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Masato Nikaido

Publications and source records attributed to Masato Nikaido.

At least 19 recordsLinked to original sources
PubMed2006

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species.

Morphological data have indicated that toothed whales form a monophyletic group. However, research published in the last several years has made the issue of the monophyly or paraphyly of toothed whales a subject of debate. Our group previously characterized three independent loci in which SINE insertions were shared among dolphins and sperm whales, thus supporting the traditional, morphologically based hypothesis of toothed whale monophyly. Although in recent years a few additional molecular works proposed this topology, there is still skepticism over this monophyly from the view point of molecular systematics. When the phylogeny of rapidly radiated taxa is examined using the SINE method, it is important to consider the ascertainment bias that arises when choosing a particular taxon for SINE loci screening. To overcome this methodological problem specific to the SINE method, we examined all possible topologies among sperm whales, dolphins and baleen whales by extensively screening SINE loci from species of all three lineages. We characterized nine independent SINE loci from the genomes of sperm whales and dolphins, all of which cluster sperm whales and dolphins but exclude baleen whales. Furthermore, we characterized ten independent loci from baleen whales, all of which were amplified in a common ancestor of these whales. From these observations, we conclude that toothed whales form a monophyletic group and that no ancestral SINE polymorphisms hinder their phylogenetic assignment despite the short divergence times of the major lineages of extant whales during evolution. These results suggest that a small population of common ancestors of all toothed whales ultimately diverged into the lineages of sperm whales and dolphins.

Animals↗
PubMed2006

New candidate species most closely related to penguins.

The phylogenetic position of the order Spenisciformes in Aves remains unclear despite several independent analyses based on morphological and molecular data. To address this issue, we determined the complete mtDNA sequence of rockhopper penguins. The mitochondrial genome, excluding the region from the D-loop to 12SrRNA, was also sequenced for petrel, albatross, frigatebird, loon and grebe, which previous studies suggest are related to penguins. A maximum likelihood analysis of the phylogenetic placement of penguins with 23 birds, including 17 species whose mtDNA sequences were previously reported, suggested that storks are the closest extant relatives of penguins, with 78% and 56% bootstrap supports, depending on the choice of outgroup species. Thus, ciconiiform birds constitute new candidates as the closest extant relatives of penguins (previously proposed candidates were either gaviiform, podicipediform, or procellariiform birds). In addition to this new evidence, our analysis gave evidence to some of ambiguous relationships in the avian tree: our analysis supported a basal split between passerines and other neoavians within Neoaves, and rejected the monophyly of Falconiformes as well as that of loons and grebes.

Animals↗
PubMed2006

Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage.

Balaenoptera omurai, formerly classified as a small form of Bryde's whale, was recently reclassified as a new baleen whale species of the family Balaenopteridae. Although researchers have investigated the evolutionary history of Balaenopteridae and their relatives using molecular phylogenetic methods, the taxonomy of the ordinary Bryde's whale (Balaenoptera brydei) and small-form Bryde's whales (Balaenoptera edeni and B. omurai) remains unclear. We have used complete mtDNA sequences and short interspersed repetitive element (SINE) insertion patterns to construct the evolutionary history of both B. omurai and the taxonomically redefined species, B. edeni. The combined results demonstrate that B. omurai forms a monophyletic lineage with B. musculus, B. brydei, B. edeni and B. borealis and that B. omurai and B. musculus successively diverged from their common ancestor. In addition, we also showed that B. edeni constitutes a sister taxon to B. brydei. Our data suggest that B. omurai evolved as an ancient independent lineage that diverged much earlier than B. borealis, B. brydei and B. edeni, which were previously believed to be closely related to B. omurai.

Animals↗
PubMed2006

Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications.

We determined the complete mitochondrial genomes of five cephalopods of the Subclass Coleoidea (Suborder Oegopsida: Watasenia scintillans, Todarodes pacificus, Suborder Myopsida: Sepioteuthis lessoniana, Order Sepiida: Sepia officinalis, and Order Octopoda: Octopus ocellatus) and used them to infer phylogenetic relationships. In our Maximum Likelihood (ML) tree, sepiids (cuttlefish) are at the most basal position of all decapodiformes, and oegopsids and myopsids form a monophyletic clade, thus supporting the traditional classification of the Order Teuthida. We detected extensive gene rearrangements in the mitochondrial genomes of broad cephalopod groups. It is likely that the arrangements of mitochondrial genes in Oegopsida and Sepiida were derived from those of Octopoda, which is thought to be the ancestral order, by entire gene duplication and random gene loss. Oegopsida in particular has undergone long-range gene duplications. We also found that the mitochondrial gene arrangement of Sepioteuthis lessoniana differs from that of Loligo bleekeri, although they belong to the same family. Analysis of both the phylogenetic tree and mitochondrial gene rearrangements of coleoid Cephalopoda suggests that each mitochondrial gene arrangement was acquired after the divergence of each lineage.

Animals↗
PubMed2006

Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes.

Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.

Animals↗
PubMed2005

The rise and fall of the CR1 subfamily in the lineage leading to penguins.

