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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Mol. Biosci.</journal-id>
<journal-title>Frontiers in Molecular Biosciences</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Mol. Biosci.</abbrev-journal-title>
<issn pub-type="epub">2296-889X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fmolb.2017.00081</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Molecular Biosciences</subject>
<subj-group>
<subject>Mini Review</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>A Matter of Taste: Lineage-Specific Loss of Function of Taste Receptor Genes in Vertebrates</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Antinucci</surname> <given-names>Marco</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Risso</surname> <given-names>Davide</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/459603/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Biology, University of Pisa</institution>, <addr-line>Pisa</addr-line>, <country>Italy</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Genome Sciences, University of Washington School of Medicine</institution>, <addr-line>Seattle, WA</addr-line>, <country>United States</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Piero Andrea Temussi, University of Naples Federico II, Italy</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Fred Robert Naider, College of Staten Island, United States; Doriano Lamba, Consiglio Nazionale Delle Ricerche (CNR), Italy</p></fn>
<fn fn-type="corresp" id="fn001"><p>&#x0002A;Correspondence: Davide Risso <email>daviderix&#x00040;gmail.com</email></p></fn>
<fn fn-type="other" id="fn002"><p>This article was submitted to Structural Biology, a section of the journal Frontiers in Molecular Biosciences</p></fn></author-notes>
<pub-date pub-type="epub">
<day>28</day>
<month>11</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection">
<year>2017</year>
</pub-date>
<volume>4</volume>
<elocation-id>81</elocation-id>
<history>
<date date-type="received">
<day>12</day>
<month>07</month>
<year>2017</year>
</date>
<date date-type="accepted">
<day>13</day>
<month>11</month>
<year>2017</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2017 Antinucci and Risso.</copyright-statement>
<copyright-year>2017</copyright-year>
<copyright-holder>Antinucci and Risso</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>Vertebrates can perceive at least five different taste qualities, each of which is thought to have a specific role in the evolution of different species. The avoidance of potentially poisonous foods, which are generally bitter or sour tasting, and the search for more nutritious ones, those with high-fat and high-sugar content, are two of the most well-known examples. The study of taste genes encoding receptors that recognize ligands triggering taste sensations has helped to reconstruct several evolutionary adaptations to dietary changes. In addition, an increasing number of studies have focused on pseudogenes, genomic DNA sequences that have traditionally been considered defunct relatives of functional genes mostly because of the presence of deleterious mutations interrupting their open reading frames. The study of taste receptor pseudogenes has helped to shed light on how the evolutionary history of taste in vertebrates has been the result of a succession of gene gain and loss processes. This dynamic role in evolution has been explained by the &#x0201C;less-is-more&#x0201D; hypothesis, suggesting gene loss as a mechanism of evolutionary change in response to a dietary shift. This mini-review aims at depicting the major lineage-specific loss of function of taste receptor genes in vertebrates, stressing their evolutionary importance and recapitulating signatures of natural selection and their correlations with food habits.</p>
</abstract>
<kwd-group>
<kwd><italic>Tas2Rs</italic></kwd>
<kwd><italic>TAS1Rs</italic></kwd>
<kwd>pseudogenes</kwd>
<kwd>sweet taste receptors</kwd>
<kwd>bitter taste receptors</kwd>
<kwd>umami taste receptors</kwd>
</kwd-group>
<contract-sponsor id="cn001">University of Washington<named-content content-type="fundref-id">10.13039/100007812</named-content></contract-sponsor>
<counts>
<fig-count count="1"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="73"/>
<page-count count="8"/>
<word-count count="6319"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="s1">
<title>Introduction</title>
<p>Pseudogenes have historically been considered genomic fossils and junk DNA, because of their classic definition of non-functional sequences of genomic DNA, originally derived from functional genes, but containing mutations or lacking promoter sequences precluding their expression (Wilde, <xref ref-type="bibr" rid="B65">1986</xref>; Balakirev and Ayala, <xref ref-type="bibr" rid="B3">2003</xref>). However, an increasing number of studies have shown how some pseudogenes have a function regulating gene expression (Pink et al., <xref ref-type="bibr" rid="B49">2011</xref>), or being transcribed into RNA (Frankish and Harrow, <xref ref-type="bibr" rid="B19">2014</xref>). Multiple studies also highlighted how pseudogenes have had a remarkable functional plasticity and a dynamic role in species&#x00027; evolution (Bekpen et al., <xref ref-type="bibr" rid="B8">2009</xref>; Korrodi-Greg&#x000F3;rio et al., <xref ref-type="bibr" rid="B35">2013</xref>; Risso et al., <xref ref-type="bibr" rid="B52">2014</xref>): chemosensory genes, in particular, have been characterized by a succession of birth-and-death processes in different lineages (Dong et al., <xref ref-type="bibr" rid="B14">2009a</xref>,<xref ref-type="bibr" rid="B15">b</xref>). The aim of this mini-review is to provide an integrative view of the evolutionary history of taste receptor genes, with a focus on the main gene losses that have occurred in different lineages, pinpointing the genetic and biological factors driving these episodes.</p>
