Hidetoshi Ota

Abstract The modern and Late Pleistocene terrestrial fauna of Miyako Jima and adjacent islands (the Miyako Islands) in the southern Ryukyu Islands, southwestern Japan, includes some endemic taxa or genetically unique populations that exclusively have closest allies in the more isolated Okinawa Jima and adjacent islands (the Okinawa Islands) than in the Yaeyama Islands, which are located southwest of the Miyako Islands with much narrower intervening straits. Those taxa or populations include representatives of lineages that have physiologically highly limited ability for over-sea dispersal and the Miyako Islands are currently separated from the Okinawa Islands by at least 300 km of open water; therefore, the formation of this phylogeographical pattern is perplexing. In this study, we review the late Cenozoic geology of the Miyako Islands, southern Okinawa Jima, the Okinawa–Miyako submarine plateau (OMSP; a plateau located between Okinawa Jima and Miyako Jima), and the Kerama gap, which is a depression between the OMSP and Okinawa Jima. We then consider the origin of the modern and Late Pleistocene terrestrial animals, including a number of non-volant vertebrates on the Miyako Islands. Finally, we propose a new hypothesis (the OMSP hypothesis) to explain the enigmatic composition of modern and Late Pleistocene terrestrial vertebrate fauna of the islands. Southern Okinawa Jima was uplifted and emerged after ca. 2 Ma and was temporarily connected to the OMSP, which is likely to have emerged earlier than southern Okinawa Jima, to form a large island extending from Okinawa Jima to the Miyako Islands with a NE–SW direction of ~ 400 km. Subsequently, Okinawa Jima became separated from the OMSP when the Ryukyu Group—which is composed of Quaternary reef and associated fore-reef and shelf deposits—began to accumulate around the island at 1.7–1.4 Ma. During the interval from 2.0 to 1.7–1.4 Ma, numerous terrestrial animals, including flightless vertebrates, extended their distribution to the OMSP. Although the Miyako Islands repeatedly underwent complete submergence during deposition of the main part of the Ryukyu Group (1.25–0.4 Ma), they were uplifted and emerged to become a land area after ca. 0.4 Ma. In contrast, the OMSP subsided after ca. 0.4 Ma and was almost completely submerged after 0.27 Ma. During ca. 0.4–0.27 Ma, terrestrial animals migrated from the OMSP to the Miyako Islands.

The Kuroiwa's eyelid gecko Goniurosaurus kuroiwae is an endangered species in a state of relict endemism in the Central Ryukyus, Japan, and is divided into five subspecies. We analyzed variations in sequence data for approximately 1900 base positions of mitochondrial 12S and 16S rRNA, and cytochrome b genes from samples representing all recognized subspecies of G. kuroiwae together with those from congeneric species in order to test the relevant previous phylogenetic hypotheses and discuss biogeographical implications in the degree and pattern of genetic divergence within G. kuroiwae. Our results, while confirming a previous molecular phylogenetic hypothesis proposed on the basis of much smaller data set, negate the relationships hypothesized on morphological grounds by explicitly supporting: 1) the primary dichotomy, with substantial genetic divergence, between G. k. splendens from the Amami Island Group and the remaining subspecies all from the Okinawa Island Group; and 2) the presence of at least six independent lineages within the latter, indicating non-monophyly for two of the subspecies, G. k. kuroiwae and G. k. orientalis, in the current taxonomic definitions. The marked genetic divergence between populations of the two island groups seems to have initiated in the middle Miocene, i.e., prior to formation of straits that have consistently been separating these two island groups since the early Pleistocene. All populations of G. kuroiwae are regarded as endangered from the viewpoint of conservation genetics.

Blue-tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well-supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine-locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent-based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re-evaluate 'deep' relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of 'scincines' and the inter-relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large 'scincine' clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large-bodied species inhabiting northern Indochina, south-eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent-based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter-relationships of the primarily small-bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887)+P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London.

