Japanese Haplotypes Research Articles

Behavioural and phylogeographic observations on Epipomponia nawai (Dyer, 1904): An East Asian moth (Lepidoptera; Epipyropidae) whose larvae are ectoparasitic on cicadas (Hemiptera; Cicadidae; Sonatini)

• Lepidopteran ectoparasite was found from cicada. • Parasitic lepidoptera was identified as Epipomponia nawai (Dyer 1904) • Hyalessa maculaticollis ( de Motschulsky 1866 ) is newly recognized as a host. • Haplotype analysis of Chinese populations showed distinct separation into two groups. • Either Korean or Japanese haplotype belongs to each group. The lepidopteran family of the Epipyropidae contains currently 32 known species of moths with larvae that are parasitic on plant and leafhoppers as well as cicadas. This paper focuses on behavioural aspects of the final instar of the cicada parasite Epipomponia nawai (Dyer 1904) on the cicada Hyalessa maculaticollis ( de Motschulsky 1866 ) and represents only the second report of the species from South Korea. This species is a new host for E. nawai in Korea, since in the past it had only been reported once from Meimuna opalifera and Oncotympana fuscata in Korea. Molecular relationships between specimens of E. nawai collected in China, Japan, and Korea were analysed. The Chinese haplotypes fell into two groups: one clearly related to the Korean haplotype, but the other tightly affiliated with the Japanese haplotype. The findings suggest two routes for the occurrence of E. nawai in mainland China. Once the host cicada was dead or too weak to move, the caterpillar crawled away from it, seeking a place to pupate. Very little is known about parasitic Lepidoptera and therefore any information on host species or behavioural aspects is of importance.

Raccoon dog (Nyctereutes procyonoides) phylogeography including the Polish population: local and global aspects

The raccoon dog (Nyctereutes procyonoides) is a representative of Canidae and is closely related to red fox-like canids, although the species exhibits high distinctiveness in the family. These animals were farmed for fur products, but thousands were intentionally released into the wild in western Russia. This newly established alien species in Europe has spread rapidly into many European countries. The aim of the study was to determine the origin of Polish populations by comparing the mitochondrial molecular marker cytochrome b (cytb) sequences of Polish wild and farm individuals with wild raccoon dogs from the western Russia and Asian specimens whose sequences were obtained from GenBank resources. The results of our phylogenetic analysis support the previous suggestions on the existence of two main clades clearly referring to continental and Island populations. Polish individuals were classified into a highly diverse continental group. The relationships between the haplotypes within the clade together with estimated values of genetic diversity parameters indicate that the Polish raccoon dog populations exhibit high genetic similarity to the Russian population. In combination with the history of introduction of the species to Europe, this suggests the most probable assignment of the Polish populations to the subspecies N. procyonoides ussuriensis. Our results indicate the presence of two Japanese haplotypes within the continental group, which is inconsistent with the assumed scenario of post-glacial expansion of raccoon dogs excluding gene flow between continental and Island populations.

Morphotype and haplotype identification of Varroa destructor (Acari: Varroidae), and its importance for apiculture in Nicaragua

The ectoparasite Varroa (Acari: Varroidae) is considered to be the main pest of honey bees (Apis mellifera L.) in Nicaragua. The aim of this study was to determine morphotypes and mitochondrial haplotypes of the Varroa mites, related to infestation levels in A. mellifera hives in Nicaragua in a cross-sectional study (2013-2016). Samples were taken from 34 sentinel apiaries in five geographical zones; from 713 Varroa females collected during the study, 153 were selected for measurement of various morphometric characters for further classification into morphotypes. The mitochondrial haplotype was assigned to one of the two (Korean or Japanese), using the restriction by SacI of the PCR product of a fragment of the gene CO-I. Morphometric measurement and sequencing revealed the affiliation to the species Varroa destructor with a mean (± SD) body width of 1699.1 ± 60.2µm and a body length of 1161.1 ± 34.9µm. Body characters were significantly different among the 34 apiaries. Varroa destructor samples were classified into four morphotypes, with no significant differences in the geographical zones. As GAGCTC SacI enzyme cleavage sequences were not observed, all PCR products were identified as V. destructor Korean haplotype. The CO-I gene nucleotide sequences from two samples V. destructor showed both 100% similarity with the Korean haplotype and 99.8% similarity to the Japanese haplotype. Although the V. destructor mite was identified as a Korean haplotype, host-parasite association in 2 decades has led into a balance without entering into severe losses in the Nicaraguan apiculture.