</sec>
<sec id="s2">
<title>Evolution of taste receptors</title>
<p>Vertebrates can perceive at least five different taste qualities, each of which is thought to have evolved to face a challenge or play a specific role in species&#x00027; evolution. Bitter taste, for instance, likely occurred as a defensive and protective mechanism to prevent species from ingesting potentially toxic and dangerous foods. Conversely, sweet foods are naturally attractive and accepted, since sugars serve as the main energy source for animals. Umami senses amino acids in proteins representing the taste of monosodium glutamate, naturally-occurring in meats, vegetables and fermented products. Salty and sour taste are additional protective mechanisms aimed at assuring internal sodium or acid-base balance, respectively. Genes encoding taste receptors for different tastes, as depicted below, are highly diversified in terms of both inter- and intra-specific conservation and differences (Bachmanov et al., <xref ref-type="bibr" rid="B2">2014</xref>). Although most authors primarily focused on vertebrates, a few studies highlighted the presence of a large GPCR gene family in <italic>Drosophila</italic> named Gustatory Receptor (GR) which shows a differential expression in feeding-related tissues and confers a fine taste sensitivity to a broad range of alkaloids and other bitter compounds (Chapman et al., <xref ref-type="bibr" rid="B10">1991</xref>; Glendinning and Hills, <xref ref-type="bibr" rid="B21">1997</xref>; Clyne et al., <xref ref-type="bibr" rid="B13">2000</xref>).</p>
<sec>
<title>Bitter taste</title>
<p>Bitter taste is recognized by receptors encoded by the <italic>TAS2R</italic> gene family (Adler et al., <xref ref-type="bibr" rid="B1">2000</xref>). These genes are expressed in type II taste bud cells, lack introns, are relatively small (&#x0007E;1,000 bp) and have a short extracellular N-terminus. <italic>TAS2R</italic> products consist of G protein-coupled receptors (GPCRs), seven-transmembrane-domains-proteins that detect and signal neurotransmitters and hormones, among other stimuli. In particular, the binding of bitter compounds to <italic>TAS2R</italic> receptors activates heterometric GTP-binding proteins, consisting of a taste-selective G&#x003B1; subunit (i.e., &#x003B1;-gustducin) and its &#x003B2;&#x003B3; and &#x003B2;3&#x003B3;13 partners (McLaughlin et al., <xref ref-type="bibr" rid="B42">1992</xref>; Huang et al., <xref ref-type="bibr" rid="B29">1999</xref>). This initiates a phosphoinositide pathway that elevates cytoplasmic Ca<sup>2&#x0002B;</sup> and depolarizes the membrane via cation channels, resulting in the intracellular release of the taste bud transmitter ATP, which conveys signals through gustatory nerves to the brain (Chaudhari and Roper, <xref ref-type="bibr" rid="B11">2010</xref>). Studies on bitter perception highlighted a differential ability to detect the bitter molecule phenylthiocarbamide (PTC) showing that this trait is linked to two haplotypes on <italic>TAS2R38</italic> producing the two phenotypes &#x0201C;taster&#x0201D; and &#x0201C;nontaster&#x0201D; (Kim et al., <xref ref-type="bibr" rid="B34">2003</xref>). Further studies on the 3D structure of <italic>TAS2R38</italic> showed how PTC and its analogous molecule 6-n-propylthiouracile (PROP) can form hydrogen bounds in the transmembrane domain of the &#x0201C;taster&#x0201D; form while this bond is not formed in the &#x0201C;nontaster&#x0201D; one (Tan et al., <xref ref-type="bibr" rid="B60">2012</xref>). The number of <italic>TAS2R</italic> genes and pseudogenes varies greatly among different vertebrate species, spanning from 0 in the bottlenose dolphin to 52 in the western clawed frog (Figure <xref ref-type="fig" rid="F1">1</xref>). A notable interspecific variation can be observed when comparing different classes of animals: mammals (<italic>n</italic> &#x0003D; 3&#x02013;34) and reptiles (<italic>n</italic> &#x0003D; 3&#x02013;10) for example, have a higher number of pseudogenes when compared to birds (<italic>n</italic> &#x0003D; 0&#x02013;3) and fishes (<italic>n</italic> &#x0003D; 0). The limited amount of studies analyzing the <italic>TAS2R</italic> genes repertoire in amphibians precludes the possibility of making general considerations on this group. Further studies analyzing multiple amphibian species are therefore necessary to better comprehend the evolutionary history of these genes. Similarly, the