Population history and genomic admixture of sea snakes of the genus Laticauda in the West Pacific.

Speciation in the open ocean has long been studied, but it remains largely elusive what factors promote or inhibit speciation in such an open environment. Marine amniotes, which evolved from terrestrial ancestors, provide valuable opportunities for studying speciation in the ocean because of their evident aquatic origins. Sea snakes are phylogenetically related to terrestrial elapid snakes and consist of two monophyletic groups (Hydrophiini and Laticaudini). These two groups migrated from land to water almost at the same time, but species diversities are remarkably different: there are approx. 60 species in 16 genera described for hydrophiins, whereas only eight species in the genus Laticauda are described for laticaudins. Here, we provide a high-quality reference genome assembly of a laticaudin L. colubrina with a scaffold N50 value of 40 Mbp, and focused on laticaudins to consider why they have seldom speciated. We performed whole-genome shotgun sequencing of several species of laticaudins sampled in their southmost (Vanuatu) and northmost (Ryukyu) habitats. Demographic histories of Vanuatu and Ryukyu populations suggest that populations of broadly distributed major species are geographically structured. Each species is genetically clearly distinguished, but there is a considerable amount of gene flow between two sibling species distributed sympatrically in Vanuatu. In addition, inter-species genomic admixture is ubiquitously observed among laticaudins even between phylogenetically distant species. Broad distribution of major species combined with such genetic mixability might have prevented laticaudins from genetic isolation and speciation.

A new species of Plestiodon (Squamata: Scincidae) from Kuchinoshima Island in the Tokara Group of the Northern Ryukyus, Japan.

A scincid lizard of the genus Plestiodon from Kuchinoshima Island in the Tokara Group of the Northern Ryukyus, Japan, has proved to be genetically and morphologically differentiated from any previously recognized species in the genus. We thus describe this island population as a new species, Plestiodon kuchinoshimensis. The new species shows characteristics of the P. latiscutatus species group, but differs from other species of this group by the combination of the following character states: postnasal absent; hatchling with five longitudinal light lines on dorsum; lateral light line on each side passing over ear opening and the sixth to eighth scale rows at midbody; dorsolateral light line beginning from behind supraoculars; patch of enlarged irregular scales on posterior femur absent; scale rows around midbody 27-32; and brownish background on the dorsal surface of the juvenile.

Divergence and long-distance overseas dispersals of island populations of the Ryukyu five-lined skink, Plestiodon marginatus (Scincidae: Squamata), in the Ryukyu Archipelago, Japan, as revealed by mitochondrial DNA phylogeography.

We assessed the historical biogeography of the Ryukyu five-lined skink, Plestiodon marginatus, and related species (P. stimpsonii and P. elegans). Our specific aims were to reveal the origin, tim- ing, and route of the colonization to three volcanic islands in the northern Tokara Group of the northern Ryukyus: Kuchinoshima, Nakanoshima, and Suwanosejima. We conducted phylogenetic analyses and divergence time estimation using a partial sequence of the mitochondrial cytochrome b gene for P. marginatus collected from across its whole range (the northern and central Ryukyus), and for P. stimpsonii (from the Yaeyama Group of the southern Ryukyus) and P. elegans (from Taiwan). Our results suggest three major clades (A, B, and C). Clades A and B consist of P. marginatus, excluding the Kuchinoshima population, and Clade C consisted of the Kuchinoshima population, P. stimpsonii, and P. elegans. These clades are estimated to have diverged during the Late Miocene to the Late Pliocene. Among the three examined northern Tokara populations, the Kuchinoshima population was shown to be a sister group of P. stimpsonii. The two other populations from Nakanoshima and Suwanosejima Islands were closely related to P. marginatus from the northern part of the Okinawa Group and that from Kodakarajima Island in the southern Tokara Group, respectively. These populations are estimated to have diverged from their respective related spe cies in various ages of the Early to Late Pleistocene, suggesting that they colonized the islands by independent overseas dispersals of approximately 50-850 km via the Kuroshio Current. Taxonomic implications for P. marginatus are also discussed.

