Genetic diversity in domestic cats Felis catus of the Tsushima Islands, based on mitochondrial DNA cytochrome b and control region nucleotide sequences

Nucleotide sequences of mitochondrial DNA (mtDNA) of 50 domestic cats (Felis catus) obtained from the Tsushima Islands were determined and the genetic diversity was analyzed. In the cats, six haplotypes of the complete cytochrome b sequences (1,140 base-pairs, bp) and ten haplotypes of the partial control region sequences (350 bp) were identified. Haplotypes obtained from both genes showed existence of at least 11 maternal lineages of domestic cats in Tsushima. Mean values of polymorphic site numbers and sequences differences in the control region were 2.4 times and 1.8 times higher than those in the cytochrome b gene, respectively. Our results support the idea that the evolutionary rate of the control region was faster than that of the cytochrome b as reported in other mammals. Molecular phylogenetic trees showed the similar clustering of haplotypes for both genes. Meanwhile, no individual variations within the Tsushima leopard cat (Felis bengalensis euptilura), which is native to Tsushima, were observed, possibly as a result of genetic drift in the small ancestral population by geographical isolation. In contrast, the diversity of the domestic cat population was higher than that of the leopard cats, because the genetic variability of the former's founders, which were repeatedly brought to Tsushima in the past, still remains. In addition, no sequences of the leopard cat mtDNA were detected in any domestic cats. However, because the possibility that the domestic cat would crossbreed with the leopard cat cannot be denied, genetic monitoring of two species is necessary to biological conservation in Tsushima.     

A genetic method to distinguish crossbred Inobuta from Japanese wild boars

To distinguish pig-wild boar crossbred Inobuta from Japanese wild boar populations, a genetic method by using mitochondrial DNA (mtDNA) haplotypes and the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) was developed. Sixteen mtDNA haplotypes from 152 wild boars from Kyushu, Shikoku and Honshu islands of Japan were distinct from those from Asian and European domestic pigs. Five alleles of GPIP were classified into two groups: 1). alleles GPIP*1, GPIP*3 and GPIP*3a from Japanese wild boars, Asian wild boars and domestic pigs; 2). alleles GPIP*4 and GPIP*4a from European wild boars and domestic pigs. An extensive genetic survey was done to distinguish the crossbred Inobuta from 60 wild boars hunted on Tsushima Island, Goto Islands, and Nagasaki and Ooita Prefectures. The mtDNA haplotypes from the 60 samples showed Japanese wild boars, but four wild boar samples from Nagasaki Prefecture had the European GPIP allele, GPIP*4. These results showed that nuclear DNA polymorphism analysis is useful, in addition to mtDNA haplotype assay, to detect "Inobuta" having the European genotype from Japanese wild boar populations.     

Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago

We investigated the sequence variation in the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene and the nuclear ribosomal internal transcribed spacers (ncITS) of the calanoid copepod Acanthodiaptomus pacificus in Japan. A. pacificus individuals were divided into three divergent mtCOI lineages (mt-A, -B and -C). mt-A was distributed in the northernmost part of Japan, from Hokkaido to the northern part of Honshu Island, whereas mt-C was the southernmost lineage, distributed from central Honshu to Shikoku and Kyushu Islands. mt-B was distributed between these former two lineages, resulting in parapatry with mt-C and mt-A. In all lineages, 80% of the localities were fixed for a single haplotype, and different localities tended to have different haplotypes. The degree of genetic differentiation among these lineages (15–22%) was at an interspecific level, according to the criteria of the DNA barcode technique. However, the topology of ncITS was not congruent with that of mtCOI, as the reciprocal monophyly was not observed within mt-B and mt-C. Therefore, we merged them into the Southern Lineage and separated it from the Northern Lineage (i.e. mt-A). Evidence of introgression was found within the Southern Lineage, while gene flow was not observed between the Northern and Southern Lineages, suggesting that A. pacificus is a cryptic species complex. We also argue that genetic differentiations of A. pacificus in Japan may reflect the history of separation, transgression and regression of the landmass during the formation of current Japanese Archipelago.     