Characterization of Varroa destructor Mites in Cuba Using Mitochondrial and Nuclear Markers

Abstract Varroa destructor has been present in Cuba since 1996, but without the use of acaricidal infestation rates remain at very low levels. The presence of Korean haplotype mites was described in 2007, but there is no information regarding the introgression of the less virulent Japanese haplotype that could account for a low pathogenicity of the mite. In this research, we carried out molecular characterization of Cuban Varroa mites through mitochondrial DNA and hypervariable nuclear loci. We applied an alternative RFLP technique and found that all the analyzed samples corresponded to Korean haplotypes. We analyzed the three STRs loci VD112, VD114 and VD016, previously described as highly variable and found new alleles in all of them, with an absolute allele size very different to those reported worldwide. We also detected genic and genotypic differentiation between samples from two nearby locations (P=0.08). We also tested a new RFLP method for mite haplotype discrimination with an intra-reaction positive control of digestion.

Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease.

To elucidate the genetics of coronary artery disease (CAD) in the Japanese population, we conducted a large-scale genome-wide association study of 168,228 individuals of Japanese ancestry (25,892 cases and 142,336 controls) with genotype imputation using a newly developed reference panel of Japanese haplotypes including 1,781 CAD cases and 2,636 controls. We detected eight new susceptibility loci and Japanese-specific rare variants contributing to disease severity and increased cardiovascular mortality. We then conducted a trans-ancestry meta-analysis and discovered 35 additional new loci. Using the meta-analysis results, we derived a polygenic risk score (PRS) for CAD, which outperformed those derived from either Japanese or European genome-wide association studies. The PRS prioritized risk factors among various clinical parameters and segregated individuals with increased risk of long-term cardiovascular mortality. Our data improve the clinical characterization of CAD genetics and suggest the utility of trans-ancestry meta-analysis for PRS derivation in non-European populations.

<p class="Body"><strong>Mitochondrial haplotype analyses of the mite <em>Varroa destructor</em> (Acari: Varroidae) collected from honeybees <em>Apis mellifera</em> (Hymenoptera, Apidae) in Uruguay</strong></p>

The ectoparasite Varroa destructor is currently the main health problem faced by honeybees Apis mellifera in the world. It has been identified that two haplotypes were able of infecting and reproducing in this species: the “Korean haplotype” (K) and the “Japanese haplotype” (J). Both haplotypes differ in their virulence, being the K haplotype more harmful than the J. V. destructor was detected for the first time in Uruguay in 1978, but its effect on honeybees is very different depending on the region of the country. Although the K haplotype predominates in South America, the presence of J haplotype in Uruguay is possible, and may be the cause of different virulence of the mites. The aims of this study were to identify the haplotype of V. destructor existing throughout Uruguay and, at the same time, to present a new strategy of RFLP which that presents an internal positive control of digestion. Despite the differences in the effect of V. destructor on honeybees in different areas of the country, all the colonies evaluated presented the K haplotype. The presence in the past of haplotype J cannot be ruled out, and could be assessed with independent nuclear markers.

