Cryptic clonal lineages and genetic diversity in the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) inferred from nuclear and mitochondrial DNA analyses

In the loach Misgurnus anguillicaudatue, the asexual lineage, which produces unreduced clonal diploid eggs, has been identified. Among 833 specimens collected from 54 localities in Japan and two localities in China, 82 candidates of other lineage(s) of cryptic clones were screened by examining RFLP (restriction fragment length polymorphism)-PCR haplotypes in the control region of mtDNA. This analysis was performed because triploid loaches arise from the accidental incorporation of the sperm nucleus into unreduced diploid eggs of a clone. The categorization of members belonging to three newly identified lineages (clones 2–4) and the previously identified clonal lineage (clone 1) was verified by evaluating the genetic identity between two or more individuals from each clonal lineage based on RAPD (random amplified polymorphic DNA)-PCR and multilocus DNA fingerprints. We detected 75 haplotypes by observing the nucleotide status at variable sites from the control region of mtDNA. Phylogenic trees constructed from such sequences showed two highly diversified clades, A and B, that were beyond the level common for interspecific genetic differentiation. That result suggests that M. anguillicaudatus in Japan is not a single species entity. Two clone-specific mtDNA sequences were included in clade A, and the loaches with such sequences may be the maternal origin of the clones. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan

The genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population harboring the lineage A mitochondria expanded in the recent past, while lineage B showed weak signals of a population expansion. It is not clear whether the two lineages of mtDNA evolved in separate or identical geographical regions. We discuss two hypotheses regarding the two lineages of mtDNA: a cryptic race/species hypothesis and a selective sweep hypothesis.     

Extensive Variation and Sub-Structuring in Lineage A mtDNA in Indian Sheep: Genetic Evidence for Domestication of Sheep in India

Previous studies on mitochondrial DNA analysis of sheep from different regions of the world have revealed the presence of two major- A and B, and three minor- C, D and E maternal lineages. Lineage A is more frequent in Asia and lineage B is more abundant in regions other than Asia. We have analyzed mitochondrial DNA sequences of 330 sheep from 12 different breeds of India. Neighbor-joining analysis revealed lineage A, B and C in Indian sheep. Surprisingly, multidimensional scaling plot based on F_ST values of control region of mtDNA sequences showed significant breed differentiation in contrast to poor geographical structuring reported earlier in this species. The breed differentiation in Indian sheep was essentially due to variable contribution of two major lineages to different breeds, and sub- structuring of lineage A, possibly the latter resulting from genetic drift. Nucleotide diversity of this lineage was higher in Indian sheep (0.014 ± 0.007) as compared to that of sheep from other regions of the world (0.009 ± 0.005 to 0.01 ± 0.005). Reduced median network analysis of control region and cytochrome b gene sequences of Indian sheep when analyzed along with available published sequences of sheep from other regions of the world showed that several haplotypes of lineage A were exclusive to Indian sheep. Given the high nucleotide diversity in Indian sheep and the poor sharing of lineage A haplotypes between Indian and non-Indian sheep, we propose that lineage A sheep has also been domesticated in the east of Near East, possibly in Indian sub-continent. Finally, our data provide support that lineage B and additional lineage A haplotypes of sheep might have been introduced to Indian sub-continent from Near East, probably by ancient sea trade route.     

Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata)

Mitochondrial DNA (mtDNA) sequence variation was examined in 131 individuals of the Rosy Boa (Lichanura trivirgata) from across the species range in southwestern North America. Bayesian inference and nested clade phylogeographic analyses (NCPA) were used to estimate relationships and infer evolutionary processes. These patterns were evaluated as they relate to previously hypothesized vicariant events and new insights are provided into the biogeographic and evolutionary processes important in Baja California and surrounding North American deserts. Three major lineages (Lineages A, B, and C) are revealed with very little overlap. Lineage A and B are predominately separated along the Colorado River and are found primarily within California and Arizona (respectively), while Lineage C consists of disjunct groups distributed along the Baja California peninsula as well as south-central Arizona, southward along the coastal regions of Sonora, Mexico. Estimated divergence time points (using a Bayesian relaxed molecular clock) and geographic congruence with postulated vicariant events suggest early extensions of the Gulf of California and subsequent development of the Colorado River during the Late Miocene-Pliocene led to the formation of these mtDNA lineages. Our results also suggest that vicariance hypotheses alone do not fully explain patterns of genetic variation. Therefore, we highlight the importance of dispersal to explain these patterns and current distribution of populations. We also compare the mtDNA lineages with those based on morphological variation and evaluate their implications for taxonomy.     

Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo

Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A. The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin.     

Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers

A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific contact zones (hybrid zones), commonly involves sequencing numerous individuals. Large‐scale sequencing is both expensive and labour‐intensive. Based on sequences from 15 individuals, we devised a simple and quick polymerase chain reaction assay for identification of divergent mtDNA lineages in a secondary contact zone of the side‐blotched lizard (Uta stansburiana). The application uses lineage‐selective primers to amplify a lineage‐diagnostic product, and is based on each group of mtDNA haplotypes being a monophyletic assemblage of haplotypes sharing the same maternal ancestry, deeply divergent from the other group. The assay was tested on a larger sample (n = 147) of specimens from the contact zone, confirming its usefulness in quick and reliable identification of mtDNA lineages. This approach can be modified for other species, provided diagnostic lineage variation is available, and may also be performed in simple laboratory settings while conducting fieldwork.     

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech,Haemadipsa japonica,in Japan

Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'_ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.     

Local parasite lineage sharing in temperate grassland birds provides clues about potential origins of Galapagos avian Plasmodium

Oceanic archipelagos are vulnerable to natural introduction of parasites via migratory birds. Our aim was to characterize the geographic origins of two Plasmodium parasite lineages detected in the Galapagos Islands and in North American breeding bobolinks (Dolichonyx oryzivorus) that regularly stop in Galapagos during migration to their South American overwintering sites. We used samples from a grassland breeding bird assemblage in Nebraska, United States, and parasite DNA sequences from the Galapagos Islands, Ecuador, to compare to global data in a DNA sequence registry. Homologous DNA sequences from parasites detected in bobolinks and more sedentary birds (e.g., brown‐headed cowbirds Molothrus ater, and other co‐occurring bird species resident on the North American breeding grounds) were compared to those recovered in previous studies from global sites. One parasite lineage that matched between Galapagos birds and the migratory bobolink, Plasmodium lineage B, was the most common lineage detected in the global MalAvi database, matching 49 sequences from unique host/site combinations, 41 of which were of South American origin. We did not detect lineage B in brown‐headed cowbirds. The other Galapagos‐bobolink match, Plasmodium lineage C, was identical to two other sequences from birds sampled in California. We detected a close variant of lineage C in brown‐headed cowbirds. Taken together, this pattern suggests that bobolinks became infected with lineage B on the South American end of their migratory range, and with lineage C on the North American breeding grounds. Overall, we detected more parasite lineages in bobolinks than in cowbirds. Galapagos Plasmodium had similar host breadth compared to the non‐Galapagos haemosporidian lineages detected in bobolinks, brown‐headed cowbirds, and other grassland species. This study highlights the utility of global haemosporidian data in the context of migratory bird–parasite connectivity. It is possible that migratory bobolinks bring parasites to the Galapagos and that these parasites originate from different biogeographic regions representing both their breeding and overwintering sites.     

Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo

The origins of the domestic water buffalo remain contentious. To better understand the origins of Chinese water buffalo, we sequenced the complete mitochondrial cytochrome b (MT-CYB) gene from 270 individuals representing 13 Chinese domestic swamp buffalo populations. We found genetic evidence of introgression of river buffalo into Chinese swamp buffalo herds. Swamp buffalo haplotypes can be divided into two highly divergent lineages (A and B), suggesting that Chinese native swamp buffalo have two maternal origins. We found that the A→G transition in the buffalo MT-CYB gene stop codon resulted in buffalo haplotypes being terminated by one of two stop codons: AGA or AGG. AGA is common to river buffalo and lineage A of swamp buffalo, while AGG is specific to lineage B of swamp buffalo. Lineage A appears to have been domesticated in China. Further genetic evidence is required to clarify the origins of lineage B.     

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.     

