Y-chromosomal DNA variation in Pakistan

Eighteen binary polymorphisms and 16 multiallelic, short-tandem-repeat (STR) loci from the nonrecombining portion of the human Y chromosome were typed in 718 male subjects belonging to 12 ethnic groups of Pakistan. These identified 11 stable haplogroups and 503 combination binary marker/STR haplotypes. Haplogroup frequencies were generally similar to those in neighboring geographical areas, and the Pakistani populations speaking a language isolate (the Burushos), a Dravidian language (the Brahui), or a Sino-Tibetan language (the Balti) resembled the Indo-European-speaking majority. Nevertheless, median-joining networks of haplotypes revealed considerable substructuring of Y variation within Pakistan, with many populations showing distinct clusters of haplotypes. These patterns can be accounted for by a common pool of Y lineages, with substantial isolation between populations and drift in the smaller ones. Few comparative genetic or historical data are available for most populations, but the results can be compared with oral traditions about origins. The Y data support the well-established origin of the Parsis in Iran, the suggested descent of the Hazaras from Genghis Khan's army, and the origin of the Negroid Makrani in Africa, but do not support traditions of Tibetan, Syrian, Greek, or Jewish origins for other populations.     

A Statistical Approach to Identify Ancient Template DNA

One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging. [Reviewing Editor: Dr. Magnus Nordborg]     

Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals

Family studies of individual tissues have shown that gene expression traits are genetically heritable. Here, we investigate cis and trans components of heritability both within and across tissues by applying variance-components methods to 722 Icelanders from family cohorts, using identity-by-descent (IBD) estimates from long-range phased genome-wide SNP data and gene expression measurements for approximately 19,000 genes in blood and adipose tissue. We estimate the proportion of gene expression heritability attributable to cis regulation as 37% in blood and 24% in adipose tissue. Our results indicate that the correlation in gene expression measurements across these tissues is primarily due to heritability at cis loci, whereas there is little sharing of trans regulation across tissues. One implication of this finding is that heritability in tissues composed of heterogeneous cell types is expected to be more dominated by cis regulation than in tissues composed of more homogeneous cell types, consistent with our blood versus adipose results as well as results of previous studies in lymphoblastoid cell lines. Finally, we obtained similar estimates of the cis components of heritability using IBD between unrelated individuals, indicating that transgenerational epigenetic inheritance does not contribute substantially to the "missing heritability" of gene expression in these tissue types.     

Atlantic salmon paramyxovirus (ASPV) infection contributes to proliferative gill inflammation (PGI) in seawater-reared Salmo salar

Proliferative gill inflammation (PGI) causes significant losses in farmed Atlantic salmon Salmo salar L. in Norway, especially during the first months following seawater transfer. The aetiology is apparently multifactorial, including infection with chlamydia-like bacteria and Atlantic salmon paramyxovirus (ASPV). In the present study, gills from diseased fish from 3 farms on the western coast of Norway were sampled. The pathological changes were briefly described and the aetiological significance of ASPV studied by immunofluorescent staining of cryosections and by immunohistochemistry on sections of formalin-fixed and paraffin-embedded tissue. The pathological changes were macroscopically characterized by palour of the gills, and histologically by inflammation, circulatory disturbances, cell death and epithelial cell proliferation. ASPV was demonstrated in fish from all farms studied, as immunostaining consistent with ASPV was obtained in lamellar epithelial and endothelial cells of pathologically altered tissues. It is concluded that ASPV is at least a contributing cause of PGI. As far as we know, this is the first demonstration of fish disease related to infection with a paramyxovirus.     

mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure

We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.     

A novel betaproteobacterial agent of gill epitheliocystis in seawater farmed Atlantic salmon (Salmo salar)

Epitheliocystis, a disease characterised by cytoplasmic bacterial inclusions (cysts) in the gill and less commonly skin epithelial cells, has been reported in many marine and freshwater fish species and may be associated with mortality. Previously, molecular and ultrastructural analyses have exclusively associated members of the Chlamydiae with such inclusions. Here we investigated a population of farmed Atlantic salmon from the west coast of Norway displaying gill epitheliocystis. Although 'Candidatus Piscichlamydia salmonis', previously reported to be present in such cysts, was detected by PCR in most of the gill samples analysed, this bacterium was found to be a rare member of the gill microbiota, and not associated with the observed cysts as demonstrated by fluorescence in situ hybridization assays. The application of a broad range 16 S rRNA targeted PCR assay instead identified a novel betaproteobacterium as an abundant member of the gill microbiota. Fluorescence in situ hybridization demonstrated that this bacterium, tentatively classified as 'Candidatus Branchiomonas cysticola', was the cyst-forming agent in these samples. While histology and ultrastructure of 'Ca. B. cysticola' cysts revealed forms similar to the reticulate and intermediate bodies described in earlier reports from salmon in seawater, no elementary bodies typical of the chlamydial developmental cycle were observed. In conclusion, this study identified a novel agent of epitheliocystis in sea-farmed Atlantic salmon and demonstrated that these cysts can be caused by bacteria phylogenetically distinct from the Chlamydiae.     