Discovery of the Masson Pine Moth, <i>Dendrolimus punctatus</i>, from Japan with Taxonomic Notes on <i>D. superans,</i> <i>D. spectabilis</i>, and <i>D. okinawanus</i>（Lepidoptera: Lasiocampidae）

The masson pine moth, Dendrolimus punctatus（Walker）（Lepidoptera: Lasiocampidae）, is a notorious pest of pine trees in Asian countries and was recorded in Japan for the first time from Ishigakijima Island and Iriomotejima Island. We performed taxonomic studies involving the male and female genitalia and clarified the distinguishable features among the following four Japanese species of the genus Dendrolimus: D. superans（Butler）, D. spectabilis（Butler）, D. okinawanus Sonan, and D. punctatus based on many specimens including the lectotype of D. punctatus. As for DNA barcoding, five of the analyzed Japanese haplotypes from Ishigakijima Island and Iriomotejima Island and three of the Chinese haplotypes registered in GenBank as D. punctatus belonged to the same clade in the NJ tree. The intraspecific divergence value within D. punctatus was higher than the interspecific divergence value between D. okinawanus and D. spectabilis. In addition, we revealed that D. punctatus induced severe damage in Pinus luchuensis Mayr on Ishigakijima Island in 2016.

Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

BackgroundImputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined.MethodsThis study was divided into two parts. In the first part, we applied imputation to genotyped SNPs from Southeast Asian populations from the Pan-Asian SNP database. Five percent of the total SNPs were removed. The remaining SNPs were applied to imputation with IMPUTE2. The imputed outcomes were verified with the removed SNPs. We compared imputation references from Chinese and Japanese haplotypes from the HapMap phase II (HMII) and the complete set of haplotypes from the 1000 Genomes Project (1000G). The second part was imputation accuracy and yield in Thai patient dataset. Half of the autosomal SNPs was removed to create Set 1. Another dataset, Set 2, was then created where we switched which half of the SNPs were removed. Both Set 1 and Set 2 were imputed with HMII to create a complete imputed SNPs dataset. The dataset was used to validate association testing, SNPs annotation and imputation outcome.ResultsThe accuracy was highest for all populations when using the HMII reference, but at the cost of a lower yield. Thai genotypes showed the highest accuracy over other populations in both HMII and 1000G panels, although accuracy and yield varied across chromosomes. Imputation was tested in a clinical dataset to compare accuracy in gene-related regions, and coding regions were found to have a higher accuracy and yield.ConclusionsThis work provides the first evidence of imputation reference selection for Southeast Asian studies and highlights the effects of SNP locations respective to genes on imputation outcome. Researchers will need to consider the trade-off between accuracy and yield in future imputation studies.

Molecular Evidence for the Expansion of the Asian Cryptic Invader Hediste diadroma (Nereididae: Annelida) into the Northeast Pacific Habitats of the Native H. limnicola.

We used previously established molecular methods to determine how far the Asian invader nereidid worm Hediste diadroma has spread into northeast Pacific estuaries that are inhabited by the native congener H. limnicola. Further, we analyzed the mitochondrial DNA of 702 Hediste specimens collected from 27 estuaries along 1,350 km of coastline in Washington, Oregon, and California, USA, to distinguish between the morphologically indistinguishable immature stages of these two species. In total, 377 specimens were identified as the invader H. diadroma and 325 were identified as the native H. limnicola. The invader H. diadroma was dominant at many sites in Puget Sound, Washington, and in the Columbia River estuary, Washington, and Oregon, suggesting that this species initially invaded estuaries in Washington or northern Oregon. In contrast, the native H. limnicola was dominant at intertidal sites in California and at subtidal sites in the Columbia River estuary. We also analyzed a partial nucleotide sequence from the mitochondrial cytochrome oxidase subunit I gene of H. diadroma in specimens collected from seven sites in the US and 11 sites in Japan, which showed no marked geographic differentiation between 18 US and 31 Japanese haplotypes. This finding suggests that H. diadroma have been introduced repeatedly into US estuaries from many regions in Japan.

