Role of feeding specialization in taste receptor loss: insights from sweet and umami receptor evolution in Carnivora.

Controversy and misunderstanding surround the role of feeding specialization in taste receptor loss in vertebrates. We refined and tested the hypothesis that this loss is caused by feeding specializations. Specifically, feeding specializations were proposed to trigger time-dependent process of taste receptor loss through deprivation of benefit of using the receptor's gustatory function. We propose that this process may be accelerated by abiotic environmental conditions or decelerated/stopped because of extragustatory functions of the receptor's protein(s). As test case we used evolution of the sweet (TAS1R2+TAS1R3) and umami (TAS1R1+TAS1R3) receptors in Carnivora (dogs, cats, and kin). We predicted these receptors' absence/presence using data on presence/absence of inactivating mutations in these receptors' genes and data from behavioral sweet/umami preference tests. We identified 20 evolutionary events of sweet (11) or umami (9) receptor loss. These events affected species with feeding specializations predicted to favor sweet/umami receptor loss (27 and 22 species, respectively). All species with feeding habits predicted to favor sweet/umami receptor retention (11 and 24, respectively) were found to retain that receptor. Six species retained the sweet (5) or umami (1) receptor despite feeding specialization predicted to favor loss of that receptor, which can be explained by the time dependence of sweet/umami receptor loss process and the possible decelerating effect of TAS1R extragustatory functions so that the sweet/umami receptor process is ongoing in these species. Our findings support the idea that feeding specialization leads to taste receptor loss and is the main if not only triggering factor for evolutionary loss of taste receptors.

Mitochondrial genomes reveal the pattern and timing of marten (Martes), wolverine (Gulo), and fisher (Pekania) diversification.

Despite recent advances in understanding the pattern and timescale of evolutionary diversification in the marten, wolverine, fisher, and tayra subfamily Guloninae (Mustelidae, Carnivora), several important issues still remain contentious. Among these are the phylogenetic position of Gulo relative to the subgenera of Martes (Martes and Charronia), the phylogenetic relationships within the subgenus Martes, and the timing of gulonine divergences. To elucidate these issues we explored nucleotide variation in 11 whole mitochondrial genomes (mitogenomes) from eight gulonine species and two outgroup meline species. Parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded fully resolved and identical patterns of relationships with high support for all divergences. The generic status of Pekania (P. pennanti), the monophyly of the genus Martes containing M. flavigula (subgenus Charronia) to the exclusion of the genus Gulo (G. gulo), and the M. foina (M. americana (M. melampus (M. zibellina, M. martes))) phylogeny of the subgenus Martes were strongly supported. Dating analyses (BEAST) using a set of five newly applied fossil calibrations provided divergence times considerably younger than previous multigene mitochondrial estimates, but similar to multigene nuclear and nuclear-mitochondrial estimates. The 95% confidence (highest posterior density) intervals of our divergence times fell within those inferred from nuclear and nuclear-mitochondrial sequence data, and were markedly narrower than in earlier studies (whether nuclear, mitochondrial, or combined). Notably, and contrary to long-held beliefs, our findings indicate that fossils older than the Tortonian-Messinian transition (late Late Miocene) do not represent Martes, excluding from this genus its putative members from the Early, Middle, and early Late Miocene. This study demonstrates the high informativeness of the mitogenome for phylogenetic inference and divergence time estimation within Guloninae, and suggests that mitogenomes can be highly informative also for other clades at similar levels of evolutionary divergence.

Brainy stuff of long-gone dogs: a reappraisal of the supposed Canis endocranial cast from the Pliocene of Poland.