number of functional <italic>TAS2Rs</italic> differs among different classes: <italic>n</italic> &#x0003D; 0&#x02013;37 in mammals, <italic>n</italic> &#x0003D; 0&#x02013;19 in birds, <italic>n</italic> &#x0003D; 52 in frogs, <italic>n</italic> &#x0003D; 1&#x02013;6 in fishes and <italic>n</italic> &#x0003D; 11&#x02013;39 in reptiles (Dong et al., <xref ref-type="bibr" rid="B14">2009a</xref>; Shi and Zhang, <xref ref-type="bibr" rid="B58">2009</xref>; Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref>; Li and Zhang, <xref ref-type="bibr" rid="B36">2013</xref>; Baldwin et al., <xref ref-type="bibr" rid="B4">2014</xref>; Wang and Zhao, <xref ref-type="bibr" rid="B63">2015</xref>; Liu et al., <xref ref-type="bibr" rid="B41">2016</xref>). Humans occupy an intermediate position, possessing 25 functional <italic>TAS2Rs</italic> and 11 pseudogenes mapping to chromosomes 5, 7, and 12 (Adler et al., <xref ref-type="bibr" rid="B1">2000</xref>; Go et al., <xref ref-type="bibr" rid="B23">2005</xref>). This remarkable variation of <italic>TAS2R</italic> repertoires among vertebrates has been explained by a birth-and-death model involving a complex evolution of this family, made of gene expansions, contractions, deletions, and duplications in different lineages in response to environmental changes (Shi et al., <xref ref-type="bibr" rid="B59">2003</xref>; Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref>; Go, <xref ref-type="bibr" rid="B22">2006</xref>; Roudnitzky et al., <xref ref-type="bibr" rid="B53">2016</xref>).</p>
<fig id="F1" position="float">
<label>Figure 1</label>
<caption><p>Distribution of bitter taste receptor genes (blue) and pseudogenes (green) (i.e., <italic>TAS2Rs</italic>) among different lineages. Data were taken from <xref ref-type="bibr" rid="B15">Dong et al. (2009b)</xref>, Shi and Zhang (<xref ref-type="bibr" rid="B58">2009</xref>); Jiang et al. (<xref ref-type="bibr" rid="B32">2012</xref>); Li and Zhang (<xref ref-type="bibr" rid="B36">2013</xref>); Wang and Zhao (<xref ref-type="bibr" rid="B63">2015</xref>), and Liu et al. (<xref ref-type="bibr" rid="B41">2016</xref>). When different references indicated different numbers of <italic>TAS2R</italic> genes, the highest estimate was considered.</p></caption>
<graphic xlink:href="fmolb-04-00081-g0001.tif"/>
</fig>
</sec>
<sec>
<title>Sweet and umami taste</title>
<p>Sweet and umami tastes are also recognized by GPCRs that activate a signal transduction cascade through &#x003B1;-gustducin. However, sweet and umami GPCRs are encoded by the <italic>TAS1R</italic> gene family, with genes bigger in size, containing introns and a large N-terminal extracellular domain (Chen et al., <xref ref-type="bibr" rid="B12">2009</xref>). This large extracellular domain is composed of two additional domains: a Venus Flytrap Domain and a cysteine-rich domain. The first is named after the carnivorous plant (i.e., <italic>Dionaea muscipula</italic>) as its structure can switch between open and closed conformations. The cysteine-rich domain links the first domain to the transmembrane ones and could facilitate the binding of allosteric proteins (Pin et al., <xref ref-type="bibr" rid="B48">2003</xref>). Both sweet and umami receptors are heterodimers formed by two members of the <italic>TAS1R</italic>s gene family: the receptor encoded by the combination of <italic>TAS1R1</italic>&#x0002B;<italic>TAS1R3</italic> genes senses umami compounds, while the one encoded by <italic>TAS1R2</italic>&#x0002B;<italic>TAS1R3</italic> is activated by sweet substances (Nelson et al., <xref ref-type="bibr" rid="B44">2001</xref>). A thorough research of the heterodimer <italic>TAS1R2</italic>&#x0002B;<italic>TAS1R3</italic>, showed how its combinations of closed-open conformations could host sweet molecules. The authors concluded that, in order to bind low molecular-weighting sweeteners, at least one monomer has to be in the open configuration. The simultaneous binding on both monomers, instead, can take place only with a combination of a closed and an open monomer, bounded to a small and a large sweetener respectively (Morini et al., <xref ref-type="bibr" rid="B43">2005</xref>). This latter observation is consistent with sweetener synergy, where the action of a sweetener upon the receptor is augmented in the presence a second sweetener; moreover, the authors found that sweet proteins can bind an external portion of the receptor other than the Venus Flytrap. Additionally, sweet and umami receptors are highly conserved among different species: most vertebrates have only three receptors sensing sweet and umami tastes (i.e., <italic>TAS1R1, TAS1R2</italic>, and <italic>TAS1R3</italic>) and this configuration rarely changes, dating the divergence of these genes before the separation of teleost fishes and tetrapods, around 400 million years ago (Ishimaru et al., <xref ref-type="bibr" rid="B31">2005</xref>; Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref>). However, some notable exceptions represented by lineage-specific changes in number of <italic>TAS1R</italic> genes, exist and will be discussed in a separate section of this mini-review.</p>
</sec>
<sec>
<title>Salty and sour taste</title>