A shared haplotype for dentatorubropallidoluysian atrophy (DRPLA) in Italian families testifies of the recent introduction of the mutation

To clarify the population history of dentatorubropallidoluysian atrophy (DRPLA) in Italy and to date back the introduction of the mutation, we reconstructed extended haplotypes flanking the CAG repeat in 10 patients of Italian ancestry, analyzing their similarity/dissimilarity as a function of distance from the CAG repeat. Our aim was to compare the hypothesis of a single, recent genealogy connecting all the observed haplotypes with the alternative hypothesis of multiple introductions by more distantly related haplotypes from outer sources. Polymorphic DNA markers were chosen to cover a region of 153 kb flanking the CAG repeat, that is, informative for dating the age of the DNA segment unaffected by recombination. In all patients, an expansion of the ATN1 CAG segment was confirmed residing onto the same narrow haplotype described to be associated with the CAG expansion in the Japanese and Portuguese populations. We also observed the disruption of the DRPLA haplotype at longer distances, on both sides of the CAG. Our results are compatible with a single founder in the last 600 years, most likely before the last 270 years. These estimates for the Sicilian population largely overlap a period in which the Japanese haplotype with the DRPLA mutation could have been introduced by the Portuguese maritime travelers.

Identification of Independent Susceptible and Protective HLA Alleles in Japanese Autoimmune Thyroid Disease and Their Epistasis

Autoimmune thyroid disease (AITD) includes Graves disease (GD) and Hashimoto thyroiditis (HT), which partially share immunological features. Determining the genetic basis that distinguishes GD and HT is a key to understanding the differences between these 2 related diseases. The aims of this study were to identify HLA antigens that can explain the immunopathological difference between GD and HT and to elucidate epistatic interactions between protective and susceptible HLA alleles, which can delineate the distinct function of HLA in AITD etiology. We genotyped 991 patients with AITD (547 patients with GD and 444 patients with HT) and 481 control subjects at the HLA-A, HLA-C, HLA-B, DRB1, DQB1, and DPB1 loci. A direct comparison of HLA antigen frequencies between GD and HT was performed. We further analyzed an epistatic interaction between the susceptible and protective HLA alleles in the development of GD and HT. We identified 4 and 2 susceptible HLA molecules primarily associated with GD and HT, respectively, HLA-B*35:01, HLA-B*46:01, HLA-DRB1*14:03, and HLA-DPB1*05:01 for GD and HLA-A*02:07 and HLA-DRB4 for HT. In a direct comparison between GD and HT, we identified GD-specific susceptible class II molecules, HLA-DP5 (HLA-DPB1*05:01; Pc = 1.0 × 10(-9)) and HLA-DR14 (HLA-DRB*14:03; Pc = .0018). In contrast, HLA components on 3 common haplotypes in Japanese showed significant protective effects against the development of GD and HT (HLA-A*24:02-C*12:02-B*52:01-DRB1*15:02-DQB1*06:01-DPB1*09:01 and HLA-A*24:02-C*07:02-B*07:02-DRB1*01:01-DQB1*05:01-DPB1*04:02 haplotypes for GD and HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01 haplotype for GD and HT). Interestingly, the representative protective HLA, HLA-DR13 (HLA-DRB1*13:02), was epistatic to susceptible HLA-DP5 in controlling the development of GD. We show that HLA exerts a dual function, susceptibility and resistance, in controlling the development of GD and HT. We also show that the protective HLA allele is partially epistatic to the susceptible HLA allele in GD.

Homozygosity for killer immunoglobin-like receptor haplotype A predicts complete molecular response to treatment with tyrosine kinase inhibitors in chronic myeloid leukemia patients