DIFFERING LEVELS OF AMONG-POPULATION DIVERGENCE IN THE MITOCHONDRIAL DNA OF PERIODICAL CICADAS RELATED TO HISTORICAL BIOGEOGRAPHY

Mitochondrial DNA (mtDNA) haplotypes were determined for 118 individuals of 13-and 17-year periodical cicadas (genus Magicicada) collected from 16 localities throughout the Midwest and eastern United States. Two distinct mtDNA lineages, identified as A and B, differ by 2.5% based on analysis of fragment patterns and restriction maps. Observed levels of mtDNA diversity within each lineage are low compared to estimates for other taxa. The two lineages are regionally segregated, with the boundary line occurring at a latitude of approximately 33° North. The levels of mtDNA diversity and population genetic structure differ within the two lineages. There is a remarkably low level of mean mtDNA divergence and no genetic structure in lineage A, whereas lineage B exhibits an order of magnitude higher level of mtDNA diversity and significant genetic structure among sampled populations. The low level of mtDNA diversity in cicadas may be attributed to (1) a population bottleneck that most likely occurred during the Pleistocene, (2) recent colonization following the retreat of the glaciers and the expansion of deciduous forests, and/or (3) high among-family reproductive variance (as a consequence of large population size, high fecundity, aggregative behavior of adults, and clumping of eggs). The difference in mtDNA diversity and population genetic structure between the lineages suggests that they experienced different biogeographic histories; we relate this to Pleistocene changes.     

Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis)

The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.     

Systematics of the Pezizomycetes--the operculate discomycetes

The Pezizomycetes (order Pezizales) is an early diverging lineage within the Pezizomycotina. A shared derived character, the operculate ascus, supports the Pezizales as monophyletic, although functional opercula have been lost in certain taxa. Phylogenetic relationships within Pezizales were studied using parsimony and Bayesian analyses of partial SSU and LSU rDNA sequences from 100 taxa representing 82 genera and 13 of the 15 families currently recognized. Three primary lineages are identified that more or less correspond to the A, B and C lineages resolved in previous analyses using SSU rDNA: (A) Ascobolaceae and Pezizaceae; (B) Discinaceae-Morchellaceae and Helvellaceae-Tuberaceae; (C) Ascodesmidaceae, Glaziellaceae, Pyronemataceae, Sarcoscyphaceae and Sarcosomataceae. In contrast the monotypic Rhizinaceae and Caloscyphaceae are resolved as two independent lineages. Bayesian analyses support a relationship among Rhizina and two species of Psilopezia (Pyronemataceae). Only lineage C is highly supported. The B and C lineages form a strongly supported monophyletic group. None of these lineages corresponds to earlier proposed suborders. The A and B lineages are supported by certain morphological features (e.g. ascus bluing reaction in iodine, cytology of spores and paraphyses, septal pore structures and excipulum structure); these characters have been subject to homoplasy. Lineage C is the largest and most heterogeneous, and no unifying morphological features support its recognition. The Pyronemataceae, in which almost half of the species in the order are found, is not monophyletic because the Ascodesmidaceae and Glaziellaceae are nested within it. The relationships among all families in the C lineage remain uncertain. The origin of various forms of ascomata, including hypogeous forms (truffles and truffle-like), epigeous cleistothecia, simple reduced apothecia and highly elaborate, stipitate forms (helvelloid and morchelloid), are discussed.     

Morphological and genetic diversity of the thermophilic cyanobacterium,Mastigocladus laminosus (Stigonematales,Cyanobacteria) from Japan and Myanmar

The morphology and phylogeny of 13 strains of a thermophilic cyanobacterium, Mastigocladus laminosus Cohn, isolated from hot springs in Japan and Myanmar were analyzed to determine taxonomy and biogeography. From the morphological observations of cell size, there were significant differences among strains. Phylogenetic analyses based on 16S rRNA gene sequences revealed two lineages: Lineages I and II. Lineage I consisted of strains collected in Japan and reference strains from a previous study (CCMEE 5329 and 5331, Hakone, Japan); Lineage II included all of the Myanmar strains and one Japanese strain, and was a novel lineage in phylogeographic studies on M. laminosus. Since strains in the Lineage II tended to have larger cells than those in the Lineage I, the morphological and phylogenetic lineages corresponded well with each other.     