Phylogeography of the two smooth skinks, Scincella boettgeri and S. formosensis (Squamata: Scincidae) in the Southern Ryukyus and Taiwan, as inferred from variation in mitochondrial cytochrome b sequences.

Scincella boettgeri and S. formosensis are respectively small-bodied, morphologically similar skinks, endemic to the Southern Ryukyus and Taiwan. To estimate the phylogeography of both species, we performed phylogenetic analyses using the mitochondrial cytochrome b (cyt b) gene sequences based on 102 individuals of S. boettgeri from 12 Southern-Ryukyu islands and 33 S. formosensis from six localities in Taiwan. A total of 67 haplotypes were recognized for S. boettgeri and 21 for S. formosensis. The phylogenetic analyses revealed that the populations of Scincella spp. in the Southern Ryukyus and Taiwan are composed of three major clades, the Yonagunijima clade from Yonagunijima Island, the Southern-Ryukyu clade from the Southern Ryukyus exclusive of Yonagunijima Island, and the Taiwan clade from Taiwan. These clades showed high levels of genetic divergence, suggesting that the species have been isolated since the Early Pliocene. The Southern-Ryukyu and Taiwan clades were further divided into three and four subclades, respectively. Two of the three Southern-Ryukyu subclades are partially sympatric on two islets of the Yaeyama Group, suggesting this population represents a secondary contact subsequent to their allopatric differentiations.

An investigation for population maintenance mechanism in a miniature garden: genetic connectivity or independence of small islet populations of the Ryukyu five-lined skink.

The Ryukyu five-lined skink (Plestiodon marginatus) is an island lizard that is even found in tiny islets with less than half a hectare of habitat area. We hypothesized that the island populations are maintained under frequent gene flow among the islands or independent of each other. To test our hypotheses, we investigated genetic structure of 21 populations from 11 land-bridge islands that were connected during the latest glacial age, and 4 isolated islands. Analyses using mitochondrial cytochrome b gene sequence (n = 67) and 10 microsatellite loci (n = 235) revealed moderate to high levels of genetic differentiation, existence of many private alleles/haplotypes in most islands, little contemporary migration, a positive correlation between genetic variability and island area, and a negative correlation between relatedness and island area. These evidences suggest a strong effect of independent genetic drift as opposed to gene flow, favoring the isolation hypothesis even in tiny islet populations. Isolation-by-distance effect was demonstrated and it became more prominent when the 4 isolated islands were excluded, suggesting that the pattern is a remnant of the land-bridge age. In a few island populations, however, the possibility of occasional overwater dispersals was partially supported and therefore could not be ruled out.

Phylogeography of Fischer's blue, Tongeia fischeri, in Japan: Evidence for introgressive hybridization.

The widespread lycaenid butterfly Tongeia fischeri is distributed from eastern Europe to northeastern Asia and represented by three geographically isolated populations in Japan. In order to clarify the phylogeographic history of the species, we used sequences of three mitochondrial (COI, Cyt b and ND5) and two nuclear (Rpl5 and Ldh) genes of 207 individuals collected from 55 sites throughout Japan and five sites on the Asian continent. Phylogenetic trees and the median-joining network revealed six evolutionary mitochondrial haplotype clades, which corresponded to the geographic distribution of the species. Common ancestors of Japanese T. fischeri might have come to Japan during the mid-Pleistocene by multiple dispersals of continental populations, probably via a land bridge or narrow channel between western Japan and the Korean Peninsula. The geographical patterns of variation of mitochondrial and nuclear markers are discordant in northeastern Kyushu, possibly as a result of introgressive hybridization during the ancient contact between the Kyushu and Shikoku populations in the last glacial maximum. The phylogeographic pattern of T. fischeri in Japan are probably related to the geological history, Pleistocene climatic oscillations and distribution of the host plant.

Pairwise comparison of orthologous olfactory receptor genes between two sympatric sibling sea kraits of the genus Laticauda in Vanuatu.

