Revealing the History of Sheep Domestication Using Retrovirus Integrations

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Afr

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

Population structure and history in East Asia

Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.

Reconstructing the evolutionary history of China: A caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modem data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (similar to 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modem populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

Studies on the toxicological effects of Asulox-40 and Emisan-6 to eggs and early life history stages of Sarotherodon mossambicus

Toxicological effects of Asulox-40 and Emisan-6 to eggs and early life history stages of Sarotherodon mossambicus were reported. 80% of egg hatching occurred in the controls, 1 p.p.m and 5 p.p.m concentrations of Asulox-40. 10 p.p.m. and 50 p.p.m. concentrations of the same toxicants had 70% and 60% hatchings while in Emisan-6 in the same concentrations the hatching were 70% and! 40%. In 100 p.p.m. concentration of both toxicants 20% incomplete hatching occurred. In Emisan-6 Lc 50 and Lc 100 values were recorded at 32 hand 96h respectively in 10 p.p.m. concentrations. In Asulox-40 the same values were recorded in 24h and 40h respectively at 50 p.p.m. concentration. The fish activity during the experimental period showed initial hyper activity. It was established that the Emisan-6 is more harmful to S. mossambicus than Asulox-40. The harmless concentrations of these chemicals were 1.2 p.p.m. for Asulox-40 and 0.6 p.p.m. for Emisan-6.

Ecology and life history of penaeid shrimps

Fourteen species of penaeid shrimps with commercial value in Batan Bay and Tigbauan-Guimbal waters were identified as follows: Penaeus monodon, P.semisulcatus, P.japonicus, Metapenaeus ensis, M.burkenroadi, M.endeavouri, Metapenaeopsis palmensis, M.stridulans, Trachypenaeus fulvus, and Parapenaeus longipes. Among the 14 penaeids, P.semisulcatus, M.ensis and M.palmensis were found to be the dominant species within each genus. There are seven existing fishing gears for shrimping in the Batan Bay and Tigbauan-Guimbal waters: fish corrals, lift net, filter net, gill net, skimming net, baby trawler and commercial trawler. In general, female penaeids are larger than males. The largest P.monodon female measured was 81 mm in carapace length with 23 g in body weight. The largest male measuring 59 mm in carapace length with 119 g of body weight was caught in Batan Bay. Judging from spermatozoa occurrence on both sexes of P.monodon, the biological minimum size for male is 37 mm in carapace length and 49 mm for female. A total of 133 Penaeus postlarvae obtained from the offshore were identified by comparison with those reared in the laboratory. The postlarvae of P.japonicus-latisulcatus complex were quite dominant (60 . 2%), followed by P.semisulcatus (18 . 0%), and P.merguiensis-indicus complex (17 . 3%). The number of P.monodon postlarvae was relatively small (4 . 5%). The modal carapace length of P.monodon postlarvae from the offshore was 1 . 3 mm with three or four dorsal and no ventral spines on the rostrum, while P.monodon fry from the shoreline had 2 . 3 mm with five or six dorsal and one or two ventral spines.

Developmental and ecological stages in the life history of milkfish Chanos chanos Forsskal

Seven stages in the life history of the milkfish C. chanos , are recognized and suggested: A, embryonic; B, yolksac larval; C, larval; D, postlarval; E, juvenile; F, subadult; G. adult. An outline is presented of the life history. It is concluded that the milkfish, throughout the known stages of their life history are well adapted and equipped for optimal survival. High swimming performance, broad flexibility in feeding habits, high adaptability to a wide range of physicochemical conditions of the environment are but a few of the adaptations. The main driving force in all developmental stages is the evolutionary response to food distribution and availability followed by predation pressure.

