The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers

Background

The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary.

Methodology and Results

We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations.

Conclusion

The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.     

Studies on theileriosis in Southern Spain

Mediterranean theileriosis is widely distributed throughout Southern Spain, where it causes economic losses of considerable importance. In recent studies on 221 fighting bulls from 29 locations of different provinces, mainly in Southern Spain, the seroprevalence was 75.1% by IFAT. On the other hand, we are carrying out studies on beef and dairy breeds from eight provinces in the southern half of Spain where the positivity by IFAT ranges from 50 to more than 90% of the sampled cattle. Studies on the isolation of T. annulata strains, the demonstration of the vectorial role of some tick species, and cattle immunisation, have been carried out as well. In order to isolate the causative agent of the disease, infected blood or biopsies of lymph nodes from infected animals were used to establish in vitro cultures of T. annulata-infected lymphoblastoid cells, in six different cell lines. Attenuation of the parasites was achieved by growth in successive passages of a cell line by in vitro culture. Nowadays, a tissue culture vaccine has been developed from a local strain which is tried in experimental calves and under field condition with successful results. Besides, some studies on the transmission of T. annulata to cattle by the tick Hyalomma lusitanicum have been done.     

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.     

Neural Markers Reveal a One-Segmented Head in Tardigrades (Water Bears)

Background

While recent neuroanatomical and gene expression studies have clarified the alignment of cephalic segments in arthropods and onychophorans, the identity of head segments in tardigrades remains controversial. In particular, it is unclear whether the tardigrade head and its enclosed brain comprises one, or several segments, or a non-segmental structure. To clarify this, we applied a variety of histochemical and immunocytochemical markers to specimens of the tardigrade Macrobiotus cf. harmsworthi and the onychophoran Euperipatoides rowelli.

Methodology/Principal Findings

Our immunolabelling against serotonin, FMRFamide and α-tubulin reveals that the tardigrade brain is a dorsal, bilaterally symmetric structure that resembles the brain of onychophorans and arthropods rather than a circumoesophageal ring typical of cycloneuralians (nematodes and allies). A suboesophageal ganglion is clearly lacking. Our data further reveal a hitherto unknown, unpaired stomatogastric ganglion in Macrobiotus cf. harmsworthi, which innervates the ectodermal oesophagus and the endodermal midgut and is associated with the second leg-bearing segment. In contrast, the oesophagus of the onychophoran E. rowelli possesses no immunoreactive neurons, whereas scattered bipolar, serotonin-like immunoreactive cell bodies are found in the midgut wall. Furthermore, our results show that the onychophoran pharynx is innervated by a medullary loop nerve accompanied by monopolar, serotonin-like immunoreactive cell bodies.

Conclusions/Significance

A comparison of the nervous system innervating the foregut and midgut structures in tardigrades and onychophorans to that of arthropods indicates that the stomatogastric ganglion is a potential synapomorphy of Tardigrada and Arthropoda. Its association with the second leg-bearing segment in tardigrades suggests that the second trunk ganglion is a homologue of the arthropod tritocerebrum, whereas the first ganglion corresponds to the deutocerebrum. We therefore conclude that the tardigrade brain consists of a single segmental region corresponding to the arthropod protocerebrum and, accordingly, that the tardigrade head is a non-composite, one-segmented structure.     

Bluetongue epidemiology in wild ruminants from Southern Spain

Serum samples from 210 wild ruminants collected between 2006 and 2007 in southern Spain were tested for antibodies against bluetongue virus (BTV) by means of a competitive ELISA assay. Eighty-seven of the 210 wild ruminants analysed (41%) showed antibodies against BTV. Statistically significant differences were found in the seroprevalence among species: 66% (65 of 98) for red deer (Cervus elaphus), 50% (ten of 20) for fallow deer (Dama dama), 33% (three of nine) for mouflon (Ovis aries musimon) and 11% (nine of 83) for Spanish ibex (Capra pyrenaica). Overall, the sites where seropositive wild ruminants were found coincide with the areas where BTV had been detected in livestock, but in eastern Sierra Morena, the virus circulated in wild ruminants, although it had not been detected in domestic ruminants in the same areas. Wild ruminants over 1-year of age (sub-adults and adults) had significantly higher seroprevalences than juvenile animals. Statistically significant differences were also observed between BTV seroprevalence and management (free-ranging vs. captivity) with higher prevalence in free-ranging animals. The high seroprevalences obtained suggest that BTV is widespread in wild ruminants in southern Spain. This factor could have an important influence on the evolution of the infection in domestic livestock and indicates the need to include wild ruminant species in BTV surveillance or control programs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enigmatic ichnites in the middle triassic of Southern Spain

In southern Spain, within the Chiclana de Segura Formation of red detrital fades, enigmatic structures were found whose origins are discussed here. Each structure is composed of the union of elongated traces, two laterals and a shorter central one. All are concave epireliefs at the top of a sandstone bed whose age is assumed to be Ladinian (Triassic). The sediments formed within a fluvial environment. We describe these imprints, their structures and measurements, and discuss their orientations and associations. The traces probably have an organic origin, and are most likely tracks made by a vertebrate, possibly an archosaur, although no osseous remains have been found to confirm this interpretation.     