Several recent reports suggest a possible role for killer immunoglobulin-like receptors (KIR) in the onset of chronic myeloid leukemia (CML) and response to therapy with tyrosine kinase inhibitors (TKIs). To explore this hypothesis, we studied KIRs and their human leukocyte antigen class I ligands in 59 consecutive patients with chronic-phase CML (mean age, 53 years; range, 23-81 years) and a group of 121 healthy control participants belonging to the same ethnic group as the patients. The 2-year cumulative incidence of complete molecular response, obtained after a median of 27 months (range, 4-52 months), was 51.2%. An increased frequency of the activating receptor KIR2DS1 (pm = 0.05) and a reduced frequency of the KIR-ligand combination KIR2DS2/2DL2 absent/C1 present (pm = 0.001) were significantly associated with CML. Moreover, KIR repertoires in patients appeared to influence response to TKI therapy. Homozygosity for KIR haplotype A (pm = 0.01), a decreased frequency of the inhibitory KIR gene KIR2DL2 (pm = 0.02), and low numbers of inhibitory KIR genes (pm = 0.05) were all significantly associated with achievement of complete molecular remission. These data suggest that a decrease in properly stimulated and activated NK cells might contribute to the occurrence of CML and indicate homozygosity for KIR haplotype A as a promising immunogenetic marker of complete molecular response that could help clinicians decide whether to withdraw treatment in patients with CML.

Phylogenetic relationship of the Brazilian isolates of the rat lungworm Angiostrongylus cantonensis (Nematoda: Metastrongylidae) employing mitochondrial COI gene sequence data

BackgroundThe rat lungworm Angiostrongylus cantonensis can cause eosinophilic meningoencephalitis in humans. This nematode’s main definitive hosts are rodents and its intermediate hosts are snails. This parasite was first described in China and currently is dispersed across several Pacific islands, Asia, Australia, Africa, some Caribbean islands and most recently in the Americas. Here, we report the genetic variability among A. cantonensis isolates from different geographical locations in Brazil using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.MethodsThe isolates of A. cantonensis were obtained from distinct geographical locations of Brazil. Genomic DNAs were extracted, amplified by polymerase reaction, purified and sequenced. A partial sequence of COI gene was determined to assess their phylogenetic relationship.ResultsThe sequences of A. cantonensis were monophyletic. We identified a distinct clade that included all isolates of A. cantonensis from Brazil and Asia based on eight distinct haplotypes (ac1, ac2, ac3, ac4, ac5, ac6, ac7 and ac8) from a previous study. Interestingly, the Brazilian haplotype ac5 is clustered with isolates from Japan, and the Brazilian haplotype ac8 from Rio de Janeiro, São Paulo, Pará and Pernambuco states formed a distinct clade. There is a divergent Brazilian haplotype, which we named ac9, closely related to Chinese haplotype ac6 and Japanese haplotype ac7.ConclusionThe genetic variation observed among Brazilian isolates supports the hypothesis that the appearance of A. cantonensis in Brazil is likely a result of multiple introductions of parasite-carrying rats, transported on ships due to active commerce with Africa and Asia during the European colonization period. The rapid spread of the intermediate host, Achatina fulica, also seems to have contributed to the dispersion of this parasite and the infection of the definitive host in different Brazilian regions.

Molecular detection of protozoan parasites infecting Apis mellifera colonies in Japan

The role of protozoan parasites in honey bee health and distribution in the world is not well understood. Therefore, we carried out a molecular survey for the presence of Crithidia mellificae and Apicystis bombi in the colonies of both non-native Apis mellifera and native Apis cerana japonica in Japan. We found that A. mellifera, but not A. c. japonica, colonies are parasitized with C. mellificae and A. bombi. Their absence in A. c. japonica colonies indicates that A. mellifera is their native host. Nevertheless, the prevalence in A. mellifera colonies is low compared with other pathogens such as viruses and Nosema microsporidia. Japanese C. mellificae isolates share well-conserved nuclear-encoded gene sequences with Swiss and US isolates. We have found two Japanese haplotypes (A and B) with two nucleotide differences in the kinetoplast-encoded cytochrome b sequence. The haplotype A is identical to Swiss isolate. These results demonstrate that C. mellificae and A. bombi distribute in Asia, Oceania, Europe, and South and North Americas.