The pre-Quaternary fossil record of Canis in the Old World is scarce, and the first appearance of this genus in Europe remains an enigma. Amongst the oldest fossils assigned to this genus, there is a natural cast of the brain (endocast) collected in Weze 1, Poland, from Pliocene deposits dated between 3.3 and 4.0 Ma. We reexamined this specimen and found that it differs from the brain of Canis in having its region medial to the coronal sulcus heart-shaped in dorsal view, its region rostral to the presylvian sulcus shorter and less constricted laterally, and its cerebellum less overlapped by the cerebrum and lacking a lateral twist of the posterior vermis. We identified this fossil, as well as another fossil canid endocast from Weze 1, as representing the raccoon dog genus Nyctereutes. The previously reported presence of Canis in Weze 1 is therefore not confirmed. Specifically, both endocasts can be referred to N. donnezani because this is the only species of Nyctereutes that has been recognised in this locality on the basis of craniomandibular and dental fossils. Our study represents a taxonomic application of comparative neuroanatomical and palaeoneurological data, an approach that may become increasingly useful with the growing knowledge of the endocranial morphology of fossil mammals.

Evolutionary and biogeographic history of weasel-like carnivorans (Musteloidea).

We analyzed a concatenated (8492 bp) nuclear-mitochondrial DNA data set from 44 musteloids (including the first genetic data for Lyncodon patagonicus) with parsimony, maximum likelihood, and Bayesian methods of phylogenetic and biogeographic inference and two Bayesian methods of chronological inference. Here we show that Musteloidea emerged approximately 32.4-30.9 million years ago (MYA) in Asia, shortly after the greenhouse-icehouse global climate shift at the Eocene-Oligocene transition. During their Oligocene radiation, which proceeded wholly or mostly in Asia, musteloids diversified into four primary divisions: the Mephitidae lineage separated first, succeeded by Ailuridae and the divergence of the Procyonidae and Mustelidae lineages. Mustelidae arose approximately 16.1 MYA within the Mid-Miocene Climatic Optimum, and extensively diversified in the Miocene, mostly in Asia. The early offshoots of this radiation largely evolved into badger and marten ecological niches (Taxidiinae, Melinae, Mellivorinae, Guloninae, and Helictidinae), whereas the later divergences have adapted to other niches including those of weasels, polecats, minks, and otters (Mustelinae, Ictonychinae, and Lutrinae). Notably, and contrary to traditional beliefs, the morphological adaptations of badgers, martens, weasels, polecats, and minks each evolved independently more than once within Mustelidae. Ictonychinae (which is most closely related to Lutrinae) arose approximately 9.5-8.9 MYA, most likely in Asia, where it diverged into the Old World Ictonychini (Vormela, Poecilictis, Ictonyx, and Poecilogale) and New World Lyncodontini (Lyncodon and Galictis) lineages. Ictonychini presumably entered Africa during the Messinian Salinity Crisis (at the Miocene-Pliocene transition), which interposed the origins of this clade (approximately 6.5-6.0 MYA) and its African Poecilictis-Ictonyx-Poecilogale subclade (approximately 4.8-4.5 MYA). Lyncodontini originated approximately 2.9-2.6 MYA at the Pliocene-Pleistocene transition in South America, slightly after the emergence of the Panamanian land bridge that provided for the Great American Biotic Interchange. As the genera Martes and Ictonyx (as currently circumscribed) are paraphyletic with respect to the genera Gulo and Poecilogale, respectively, we propose that Pekaniaand Poecilictis be treated as valid genera and that "Martes"pennanti and "Ictonyx"libyca, respectively, be assigned to these genera.

Loss or major reduction of umami taste sensation in pinnipeds.

Umami is one of basic tastes that humans and other vertebrates can perceive. This taste is elicited by L-amino acids and thus has a special role of detecting nutritious, protein-rich food. The T1R1 + T1R3 heterodimer acts as the principal umami receptor. The T1R1 protein is encoded by the Tas1r1 gene. We report multiple inactivating (pseudogenizing) mutations in exon 3 of this gene from four phocid and two otariid species (Pinnipedia). Jiang et al. (Proc Natl Acad Sci U S A 109:4956-4961, 2012) reported two inactivating mutations in exons 2 and 6 of this gene from another otariid species. These findings suggest lost or greatly reduced umami sensory capabilities in these species. The widespread occurrence of a nonfunctional Tas1r1 pseudogene in this clade of strictly carnivorous mammals is surprising. We hypothesize that factors underlying the pseudogenization of Tas1r1 in pinnipeds may be driven by the marine environment to which these carnivorans (Carnivora) have adapted and may include: the evolutionary change in diet from tetrapod prey to fish and cephalopods (because cephalopods and living fish contain little or no synergistic inosine 5'-monophosphate that greatly enhances umami taste), the feeding behavior of swallowing food whole without mastication (because the T1R1 + T1R3 receptor is distributed on the tongue and palate), and the saltiness of sea water (because a high concentration of sodium chloride masks umami taste).

Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora).

Missing data are commonly thought to impede a resolved or accurate reconstruction of phylogenetic relationships, and probabilistic analysis techniques are increasingly viewed as less vulnerable to the negative effects of data incompleteness than parsimony analyses. We test both assumptions empirically by conducting parsimony and Bayesian analyses on an approximately 1.5 × 106 -cell (27 965 characters × 52 species) mustelid-procyonid molecular supermatrix with 62.7% missing entries. Contrary to the first assumption, phylogenetic relationships inferred from our analyses are fully (Bayesian) or almost fully (parsimony) resolved topologically with mostly strong support and also largely in accord with prior molecular estimations of mustelid and procyonid phylogeny derived with parsimony, Bayesian, and other probabilistic analysis techniques from smaller but complete or nearly complete data sets. Contrary to the second assumption, we found no compelling evidence in support of a relationship between the inferior performance of parsimony and taxon incompleteness (i.e. the proportion of missing character data for a taxon), although we found evidence for a connection between the inferior performance of parsimony and character incompleteness (i.e. no overlap in character data between some taxa). The relatively good performance of our analyses may be related to the large number of sampled characters, so that most taxa (even highly incomplete ones) are represented by a sufficient number of characters allowing both approaches to resolve their relationships. © The Willi Hennig Society 2009.

Deciphering and dating the red panda's ancestry and early adaptive radiation of Musteloidea.

Few species have been of more disputed affinities than the red or lesser panda (Ailurus fulgens), an endangered endemic Southeast Asian vegetarian member of the placental mammalian order Carnivora. This peculiar carnivoran has mostly been classified with raccoons (Procyonidae) or bears (Ursidae), grouped with the giant panda (Ailuropoda melanoleuca) in their own family, or considered a separate lineage of equivocal ancestry. Recent molecular studies have indicated a close affinity of the red panda to a clade of procyonids and mustelids (weasels, otters, martens, badgers, and allies), but have failed to unambiguously resolve the position of this species relative to mephitids (skunks and stink badgers). We examined the relationship of the red panda to other extant species of the carnivoran suborder Caniformia using a set of concatenated approximately 5.5-kb sequences from protein-coding exons of five nuclear genes. Bayesian, maximum likelihood, and parsimony phylogenetic analyses strongly supported the red panda as the closest living relative of a clade containing Procyonidae and Mustelidae to the exclusion of Mephitidae. These three families together with the red panda (which is classified here as a single extant species of a distinct family, Ailuridae) compose the superfamily Musteloidea, a clade strongly supported by all our phylogenetic analyses as sister to the monophyletic Pinnipedia (seals, sea lions, walruses). The approximately unbiased, Kishino-Hasegawa, and Templeton topology tests rejected (P<0.05) each of all possible alternative hypotheses about the relationships among the red panda and mephitids, procyonids, and mustelids. We also estimated divergence times for the red panda's lineage and ones of other caniform taxa, as well as the ages of the first appearance datums for the crown and total clades of musteloids and the total clades of the red panda, mephitids, procyonids, and mustelids. Bayesian relaxed molecular-clock analysis using combined information from all sampled genes yielded a approximately 42-Myr timescale to caniform evolution and provided evidence of five periods of increased diversification. The red panda's lineage and those of other extant musteloid families are estimated to have diverged during a 3-Myr interval from the mid-Early Oligocene to near the Early/Late Oligocene boundary. We present fossil evidence that extends the early adaptive radiation of the total clade of musteloids to the Eocene-Oligocene transition and also suggests Asia as a center of this radiation.