韩国豹猫与其它豹猫及西表猫之间的遗传分化:基于IRBP、12S rRNA 和Cyt b 序列的分析

利用韩国豹猫的IRBP、12S rRNA 和细胞色素b (Cyt b)序列,并将其与GenBank 中的豹猫及西表猫的上述基因进行比较,以此来重新分析韩国豹猫和其它豹猫及西表猫之间的遗传分化情况。首先,我们从18 只韩国豹猫的IRBP、12S rRNA 和Cyt b 序列分析中分别检测到6 个等位基因、1 个单倍型和3 个单倍型,推测曾经发生 在豹猫种群的瓶颈事件可能是本文发现的不同分子标记之间存在基因型丢失差异的原因。基于Cyt b 序列分析,证实东亚的豹猫形成一个单独的进化枝,本文得到的Cyt b 序列和之前发布结果支持一个分类理论,即认为东亚的豹猫就是东北森林猫。我们发现在IRBP、12S rRNA 基因上,韩国豹猫和西表猫存在相同的序列,支持将西表猫和豹猫视为同一物种。     

Genetic diversity and population structure of wintering Western Sandpipers from the Sinaloa coast,Mexico

ABSTRACT Although Western Sandpipers (Calidris mauri) are one of the best‐studied shorebirds along the Pacific Flyway, their genetic identity and population structure is poorly known. We studied the genetic population structure of nonbreeding Western Sandpipers at Bahia Santa María in Sinaloa, northwestern Mexico. A 685‐bp fragment of the mtDNA control region was sequenced for 162 individuals, resulting in 29 variable positions that defined 41 haplotypes. The most common haplotype (WESA01) occurred in 44% of all individuals, whereas 15 were unique to single individuals. Nucleotide diversity was low (π= 0.0030 ± 0.0019 [SE]), but haplotype diversity was moderately high (h= 0.802 ± 0.033 [SE]). The main two maternal lineages exhibited a slightly different local scale distribution that appeared to be related to migratory chronology. Lineage A represented 71% of the haplotypes and was evenly distributed across the nonbreeding season and habitat types, whereas Lineage B represented only 29% of the haplotypes and was disproportionately represented in January in some habitat types. Overall, the low level of nucleotide diversity, the star‐shape of the haplotype tree, the mismatch distribution, and the significantly negative Tajima's D values suggest that Western Sandpipers underwent a recent demographic expansion. Although our results are based on a small sample size from one of several wintering sites along the Pacific Flyway, Santa María likely contains a relatively high proportion of the species genetic variability because it is the wintering ground of nearly 10% of the global population.     

Evaluation of genetic introgression from domesticated pigs into the Ryukyu wild boar population on Iriomote Island in Japan

We evaluated genetic introgression from domesticated pigs into the Ryukyu wild boar (RWB) population on Iriomote Island based on their genetic structure and diversity. We used a combination of mitochondrial DNA D‐loop region (596 bp) polymorphisms and 23 microsatellite markers. RWBs (n = 130) were collected from 18 locations on Iriomote Island and compared with 66 reference samples of European and Asian domestic pigs. We identified six distinct haplotypes, involving 22 single nucleotide polymorphisms (including one insertion) in the RWB population. The phylogenetic tree had two branches: the RWB group and domestic lineage. Fourteen of 130 RWBs (10.8%) belonged to the European domestic lineage, including 11 RWBs from the Panari Islands, northwest of Iriomote Main Island (IMI). The heterozygosity values, total number of alleles, number of effective alleles and polymorphism information content of the RWB groups were lower than those of the European domestic groups. The RWB population on IMI had a lower heterozygous deficiency index (F_IS = 0.059) than did the other populations, which indicates that this population was more inbred. There was a large genetic distance (F_ST = 0.560) between RWBs on IMI and the Meishan populations. Structure analysis using the 23 microsatellite markers revealed that 16 RWBs had an admixture pattern between RWB and domesticated pig breeds. These results suggest that gene flow may have occurred from domestic pigs to RWBs and demonstrate that there was low genetic variation in the IMI population.     