Identifying and dating historical biological events is a fundamental goal of evolutionary biology, and recent analytical advances permit the modeling of factors known to affect both the accuracy and the precision of molecular date estimates. As the use of multilocus data sets becomes increasingly routine, it becomes more important to evaluate the potentially confounding effects of rate heterogeneity both within (e.g., codon positions) and among loci when estimating divergence times. Here, using Plestiodon lizards as a test case, we examine the effects of accommodating rate heterogeneity among data partitions on divergence time estimation. Plestiodon inhabits both East Asia and North America, yet both the geographic origin of the genus and timing of dispersal between the continents have been debated. For each of the eight independently evolving loci and a combined data set, we conduct single model and partitioned analyses. We found that extreme saturation has obscured the underlying rate of evolution in the mitochondrial DNA (mtDNA), resulting in severe underestimation of the rate in this locus. As a result, the age of the crown Plestiodon clade was overestimated by 15-17 Myr by the unpartitioned analysis of the combined loci data. However, the application of partition-specific models to the combined data resulted in ages that were fully congruent with those inferred by the individual nuclear loci. Although partitioning improved divergence date estimates of the mtDNA-only analysis, the ages were nonetheless overestimated, thus indicating an inadequacy of our current models to capture the complex nature of mtDNA evolution in over large time scales. Finally, the statistically incongruent age distributions inferred by the partitioned and unpartitioned analyses of the combined data support mutually exclusive hypotheses of the timing of intercontinental dispersal of Plestiodon from Asia to North America. Analyses that best capture the rate of evolution in the combined data set infer that this exchange occurred via Beringia ∼18.0-30 Ma. © The Author(s) 2010.

The Quaternary terrestrial turtle fauna of the Ryukyu Archipelago was reviewed on the basis of recently excavated fossils, as well as literature information. As a result, five extinct species (four geoemydids [Cuora sp., Geoemyda amamiensis, Mauremys sp., and another species with undetermined generic and specific status] and one testudinid [Manouria oyamai]) were recognized from Late Pleistocene cave and fissure deposits. Two of the three turtles currently occurring in this archipelago (C. flavomarginata and G.japonica) were also recognized from comparable deposits on islands, including those where they do not occur at present. These records indicate that the terrestrial turtles of the Ryukyus were much more diverse during the Late Pleistocene than at present, and that extinction has occurred during the last few tens of thousands of years not only for those five fossil species bur also for some island populations of the extant species. Distributions of three of the extinct species (G. amamiensis, Cuora sp., and the geoemydid [genus and species undetermined]), confined to the central Ryukyus, are concordam with the currently prevailing hypothesis of Ryukyu paleogeography, which assumes a relatively long isolation of this region and much more recent insularization of the southern Ryukyus. In contrast, distributions of the remaining two extinct species (Man. oyamai and Mau. sp.) must be explained by some ad hoc scenario or, otherwise, drastic modification of the current hypothesis. © 2008 by University of Hawai'i Press. All rights reserved.

A female Hemidactylus frenatus, collected on 7 June 2004 and housed alone in a cage, produced a total of six clutches, each consisting of one or two eggs, until 24 June 2005. All eggs but one, including the one egg composing the last clutch, hatched to produce hatchlings that included a male. This indicates that females of this broadly distributed gecko can store functional sperms for more than one year. Such ability may have played an important role in the colonization by this gecko of tropical and particularly subtropical regions of Asia and the Pacific islands. © 2006, The Herpetological Society of Japan. All rights reserved.

A mark and recapture study was carried out for three years on a population of the Ijima's sea snake, Emydocephalus ijimae, in the coastal shallow water of Zamamijima Island, central Ryukyus, Japan. The relatively high recapture (47% of 167 marked snakes) suggests that E. ijimae is a particularly philopatric, sedentary species among the sea snakes. The sex ratio (male: female), approximately 1.6:1, significantly skewed from 1:1. The growth rate in SVL declined with growth, with females thoroughly growing better than males. Males and females were estimated to begin reproductive activity in the second or third summer and the third spring after birth, respectively. Frequency of female reproduction is guessed to vary from annual to biennial, or even less frequent.