A worldwide phylogeography of the whiteworm lichens Thamnolia reveals three lineages with distinct habitats and evolutionary histories

Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia . By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems. Molecular dating analysis indicated that the split of the three lineages is older than the last glacial maximum, but the distribution ranges and the population genetic analyses suggest an influence of last glacial period on the present‐day population structure of each lineage. We found a very low diversity of Lineage B, but a higher and similar one in Lineages A and C. Demographic analyses suggested that Lineage C has its origin in the Northern Hemisphere, possibly Scandinavia, and that it has passed through a bottleneck followed by a recent population expansion. While all three lineages reproduce clonally, recombination tests suggest rare or past recombination in both Lineages A and C. Moreover, our data showed that Lineage C has a comparatively low photobiont specificity, being found associated with four widespread Trebouxia lineages (three of them also shared with other lichens), while Lineages A and B exclusively harbor T. simplex s. lat. Finally, we did not find support for the recognition of taxa in Thamnolia based on either morphological or chemical characters.     

Mitochondrial diversity of European pond turtles (Emys orbicularis) in Anatolia and the Ponto-Caspian Region: Multiple old refuges, hotspot of extant diversification and critically endangered endemics

The European pond turtle, Emys orbicularis (Linnaeus, 1758), is one of the world's most widely distributed chelonian species. We investigated its mitochondrial phylogeography and demography using ∼1300 cyt b sequences from the entire range, with a focus on the eastern part, in particular on Turkey, where the species currently suffers massive losses. Coloration data from >1450 turtles were compared with mtDNA differentiation to assess the validity of the currently accepted subspecies from Turkey, the Black Sea Region, the Transcaucasus, and Iran. Our study region harbors considerable part of the mtDNA diversity of Emys, including a newly discovered lineage and 16 new haplotypes. In this area corresponding to approximately one-third of the entire distribution range, six out of the ten mitochondrial lineages and about half of all 72 haplotypes occur. Two mitochondrial lineages (VIII, X) are confined to small ranges along the southern coast of Turkey, another lineage (I) occupies the remainder of Turkey, the entire Black Sea Region, and the north-eastern part of the species’ range. In the south-western corner of the Black Sea and in the Aegean Region, two lineages (II, IV) occur that have their main distribution areas farther west. In the Transcaucasus and northern Iran, another endemic lineage (VII) is found. Lineage I is the largest and most diverse of all lineages and has its greatest diversity in Anatolia. Phylogeographic and demographic data suggest Anatolia as an ancient glacial refuge for turtles harboring mitochondrial lineages I, VIII and X, and that Anatolia and the Black Sea coasts constitute a hotspot for a younger burst of diversification within lineage I. These two regions correspond to the glacial refuge from which lineage I turtles recolonized more northerly parts of the range in the Holocene; lineage II represents an off-shoot of lineage I that became isolated in a westward-located refuge in the south-eastern Balkans during a previous Pleistocene glacial. Our data on coloration indicate that such characters have only limited value for delineating evolutionarily significant units. We propose to reduce the number of subspecies using mtDNA lineages as arbiter, and to recognize three subspecies as valid in Turkey, the Black Sea Region, the Transcaucasus and Iran: Emys orbicularis orbicularis (mtDNA lineage I); E. o. eiselti Fritz et al., 1998 (X); and E. o. persica Eichwald, 1831 (VII). However, the southern Turkish lineage VIII most probably represents an additional undescribed subspecies. Both southern Turkish endemics are critically endangered, with only three surviving populations of fewer than 30 adults each. We recommend establishing sanctuaries for them, and including them in the IUCN Red List.     

Retrospective Estimation of Genetic Diversity of an Extinct Oriental White Stork (Ciconia boyciana) Population in Japan Using Mounted Specimens and Implications for Reintroduction Programs

The Japanese regional population of the Oriental white stork (Ciconia boyciana) became extinct in 1986. Mitochondrial DNA (mtDNA) D-loop region from 20 mounted specimens preserved at public facilities in Toyooka City, Hyogo Prefecture, Japan and its vicinity (n = 17), the area inhabited by the last of the Japanese population, and samples originating from China (n = 3) which were kept at a zoo was analyzed. After extracting DNA from small pieces of skin from mounted specimens, a 1210-bp region of the mtDNA D-loop region was analyzed. The haplotypes among 11 specimens of storks captured or found dead at Toyooka City just before the population became extinct were completely identical. Four haplotypes observed among the mounted specimens preserved in the vicinity of Toyooka City were differentiated from those of captive storks originating from China and Russia in a previous study. Therefore, the last Japanese population might have been a genetically unique group. However, phylogenetic analysis using the maximum likelihood method showed that haplotypes found in the Japanese regional population were closely related to the Chinese and Russian lineages (sequence difference = 2.1%). One mounted specimen collected in 1935 at Izushi village, in the vicinity of Toyooka City, showed the same haplotype as the captive storks from China, suggesting that genetic flow may have historically occurred between the populations of Japan and the continent. Recently, reintroduction for the Oriental white stork has been planned in Toyooka City. The planning for the recovery of extinct populations should not only involve translocation of species to the range from which it disappeared, but also reconstruction of regional populations while considering the genetic lineage between the extinct and introduced populations.     

