Tetsuji Hosoda

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

Abstract 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.

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 pandas 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 pandas 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.

Evidence from Nuclear DNA Sequences Sheds Light on the Phylogenetic Relationships of Pinnipedia: Single Origin with Affinity to Musteloidea

Abstract 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.

Molecular Phylogeny of Arctoids (Mammalia: Carnivora) with Emphasis on Phylogenetic and Taxonomic Positions of the Ferret-badgers and Skunks

Abstract 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.

Genetic Diversity of the Japanese Marten (Martes melampus) and Its Implications for the Conservation Unit

Molecular phylogenetic analyses of combined mitochondrial DNA sequences (2814 bp; cytochrome b gene, displacement loop region, and NADH dehydrogenase subunit 2 gene) identified nine groups among 49 individual Japanese martens, Martes melampus, collected from several areas in Japan. The grouping was not correlated with winter coat color, but was consistent with geography. In particular, the monophyly of 29 Tsushima martens, M. m. tsuensis, was supported by strong clade support and topological tests. Haplotype and nucleotide diversities were much lower for the Tsushima population than for any population on the Japanese main islands. In addition, analyses of heterozygosity in nuclear growth hormone receptor gene sequences (654 bp) showed genetic homogeneity for the Tsushima population. This evidence supports the view that the Tsushima martens long history of isolation on small islands is responsible for its genetic distinctiveness and uniformity, validating the Tsushima population as an evolutionarily significant unit.

Genetic diversity of the sable (Martes zibellina, Mustelidae) in Russian Far East and Hokkaido inferred from mitochondrial NADH dehydrogenase subunit 2 gene sequences

Abstract. Intra-species genetic variations of the sable Martes zibellina (Carnivora, Mustelidae), originating from Russian Far East and Hokkadio, were assessed by using nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs). Evaluation of the genetic diversity of the sables demonstrated that populations in the southern Primorsky territory in Russian Far East harbors high genetic diversity. We assumed that the high genetic variations might have been due to effects of refugia, secondary admixture of allopatrically differentiated lineages, or massive anthropogenic introductions. Molecular phylogenetic (maximum likelihood and Bayesian inference approaches) and network (median joining method) analyses clarified that sables in Hokkaido was monophyletic. Bayesian-relaxed molecular dating approach estimated the date for migration of sables into Hokkaido to lie between 0.10–0.27 Myr BP. Considering the geological evidence, the Late Pleistocene was presumed to be the plausible epoch for the establishment of the sables in Hokkaido. Lower genetic diversity of the sables in Hokkaido observed in this study was probably caused by the foundation effects or anthropogenic hunting pressures. Mammalian faunal construction in Hokkaido was also discussed.

Colonization history of the sable Martes zibellina (Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia

We examined the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs) for 279 individuals of the sable Martes zibellina (Carnivora, Mustelidae), derived from diverse areas throughout the regions of the Ural Mountains to the Russian Far East on the Eurasian continent and the peripheral peninsula (Kamchatka) and islands (Sakhalin, Hokkaido, and southern Kurils). The demographic history of the sable and its migration history to the eastern peripheral peninsula and islands were inferred using phylogeographic approaches. The analyses confirmed the previously found major lineages for the examined sables and further identified novel sublineages. Our data also support that a lineage, which is endemic to the eastern marginal islands (Sakhalin, Hokkaido, and southern Kurils), was produced by the demographic expansion of an ancestral lineage in the Eurasian continent. The most recent common ancestor of the Sakhalin, Hokkaido, and southern Kuril sables was estimated to exist during the Late Pleistocene. We also determined that another lineage exists on Sakhalin and is shared by the Far East Primorsky population. Our results indicate multiple migration events onto Sakhalin from the continent and suggest the importance of the formation of several straits to the distribution of sable lineages. Meanwhile, Kamchatka is dominated by a sole lineage which would also have followed the demographic expansion on the Eurasian continent. The Russian Far East was indicated as the source area for lineage diversifications; in this region, genetic diversity was relatively high, which is consistent with previous studies.

Factors Affecting the Distribution of the Japanese Weasel Mustela itatsi and the Siberian Weasel M. sibirica in Japan

Abstract. The vertical distribution of introduced Siberian weasels Mustela sibirica and endemic Japanese weasels M. itatsi in the Seburi Mountains in Kyushu, Japan, was examined from October 1996 to February 1998. Siberian weasels occurred near villages with paddy and cultivated fields, whereas Japanese weasels occurred in grasslands and plantations. The dispersion of yearlings destabilized the distributions of both weasel species. The horizontal distribution of both species throughout Japan was examined by means of collection of dead specimens and by trapping from March 1998 to March 2002. The eastern boundary of the distribution of the Siberian weasel was Fukui, Nagano, and Aichi prefectures; however, the distribution is expanding slowly eastward. The Siberian weasel cannot invade new habitats that lack nearby villages in Seburi, and cannot expand its range in the eastern area of Aichi, where Japanese weasels are dominant. The presence of the Japanese weasel likely prevents expansion of the distribution of the Siberian weasel.