Olfaction-based reproductive isolation is widely observed in animals, but little is known about the genetic basis of such isolation mechanisms. Two species of sibling amphibious sea snakes, Laticauda colubrina and L. frontalis live in Vanuatu sympatrically and syntopically, but no natural hybrids have been reported. Adult females of both taxa possess distinctive lipids in the skin, and male L. frontalis distinguishes conspecific females based on olfactory cues. To shed light on the molecular basis of the evolution of olfaction-based isolation mechanisms, olfactory receptor (OR) gene repertoires of both taxa were identified using pyrosequencing-based technology, and orthologous OR gene sets were identified. Few species-specific gene duplications or species-specific gene losses were found. However, the nonsynonymous-to-synonymous substitution rate ratio was relatively higher between orthologous OR genes of L. frontalis and L. colubrina, indicating that L. frontalis and L. colubrina have evolved to possess different olfactory senses. We suggest that L. frontalis and L. colubrina have evolved allopatrically, and this may be a byproduct of the allopatric evolution, and that this dissimilarity may function as a premating isolation barrier, since L. frontalis has returned to the ancestral range (Vanuatu).

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.

A new species of the genus Scincella (Squamata: Scincidae) from Yonagunijima Island, Southern Ryukyus, Japan.

We performed a molecular phylogenetic analysis for the ground skink populations of the genus Scincella Mittleman, 1950 on Yonagunijima Island, Southern Ryukyus and representative samples of Scincella species known from other islands of the East Asian Archipelago. Partial mitochondrial cytochrome c oxidase subunit I and cytochrome b sequence data were used. Additionally, we examined the nuclear genetic variation between the Yonagunijima samples and those of closely related species. The genetic distances were largely equivalent between the Yonagunijima population and the two closest species, S. boettgeri from other southern Ryukyu Islands and S. formosensis from Taiwan. Moreover, there were nuclear haplotypes unique to the Yonagunijima population. We thus recognize the Yonagunijima population as a distinct species and describe it as Scincella dunan sp. nov. Morphologically, S. dunan sp. nov. is similar to S. boettgeri, but differs in some morphometric and meristic characters, and dorsolateral stripe pattern. These findings further support the biogeographically unique status of Yonagunijima Island among the southern Ryukyus islands.

Another New Bent-toed Gecko, genus Cyrtodactylus Gray 1837 (Squamata: Gekkonidae), from Borneo.

To reveal the diversity of Indonesian bent-toed geckos, we pay attention to Kalimantan (Borneo)an island which has received less attention than other Indonesian islands such as Sumatra, Java, Sulawesi, the Moluccas, and the Lesser Sunda archipelagos. About 30 years after Hikida (1990) described three new Cyrtodactylus from Borneo, four more species were described, namely C. limajalur and C. muluensis in 2019, and C. hantu and C. miriensis in 2021, all by Davis et al. Through examination of the collection at MZB and three addition specimens collected from Tawau, we found several undescribed species, one of which we describe here. This new species is easily differentiated from all other congeners by the combination of the following characters: maximum SVL of at least 65.8 mm; no tubercles on dorsal surface of upper arm; tubercles present in the ventrolateral body folds; 2830 paravertebral tubercles; 1720 longitudinal dorsal tubercle rows; 3946 ventral scale rows at midbody; 1719 subdigital lamellae on fourth toe; precloacal pit with 57 pores in males arranged in a wide -shape but absent in females; no enlarged transverse median subcaudals; paired dark brown semilunar-shaped markings on the upper nape. Further study is needed to reveal its molecular phylogenetic position and biogeographical history.

Geographic variation in morphological traits of the large Japanese field mouse, Apodemus speciosus (Rodentia, Muridae), from the Izu Island Group, Japan.

We investigated geographic variation in morphological traits of the large Japanese field mouse (Apodemus speciosus) from the Izu Island Group, Japan. There was sexual dimorphism in external characters and cranial measurements; hence, these were considered in subsequent analyses. There was geographic divergence in morphometric characters among populations of the Izu Island Group and Honshu. Mice from the Miyakejima Island and Niijima-Shikinejima Islands differed from those of other populations and from each other; Oshima Island mice also differed, but to a lesser degree. Mice from three populations from Honshu were similar to one another, and mice from Kozushima Island were more similar to those from Honshu populations than those from Izu Island Group populations. These results suggest that A. speciosus populations in the Izu Island Group may have had multiple origins. One possible hypothesis to explain these patterns of variation is that the Miyakejima, Niijima, and Shikinejima populations may share a relatively longer history of overseas dispersal, whereas the Kozushima populations may have experienced a recent invasion from Honshu via human activities.