The evolution of penguins has been investigated extensively, although inconclusively, by morphologists, biogeographers and molecular phylogeneticists. We investigated this issue using retroposon analysis of insertions of CR1, which is a member of the LINE (long interspersed element) family, in the genomes of penguins and penguin relatives. The retroposon method is a powerful tool for identifying monophyletic groups. Because retroposons often show different relative frequencies of retroposition during evolution, it is first necessary to identify a certain subgroup that was specifically active during the period when the species in question diverged. Hence, we systematically analyzed many CR1 members isolated from penguin and penguin-related genomes. These CR1s are divided into at least three distinct subgroups that share diagnostic nucleotide insertions and/or deletions, namely, penguin CR1 Sph I, Sph II type A and Sph II type B. The analysis of the inserted retroposons by PCR revealed that different CR1 subfamilies or types had amplified at different rates among different periods during penguin evolution. Namely, the penguin CR1 Sph I subfamily had higher rates of retroposition in a common ancestor of all orders examined in this study or at least in a common ancestor of all extant penguins, and the subfamily Sph II type A also had the same tendency. Therefore, these CR1 members can be used to elucidate the phylogenetic relationships of Sphenisciformes (penguins) among different avian orders. In contrast, the penguin CR1 Sph II type B subfamily had higher rates of retroposition just before and after the emergence of the extant genera in Spheniscidae, suggesting that they are useful for elucidating the intra-relationships among extant penguins. This is the first report for the characterization among the members of CR1 family in avian genomes excluding those of chickens. Hence, this work will be a cornerstone for elucidating the phylogenetic relationships in penguin evolution using the retroposon method.

Animals↗
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis.

Baleen whales (suborder Mysticeti) comprise 11 extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using short interspersed repetitive element (SINE) insertion data, which now are regarded as almost ideal shared, derived characters at the molecular level. We reconstructed the phylogenetic relationships of baleen whales by characterizing 36 informative SINE loci. One of the intriguing conclusions is that balaenopterids and eschrichtiids radiated very rapidly during a very short evolutionary period. During this period, speciation occurred in balaenopterids and eschrichtiids while newly inserted SINE loci remains polymorphic. Later on, these SINEs were sorted incompletely into each lineage. Thus, there are now inconsistencies among species regarding the presence or absence of a given SINE. This is in sharp contrast to the phylogeny of toothed whales, for which no SINE inconsistencies have been found. Furthermore, we found monophyletic groupings between humpback and fin whales as well as between (sei+Bryde's) whales and blue whales, both of which have not previously been recognized. The comprehensive SINE insertion data, together with the mitochondrial DNA phylogeny that was recently completed (Sasaki, T., M. Nikaido, H. Healy et al. 2005. Mitochondrial phylogenetics and evolution of mysticete whales. Syst. Biol. 56:77-90; Rychel, A. L., T. W. Reeder, and A. Berta. 2004. Phylogeny of mysticete whales based on mitochondrial and nuclear data. Mol. Phylogenet. Evol. 32:892-901), provide a nearly complete picture of the evolutionary history of baleen whales.

Animals↗
PubMed2005

A retroposon analysis of Afrotherian phylogeny.

Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.

Amino Acid Sequence↗
PubMed2005

Mitochondrial phylogenetics and evolution of mysticete whales.

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.

Animals↗
PubMed2004

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea.

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.

Amino Acid Sequence↗
PubMed2004

Retroposon mapping in molecular systematics.

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

Animals↗
PubMed2003

Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources.

Short interspersed nuclear elements (SINEs) are dispersed repetitive DNA sequences that are major components of all mammalian genomes. They have been described in almost all lineages of Euarchontoglires (rodents, rabbits, primates, flying lemurs, and tree shrews), except in flying lemurs. Most SINE family members are composed of three distinct regions: a 5' tRNA-related region, a tRNA-unrelated region, and a short tandem repeat at the 3' end that is AT-rich. The newly discovered SINE family in Cynocephalus deviates from this common structure. All 30 SINE loci analyzed in this family lack a tRNA-unrelated region and are composed exclusively of tRNA-related elements. Therefore, this novel SINE structure, described for the first time in mammalian genomes, was designated as t-SINE. The t-SINE family exhibits a high copy number and is specific to flying lemurs. Three major t-SINE subfamilies could be distinguished on the basis of characteristic nucleotides, deletions, insertions, and duplications. These sequence-specific characteristics within subfamilies and sub-subfamilies reveal that they are derived copies of distinct progenitors. We present evolutionary relationships between subfamilies and compare relationships between the subfamilies and the isoleucine tRNA gene. t-SINE amplification occurred through multiple sources and is supposedly mobilized via the L1-encoded reverse transcriptase-dependent retrotranspositional mechanism in trans.

Animals↗
PubMed2003

Ancient SINEs from African endemic mammals.