基于粪便DNA的青藏高原雪豹种群调查和遗传多样性分析

基于非损伤性取样,利用mtDNA和微卫星DNA遗传标记,对来自青藏高原三江源国家级自然保护区、羌塘国家级自然保护区和甘肃党河南山地区等地的277 份疑似雪豹粪便样品进行了物种鉴定、个体识别和遗传多样性研究。结果显示：在190份成功扩增的mtDNA cyt b基因片段中,确定有89份属于雪豹;微卫星分析确定其属于48个不同的个体。在48个雪豹mtDNA cyt b基因片段中,共检测出13个多态性位点,定义了9个单倍型,单倍型多态性为0.776,核苷酸多态性为 1.50%, 9个单倍型的遗传距离为 0.009-0.058。研究表明在研究区域均存在雪豹分布,并具有一定的遗传多态性,地理距离分布较远的羌塘国家级自然保护区和甘肃党河南山地区的雪豹样品具有一定的遗传差异。     

mtDNA variation of the critically endangered hawksbill turtle (Eretmochelys imbricata) nesting on Iranian islands of the Persian Gulf

Genetic diversity of sea turtles (hawksbill turtle) was studied using sequencing of mitochondrial DNA (mtDNA, D-loop region). Thirty dead embryos were collected from the Kish and Qeshm Islands in the Persian Gulf. Analysis of sequence variation over 890 bp of the mtDNA control region revealed five haplotypes among 30 individuals. This is the first time that Iranian haplotypes have been recorded. Nucleotide and haplotype diversity was 0.77 and 0.001 for Qeshm Island and 0.64 and 0.002 for Kish Island, respectively. Total haplotype diversity was calculated as 0.69, which demonstrates low genetic diversity in this area. The data also indicated very high rates of migration between the populations of these two islands. A comparison of our data with data from previous studies downloaded from a gene bank showed that turtles of the Persian Gulf migrated from the Pacific and the Sea of Oman into this area. On the other hand, evidence of migration from populations to the West was not found.     

Characterization of six microsatellite loci in the mangrove cricket Apteronemobius asahinai

The mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors in China, Southeast Asia and the Ryukyu archipelago (Amamiohsima, Okinawa, Miyako, Ishigaki and Iriomote Islands) of Japan. We developed six polymorphic microsatellite markers for the mangrove cricket from genomic DNA libraries enriched for CA, GA, AAG and ATG motifs. The M13‐tailed primer method was used in the process of screening of amplification and polymorphism of primers. A total of 64 specimens from two populations (one from Okinawa and the other from Iriomote) were genotyped for allelic diversity. The average number of alleles per locus was 4.67 and 6.67 for Okinawa and Iriomote populations, respectively. A significant genetic differentiation was detected between the two populations (pairwise F_ST 0.2404). These polymorphic microsatellite loci will be useful in ongoing studies of the population genetic structure of the mangrove cricket including several populations in the Ryukyu archipelago.     

Phylogenic and geographic analysis of chum salmon Oncorhynchus keta (Walbaum) in Asian populations based on mitochondrial DNA variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993-2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community

Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.     

Genetic Divergence of an Avian Endemic on the Californian Channel Islands

The Californian Channel Islands are near–shore islands with high levels of endemism, but extensive habitat loss has contributed to the decline or extinction of several endemic taxa. A key parameter for understanding patterns of endemism and demography in island populations is the magnitude of inter–island dispersal. This paper estimates the extent of migration and genetic differentiation in three extant and two extinct populations of Channel Island song sparrows (Melospiza melodia graminea). Inter–island differentiation was substantial (G''''_ST: 0.14–0.37), with San Miguel Island having the highest genetic divergence and lowest migration rates. Santa Rosa and Santa Cruz Island populations were less diverged with higher migration rates. Genetic signals of past population declines were detected in all of the extant populations. The Channel Island populations were significantly diverged from mainland populations of M. m. heermanni (G''''_ST: 0.30–0.64). Ten mtDNA haplotypes were recovered across the extant and extinct Channel Island population samples. Two of the ten haplotypes were shared between the Northern and Southern Channel Islands, with one of these haplotypes being detected on the Californian mainland. Our results suggest that there is little contemporary migration between islands, consistent with early explanations of avian biogeography in the Channel Islands, and that song sparrow populations on the northern Channel Islands are demographically independent.     