Molecular diversity and phylogeography of the Asian leopard cat, Felis bengalensis, inferred from mitochondrial and Y-chromosomal DNA sequences

To investigate genetic diversity and phylogeography of the Asian leopard cat (Felis bengalensis), mitochondrial DNA (mtDNA) sequences were determined for 39 individuals from various areas. Sequences combining the complete cytochrome b gene (1,140 bp) with the partial control region (646-810 bp) were classified into 24 haplotypes: 21 types from 21 animals, one from eight animals from Tsushima Islands, one from eight animals from Iriomote Island, and one from two animals from Southeast Asia. Phylogenetic trees of the 24 haplotypes clearly showed three clades: a Northern Lineage and Southern Lineages 1 and 2. The Northern Lineage consisted of animals from Tsushima Islands, the Korean Peninsula, the continental Far East, Taiwan, and Iriomote Island. Within the Northern Lineage, genetic contacts could have occurred between geographically neighboring populations before isolation by straits. Southern Lineage 1, comprising Southeast Asian animals, showed higher genetic diversity. Southern Lineage 2 had large genetic distances from other lineages. Within the control region, the Asian leopard cats shared two to four repetitive motifs, and the number of motifs and their constitution were highly variable among individuals. The motifs were polymorphic even within individuals and could be classified into 31 types. Finally, males of mtDNA Southern Lineage 1 had either of two types of the Y-chromosomal gene ZFY, whereas all males of Northern Lineage shared only one type. Our results indicate that the diversity of southern populations is higher and that genetic differentiation among northern local populations reflects past geographical isolation.     

Mitochondrial DNA analysis provides new insights into the origin of the Chinese domestic goat

Many studies have focused on modern goats, however, few reports focused on origin and genetic structure of Chinese ancient goats. In this study, we analyzed the 289-bp fragment of mitochondrial DNA (mtDNA) control region from 14 Chinese ancient goats excavated from two archaeological sites in Inner Mongolia, China dating back about 2500 years. 10 haplotypes were successfully obtained from the 14 ancient goats. Phylogenetic analysis revealed the multiple maternal origins of Chinese domestic goats, three mtDNA lineages A, B, and D were identified in the Chinese ancient individuals, in which lineage A was predominant (70%), lineages B was moderate (20%), and lineage D was present at low frequency (10%). The network analysis showed that lineage B was subdivided into two subgroups B1 and B2. One of the Chinese ancient goats shared the founder haplotype in the center of subgroup B1, and the shared sequences of the founder haplotypes of subgroups B1 and B2 distributed mainly in China. These results implied that lineage B including subgroups B1 and B2 probably originated from China, and further supported the hypothesis that China may be one of the goat domestication centers. In addition, the analysis of shared sequences indicated that the ancient goats from Inner Mongolia were closely genetically related to Chinese modern goats, suggesting that the ancient goats from Inner Mongolia had the genetic contribution to Chinese modern goats.     

Evidence for two independent lineages of shiitake of the americas (Lentinula boryana) based on rDNA and beta-tubulin gene sequences

Portions of ribosomal RNA genes (rDNA) were sequenced from members of the genus Lentinula and were used, along with partial beta-tubulin gene sequences, for phylogenetic reconstructions. The rDNA sequences of L. boryana were separated into two well-defined lineages. Lineage 1 was composed of isolates from Mexico and Costa Rica while lineage 2 encompassed isolates from the United States, Venezuela, and Brazil. The two South American isolates of L. boryana had nearly identical ITS sequences and very closely related beta-tubulin sequences. This high level of similarity may indicate that sexual reproduction occurs among the sampled populations, although this is difficult to reconcile with the large geographic distances (over 4000 km) that separate some of the collecting locations. An alternative explanation may be that the isolates sampled are the product of a rapid population expansion over a large geographic area. Analyses of partial beta-tubulin gene sequences that were rooted using Pleurotus spp. support the hypothesis that L. boryana is monophyletic.