<p>Unlike bitter, sweet, and umami, the receptors responsible for salt and sour perception are not well-known. However, candidates have been identified for both tastes: studies have shown how salt and sour taste sensations are presumably not detected through GPCRs like the other tastes, but through ion channels. The amiloride-specific and sodium-specific epithelial sodium channel (ENaC) has been proposed as a candidate for salt taste perception in vertebrates (Heck et al., <xref ref-type="bibr" rid="B27">1984</xref>). This membrane-bound ion-channel permeable to Na<sup>&#x0002B;</sup> is a heteromer constituted by four subunits named &#x003B1;, &#x003B2;, &#x003B3;, and &#x003B4; and encoded by the closely-linked <italic>SCNN1A, SCNN1B, SCNN1G</italic>, and <italic>SCNN1D</italic> genes. These subunits are organized in two transmembrane domains, forming the pore through which Na<sup>&#x0002B;</sup> can enter the intracellular environment. Modeling studies propose ligand binding-induced rotational movements of the pore altering the position of residues and enabling cation entrance (Kashlan and Kleyman, <xref ref-type="bibr" rid="B33">2011</xref>). Genes encoding for them were found in both tetrapods and the coelacanth, indicating their ancient evolutionary origin (Giraldez et al., <xref ref-type="bibr" rid="B20">2012</xref>). Many ion channels have also been proposed as sour taste perception mediators, even though the genetic basis of the perception of this taste are still poorly known. However, two transient receptor potential (TRP) channels, PKD1L1 and PKD2L3 (polycystic kidney disease-1- and &#x02212;3-like), have been identified as potential candidates for sour transduction (Ishimaru et al., <xref ref-type="bibr" rid="B30">2006</xref>). TRP structure comprises six transmembrane domains with a pore loop situated between the fifth and the sixth domains (Venkatachalam and Montell, <xref ref-type="bibr" rid="B62">2007</xref>). PKD1 and PKD2 possess a domain with an apical pore at the top of such TRP structure, surrounded by negatively charged residues possibly drawing cations to this molecular entrance. Movements of the transmembrane helices are involved in the opening of the pore loop and thus in the activation of the receptor (Grieben et al., <xref ref-type="bibr" rid="B24">2017</xref>). Although these remarkable efforts have been made to identify potential candidates for the transduction of salty and sour taste, a deep understanding of the molecular basis of these tastes is still lacking and further studies are therefore necessary to better support the physiological and genetic evidence on such candidate genes.</p>
</sec>
</sec>
<sec id="s3">
<title>Lineage-specific gene losses</title>
<p>Although most vertebrates can detect the same five basic tastes, some have lost particular tastes along their evolutionary paths. For most cases, these lineage-specific losses have occurred in response to specific dietary changes, feeding ecologies or changes in the environment. This complex network of co-evolution between organisms and niches is explored by the niche construction theory, where modifications of species&#x00027; niches cause diverse evolutionary constraints and ecological inheritances (Odling-Smee et al., <xref ref-type="bibr" rid="B45">1996</xref>). Table <xref ref-type="table" rid="T1">1</xref> recapitulates the major lineage-specific taste losses occurred in different vertebrate lineages, together with their genetic signatures, as a consequence of the intimate correlation between taste behavior, feeding ecology and taste receptor function. Most of the taste losses regard sweet or umami tastes, associated with the pseudogenization of <italic>Tas1r2</italic> and either <italic>Tas1r1</italic> or <italic>Tas1r3</italic> respectively: in particular, the loss of sweet taste perception for obligate carnivores is hypothesized to have been the result of their meat-only diets. Other animals have lost more than one taste quality, being adapted to swallowing their food whole: this has been associated with the loss of bitter <italic>Tas2rs</italic> and sour <italic>Pkd2l1</italic> genes (Beauchamp and Jiang, <xref ref-type="bibr" rid="B5">2015</xref>; Zhao et al., <xref ref-type="bibr" rid="B69">2015</xref>). In this paragraph, we explore some of the most exemplifying cases of taste losses, focusing on the genetic basis of these episodes.</p>
<table-wrap position="float" id="T1">
<label>Table 1</label>
<caption><p>Correlation of pseudogene and taste losses in different lineages.</p></caption>
<table frame="hsides" rules="groups">
<thead><tr>
<th valign="top" align="left"><bold>Species</bold></th>
<th valign="top" align="left"><bold>Pseudogene/Absent</bold></th>
<th valign="top" align="left"><bold>Taste loss</bold></th>
<th valign="top" align="left"><bold>Reference(s)</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left" colspan="4" style="background-color:#bbbdc0"><bold>MAMMALS</bold></td>
</tr>
<tr>
<td valign="top" align="left">African lion (<italic>Panthera leo krugeri</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Li et al., <xref ref-type="bibr" rid="B38">2009</xref></td>
</tr>
<tr>