Afrotheria is a newly recognized taxon comprising elephants, hyraxes, sea cows, aardvarks, golden moles, tenrecs, and elephant shrews, each of which originated in Africa. Although some members of this taxon were once classified into distantly related groups, recent molecular studies have demonstrated their close relationships. It was suggested that this group emerged as a result of physical isolation of the African continent during the successive breakup events of Gondowanaland. In this study, a novel family of SINEs, designated AfroSINEs, was isolated and characterized from the genomes of afrotherians. This SINE family is distributed exclusively among the afrotherian species, confirming their monophyletic relationships. Furthermore, a distinct subfamily, which shares a deletion in the middle region of the SINE, was identified. The distribution of this subfamily is apparently restricted to the genomes of hyraxes, elephants, and sea cows, suggesting monophyly of these three groups, which was previously proposed as Paenungulata. We characterized the structures of the AfroSINEs from all afrotherian representatives by PCR, and we discuss how they were generated as well as the phylogenetic relationships of their host species.

Africa↗
PubMed2003

Afrotherian phylogeny as inferred from complete mitochondrial genomes.

Afrotheria is a huge assemblage of various mammals encompassing six orders that were once classified as distantly related groups. This superordinal relationship may have resulted from the break-up of Gondowanaland followed by the isolation of the African continent between 105 and 40 million years ago. Although the monophyly of Afrotheria is well supported by recent molecular studies, the interrelationships within afrotherian mammals remain unclarified. In this study, we determined the sequence of the complete mitochondrial genomes of hyrax, golden mole, and elephant shrew. These sequences were compared with those of other eutherians to analyze the phylogenetic relationships among afrotherians and, in particular, those among paenungulates. Our mitochondrial genome analysis supports the monophyly of Tethytheria.

Animals↗
PubMed2003

Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla.

We sequenced the complete mitochondrial (mt) genomes of three insectivores: the long-eared hedgehog Hemiechinus auritus, the Japanese mole Mogera wogura, and the greater Japanese shrew-mole Urotrichus talpoides. These mtDNA data together with other previously sequenced mtDNAs were analyzed using a maximum likelihood method to infer their phylogenetic relationships among eutherians. Previous mitochondrial protein analyses used a simple model that did not consider site-heterogeneity, and Erinaceoidea (hedgehogs and moonrats) was placed at the basal eutherian position that is separated from Soricoidea (shrews) and Talpoidea (moles), suggesting the exclusion of the Erinaceoidea-Eulipotyphla tree. By including the new mtDNA sequences and introducing site-heterogeneity into the model, the Erinaceoidea-Eulipotyphla tree emerges as the best tree or as a tree with a log-likelihood score indistinguishable from that of the best tree. However, this conclusion depends on species sampling in Erinaceoidea, demonstrating the importance of both species sampling and use of an appropriate substitution model when inferring phylogenetic relationships.

Amino Acid Sequence↗
PubMed2003

The status of the Japanese and East Asian bats of the genus Myotis (Vespertilionidae) based on mitochondrial sequences.

The genus Myotis includes the largest number of species in the family Vespertilionidae (Chiroptera), and its members are distributed throughout most of the world. To re-evaluate the phylogenetic position of East Asian Myotis species with respect to Myotis species worldwide, we analyzed mitochondrial gene sequences of NADH dehydrogenase subunit 1 and cytochrome b from 24 East Asian individuals as well as 42 vespertilionid bats determined previously. The results suggest that: (1) some individuals having the same species name in Europe and Japan do not form a monophyletic clade, indicating that some bat species exhibit morphological convergence, (2) Japanese Myotis mystacinus forms a sister relationship with Myotis brandtii (Palaearctic), and both species are included in the American clade implying that an ancestor of these species originated in North America, and (3) the Black whiskered bat, Myotis pruinosus, is endemic to Japan and forms sister relationships with Myotis yanbarensis and Myotis montivagus collected from Okinawa (Japan) and Selangor (Malaysia), respectively, implying that M. pruinosus originated from the south. The systematics of Japanese and East Asian Myotis bats were revisited by considering their phylogenetic relationships. Our study provides the first extensive phylogenetic hypothesis of the genus Myotis that includes East Asian and Japanese species.

Adaptation, Biological↗
PubMed2003

The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondrial genome.

The complete mitochondrial genome of a lesser hedgehog tenrec Echinops telfairi was determined in this study. It is an endemic African insectivore that is found specifically in Madagascar. The tenrec's back is covered with hedgehog-like spines. Unlike other spiny mammals, such as spiny mice, spiny rats, spiny dormice and porcupines, lesser hedgehog tenrecs look amazingly like true hedgehogs (Erinaceidae). However, they are distinguished morphologically from hedgehogs by the absence of a jugal bone. We determined the complete sequence of the mitochondrial genome of a lesser hedgehog tenrec and analyzed the results phylogenetically to determine the relationships between the tenrec and other insectivores (moles, shrews and hedgehogs), as well as the relationships between the tenrec and endemic African mammals, classified as Afrotheria, that have recently been shown by molecular analysis to be close relatives of the tenrec. Our data confirmed the afrotherian status of the tenrec, and no direct relation was recovered between the tenrec and the hedgehog. Comparing our data with those of others, we found that within-species variations in the mitochondrial DNA of lesser hedgehog tenrecs appear to be the largest recognized to date among mammals, apart from orangutans, which might be interesting from the view point of evolutionary history of tenrecs on Madagascar.

Animals↗