Dental integration and modularity in pinnipeds.

Morphological integration and modularity are important for understanding phenotypic evolution because they constrain variation subjected to selection and enable independent evolution of functional and developmental units. We report dental integration and modularity in representative otariid (Eumetopias jubatus, Callorhinus ursinus) and phocid (Phoca largha, Histriophoca fasciata) species of Pinnipedia. This is the first study of integration and modularity in a secondarily simplified dentition with simple occlusion. Integration was stronger in both otariid species than in either phocid species and related positively to dental occlusion and negatively to both modularity and tooth-size variability across all the species. The canines and third upper incisor were most strongly integrated, comprising a module that likely serves as occlusal guides for the postcanines. There was no or weak modularity among tooth classes. The reported integration is stronger than or similar to that in mammals with complex dentition and refined occlusion. We hypothesise that this strong integration is driven by dental occlusion, and that it is enabled by reduction of modularity that constrains overall integration in complex dentitions. We propose that modularity was reduced in pinnipeds during the transition to aquatic life in association with the origin of pierce-feeding and loss of mastication caused by underwater feeding.

Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: single origin with affinity to Musteloidea.

Considerable long-standing controversy and confusion surround the phylogenetic affinities of pinnipeds, the largely marine group of "fin-footed" members of the placental mammalian order Carnivora. Until most recently, the two major competing hypotheses were that the pinnipeds have a single (monophyletic) origin from a bear-like ancestor, or that they have a dual (diphyletic) origin, with sea lions (Otariidae) derived from a bear-like ancestor, and seals (Phocidae) derived from an otter-, mustelid-, or musteloid-like ancestor. We examined phylogenetic relationships among 29 species of arctoid carnivorans using a concatenated sequence of 3228 bp from three nuclear loci (apolipoprotein B, APOB; interphotoreceptor retinoid-binding protein, IRBP; recombination-activating gene 1, RAG1). The species represented Pinnipedia (Otariidae: Callorhinus, Eumetopias; Phocidae: Phoca), bears (Ursidae: Ursus, Melursus), and Musteloidea (Mustelidae: Mustela, Enhydra, Melogale, Martes, Gulo, Meles; Procyonidae: Procyon; Ailuridae: Ailurus; Mephitidae: Mephitis). Maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of separate and combined datasets produced trees with largely congruent topologies. The analyses of the combined dataset resulted in well-resolved and well-supported phylogeny reconstructions. Evidence from nuclear DNA evolution presented here contradicts the two major hypotheses of pinniped relationships and strongly suggests a single origin of the pinnipeds from an arctoid ancestor shared with Musteloidea to the exclusion of Ursidae.

Tooth Size Variation in Pinniped Dentitions.

It is contentious whether size variation among mammalian teeth is heterogeneous or homogeneous, whether the coefficient of variation is reliable, and whether the standard deviation of log-transformed data and the residual of standard deviation on mean variable size are useful replacements for the coefficient of variation. Most studies of tooth size variation have been on mammals with complex-crowned teeth, with relatively little attention paid to taxa with simple-crowned teeth, such as Pinnipedia. To fill this gap in knowledge and to resolve the existing controversies, we explored the variation of linear size variables (length and width) for all teeth from complete permanent dentitions of four pinniped species, two phocids (Histriophoca fasciata, Phoca largha) and two otariids (Callorhinus ursinus, Eumetopias jubatus). Size variation among these teeth was mostly heterogeneous both along the toothrow and among species. The incisors, canines, and mesial and distal postcanines were often relatively highly variable. The levels of overall dental size variation ranged from relatively low as in land carnivorans (Phoca largha and both otariids) to high (Histriophoca fasciata). Sexual size dimorphism varied among teeth and among species, with teeth being, on average, larger in males than in females. This dimorphism was more pronounced, and the canines were larger and more dimorphic relative to other teeth in the otariids than in the phocids. The coefficient of variation quantified variation reliably in most cases. The standard deviation of log-transformed data was redundant with the coefficient of variation. The residual of standard deviation on mean variable size was inaccurate when size variation was considerably heterogeneous among the compared variables, and was incomparable between species and between sexes. The existing hypotheses invoking developmental fields, occlusal complexity, and the relative timing of tooth formation and sexually dimorphic hormonal activity do not adequately explain the differential size variation along the pinniped toothrow.