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Survey of exist specifications morphometric, meristic and inter species molecular genetic on Bream (Abramis brava orientalis) in Anzali wetland, southern coast of Caspian Sea, Aras Dam Lake and Azerbijan Republic

Bream (Abramis brava orientalis) is one of Cyprindae the Caspian Sea and its basin which has a special ecological, biological and economical role. Stock of this fish in the Caspian Sea has reduced during several years for different reason the over fishing, different industrial, agriculture, urban pollution and destroy of the spawning habitat. So that fishery company decided to recover the stock of this fish by the way of artificial reproduction of a Bream couple hunted from south coast of the Caspian Sea (Iran) and setting the fingerling to the rivers and inflow wetlands of the Caspian Sea.This activity has due to 20 tons Bream annual fishing in the Iranian South coast of the Caspian Sea (Gilan province coast and Anzali wetland), The artificial reproduction has decreased Bream population diversity of Caspian sea and Anzali wetland.So it has been declined to improve Braem population diversity by the entrance of Azerbijan republic Bream and encounter to the Caspian sea Bream. Meanwhile there is Bream in the Aras Dam Lake which had been forgotten by the Fishery Company of Iran .For this reason specifications morphometric, meristic and inter species Molecular Genetic have been surveyed in Anzali wetland,Southern coast of Caspian Sea ,Aras Darn Lake and Azerbijan republic during 2003-2005. According to the research on specifications of Morphometric and Meristic of Anzali wetland(120 species),Southern coast of Caspian Sea(90 species), Aras Dam Lake(110 species) and Azerbijan Republic(125 species)has Morphometric and Meristic differences. So that average weight and total length of Anzali wetland Bream respectively was 167 g and 23/76 cm, 102 g and 27/62 cm in Caspian Sea , 461 g and 3 5/38 cm in Aras Darn Lake and 3 4189 g and 15/21 cm in Azerbijan republic (We forced to use 1 year Bream of artificial reproduction in Iran). Also variation coefficient average Morphometric, Morphometric specification Ration and meristic in Anzali wetland Bream was 17/45, 21/56 and 4/63, in Caspian Sea bream 22/58, 15/27 and 3124, in Aras Dam lake Lake 17145. 1.5/27 and 3/57 and Azerbaijan republic Bream 22/29, 19/66 and 4/22. Also Bream of these four regions in general status had Morphometric significant differences based on One Way ANOVA Analysis. Meanwhile Anzali wetland Bream with Caspian Sea Bream from 41 Morphometric surveyed factors in 33 factors, with Aras Darn Lake Bream in 41 factors, with Azerbkjan republic Bream in 41 factors,Caspian Sea Bream with Aras Darn Lake Bream in 36 factors,with Azerbijan republic B ream in 40 factors and A ras Dam L ake Bream with Azerbijan republic Bream in 38 factors had significant statistical differences. These four regions Bream had differences according to the Morphomertric specification ration based on One Way ANOVA Analysis. Also Anzali wetland Bream was surveyed with Caspian Sea Bream from 37 factors i n 27 factors, Anzali wetland Bream with Aras Dam 1ake in 37 factors Anzali wetland Bream with Azerbijan republic Bream in 32 factors,Caspian sea bream with Arsa Dam Lake Bream in 26 factors, Caspian Sea Bream with Azerbijan republic Bream in 29 factors and Aras Dam Lake Bream with Azerbijan republic Bream in 34 factor had significant statistical differences. Based on Meristic factor of four regions bream in 16 surveyed factors in 10 factors had meaningful differences according to the One Way ANOVA Analysis. While Anzali wetland Bream was surveyed with Caspian Sea Bream from in 3 factors,Anzali wetland Bream with Aras Dam lake in 8 factors,Anzali wetland Bream with Azerbijan republic B ream in 6 factors,Caspian Sea bream with Arsa Dam Lake Bream in 6 factors,Caspian sea Bream with Azerbijan republic Bream in 3 factors and Aras Dam Lake Bream with Azerijan republic Bream in 8 factor had significant statistical differences.Meanwihle based on Factor Analysis and Discriminant Breams had differences. Also according to the resrarchs Anzali wetland Bream in 0+ age group till 5+ (6 age groups),Caspian Sea bream in 1+ - 5+(5 age groups),Aras Darn Lake Bream in 1+ - 7+ (7 age groups) and Azerbijan republic Bream for Morphometric and Meristic studies in 1+age group and for molecular Genetic reaserch were in 8+and 9+ age groups. According to the research 4 ecosystems Bream in status of same age, Aras lake Bream were bigger according to weight and length.Also in this research genetic diversity between four population was researched by PCR-RFLP technic on a piece of mitochondrion genome with the length of 3500bp contain of tRNA-leu,tRNA-glu,ND5/6,Cytb. Between 17 used enzyme. 4 enzyme, Dral, Bc11, Haefll and Banff showed diversity in totally 6 composite haplotype was detected. Maximum nucleotide diversity by the value% 0/58 in Azerbijan republic Bream by all haplotype. Aras darn Lake Bream had 2 haplotype and nucleotide diversity of %0/35.Anzali wetland and Caspian Sea Bream had no diversity. Statistical analysis by the usage of Monte Carlo with 1000 repeat showed significant differences between Azerbaijan Bream and other Bream(P<0/0001) but there was no significant difference between 3 regions Bream(P>0/5).

