertebrates. This system was so successful that, once established, it has been maintained in all classes of jawed vertebrates with only minor modifications. One event thought to have contributed to the emergence of this form of AIS is two rounds of whole-genome duplication. This event enabled jawed vertebrate ancestors to acquire many paralogous genes, known as ohnologs, with essential roles in T cell and B cell immunity. Ohnologs encode the key components of the antigen presentation machinery and signal transduction pathway for lymphocyte activation as well as numerous transcription factors important for lymphocyte development. Recently, it has been discovered that jawless vertebrates have developed an AIS employing antigen receptors unrelated to T/B cell receptors, but with marked overall similarities to the AIS of jawed vertebrates. Emerging evidence suggests that a common ancestor of all vertebrates was equipped with T-lymphoid and B-lymphoid lineages.

Genomic transformations during early vertebrate evolution, including two rounds of whole-genome duplication, laid the groundwork for the emergence of novel morphological features in jawed vertebrates. Among these innovations, paired appendages represent a major evolutionary milestone, whose development and diversification enabled vertebrates to exploit diverse ecological niches in aquatic, terrestrial, and aerial environments. Here, we combined phylogenetic and local genomic synteny analyses to investigate the evolutionary history of chordin-like homologs in vertebrates. Our results indicate that chordin-like1 first appeared in jawed vertebrates, suggesting a possible link between its origin and the emergence of paired appendages. To explore this hypothesis, we examined chordin-like1 expression in representatives of basal jawed vertebrate lineages - cartilaginous fishes (grey catshark, Chiloscyllium griseum) and sturgeons (sterlet, Acipenser ruthenus). We further assessed the expression and functional properties of the chordin-like1 ortholog in the African clawed frog (Xenopus laevis), a representative terrestrial vertebrate with limb morphology that markedly differs from the fins of basal gnathostomes. Together with published data, our findings support a potential role for chordin-like1 in the evolution of paired appendages. In particular, chordin-like1 may have contributed to the development of the metapterygial element and its derivatives, which formed the structural basis

found in jawed fish (cladistically including mammals). Most elements of the jawed fish system are in place thanks to the second round of whole-genome duplication The adaptive immune system (AIS), also known as the acquired immune system or specific immune system, is a subsystem of the immune system that is composed of specialized cells, organs, and processes that eliminate pathogens specifically. The acquired immune system is one of the two main immunity strategies found in vertebrates (the other being the innate immune system). Like the innate system, the The adaptive immune system… Primitive jawless vertebrates, such as the lamprey and hagfish, have an adaptive immune system that shows 3 different cell lineages, each sharing a common origin with B cells, αβ T cells, and innate-like γΔ T cells. Instead of the classical antibodies and T cell receptors, these animals possess a large array of molecules called variable lymphocyte receptors (VLRs for short) that, like the antigen receptors of jawed vertebrates, are produced from only a small number (one or two) of genes. These molecules are believed to bind pathogenic antigens in a similar way to antibodies, and with the same degree of specificity. The jawless fish are vertebrates like the jawed fish, but belong on a different branch. In jawless fish, three subsets of lymphocytes use variable lymphocyte receptors (VLRs) for antigen binding. The VLRs are derived from pattern recognition receptors (PRRs) of the innate immune system. Diversity is generated by a cytosine deaminase-mediated rearrangement of LRR-based DNA segments. The functional dichotomy between two of the lymphocyte subsets parallels Ig and TCR molecules.

bitterness evolved in the common ancestor of jawed vertebrates: the bitter taste receptor gene family TAS2R is limited to jaw vertebrates, a group that originated The sensation of bitterness evolved in the common ancestor of jawed vertebrates: the bitter taste receptor gene family TAS2R is limited to jaw vertebrates, a group that originated about 500 million years ago. The TAS2R gene cluster in tetrapods is massive compared to those in fishes, with great variation from species to species indicating a rich history of evolution. In tetrapods, TAS2R detect tox The sensation of bitterness evolved in the common ancestor of jawed vertebrates: the bitter taste receptor gene family TAS2R is limited to jaw vertebrates, a group that originated about 500 million years ago. The TAS2R gene cluster in tetrapods is massive compared to those in fishes, with great variation from species to species indicating a rich history of evolution. In tetrapods, TAS2R detect toxins, mostly of a plant origin, as a bitter taste. Expansion of the gene cluster via gene duplication allows variants to arise, potentially leading to the detection of more types of toxins. As a result, TAS2R expansion usually coincides with changes in a species' diet. The TAS2R cluster has been well characterized in humans and several common laboratory animals such as primates and mice. In humans, the family contains 25 functional loci as well as 11 pseudogenes. The current human genetic diversity in this cluster indicates ongoing evolution. It also tells a story about changes in hominid diets with a shift to foods that are less likely to contain bitter toxins.