Developmental changes in external morphological characters were examined for the whole embryonic-larval period of Microhyla ornata from Okinawajima Island, Ryukyu Archipelago, Japan. By considering the extent of morphological changes observed and compatibility with standard developmental tables hitherto proposed for other anuran groups, a developmental table consisting of 45 developmental stages was proposed for this species. Eight developmental terms, each consisting of several successive stages, were also defined-Cleavage-Blastula [stages 1-10], Gastrula [stages 11-14], Neurula [stages 15-18], Tail bud [stages 19-21], External gill [stages 22-28], Hind limb bud [stages 29-33], Hind limb formation [stages 34-41], and Metamorphosis [stages 42-45]). From previously described conspecific samples from other localities, our sample exhibited appreciable differences in the egg diameter, timing of pigmentaion at the position of the stomodium, and a few other tadpole characters. © 2003, The Herpetological Society of Japan. All rights reserved.

Historical relationships were inferred for the oriental lizards of the genus Takydromus Daudin 1802 (Lacertidae) on the basis of DNA sequences. Of the 17 species currently recognized for the genus, 13 species represented by 42 specimens from 29 localities were examined. Maximum-likelihood and maximum-parsimony analyses of data for 829 aligned sites from parts of the mitochondrial 12S and 16S rRNA genes yielded relationships that, while showing no substantial discrepancy with each other, were strikingly different from a currently prevailing phylogenetic hypothesis from a parsimony analysis of morphological characters. Based on the results of these molecular analyses, supplemented by results of the morphological analysis that offered robust evidence for positions of two additional species (T. khasiensis and T. sylvaticus), the following interrelationships were hypothesized as the most preferred phylogeny: (kuehnei (sexlineatus khasiensis))(tachydromoides ((smaragdinus (sauteri (dorsalis sylvaticus))) (amurensis (((formosanus wolteri) hsuehshanensis)(toyamai (septentrionalis stejnegeri)))))). These interrelationships indicate: (1) invalidity of Platyplacopus Boulenger 1917, which was recently resurrected as a subgenus of Takydromus on the basis of the morphological analysis; (2) homoplasy in states of some morphological characters, such as green dorsal coloration, that were considered as synapomorphs of certain nodes in the morphological analysis; and (3) involvement of the genus in a series of vicariances in both the continental and insular parts of eastern Eurasia. Due to the paucity of available samples, phylogenetic status of T intermedius and T. haughtonianus remain to be examined in future studies. (C) 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 76,493-509.

An electrophoretic survey of samples of the gekkonid lizard, Gekko hokouensis, from the East Asian islands demonstrated that two genetically divergent, but morphologically almost identical, entities occur on five islands of the Okinawa Group, Ryukyu Archipelago, Japan. These entities, while sharing all of the external character states diagnostic of G. hokouensis, exhibited fixed allele differences at six to eight out of 30 loci examined and great overall genetic distances [Nei's (1978) D = 0.489-0.654]. On Kumejima and Tonakijima Islands of the Okinawa Group, the two entities were collected together from identical microhabitats. These results indicate that the two entities represent separate biological species. Genetic comparisons of these two cryptic species from the Okinawa Group with 'G. hokouensis' from other island groups revealed that one occurs broadly in the insular region of East Asia, whereas the other is restricted to the Okinawa Group. Implications of the present findings for the morphological evolution of 'G. hokouensis' are also discussed.