A new species of the genus Larutia (Squamata: Scincidae) from Gunung Penrissen, Sarawak, Borneo.

We collected a specimen of a scincid lizard of Larutia Böhme, 1981 from the edge of a primary forest on Gunung Penrissen, Kuching Division, Sarawak, Malaysian Borneo. The single specimen of the new species differs from all other known congeners by the molecular divergence in the mitochondrial ND1 gene and morphological characters including small adult body size (SVL 84 mm); 22 longitudinal scale rows around midbody; first pair of chinshields contacting second infralabial; second pair of chinshields separated from infralabials by an elongated scale; two subdigital lamellae on second toe; and body without yellow or pale bands or spots. It is the ninth species described in the genus and the second species of Larutia in Borneo.

A new species of Plestiodon (Squamata: Scincidae) from the Senkaku Group, Ryukyu Archipelago, Japan.

A new scincid lizard, Plestiodon takarai sp. nov., is described from the Senkaku Group, Ryukyu Archipelago, Japan. The Plestiodon lizards in this island group have previously been identified as P. elegans because they all exhibit a patch of enlarged and irregularly arranged scales on the posterior surface of their femurs. However, detailed molecular analyses revealed that the Senkaku population, although closely related to P. elegans and other species in the P. latiscutatus species group, is substantially diverged from all other recognized species. Furthermore, although the Senkaku population largely exhibits the characteristic morphological features of this species group, it can be differentiated from all recognized species by the scutellation and hatchling tail coloration. The biogeographical and conservation implications of these findings are briefly discussed.

A new species of Rock Gecko genus Cnemaspis (Squamata: Gekkonidae) from Western Sarawak, Malaysia.

A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian Cnemaspis species in its unique combination of snout-vent length (up to 62.7 mm), 4-9 precloacal pores in males, keeled subcaudals with an enlarged, smooth, median row, presence of ventrolateral caudal tubercles, and coloration (head and upper flanks dark-yellow; anterior portion of tail black; posterior portion of tail white with black, paravertebral blob). Phylogenetic relationships within the C. nigridia group and the distributional ranges of species within the group suggest allopatric speciation by geographic isolation.

Taxonomic reassessment of two subspecies of Chinese skink in Taiwan based on morphological and molecular investigations (Squamata, Scincidae).

The Chinese skink, Plestiodon chinensis (Gray, 1838), is widely distributed across continental China, Taiwan, the Korean Peninsula, and offshore islets, and consists of several subspecies. Here morphological and molecular methods have been used to reassess the taxonomic status and distributions of P. c. formosensis (Van Denburgh, 1912) and P. c. leucostictus (Hikida, 1988), which are endemic to Taiwan and Green Island (an islet off the east coast of Taiwan), respectively. It can be confirmed that the eastern Taiwanese populations of P. c. formosensis exhibit similar juvenile color patterning and genetic composition to the islet subspecies P. c. leucostictus, and are distinct from consubspecific populations in western Taiwan. Therefore, the eastern Taiwanese populations are assigned to P. c. leucostictus, and this subspecies is recognized as a distinct species, Plestiodon leucostictus (Hikida, 1988), based on their unique juvenile coloration and highly divergent DNA sequences. Our results also revealed that P. c. formosensis in western Taiwan is close to nominotypical subspecies from the continent, suggesting the necessity of a comprehensive taxonomic analysis in the future.

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

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.

Phylogeny of the lizard subfamily Lygosominae (Reptilia: Scincidae), with special reference to the origin of the new world taxa.