Colonization of floating seaweed by pelagic and subtidal benthic animals in southwestern Iceland

Coastal floating seaweed, originating from the intertidal, is colonized by various pelagic and subtidal benthic animals. At southwestern Iceland, common macrofaunal colonizers include the fish Cyclopterus lumpus L., the harpacticoid Parathalestris croni (Krøyer), the amphipods Calliopius laeviusculus (Krøyer), Gammarellus angulosus(Rathke), Dexamine thea Boeck and Ischyrocerus anguipes (Krøyer), and the isopod Idotea baltica Pallas. The colonization patterns of these species were studied by collecting samples from experimental and natural clumps of floating seaweed at approximately monthly intervals for ca. 18 months. The occurrence of colonizers was highly seasonal with maximum numbers between April and September. For most species, numbers were correlated with weight of clumps. The relationship of density (numbers/100 g algae) to weight of clump and distance from shore varied between species. The algal species composition of clumps appeared to influence some colonizers. Only juvenile C. lumpus were found, while all P. croni were sexually mature; juveniles predominated in other species. The different colonization patterns of the species can be explained partly by their biological traits. The clumps are vital for the breeding of P. croni and are used for feeding by C. lumpus fry. Other species possibly colonize floating algae accidentally, being programmed to seek attached vegetation. Floating clumps may, nevertheless, serve to disperse these species.     

Evidence of phenotypic plasticity and local adaption in metabolic rates between components of the Icelandic cod (Gadus morhua L.) stock

Phenotypic plasticity and local adaptations are important considerations in delineating population structure of marine fishes and critical to their conservation and management. We compared the weight-specific oxygen consumption rates (VO₂/M) of juvenile cod from the northern and southern components of the Icelandic stock acclimated to 4.0°C, 8.5°C, and 12.6°C and their metabolic response to abrupt temperatures changes within this range. Southern individuals exhibited VO₂/M up to 50% higher than their northern counterparts when tested at their acclimation temperature. However, northern fish generally experienced greater changes in VO₂/M, three to six-fold increases, relative to that expected at acclimation when moved to higher temperatures. Southern cod showed a greater decrease in VO₂/M when exposed to lower temperatures. Our results indicate physiological differences exist between the northern and southern components of the Icelandic cod stock and warrant considering them as two distinct populations.     

HYBRIDIZATION OF GLAUCOUS GULLS LARUS HYPERBOREUS AND HERRING GULLS L. ARGENTATUS IN ICELAND

Until recently, the Herring Gull Larus argentatus and the Glaucous Gull L. hyperboreus were completely allopatric in western Europe, although having overlapping distributions in Canada and the Soviet Union. But beginning about 1925–1930 a large-scale invasion of argentatus from the Faroe Islands and/or Britain into Iceland occurred, resulting in extensive hybridization with hyperboreus, already present there. The hybrids are viable and apparently fully fertile. In the summers of 1964–1966 371 gulls were collected from breeding colonies in various parts of Iceland and the samples analysed by the use of hybrid indices based on the colour of the five outermost primaries. The populations of northwestern Iceland, where the greatest concentration of hyperboreus was found at the time of the argentatus invasion, were found still to consist largely of pure hyperboreus, with 18–23% of the birds showing signs of argentatus admixture. In eastern Iceland, where argentatus first appeared in numbers, and along the south coast, birds of hybrid origin predominate, 3–43% of the birds being pure argentatus while pure hyperboreus are absent except for one colony in southeastern Iceland where they made up 23% of the birds. Significant differences in composition are found among several of the colonies of eastern and southern Iceland, and possible reasons for this are discussed. Among 53 mated pairs no deviation from random matings with respect to hybrid indices was indicated. The high proportion of pure argentatus found in some colonies in spite of this indicates that pure argentatus are still immigrating from abroad. Two colonies in eastern Iceland sampled both in 1965 and 1966 showed a significant change in composition towards argentatus, further evidence for continued immigration of argentatus. A few other colonies have changed in the same direction over longer periods. Although there must be some differences between the two forms in ecological requirements as shown by their distributions, their ecologies appear similar in Iceland. Both forms take a large portion of their food from the intertidal zone of the sea-shore, and although a slight difference in the selection of foods from the shore was seen in winter in one locality, this probably did not have a genetic basis. However, argentatus may feed to a larger extent on refuse than hyperboreus. This may enable argentatus-like birds to occupy the relatively barren (with respect to intertidal foods) east coast of Iceland in numbers. An examination of several hundred museum skins of argentatus and hyperboreus from other areas shows that occasional hybridization occurred in western Europe long before the extensive contact was established in Iceland, but gene flow between the two was always limited as their ranges were widely separated. The two gulls are effectively reproductively isolated from each other where synipatric in Canada, while the situations in Alaska and in parts of the Soviet Union are unclear. Since the area of overlap without hybridization is much larger than the area of hybridization, the two forms are best regarded as separate species. Future studies may show in which direction the hybrid situation in Iceland will develop, but meanwhile it is suggested that the hybrid populations in which birds of hybrid origin amount to 50% or more be referred to as Larus argentatus/hyperboreus.