<td valign="top" align="left">Asian small-clawed otter (<italic>Aonyx cinerea</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Baleen whales (Mysticei, five species)</td>
<td valign="top" align="left"><italic>Tas1r1, Tas1r2, Tas2rs, Pkd2l1</italic></td>
<td valign="top" align="left">Sweet, umami, bitter, sour</td>
<td valign="top" align="left">Feng et al., <xref ref-type="bibr" rid="B17">2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Banded linsang (<italic>Prionodon linsang</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Bats (31 species)</td>
<td valign="top" align="left"><italic>Tas1r1</italic></td>
<td valign="top" align="left">Umami</td>
<td valign="top" align="left">Zhao et al., <xref ref-type="bibr" rid="B73">2010b</xref>, <xref ref-type="bibr" rid="B70">2011</xref></td>
</tr>
<tr>
<td valign="top" align="left">Bottlenose dolphin <italic>(Tursiops truncatus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r1, Tas1r2, Tas2rs, Pkd2l1</italic></td>
<td valign="top" align="left">Sweet, umami, bitter, sour</td>
<td valign="top" align="left">Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref>; Feng et al., <xref ref-type="bibr" rid="B17">2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">California sea lion (<italic>Zalophus californianus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2, Tas1r3</italic></td>
<td valign="top" align="left">Sweet, umami</td>
<td valign="top" align="left">Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Cheetah (<italic>Acinonyx jubatus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Li et al., <xref ref-type="bibr" rid="B39">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Domestic cat (<italic>Felis catus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Li et al., <xref ref-type="bibr" rid="B39">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Fossa (<italic>Cryptoprocta ferox</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Fur seal (<italic>Arctocephalus australis</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref></td>
</tr>
<tr>
<td valign="top" align="left">Giant panda (<italic>Ailuropoda melanoleuca</italic>)</td>
<td valign="top" align="left"><italic>Tas1r1</italic></td>
<td valign="top" align="left">Umami</td>
<td valign="top" align="left">Li et al., <xref ref-type="bibr" rid="B37">2010</xref>; Zhao et al., <xref ref-type="bibr" rid="B71">2010a</xref></td>
</tr>
<tr>
<td valign="top" align="left">Pacific harnor seal (<italic>Phoca vitulina</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Red panda (<italic>Ailurus fulgens</italic>)</td>
<td valign="top" align="left"><italic>Tas1r1</italic></td>
<td valign="top" align="left">Umami</td>
<td valign="top" align="left">Hu et al., <xref ref-type="bibr" rid="B28">2017</xref></td>
</tr>
<tr>
<td valign="top" align="left">Spotted hyena (<italic>Crocuta crocuta</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Tiger (<italic>Panthera tigris</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Li et al., <xref ref-type="bibr" rid="B39">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Toothed whales (Odontoceti, seven species)</td>
<td valign="top" align="left"><italic>Tas1r1, Tas1r2, Tas2rs, Pkd2l1</italic></td>
<td valign="top" align="left">Sweet, umami, bitter, sour</td>
<td valign="top" align="left">Feng et al., <xref ref-type="bibr" rid="B17">2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Vampire bats (genus <italic>Desmodus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2, Tas1r3</italic></td>
<td valign="top" align="left">Sweet, umami</td>
<td valign="top" align="left">Zhao et al., <xref ref-type="bibr" rid="B73">2010b</xref>, <xref ref-type="bibr" rid="B70">2011</xref></td>
</tr>
<tr>
<td valign="top" align="left" colspan="4" style="background-color:#bbbdc0"><bold>BIRDS</bold></td>
</tr>
<tr>
<td valign="top" align="left">Birds (ten species)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Baldwin et al., <xref ref-type="bibr" rid="B4">2014</xref></td>
</tr>
<tr>
<td valign="top" align="left">Chicken (<italic>Gallus gallus domesticus</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref></td>
</tr>
<tr>
<td valign="top" align="left">Penguins (three species)</td>
<td valign="top" align="left"><italic>Tas1r2, Tas1r3, Tas2rs</italic></td>
<td valign="top" align="left">Sweet, umami, bitter</td>
<td valign="top" align="left">Zhao et al., <xref ref-type="bibr" rid="B69">2015</xref></td>
</tr>
<tr>
<td valign="top" align="left">Turkey (genus <italic>Meleagri</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Feng and Zhao, <xref ref-type="bibr" rid="B16">2013</xref></td>
</tr>
<tr>
<td valign="top" align="left">Zebra finch (<italic>Taeniopygia guttata</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Feng and Zhao, <xref ref-type="bibr" rid="B16">2013</xref></td>
</tr>
<tr>
<td valign="top" align="left" colspan="4" style="background-color:#bbbdc0"><bold>AMPHIBIAN</bold></td>
</tr>
<tr>
<td valign="top" align="left">Tongueless western clawed frog (<italic>Xenopus tropicalis</italic>)</td>
<td valign="top" align="left"><italic>Tas1r2</italic></td>
<td valign="top" align="left">Sweet</td>
<td valign="top" align="left">Shi and Zhang, <xref ref-type="bibr" rid="B57">2005</xref></td>
