Tsutomu Hikida

Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards

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.

Phylogenetic relationships of the family Agamidae (Reptilia : Iguania) inferred from mitochondrial DNA sequences

Abstract Phylogenetic relationships of the family Agamidae were inferred from 860 base positions of a mitochondrial DNA sequence of 12S and 16S rRNA genes. Results confirmed the monophyly of this family including Leiolepis and Uromastyx (Leiolepidinae), and indicated the sister relationship between Agamidae and Chamaeleonidae. Our results also indicated the presence of two major clades in Agamidae. In one of these major clades, “Leiolepidinae” was first diverged, followed by the Lophognathus and Hypsilurus in order, leaving Physignathus, Chlamydosaurus and Pogona as monophyletic. This result contradicts the currently prevailing hypothesis for the agamid phylogeny, which, on the basis of morphological data, assumes the primary dichotomy between Leiolepidinae and the remainder (Agaminae). The phylogenetic diversity of agamid lizards in the Australian region is supposed to have increased through an in situ continental radiation rather than through multiple colonizations from Southeast Asia. Distributions of some species in Asia and Melanesia are attributed to the secondary dispersals subsequent to this radiation.

Phylogenetic Relationships of the Flying Lizards, Genus Draco (Reptilia, Agamidae)

Abstract Phylogenetic relationships among 12 species of the genus Draco were inferred from 779 base pairs of mitochondrial 12S and 16S rRNA genes and allozymes for 20 presumptive loci. Results indicated the presence of at least four distinct lineages within the genus. The first lineage consists of D. volans and D. cornutus, whereas the second only of D. lineatus, which exhibits a great genetic divergence between two subspecies. The third is monotypic with D. dussumieri, the only species distributed in southern India. The fourth included all the remaining species. The third and fourth lineages are supposed to exclusively share a common ancestor. It is likely that the common ancestor of whole Draco originally diverged into three groups, the ancestors of the first, second, and third and fourth lineages, by vicariance. In the fourth lineage, D. blanfordii, D. haematopogon, D. melanopogon, D. obscurus and D. taeniopterus are likely to be exclusively close to each other. The resultant phylogenetic tree contradicts the dichotomous relationships previously hypothesized on the basis of morphological characters.

Phylogenetic Relationships of Eublepharid Geckos (Reptilia: Squamata): A Molecular Approach

Abstract 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.

Evolution of Asian and African Lygosomine Skinks of the Mabuya Group (Reptilia: Scincidae): A Molecular Perspective

Abstract Phylogenetic relationships among Asian and African lygosomine skinks of the Mabuya group were inferred from 825 base pairs of DNA sequences of mitochondrial 12S and 16S rRNA genes. Results indicated the presence of two distinct lineages within this group, of which one consisted of Lamprolepis and Lygosoma, and the other of Apterygodon, Dasia, and Asian and African Mabuya. Within the latter, African species of Mabuya first diverged from the remainder, leaving the Asian congeners together with the Apterygodon–Dasia clade. Our results, while suggesting the non-monophyly of the genus Mabuya, do not support the currently prevailing phylogeographical hypothesis which assumes the independent origins of Lamprolepis and Lygosoma from the Asian Mabuya-like stock. On the other hand, our results suggest that morphological and karyological similarities between the Apterygodon–Dasia clade and Lamprolepis are attributable to symplesiomorphy, while their ecological similarity to convergence. Morphological and karyological character states unique to Apterygodon are supposed to have evolved from those exhibited by Dasia.

Field observations on the social behavior of the flying lizard, Draco volans sumatranus, in Borneo

KUITER, R. H. 1992. Tropical reef-fishes of the western Pacific Indonesia and adjacent waters. PT Gramedia Pustaka Utama, Jakarta, Indonesia. MASUDA, H., C. ARAGA, AND T. YOSHINO. 1975. Coastal fishes of southern Japan. Tokai Univ. Press, Tokyo, Japan. MULLER, K. 1992. Underwater Indonesia a guide to the worlds greatest diving. Passport Books, Lincolnwood, Illinois. RANDALL, J. E. 1955. An analysis of the genera of surgeon fishes (family Acanthuridae). Pacif. Sci. 9:359-367. , AND L. J. BELL. 1992. Naso caesius, a new acanthurid fish from the central Pacific. Ibid. 46: 344-352.