Genetic and geographical differentiation of <Emphasis Type="Italic">Pandaka</Emphasis> gobies in Japan

The mitochondrial DNA (mtDNA) phylogeny of Japanese Pandaka species (Perciformes: Gobiidae) was inferred from partial nucleotide sequences of the mitochondrial 12S and 16S rRNA genes (1083bp). The resultant mtDNA tree showed two major clades (clade I and clade II), which were inconsistent with the present taxonomic classification. One of the major clades was further divided into two geographical groups, distributed on the Japanese Major Islands (clade I-A) and from Amami-oshima Island to Iriomote Island (clade I-B). The mtDNA haplotypes in clade II were found only on Iriomote Island. The mtDNA divergences in clade I indicated that the Japanese Major Island (clade I-A) and Ryukyu (clade I-B) groups have been geographically isolated from each other for millions of years, based on the putative molecular divergence rate. The geographical distributions of mtDNA haplotypes in clade I-A and clade I-B also suggested that Pandaka gobies had not dispersed to distant offshore islands, indicating that their geographical differentiation may be closely associated with the geological history of the Japanese and Ryukyu Archipelagos.This revised version was published online in January 2005 with corrections to the repetition of the 1st authors name.     

Phylogeographic Analysis of Chum Salmon Oncorhynchus keta Walbaum in Asian Populations Based on mtDNA Variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993–2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

Population Structure of Wild Musk Shrews (Suncus murinus) in Asia Based on Mitochondrial DNA Variation, with Research in Cambodia and Bhutan

The musk shrew (Suncus murinus) is a small mammalian species belonging to Insectivora. It is widely distributed in Asia. To identify the genetic relationship among wild musk shrew populations and examine its migration route, we investigated the populations of Cambodia and Bhutan by using mitochondrial DNA restriction fragment length polymorphism analysis and compared them with other Asian populations previously described. Four haplotypes were detected in Cambodia and eight in Bhutan. A total of 53 haplotypes were detected in Asia and were classified largely into two groups, the Continental and Island types, based on a minimum spanning network. From the distribution of mtDNA types in wild musk shrews, three major population groups are identified in Asia: South Asia, Southeast Asia, and Malay. It is suggested that the Malay population group was a mix of South and Southeast Asian population groups and that this was a contact area of the two groups. In addition, other contact areas between the South and Southeast Asian groups exist in Myanmar, but unlike the Malay, the Myanmar area was the border of these groups.     

中国黄牛mtDNA D-loop遗传多样性及起源

黄牛自古以来就是我国一个重要的畜种,其经济、文化价值很高。我国是世界上黄牛品种资源最丰富的国家之一。据《中国牛品种志》介绍,把一些地区同种异名的黄牛品种合并以后,尚有28个地方黄牛品种,按照其地理分布区域分为北方黄牛、中原黄牛和南方黄牛三大类型(邱怀,1986)。如果把中国地方黄牛品种分得更细,则有49个固有品种(常洪,1995)。关于中国黄牛的起源,历来有不同的观点。一般认为,中国黄牛是多元起源的,但究竟起源于哪几个牛种,观点不一(陈宏等,1993;于汝梁等,1993;Yu et al.,1999;陈幼春,1990)。主要的观点有:(1)中国黄牛主要起源于…     

Mitochondrial DNA variation in Nicobarese Islanders.

The aboriginal populations living in the Nicobar Islands are hypothesized to be descendants of people who were part of early human dispersals into Southeast Asia. However, analyses of ethnographic histories, languages, morphometric data, and protein polymorphisms have not yet resolved which worldwide populations are most closely related to the Nicobarese. Thus, to explore the origins and affinities of the Nicobar Islanders, we analyzed mitochondrial DNA (mtDNA) hypervariable region 1 sequence data from 33 Nicobarese Islanders and compared their mtDNA haplotypes to those of neighboring East Asians, mainland and island Southeast Asians, Indians, Australian aborigines, Pacific Islanders, and Africans. Unique Nicobarese mtDNA haplotypes, including five Nicobarese mtDNA haplotypes linked to the COII/tRNA(Lys) 9-bp deletion, are most closely related to mtDNA haplotypes from mainland Southeast Asian Mon-Kmer-speaking populations (e.g., Cambodians). Thus, the dispersal of southern Chinese into mainland Southeast Asia may have included a westward expansion and colonization of the islands of the Andaman Sea.     