The mourning gecko, Lepidodactylus lugubris, is an all-female parthenogenetic species widely distributed in tropical and subtropical regions. We examined clonal diversity of L.. lugubris in southern Japan, the northernmost extremity of the species' range. Results indicated that the assemblages of the Ogasawara Islands are composed solely of diploid clone A, which may have originated from artificial transportation after World War II. Assemblages of L. lugubris in the Ryukyu Archipelago were composed solely of triploid clone C. This, along with literature records, suggests that the gecko recently colonized the Ryukyu Archipelago on limited opportunities from limited sources. Samples from the Daito Islands included both diploid and triploid individuals representing one and 11 different clones, respectively. Except for one triploid clone (clone B), these clones were most likely to be endemic to the Daito Islands. Analyses of genotypic pattern suggest that most of the putative endemic triploid clones of the Daito Islands originated from iterative crosses between sympatric diploid clones and males of closely related bisexual species that were most likely extirpated subsequently.

This article compares amphibian and reptile components of the original and revised versions of the Red List of Japan, and analyzes geographic patterns of, and major threats to, species and subspecies now assigned to the threatened categories. The numbers of both amphibians and reptiles categorized as threatened in the Red List of Japan have increased greatly through its revision as a result of recent progress in the taxonomy of these groups in Japan, the introduction of new criteria for risk assessment, and unexpectedly rapid declines in the status of several taxa. Threatened taxa of amphibians and reptiles in the revised list tend to be concentrated in the Ryukyu Archipelago, where deforestation seems to be the major ultimate cause of declines. Reduction in the quality and quantity of inland water environments seems to be the major cause of declines in several endemic amphibians from the main islands of Japan. The importance of conservation was emphasized in the revised list by progress in taxonomy, by new insights and data on the estimation of temporal dynamics of population density or habitat size for threatened taxa, and by the impacts of and need to prevent further deforestation in the Ryukyus and of the ongoing destruction of inland water habitats on the main islands of Japan.

Phylogenetic analyses were carried out for representatives of all eublepharid genera and a few other gekkonoid taxa using sequence data for 879 base pairs of mitochondrial 12S and 16S ribosomal RNA genes. Neighbor-joining (NJ) distance analysis of the data suggested independent great divergences of Coleonyx and Aeluroscalabotes, and monophyly of the remainder within Eublepharidae (bootstrap proportion [BP]=76%). Of the latter, the two African genera, Hemitheconyx and Holodactylus, were almost certainly monophyletic altogether (BP=99%), whereas their sister-group relationship with Eublepharis received a weaker, but still substantial support (BP=68%). Within Goniurosaurus kuroiwae, G. k. splendens first diverged from the remainder (BP=100%), followed by G. k. kuroiwae from the northern part of Okinawajima (BP=100%): G. k. kuroiwae from the southern part of Okinawajima and G. k, orientalis, differing from each other at only seven bases, diverged finally (BP=99%). Parsimony analysis yielded results consistent with those of NJ analysis with respect to the monophyly of the two African genera and relationships within G. kuroiwae, but retained the other relationships within Eublepharidae unresolved. Our results, while showing no serious discrepancies with the relationships among eublepharid genera hypothesized from morphological data, cast a serious doubt to the currently accepted population systematics within G. kuroiwae. Furthermore, results of both analyses suggested a closer affinity of Diplodactylinae (as represented by Rhacodactylus trachyrhynchus) with Eublepharidae, rather than with Gekkoninae. Our study lends a robust support to the Laurasian origin of the family Eublepharidae.

Variation in 28 quantitative characters and one qualitative character in the endemic Ryukyu skink Ateuchosaurus pellopleurus was analyzed. Multivariate analysis of the quantitative characters revealed extensive variation among the insular populations. Branching topology in the neighbor-joining phenogram deriving from Mahalanobis distances among island samples coincides well with their geographic arrangement, suggesting a great contribution of geohistory to the branching pattern. By contrast, branch length in the phenogram does not seem to reflect the paleogeography well, presumably due to noise from rapid morphological changes in small island populations. None of our analyses demonstrated distinct divergence between populations on islands northeast and southwest of the Tokara Tectonic Strait. Accepting the current paleogeographical hypothesis that this strait has consistently existed since its initial formation in the Pliocene, we interpret this result as indicative of recent oversea dispersal across the strait. Results of the analyses also suggested that in A. pellopleurus primary divergence occurred between populations of the Okinawa Group and the remainder. Nevertheless, because of the absence of even a single discriminant character between these two groups, we reject taxonomic subdivision of the species proposed by a few previous authors.