Genetic structure of Varroa destructor populations infesting Apis mellifera colonies in Argentina

Although mitochondrial DNA mapping of Varroa destructor revealed the presence of several haplotypes, only two of them (Korean and Japanese haplotypes) were capable to infest Apis mellifera populations. Even though the Korean haplotype is the only one that has been reported in Argentina, these conclusions were based on mites sampled in apiaries from a specific geographical place (Buenos Aires province). To study mites from several sites of Argentina could reveal the presence of the Japanese genotype, especially considering sites near to Brazil, where Japanese haplotype was already detected. The aim of this work was to study the genetic structure of V. destructor populations from apiaries located in various provinces of Argentina, in order to determine the presence of different haplotypes. The study was carried out between January 2006 and December 2009. Phoretic adult Varroa mites were collected from honey bee workers sampled from colonies of A. mellifera located in Entre Ríos, Buenos Aires, Corrientes, Río Negro, Santa Cruz and Neuquén provinces. Twenty female mites from each sampling site were used to carry out the genetic analysis. For DNA extraction a nondestructive method was used. DNA sequences were compared to Korean haplotype (AF106899) and Japanese haplotype (AF106897). All DNA sequences obtained from mite populations sampled in Argentina, share 98% of similitude with Korean Haplotype (AF106899). Taking into account these results, we are able to conclude that Korean haplotype is cosmopolite in Argentina.

Genetics of Microscopic Polyangiitis in the Japanese Population

The epidemiology of ANCA-associated vasculitis is substantially different between Caucasians and Japanese, which may be related to differences in genetic backgrounds. In this review, I discussed our findings on the genetics of microscopic polyangiitis (MPA) in Japanese. Analysis of HLA genes revealed a significant increase in the HLA-DRB1*09:01-DQB1*03:03 haplotype MPA. This is one of the most frequent haplotypes in Japanese, but is nearly absent in Caucasians, and has been shown to be associated with multiple autoimmune diseases. Analysis of KIR genes revealed significant decreases in the carrier frequency of an activating receptor KIR2DS3 in MPA. When KIRs were analyzed in combination with HLA ligands, the proportion of individuals carrying KIR3DL1 and HLA-Bw4 but not KIR3DS1, the most inhibitory of all KIR3DS1/3DL1/HLA-B combinations, was significantly increased in MPA. These results suggested that decreased activation of NK and/or T cells may cause a predisposition to MPA. LILRA2 is an activating receptor involved in granulocyte and macrophage activation. LILRA2 SNP rs2241524 G >A, which disrupts the intron 6 splice acceptor site, was significantly associated with MPA. The risk allele produces an LILRA2 isoform lacking three amino acids in the linker region. These findings, when confirmed by larger-scale studies, will shed light on the molecular mechanisms of MPA. (*English Translation of J Jpn Coll Angiol 2009; 49: 31-37.).

Identification and Molecular Variations of CAN-SINEs from theZFYGene Final Intron of the Eurasian Badgers (GenusMeles)

The short interspersed nucleotide elements (SINEs) are specific to the taxa and thought to be one of powerful phylogenetic gene markers. Especially, the SINE sequences, which exist uniquely in genome of order Carnivora, are named CAN-SINEs. Among the Eurasian badgers (genus Meles), a member of the family Mustelidae in order Carnivora, the Japanese badger (M. anakuma) was previously reported to have an insertion of CAN-SINE in the final intron of the zinc finger protein gene on Y chromosome (ZFY). In the present study, we examined occurrence of the CAN-SINE of the ZFY final intron in the Eurasian badgers, and three continental and four Japanese haplotypes were identified from a total of 40 male badgers. Among the Eurasian badger CAN-SINEs, a 12-bp deletion specific to the Japanese haplotypes was found, whereas the 12-bp region (non-deletion) in the continental haplotypes consisted of one 6-bp direct repeat and 6-bp microsatellite-like sequences. Moreover, the continental haplotypes were phylogenetically divided into three lineages: eastern Eurasia, Caucasus and western Eurasia. These genetic differentiations supported the classification recently proposing that genus Meles are grouped into the European badger (M. meles), the Southwest Asian badger (M. canescens), the Northwest & Central Asian badger (M. leucurus) and the Japanese badger (M. anakuna). In addition, the number of adenines in the poly A/T rich tails was polymorphic among all lineages of Eurasian badgers, and geographically variable within the Japanese badgers.