Independent maternal origin of Chinese swamp buffalo (Bubalus bubalis)

To obtain more knowledge on the origin and genetic diversity of the swamp buffalo (Bubalus bubalis) in China, the complete mitochondrial D-loop sequences of 119 samples representing seven native types were compared. Two mitochondrial DNA (mtDNA) lineages (lineages A and B) were determined for the Chinese swamp buffalo. Examination of the diversity patterns suggest that lineage A has undergone a population expansion event. Divergence of lineages A and B was estimated at 18,000 years ago. Combined analyses of mtDNA sequences from Chinese, Indian, Brazilian/Italian and Southeast Asian/Australian buffalo samples showed independent domestication events in the swamp buffalo from China and the river buffalo from the India subcontinent. The spread of swamp and river buffalo from China and India respectively to mainland Southeast Asia suggests that Southeast Asia is a hybrid zone for buffalo. Our data support the hypothesis of the evolution of domesticated swamp and river buffalo from ancestral swamp-like animals. These ancestral animals were extensively distributed across mainland Asia and most likely are represented today by the wild Asian buffalo (Bubalus arnee).     

Phylogeographic origin of Hokkaido house mice (Mus musculus) as indicated by genetic markers with maternal, paternal and biparental inheritance

We examined intraspecies genetic variation in house mice (Mus musculus molossinus) from the northern third of the Japanese Islands, in order to obtain evidence of the history of mouse colonization that might have shaped the current genetic diversity. We extended the previous sampling of mitochondrial cytochrome b sequence and added information from the Y-linked Sry gene and ribosomal RNA gene surveys. We distinguish mitochondrial haplotypes characteristic of the North Asian musculus subspecies group (involving M. m. musculus and M. m. molossinus) as 'MUS', and that of the Southeast Asian castaneus subspecies group as 'CAS' (although the mice resemble MUS morphologically). There was a clear geographic partition of MUS and CAS types into southern and northern Hokkaido, respectively. Conversely, on Tohoku, the MUS and CAS types were interspersed without clear geographic subdivision. In contrast to the mtDNA data, all Hokkaido and Tohoku mice examined were found to possess a unique type for the Y-linked Sry gene, specific to Korea and Japan. Restriction site analysis of nuclear rDNA probe showed a consistent distribution of MUS and CAS types, as major and minor components, respectively, in the Hokkaido and Tohoku mice. These data support the previous notion that the Hokkaido and Tohoku mice experienced genetic hybridization between primary residents of CAS origin and MUS newcomers arriving via a southern route. The invasion of the MUS type could correspond with the evidence for arrival of prehistoric peoples. There are, however, alternative interpretations, including genetic admixture between MUS arriving by a southern route and CAS from a northern route.     

Mitochondrial and nuclear DNA analyses reveal pronounced genetic structuring in Tunisian wild boar <Emphasis Type="Italic">Sus scrofa</Emphasis>

We analysed 74 wild boars from Tunisia with respect to patterns of genetic differentiation and diversity based on sequences of the mitochondrial control region and genotypes at eight nuclear microsatellite loci. Analysis of molecular variance for both marker systems and Bayesian structure analysis of our microsatellite data revealed a clear break between northern and southern populations. Southern wild boar were monomorphic for one of three mtDNA haplotypes; the other two (one of which only occurred in three individuals) were confined to the north. A comparison with published sequences showed all three haplotypes to belong to the major European clade E1. Microsatellite diversity was similar to that found in earlier studies of wild boar (expected heterozygosity of 0.695 and 0.597 for the north and south, respectively). Contrary to the mtDNA results, we did not find unequivocal evidence of a bottleneck in Tunisian wild boar based on our microsatellite data. The clear distinction between northern and southern populations may be due to an Algerian origin of the southern animals.