Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies

Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive pr

Origins and pathways of the subsurface and intermediate water masses of the Indonesian Throughflow derived from historical and Argo data

On the basis of Argo data and historic temperature/salinity data from the World Ocean Database 2001 (WOD01 origins and spreading pathways of the subsurface and intermediate water masses in the Indonesian Throughflow (ITF) region were discussed by analyzing distributions of salinity on representative isopycnal layers. Results were shown that, Subsurface water mostly comes from the North Pacific Ocean while the intermediate water originates from both the North and South Pacific Ocean, even possibly from the Indian Ocean. Spreading through tire Sulawesi Sea, the Makassar Strait, and the Flores Sea, the North Pacific subsurface water and the North Pacific Intermediate water dominate the western part of the Indonesian Archipelago. Furthermore its the depth increases, the features of the North Pacific sourced water masses become more obvious. In the eastern part of the waters, high salinity South Pacific subsurface water is blocked by a strong salinity front between Halmahera and New Guinea. Intermediate water in the eastern interior region owns salinity higher than the North Pacific intermediate water and the antarctic intermediate water (AAIW), possibly coming from the vertical mixing between subsurface water and the AAIW from the Pacific Ocean, and possibly coming front the northward extending of the AAIW front the Indian Ocean as well.

Phylogeography of Schizothorax o'connori (Cyprinidae: Schizothoracinae) in the Yarlung Tsangpo River, Tibet

Schizothorax o'connori is endemic to the Yarlung Tsangpo River on the Tibetan Plateau. We assessed the relative impacts of historical and contemporary factors in organizing genetic variation in S. o'connori populations using mitochondrial cytochrome b sequences. We analyzed 191 samples from 11 populations and identified 78 haplotypes. The phylogenetic analyses and analysis of molecular variance all supported the same conclusions of two well-differentiated east-west phylogroups, separated by the Tsangpo Great Gorge. The split between the two clades accounted for 58% of the genetic variance observed among the examined samples. Waterfalls as effective barriers played an important role in shaping the phylogeographical structure of this species. Analyses of migration rates revealed that upstream dispersal was limited crossing waterfalls. Our study revealed substantial spatial and temporal variation in the influence of landscape features on contemporary patterns of genetic structure in S. o'connori. Interglacial range expansions clearly left their mark on contemporary populations above the Tsangpo Great Gorge.

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.

The status and characteristics of eutrophication in the Yangtze River (Changjiang) estuary and the adjacent East China Sea, China

Eutrophication has become increasingly serious and noxious algal blooms have been of more frequent occurrence in the Yangtze River Estuary and in the adjacent East China Sea. In 2003 and 2004, four cruises were undertaken in three zones in the estuary and in the adjacent sea to investigate nitrate (NO3-N), ammonium (NH4-N), nitrite (NO2-N), soluble reactive phosphorus (SRP), dissolved reactive silica (DRSi), dissolved oxygen (DO), phytoplankton chlorophyll a (Chl a) and suspended particulate matter (SPM). The highest concentrations of DIN (NO3-N+NH4-N+NO2-N), SRP and DRSi were 131.6, 1.2 and 155.6 mu M, respectively. The maximum Chl a concentration was 19.5 mg m(-3) in spring. An analysis of historical and recent data revealed that in the last 40 years, nitrate and SRP concentrations increased from 11 to 97 mu M and from 0.4 to 0.95 mu M, respectively. From 1963 to 2004, N:P ratios also increased from 30-40 up to 150. In parallel with the N and P enrichment, a significant increase of Chl a was detected, Chl a maximum being 20 mg m(-3), nearly four times higher than in the 1980s. In 2004, the mean DO concentration in bottom waters was 4.35 mg l(-1), much lower than in the 1980s. In comparison with other estuaries, the Yangtze River Estuary was characterized by high DIN and DRSi concentrations, with low SRP concentrations. Despite the higher nutrient concentrations, Chl a concentrations were lower in the inner estuary (Zones 1 and 2) than in the adjacent sea (Zone 3). Based on nutrient availability, SPM and hydrodynamics, we assumed that in Zones 1 and 2 phytoplankton growth was suppressed by high turbidity, large tidal amplitude and short residence time. Furthermore, in Zone 3 water stratification was also an important factor that resulted in a greater phytoplankton biomass and lower DO concentrations. Due to hydrodynamics and turbidity, the open sea was unexpectedly more sensitive to nutrient enrichment and related eutrophication processes.