Parapatric distribution of the lizards Plestiodon (formerly Eumeces) latiscutatus and P. japonicus (Reptilia: Scincidae) around the Izu Peninsula, Central Japan, and its biogeographic implications.

Abstract The scincid lizard Plestiodon latiscutatus is found in the Izu Islands and Izu Peninsula of central Japan, whereas P. japonicus, a close relative, is found over the entire main island group of Japan, except the Izu Peninsula. The precise area of occupancy of these species was surveyed around the Izu Peninsula. Species identification was made through comparison of mitochondrial DNA partial sequences of specimens from the Izu Peninsula with those from the other regions, since morphological differences between these species have not yet been characterized. This study determined that these species are deeply diverged from each other in mitochondrial DNA sequence, and that the ranges of these species overlap only in a narrow zone. The results imply that gene flow between these species, if any, is restricted to a low level, without physical barriers. The boundary between the geographic ranges of these species was established as occurring along the lower Fuji River, Mt. Fuji, and the Sakawa River. This region is concordant with that of the old sea that is assumed to have separated the Izu Peninsula from other parts of the Japanese main island group until the middle Pleistocene. This pattern suggests that P. latiscutatus and P. japonicus were differentiated allopatrically before the connection of land areas of the Izu Peninsula and Honshu, the main island of Japan, and come into secondary contact through this connection. Thus, the species boundary is likely to have been maintained in situ, without physical barriers, since the secondary contact in the middle Pleistocene.

Biochemical systematics of the Latiscutatus species-group of the genus Eumeces (Scincidae: Reptilia) from east asian islands

Abstract Genetic differentiation and phylogenetic relationships were examined for populations belonging to six species and one subspecies of the latiscutatus species-group of the genus Eumeces from East Asia by use of allozyme data. Results indicate that the population of Kuchinoshima of the northern Ryukyus, formerly assigned to E. latiscutatus , actually belongs to E. marginatus . This suggests the past dispersal of the species over Tokara Tectonic Strait, which is considered to have existed since the Pliocene. Current outlines for the two subspecies of E. marginatus ( E. m. marginatus and E. m. oshimensis ) were not supported; our data strongly suggested that Okinoerabujima and Yoronjima populations, currently assigned to E. m. oshimensis on the basis of color pattern, are actually more closely related to the nominotypical subspecies in the Okinawa Group. The UPGMA phenogram and the Wagner tree obtained from the genetic distance matrices seem to support Hikidas (1993) recently proposed phylogram constructed on the basis of distance matrix of morphological data in confirming the exclusively close relationships between E. okadae and E. latiscutatus , and E. marginatus and E. stimpsonii .

Phylogeny and biogeography of water skinks of the genus Tropidophorus (Reptilia: Scincidae): a molecular approach

Phylogenetic relationships of the Oriental semiaquatic lygosomine skinks of the genus Tropidophorus were inferred from 1219 base positions of mitochondrial 12S and 16S rRNA genes. Results of the phylogenetic analyses incorporating data for representatives of other lygosomine genera indicated that the basal phylogenetic split within Tropidophorus separated a clade of continental Indochinese species exclusive of T. cocincinensis and T. microlepis from one comprising T. cocincinensis, T. microlepis and species from Borneo, Sulawesi and the Philippines. Of the latter group, the two continental species form the sister taxon to a clade comprising the island species. Diversification among species in Indochina and among Borneo, the Philippines and Sulawesi was likely concentrated in the Miocene, with no apparent dispersal among these regions during the Pleistocene. The body depression recognized in several Indochinese species is likely to have occurred twice in parallel as an adaptation to saxicolous habitats.

Discovery of sympatric cryptic species within Gekko hokouensis (Gekkonidae: Squamata) from the Okinawa Islands, Japan, by use of allozyme data

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.