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

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Seroprevalence of Toxoplasma gondii in equids from Southern Spain

Antibodies to Toxoplasma gondii were determined in serum samples from 616 equids (454 horses, 80 mules and 82 donkeys) in a cross-sectional study of 420 herds in Andalusia (Southern Spain), the region with the highest number of equids in Spain. Antibodies to T. gondii were found in 10.8% horses, 15.0% mules and 25.6% donkeys by using the modified agglutination test (MAT) at a cut-off of 1:25. Herd seroprevalence for horses, mules and donkeys was 14.7% (48/327), 23.9% (11/46) and 34.0% (16/47), respectively, and 75 herds (17.8%) had at least one seropositive animal. Significant differences in T. gondii seroprevalence were observed among species, with donkeys having the highest seroprevalence and horses the lowest (P=0.04). Seroprevalence was significantly higher in herds with presence of domestic ruminants. This study is the first report of the presence of T. gondii antibodies in equine species in Spain and the first reporting T. gondii infection in donkeys in Europe. The presence of antibodies is indication of contact with the parasite and therefore, consumption of equine meat could be a potential source of human infection in Spain.     

Polymorphism of Y-Chromosomal Microsatellites in Russian Populations from the Northern and Southern Russia as Exemplified by the Populations of Kursk and Arkhangelsk Oblast

Allelic polymorphisms at five Y-chromosomal microsatellite loci (DYS19, DYS390, DYS391, DYS392, and DYS393) were typed in 87 individuals from male population samples from two geographically isolated regions (Arkhangelsk oblast and Kursk oblast) of the European part of Russia. The populations examined demonstrated substantial differences in the distribution of the DYS392 (P = 0.005) and DYS393 (P = 0.003) alleles. Estimates of genetic relationships between these populations and some other European populations (including Eastern-Slavic) showed that irrespectively of the measure of genetic distance chosen, Arkhangelsk population was closer to the populations belonging to the Finno-Ugric linguistic group (Saami and Estonians) and to the Estonian geographical neighbors, Latvians, while Kursk population was the member of a cluster formed by Eastern-Slavic populations (Russians of Novgorod oblast, Ukrainians, and Belarussians). Phylogenetic analysis of the most frequent haplotypes indicated that these differences between Kursk and Arkhangelsk populations were associated with high prevalence in the latter of major haplotypes characteristic primarily of the Finno-Ugric populations.__________Translated from Genetika, Vol. 41, No. 8, 2005, pp. 1125–1131.Original Russian Text Copyright © 2005 by Khrunin, Bebyakova, Ivanov, Solodilova, Limborska.     

Interspecific Introgression in Cetaceans: DNA Markers Reveal Post-F1 Status of a Pilot Whale

Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus) are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region) and eight nuclear loci (microsatellites) as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain), one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.     

Microsatellite Markers Reveal Genetic Variation within Sclerotinia sclerotiorum Populations in Irrigated Dry Bean Crops in Brazil

Microsatellites are powerful markers to infer population genetic parameters. We used 10 microsatellite loci to characterize the genetic diversity and structure of 79 samples of Sclerotinia sclerotiorum isolated from four Brazilian dry bean populations and observed that eight of them were polymorphic within populations. We identified 102 different haplotypes ranging from 6 to 18 per locus. Analyses based on genetic diversity and fixation indices indicated variability among and within populations of 28.79% (F_ST = 28793) and 71.21%, respectively. To examine genetic relatedness among S. sclerotiorum isolates, we used internal spacer (ITS1‐5.8S‐ITS2) restriction fragment length polymorphism (PCR‐RFLP) and sequencing analysis. PCR‐RFLP analysis of these regions failed to show any genetic differences among isolates. However, we detected variability within the sequence, which does not support the hypothesis of clonal populations within each population. High variability within and among populations may indicate the introduction of new genotypes in the areas analysed, in addition to the occurrence of clonal and sexual reproduction in the populations of S. sclerotiorum in the Brazilian Cerrado.     

Relationships between vegetation zonation and altitude in a salt-marsh system in northwest Spain

Abstract. Vegetation zonation in salt marshes has traditionally been attributed largely to altitudinal differences, since altitude determines the temporal pattern of tidal flooding and is thus closely related to proximate determinants of the distribution of species and plant communities. We investigated the distribution of vascular plants and plant communities along a series of altitudinal transects in two salt marshes in the northwestern Iberian Peninsula. Our results indicate that altitudinal range varies significantly both among species and among communities, and confirm that salt-marsh vegetation characteristics (species cover and composition) can be predicted on the basis of altitude, particularly at the lower levels of the profile.     

Men and Women in Southern Spain: "Domestic Power" Revisited

This article offers a definition of "domestic power" and attempts to operationalize this for comparative study of gender relations in southern Europe. It describes male-female relations in two stratified rural towns in Andalusia (southern Spain). The data show that working-class women in these towns, often united with their mothers, are able in many cases to prevail in domestic decision making despite opposition from their husbands. The article explores the cultural and psychological reasons for this apparent inversion of a constituted patriarchal ideal and the relative effect of social class upon male and female power asymmetries. The implications of limited access of male fieldworkers to Andalusian women are briefly addressed. Finally, these findings are discussed in the light of broader epistemological issues in gender study.     

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.     

用SSR标记研究柑橘属及其近缘属植物的亲缘关系

用SSR标记分析了29份柑橘属及近缘属植物的亲缘关系。7对SSR引物在29个样品中扩增得到114个等位基因,平均每个位点有16.3个等位基因。计算匹配系数后用邻接法进行聚类,结果表明,澳洲指橘与柑橘属的亲缘关系很近;SSR位点的高纯合频率支持富民枳种的地位;枳与柑橘属的关系较远,枳不大可能是从柑橘属衍生而来;Swingle的亚属的划分以及田中的原生柑橘类和后生柑橘类的划分界线不清晰;现代栽培柑橘的起源与大翼橙关系密切;柑橘属的枸橼、柚和宽皮橘都很好地分离,支持其为现代栽培柑橘的3个基本种的观点。