</tr>
</tbody>
</table>
</table-wrap>
<sec>
<title>Aquatic mammals</title>
<p>Several terrestrial mammals have returned to the water for a fully aquatic lifestyle: among these, Cetacea and Carnivores represent two orders that returned to the sea around 50 and 35 million years ago, respectively (Uhen, <xref ref-type="bibr" rid="B61">2007</xref>; Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref>). This change in lifestyle and habitat inevitably caused more or less dramatic changes in the anatomy and behavior of these creatures, depending on the lineage. One change in common to all these lineages is their feeding behavior: this dietary switch introducing meat in their diets reduced the importance of some tastes (i.e., bitter and sweet), because of the presence of little or no bitter and sweet compounds in meat. Many species of these orders also swallow their prey whole without mastication, reducing the importance of tasting their food. In addition, the high sodium concentration in oceans masks other tastes, further decreasing the need for taste in the feeding behaviors of these animals. These behavioral observations are consistent with anatomical evidence, showing how some aquatic mammals have atrophied taste systems with few or no taste buds (Yoshimura and Kobayashi, <xref ref-type="bibr" rid="B67">1997</xref>; Yoshimura et al., <xref ref-type="bibr" rid="B68">2002</xref>). A survey of taste receptor genes analyzed these loci in 12 species of toothed and baleen whales and compared it to various other species (i.e., rat, dog, human). The study better defined the repertoire of taste genes in the examined species, highlighting a relaxation of selection forces since the common ancestor of whales (between 36 and 53 Ma) and showing how all members of bitter and sweet/umami gene families have been pseudogenized because of shared premature stop codons. Moreover, the authors noted how the candidate gene for sour perception (i.e., <italic>Pkd2l1</italic>) is a pseudogene as well, while the candidate salty taste receptor genes (<italic>Scnn1a, Scnn1b</italic>, and <italic>Scnn1g</italic>) are intact and have experienced strong purifying selection (Feng et al., <xref ref-type="bibr" rid="B17">2014</xref>). Another study showed how <italic>Tas1r1, Tas1r2</italic>, and <italic>Tas1r3</italic> are also pseudogenized in the sea lion, because of deletions or nonsense mutations (Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref>).</p>
</sec>
<sec>
<title>Terrestrial carnivores</title>
<p>Carnivores that remained on mainland also experienced taste losses during their evolutionary history. Remarkably, sweet taste was independently lost in several lineages: dietary specializations, rather than dietary switches, were likely the drivers of these events. A study on the Carnivore order with different dietary habits (i.e., obligate carnivores, omnivorous and herbivores), for example, showed how the pseudogenization of the sweet taste receptor gene, <italic>Tas1r2</italic>, was widespread but independent in many lineages, because of mutations disrupting its open-reading-frame. This pseudogenization is also related to animals&#x00027; diets: exclusive meat eaters are in fact lacking an intact form of this gene. In addition, Jiang et al. (<xref ref-type="bibr" rid="B32">2012</xref>) analyzed <italic>Tas1r2</italic> sequences in the order Carnivora: the authors calculated the nonsynonymous-to-synonymous substitution ratio (dN/dS) finding a ratio significantly lower than one. This led to the conclusion that purifying selection may have been acting on these genes of this order. However, despite their carnivorous diet, both the Canadian otter and the ferret have an intact <italic>Tas1r2</italic> (sweet) receptor sequence, suggesting that additional factors may have been involved in shaping feeding strategies and gene loss/retention. Nonetheless, further studies showed how cats and felids&#x00027; (i.e., tigers, cheetahs and lions) indifference toward sugar can be accounted by the pseudogenization of <italic>Tas1r2</italic>, reflecting their eating behaviors. As obligate carnivores, cats and other felids possess a high-protein diet, with little carbohydrates and no simple sugars contained in plants (Li et al., <xref ref-type="bibr" rid="B39">2005</xref>, <xref ref-type="bibr" rid="B38">2009</xref>). Conversely, despite their herbivorous diet, horses miss <italic>Tas1r2</italic> (Zhao et al., <xref ref-type="bibr" rid="B73">2010b</xref>). Thus, the correlation between diet and disrupting events upon this sequence may not always be the best explanation. Nonetheless, domestic cats with a carnivore diet still retain functional bitter taste receptor genes (Sandau et al., <xref ref-type="bibr" rid="B54">2015</xref>). Considering that bitter receptors are expressed in extra oral tissues (Behrens and Meyerhof, <xref ref-type="bibr" rid="B6">2011a</xref>,<xref ref-type="bibr" rid="B7">b</xref>), selective forces could have also acted on these compartments. Further studies investigating these extra-oral bitter taste receptors will be crucial in understanding the selective forces acting in these gain-and-loss mechanisms. Another example comes from