External characters, hemipenial morphology, karyotype, and reproductive mode were examined for the three subspecies of the endemic Ryukyu natricine, Amphiesma pryeri. Results revealed that populations of the Yaeyama Group, currently regarded as comprising a subspecies, A. P. ishigakiense, have several unique features such as the brownish ground colour of head, termination of sulcus spermaticus in the crotch between apical lobes of the hemipenis, terminal location of centromeres in the largest microchromosome pair, and the viviparous mode of reproduction. In the other populations, ground colour of head is black or dark greyish tan; sulcus spermaticus terminates near the tip of the left lobe of the hemipenis; the largest microchromosome pair is metacentric; and the reproductive mode is oviparous. Of these, however, the Miyakojima population, which currently consists solely of the subspecies, A. p. concelarum, differs from the nominotypical subspecies from the central Ryukyus in having only 94-102 subcaudal scales and telocentric W chromosome; A. P. pryeri has 112-130 subcaudal scales and submetacentric W chromosomes. These strongly suggest that the two subspecies have also substantially diverged from each other, constituting distinct evolutionary lineages. We thus accord full-species status to each of pryeri, concelarum and ishigakiense, and revise their definitions on the basis of the present results. A dichotomous key to the Japanese species and subspecies of Amphiesma is provided. (C) 1997 The Linnean Society of London.

The batagurid turtle, Mauremys mutica, is widely distributed in tropical to temperate East Asia. Analyses of morphometric characters and coloration revealed that the southern Ryukyu populations of this species are much diverged from the other populations, presumably as a result of their long geographical isolation. We describe those populations as a new subspecies, M. m. kami. Analysis of geographic variation also suggested that distinctly isolated populations of the central and northern Ryukyus, and Kyoto and Shiga Prefectures of central Japan have originated from animals artificially introduced from the Yaeyama Group, and Taiwan, respectively. We confirmed the absence of ''larger female'' sexual size dimorphism (SSD) in M. mutica unlike most other aquatic batagurids, and further demonstrated variation in SSD pattern between the subspecies: in M. m. kami, the adult male has a significantly greater carapace length than adult females, whereas the adult carapace length does not differ significantly between sexes in the nominotypical subspecies. It is hypothesized that these dimorphic patterns evolved from the widely prevailing ''larger female'' condition through epigamic selection involving forcible copulatory behavior.

Bisexual populations of the gekkonid genus Lepidodactylus from Belau and other Micronesian islands are reviewed taxonomically on the basis of museum and newly collected materials. Specimens from the Ngerukewid Island Group of Belau, having an entire terminal scansor and a few divided or deeply notched subterminal scansors on digits II to V, are distinct from other Micronesian congeneric populations and are assigned to the species group which has previously been known from New Guinea and other Melanesian islands. The Ngerukewid specimens, however, differ from any other members of this species group in several characteristics such as a relatively few body scale rows; and, hence, it is described herein as a new species, Lepidodactylus paurolepis. Remaining specimens from Micronesia, all having a divided terminal scanser on digits II to V, include the parthenogenetic L. lugubris, one bisexual species, and possible hybrids between them. The bisexual form closely resembles L. lugubris and L. aureolineatus from the Philippines but differs from them in having smaller body, characteristic dorsal pattern, and only barely developed lateral serrations on tail. Because the one extant syntype of Gecko moestus Peters, a species first described in 1867 from Belau but subsequently synonymized with L. lugubris, is apparently conspecific with that bisexual form, we designate this specimen as lectotype and resurrect the validity of the species as Lepidodactylus moestus (Peters).