Phylogenetic relationships of the three lygosomine skink genera occurring both in the Old World and the New World (Mabuya, Scincella and Sphenomorphus) were inferred from mitochondrial DNA sequence of 12S and 16S rRNA genes. Results strongly suggested the non-monophyly for any of these three genera. Within the Mabuya group, Asian members appear to have diverged first, leaving the Neotropical and the Afro-Malagasy Mabuya as sister groups. These relationships, together with the absence of extant or fossil representatives of the Mabuya group from North America, strongly suggest the trans-Atlantic dispersals of Mabuya from Africa to Neotropics. Our results also indicated a closer affinity of the New World Scincella with the New World Sphenomorphus than with the Old World Scincella. Such relationships suggest the trans-Beringian dispersal of the common ancestor from Asia and its subsequent divergence into the North American Scincella and the Neotropical Sphenomorphus.

Genetic variation and differentiation in the Japanese five-lined skink, Eumeces latiscutatus (Reptilia: Squamata).

The genetic variation in Eumeces latiscutatus from the main islands of Japan and the northern Ryukyus was investigated and compared with that of its close relatives (E. okadae and E. marginatus) using allozyme data. All three samples from the northern Tokara Island Group, currently identified as E. latiscutatus, were shown to belong to E. marginatus and not to E. latiscutatus. The non-monophyly of the northern Tokara samples and the great genetic differences within these samples may have resulted from colonization from more than one source population by northeastward overseas dispersal. The samples from the Izu Peninsula were genetically much closer to E. okadae than the other conspecific ones. This indicates that the samples from the Izu Peninsula and the other samples of E. latiscutatus should be treated as distinct species, and that E. latiscutatus from the Izu Peninsula and E. okadae from the Izu Island Group may be treated as conspecific. Samples from western Japan were genetically well differentiated from those of eastern Japan. Within the western group, the samples from the Osumi Island Group was genetically distinct from those from the other regions, by possessing unique alleles. Our phenograms also reveal a distant affinity between samples from the Danjo Island Group and the main islands of Japan. This may be the result of long geographic isolation of the Osumi and Danjo Island Groups from Kyushu. By contrast, samples from Sapporo and Aomori were poorly differentiated genetically in spite of the long separation of these two localities by the Tsugaru Strait. This suggests that overseas dispersal of E. latiscutatus occurred across this strait after its formation.

Molecular evaluation of phylogenetic significances in the highly divergent karyotypes of the genus Gonocephalus (Reptilia: Agamidae) from tropical Asia.

The Oriental large-bodied crested dragons of the genus Gonocephalus are known to include two distinct karyomorphs. To evaluate their phylogenetic significances, we conducted phylogenetic analyses of the genus together with other agamid genera on the basis of 862 base positions of mitochondrial 12S and 16S rRNA genes. Results suggested the presence of two distinct lineages within Gonocephalus, of which one, represented by G. robinsonii that has a 2n = 32 karyotype, was closer to other Oriental agamid genera than to the other congeneric lineage. Monophyly of the latter, characterized by unique chromosomal arrangement among agamid genera (2n = 42 karyotype), was confirmed. It is thus likely that states of morphological characters shared between the two lineages are derived through convergence, or represent symplesiomorphy. Our results also suggest that the karyological similarity between G. robinsonii and several Australian agamids, pointed out in a previous study, is actually attributable to homoplasy rather than their recent common ancestry.

Proportion and cluster analyses of the skull in various species of the tree shrews.

The skull adaptation was functional-morphologically examined in 14 species of the tree shrews. From the data of the proportion indices, the similarities were confirmed between T. minor and T. gracilis, T. tana and T. dorsalis, and T. longipes and T. glis. We demonstrated that the splanchnocranium was elongated in terrestrial T. tana and T. dorsalis and shortened in arboreal T. minor and T. gracilis from the proportion data. In both dendrogram from the matrix of the Q-mode correlation coefficients and scattergram from the canonical discriminant analysis, the morphological similarities in the skull shape suggested the terrestrial-insectivorous adaptation of T. tana and T. dorsalis, and the arboreal adaptation of T. minor and T. gracilis. Since the osteometrical skull similarities were indicated among the three species of Tupaia by cluster and canonical discriminant analyses, the arbo-terrestrial behavior and its functional-morphological adaptation may be commonly established in T. montana, T. longipes and T. glis.