Molecular phylogeny of arctoids (Mammalia: Carnivora) with emphasis on phylogenetic and taxonomic positions of the ferret-badgers and skunks.

Phylogenetic relationships among the ferret-badger Melogale moschata, the skunk Mephitis mephitis, and 21 other arctoid carnivorans, representing Mustelidae (Mustelinae: Mustela, Martes, Gulo; Lutrinae: Enhydra; Melinae: Meles), Procyonidae (Procyon), and Ursidae (Ursus, Melursus), were evaluated through maximum-parsimony phylogenetic analysis of concatenated partial nucleotide sequences of the nuclear recombination-activating gene 1 (RAG1) and gene encoding interphotoreceptor retinoid-binding protein (IRBP). The analysis strongly supports Melogale as more closely related to a musteline-lutrine clade (containing Mustela and Enhydra) than to Meles or another musteline clade containing Martes and Gulo (causing Melinae and Mustelinae, as traditionally circumscribed, to be nonmonophyletic). This, together with known morphological and karyological evidence for nonmeline affinities of Melogale, justify the exclusion of the ferret-badgers from the monophyletic Melinae. Therefore, we recommend that Melogale be classified in a distinct mustelid subfamily, the monotypic Helictidinae. Our analysis also strongly supports an outgroup position of the skunks to a clade containing Procyonidae and the nonmephitine Mustelidae (causing Mustelidae, as traditionally circumscribed, to be paraphyletic). This position of the skunks agrees with results of most previous genetic studies. However, it is contradicted by known morphological evidence from both living and fossil taxa, as well as genetic evidence from protein electrophoresis. These consistently support the traditional placement of the skunks within the monophyletic Mustelidae (recently in a close relationship to Lutrinae). Therefore, we consider the recent elevation of the skunks to the level of family as premature, and recommend that this clade be left at the subfamily level (Mephitinae) within the family Mustelidae, pending further evidence.

Phylogenetic relationships and divergence times among mustelids (Mammalia: Carnivora) based on nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein and mitochondrial cytochrome b genes.

Phylogenetic relationships among 20 species-group taxa of Mustelidae, representing Mustelinae (Mustela, Martes, Gulo), Lutrinae (Enhydra), and Melinae (Meles), were examined using nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein (IRBP) and mitochondrial cytochrome b genes. Neighbor-joining and maximum-parsimony phylogenetic analyses on these genes separately and combined were conducted. While IRBP performed better than cytochrome b in recovering more-inclusive clades, cytochrome b demonstrated more resolving power in recovering less-inclusive clades. Strong support was found for a close affinity of Enhydra with Mustela to the exclusion of Martes and Gulo (causing Mustelinae to be paraphyletic); the most-basal position of Mustela vison within Mustela, followed by Mustela erminea; an association of Mustela lutreola, Mustela itatsi, Mustela sibirica, and the subgenus Putorius (including Mustela putorius and Mustela eversmanii), to the exclusion of Mustela nivalis and Mustela altaica; and a basal position of Mustela itatsi to a clade containing Mustela sibirica and Putorius. Whereas cytochrome b strongly supported Mustela lutreola as the sister species to Putorius, IRBP strongly supported its basal placement to the Mustela itatsi-Mustela sibirica-Putorius clade. The low level of sequence divergence in cytochrome b between Mustela lutreola and Putorius is therefore a result of interspecific mitochondrial introgression between these taxa, rather than a recent origin of Mustela lutreola in a close relationship to Putorius. Time estimates inferred from IRBP and cytochrome b for mustelid divergence events are mostly in agreement with the fossil record.