the giant panda and red panda, with specialized herbivore bamboo-based diets, have a functional copy of <italic>Tas1r2</italic> but a pseudogenized <italic>Tas1r1</italic> (encoding the umami receptor) because of insertions or deletions interrupting its open-reading-frame. This was interpreted as convergent evolution in response to adaptation to a specialized diet (Li et al., <xref ref-type="bibr" rid="B37">2010</xref>; Zhao et al., <xref ref-type="bibr" rid="B71">2010a</xref>; Hu et al., <xref ref-type="bibr" rid="B28">2017</xref>). Unlike panda, horse and cow intriguingly retain a functional <italic>Tas1r1</italic> and have an herbivorous diet (Zhao et al., <xref ref-type="bibr" rid="B71">2010a</xref>). Similarly, vampire bats lack a proper <italic>Tas1r2</italic> even though sugars are present in blood, their sole food source (Zhao and Zhang, <xref ref-type="bibr" rid="B72">2012</xref>).</p>
</sec>
<sec>
<title>Birds</title>
<p>An additional example of how evolution accounts for taste comes from birds, descendants from theropod dinosaurs with a carnivorous diet (Sereno, <xref ref-type="bibr" rid="B55">1999</xref>). A study analyzing <italic>Tas1r</italic> genes in 10 bird species with different diets (i.e., insectivorous, nectarivorous, and frugivores) demonstrated how birds were lacking <italic>Tas1r2</italic>, while the two other <italic>Tas1r</italic> genes (i.e., <italic>Tas1r1</italic> and <italic>Tas1r3</italic>) were present and intact. It was also suggested that the <italic>Tas1r2</italic> loss likely occurred within Dinosauria, before the non-avian reptile and bird lineages split (Beauchamp and Jiang, <xref ref-type="bibr" rid="B5">2015</xref>). However, the observation that hummingbirds, differently from other birds, showed a distinctive preference for nectar and sugar solutions, initially represented a paradox. This was solved by the striking finding that hummingbirds&#x00027; <italic>Tas1r1</italic> and <italic>Tas1r3</italic>, responsible for umami sensitivity in other species, were repurposed through the appearance of mutations leading to the acquisition of sugar responsiveness. <italic>In vitro</italic> reconstructions of chicken and hummingbird chimeric T1R1/T1R3 receptors, highlighted in fact how 19 amino acids in the hummingbird&#x00027;s T1R3 Venus Flytrap domain are responsible of modulating sucrose and sucralose perception. Intriguingly, a response to sucrose was only detected when all 19 amino acids were tested in the same chimeric receptor. These mutations were also found to be under positive selection, suggesting a new energy source unavailable to other birds (Baldwin et al., <xref ref-type="bibr" rid="B4">2014</xref>).</p>
<p>In addition, other birds have lost more than one taste quality (similar to aquatic mammals): penguins, for example, have lost three basic tastes along their evolutionary path. A study analyzing genomes of 16 bird species has shown how penguins lack functional <italic>Tas1r1, Tas1r2</italic>, and <italic>Tas1r3</italic>. Further analyses showed that the pseudogenization of <italic>Tas1r1</italic> happened in the common ancestor of all penguins, since its separation from tubenose seabirds (Zhao et al., <xref ref-type="bibr" rid="B69">2015</xref>). These taste losses correlate well with penguins&#x00027; feeding behaviors of swallowing food whole and their tongue structure and function, suggesting that these animals don&#x00027;t have a real need of perceiving the taste of their food.</p>
</sec>
<sec>
<title>Primates</title>
<p>The evolutionary role of bitter taste receptors (i.e., <italic>TAS2Rs</italic>) for avoiding potentially toxic and harmful compounds is of particular importance when considering that even small changes in the <italic>TAS2R</italic> gene repertoire could affect feeding habits of different animals, considering ligand-receptor specificity (Bachmanov et al., <xref ref-type="bibr" rid="B2">2014</xref>). Analysis of primates showed a higher level of pseudogenes accumulation after the separation from the common ancestor of other species, such as rodents (Go et al., <xref ref-type="bibr" rid="B23">2005</xref>). Nonhuman primates differ significantly in the <italic>TAS2R</italic> repertoire in respect to humans, showing higher pseudogenization rates. However, a relaxation of selective constraint on human <italic>TAS2Rs</italic> occurred instead of positive selection (Fischer et al., <xref ref-type="bibr" rid="B18">2004</xref>; Wang et al., <xref ref-type="bibr" rid="B64">2004</xref>; Go et al., <xref ref-type="bibr" rid="B23">2005</xref>; Risso et al., <xref ref-type="bibr" rid="B51">2016</xref>). In primates, lineage-specific gene duplication and pseudogenization events played a major role in shaping the <italic>TAS2R</italic> gene repertoire. In particular, only eight pseudogenes are in common to more than one primate species, while the majority (<italic>n</italic> &#x0003D; 23) of these pseudogenization events occurred specifically in different lineages: five in prosimians and tupais, and 19 in anthropoidea, respectively. Interestingly, three of these pseudogenes (<italic>TAS2R2, TAS2R62</italic>, and <italic>TAS2R64</italic>) are uniquely confined to <italic>Homo sapiens</italic> because of a two-base deletion at codon position 160, two fixed nonsense mutations at codon positions 235 and 292 and one fixed nonsense mutation at codon position 280, respectively. In addition, the two-base deletion inactivating <italic>TAS2R2</italic> is polymorphic in modern human populations and archaic humans, and <italic>TAS2R64</italic> also became a pseudogene in the orangutan because of a different nonsense mutation, showing convergent evolution (Go et al., <xref ref-type="bibr" rid="B23">2005</xref>; Perry et al., <xref ref-type="bibr" rid="B47">2015</xref>; Risso et al., <xref ref-type="bibr" rid="B50">2017</xref>). These lineage-specific gene losses likely reflect different responses to environmental changes, resulting from species-specific food preferences during primates&#x00027; evolution (Go et al., <xref ref-type="bibr" rid="B23">2005</xref>); (Liman, <xref ref-type="bibr" rid="B40">2006</xref>; Hayakawa et al., <xref ref-type="bibr" rid="B25">2012</xref>, <xref ref-type="bibr" rid="B26">2014</xref>; Risso et al., <xref ref-type="bibr" rid="B50">2017</xref>). In particular, an <italic>in vitro</italic> study showed how the receptors encoded by the reconstructed human-specific pseudogenes and the respective chimpanzee orthologues recognized different ligands because of interspecific amino acid changes, likely allowing the adaptation to different environments and the identification of compounds of species-specific relevance (Risso et al., <xref ref-type="bibr" rid="B50">2017</xref>). Similarly, a marked diversification of the <italic>TAS2R</italic> repertoire in terms of whole-gene deletions, gene-conversion variations and copy number variations was identified among subspecies of chimpanzees, likely reflecting their subspecies-specific dietary habits (Hayakawa et al., <xref ref-type="bibr" rid="B25">2012</xref>; Wooding et al., <xref ref-type="bibr" rid="B66">2012</xref>).</p>
</sec>
</sec>
<sec sec-type="conclusions" id="s4">
<title>Conclusion</title>
<p>Maynard Olson&#x00027;s &#x0201C;less-is-more&#x0201D; hypothesis sees gene loss as an engine of evolutionary change, representing a common response of different lineages undergoing similar environmental shifts (Olson, <xref ref-type="bibr" rid="B46">1999</xref>; Callaway, <xref ref-type="bibr" rid="B9">2012</xref>). Some of the lineage-specific pseudogenization events discussed in this mini-review have been related to specific feeding behavior, dietary switches or environmental changes at both large and small scales, highlighting the plasticity and dynamism of the taste system (Li et al., <xref ref-type="bibr" rid="B39">2005</xref>; Liman, <xref ref-type="bibr" rid="B40">2006</xref>; Zhao et al., <xref ref-type="bibr" rid="B71">2010a</xref>, <xref ref-type="bibr" rid="B70">2011</xref>; Hayakawa et al., <xref ref-type="bibr" rid="B25">2012</xref>; Jiang et al., <xref ref-type="bibr" rid="B32">2012</xref>; Baldwin et al., <xref ref-type="bibr" rid="B4">2014</xref>; Feng et al., <xref ref-type="bibr" rid="B17">2014</xref>; Wang and Zhao, <xref ref-type="bibr" rid="B63">2015</xref>; Risso et al., <xref ref-type="bibr" rid="B50">2017</xref>). In addition, the repertoire of bitter taste receptor genes has been associated with species&#x00027; feeding behaviors, correlating with the fraction of plants in their diet as an evolutionary mechanisms protecting from ingesting potentially toxic compounds (Li and Zhang, <xref ref-type="bibr" rid="B36">2013</xref>; Wang and Zhao, <xref ref-type="bibr" rid="B63">2015</xref>; Liu et al., <xref ref-type="bibr" rid="B41">2016</xref>; Shang et al., <xref ref-type="bibr" rid="B56">2017</xref>). However, birth-and-death events of taste receptor genes are not always correlated with species&#x00027; feeding behaviors, where putative useless taste receptor genes are still present, making it possible to detect a taste quality that should not be present in their diet. These data suggest that there is still a gap in our understanding of the physiological function of these genes (Zhao and Zhang, <xref ref-type="bibr" rid="B72">2012</xref>; Feng and Zhao, <xref ref-type="bibr" rid="B16">2013</xref>; Liu et al., <xref ref-type="bibr" rid="B41">2016</xref>). This encourages further genetic and behavioral studies aimed at better identifying the role of taste receptor genes and pseudogenes in different species, in order to shed light on the evolutionary mechanisms that have inactivated genes exclusively in specific lineages.</p>
</sec>
<sec id="s5">
<title>Author contributions</title>
<p>MA wrote the first draft of the manuscript. DR contributed to writing and editing the manuscript and created the figures/tables.</p>
<sec>
<title>Conflict of interest statement</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
</sec>
</body>
<back>
<ack><p>DR would like to thank the University of Washington, School of Medicine, for providing scholarship for his postgraduate work. MA is grateful to Mirko Di Franco for help creating Figure <xref ref-type="fig" rid="F1">1</xref>. The authors thank Andrew R Bogaard for help editing the final version of the manuscript.</p>
</ack>
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