The natural life history of milkfish

Following brief descriptions of the various phases in the natural life history of the milkfish (Chanos chanos), namely adults, eggs and embryos, larvae, fry and metamorphosis, juveniles and sub-adults, a summary is provided of the life history, providing also a schematic diagram.

The history of fish communities, biodiversity and environment of Lake Victoria and the lessons learnt

The first fishery survey of Lake Victoria was conducted between 1927 and 1928 (Graham 1929). Atthat time, the lake had a diverse fish fauna and the fishery was dominated by two endemic tilapiine cichlids; Oreochromis esculentus (Graham 1929) and O. variabilis (Boulenger 1906). There were a number of other species such as Protopterus aethiopicus Heckel 1851, Bagrus docmac (Forsk.) 1775, Clarias gariepinus (Burchell), Barbus species, mormyrids, Synodontis spp, Schilbe intermedius (Linn.) 1762 and Rastrineobola argentea Pellegrin, 1904 that were also abundant in the lake most of which made a significant contribution to the fishery (Graham 1929, Worthington 1929, 1932, Kudhongania & Cordone 1974). Haplochromine cichlids were represented by at least 300 species more than 99% of them endemic (Greenwood, 1974; Witte et al., 1992 a & b). The fishery of Lake Victoria was similar to that of lakes Kyoga and Nabugabo (Worthington 1929; Trewavas 1933; Greenwood 1965, 1966; Beadle 1962, 1981). There were also important fisheries on the inflowing rivers of Lake Victoria, the most important of which were Labeo victorianus and Barbus altianalis (Cadwallader 1965). The small sized species notably Rastrineobola argentea and haplochromines cichlids were not originally commercially exploited.

Survey of veterinery [sic] drug residues, environmental contaminants and mycotoxins of cultured shirmp [sic] in Iran

Economical achievement of optimal growth in developing countries may lead to sustainable poverty reduction. Agricultural activities play an important role in economy and human being welfare, which leads to establishment of food security and quality. Aquaculture products in developing countries share 51.4 percent of total agricultural production.7—percent in developed countries. Therefore undoutedly food production by means of quality and quantity has to be increased .The history of shirmp production goes back to 500 years ago. Today 50 countries of the world produce shirmp .In Islamic Republic of Iran shrimp production started since 1992 in the coastal region of Persian Gulf. The shrimp culture farms canbe classified in to 4 different categories; Extensive, semi-extensive, intensive and super instensive. Global ecological manitenanc is one of the major concerns of authorities Human manipulation of nature is the most destructive activity. Industrial sweage leakage in to the rivers and water sources is a big issue that causes reduction in the aquatic population. Heavy metals have an inhibitory effect in the production and growth of sealife. Human intake of food treated with anti microbial cause's allergy, hypersensitivity and develops microbial resistance. Organochlorine compounds contamination may found in hepato pancreatic tissues of aquatic products, Aresnic may transfer to man via plant & animal product contamination. In 1991 during Persian Gulf Mir 700 oil well set

Laboratory measurement of strength mobilisation in kaolin: Link to stress history

This letter presents data from triaxial tests conducted as part of a research programme into the stress-strain behaviour of clays and silts at Cambridge University. To support findings from earlier research using databases of soil tests, eighteen CIU triaxial tests on speswhite kaolin were performed to confirm an assumed link between mobilisation strain (γ M=2) and overconsolidation ratio (OCR). In the moderate shear stress range (0.2c u to 0.8c u) the test data are essentially linear on log-log plots. Both the slopes and intercepts of these lines are simple functions of OCR.