Evaluation of Genetic Diversity of Wild Oriental White Stork (Ciconia boyciana) in Russia and Their Phylogenetic Relationship with Extinct Populations in Japan

Genetic diversity evaluation of Oriental white storks distributed in the Russian Far East was conducted based on D-loop haplotype data. In addition, to study the relationship between the wild Russian population and extinct Japanese populations, we compared the Russian haplotypes and reported Japanese haplotypes obtained from mounted specimens. The results showed that eight haplotypes with mutations at 18 sites were found in ten individuals. Two types of them were previously reported types and six haplotypes of them were previously unreported type. The haplotype diversity was 0.933. The average of pairwise difference among eight sequences was 0.007. Phylogenetic analysis suggested that there were three evolutionary lineages in the Russian population and the populations in the study area were genetically related to extinct Japanese population.

Additional records of Gelidiella fanii (Gelidiales, Rhodophyta) from the western Pacific based on morphology, rbcL and cox1 analyses

Abstract This is a first report on the occurrence of Gelidiella fanii outside of Taiwan, where it was recently described as a new species. New specimens have been collected from Thailand, Indonesia, Japan, and the Philippines. The species commonly occurred on rocks and crustose algae in the intertidal zone at locations visited. Thalli had downward curving unilateral branchlets, numerous hairs around branch tips, iridescent color under water, and clublike tetrasporangial stichidia with blunt tips. Two genes were analyzed from different organelle genomes: plastid rbcL from 13 specimens and mitochondrial cox1 from 24 specimens including putative relatives. Analyses of both rbcL and cox1 sequences revealed that G. fanii was strictly separated from other species in the genus. This is the first report on cox1 gene sequences in the order Gelidiales. Nine cox1 haplotypes were found in G. fanii; there was a biogeographic structure, except for the Japanese haplotype, which grouped with those from Thailand. The present study indicates that G. fanii is common in Thailand and probably in the southeastern Asia region. G. fanii was more closely related to an identified Gelidiella sequence from South Africa, which is morphologically similar to G. acerosa. Detailed observations of field-collected material will enable a more realistic evaluation of the distribution of G. fanii in tropical and subtropical waters of the world.

Evaluation of Haplotype Inference Using Definitive Haplotype Data Obtained from Complete Hydatidiform Moles, and Its Significance for the Analyses of Positively Selected Regions

The haplotype map constructed by the HapMap Project is a valuable resource in the genetic studies of disease genes, population structure, and evolution. In the Project, Caucasian and African haplotypes are fairly accurately inferred, based mainly on the rules of Mendelian inheritance using the genotypes of trios. However, the Asian haplotypes are inferred from the genotypes of unrelated individuals based on population genetics, and are less accurate. Thus, the effects of this inaccuracy on downstream analyses needs to be assessed. We determined true Japanese haplotypes by genotyping 100 complete hydatidiform moles (CHM), each carrying a genome derived from a single sperm, using Affymetrix 500 K Arrays. We then assessed how inferred haplotypes can differ from true haplotypes, by phasing pseudo-individualized true haplotypes using the programs PHASE, fastPHASE, and Beagle. We found that, at various genomic regions, especially the MHC locus, the expansion of extended haplotype homozygosity (EHH), which is a measure of positive selection, is obscured when inferred Asian haplotype data is used to detect the expansion. We then mapped the genome using a new statistic, XDiHH, which directly detects the difference between the true and inferred haplotypes, in the determination of EHH expansion. We also show that the true haplotype data presented here is useful to assess and improve the accuracy of phasing of Asian genotypes.