Multiple domestications of Asian rice.

The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.

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This study aimed to examine the responses of persistent soil seed bank to future precipitation reduction of global climate change in the forest-steppe ecotone of Hulunbuir. Samples of soil seed bank were collected from 0-10 cm soil layer along a precipitation gradient. We examined the density, species composition, diversity of seed bank and their relationship with vegetation. Structural equation model was used to explore the direct impact of annual precipitation on soil seed bank and the indirect impact through vegetation, soil nitrogen, soil phosphorus, and soil pH. The results showed that seed bank density and species richness were negatively correlated with annual precipitation. The species diversity of soil seed banks in grasslands was higher than that in forests. The similarity between soil seed bank and vegetation was generally low. The results of structural equation model showed that the effects of annual precipitation on seed bank density and species richness were negative, with the standard path coefficients of -0.051 and -0.122, respectively. The direct effect of annual precipitation on seed bank density and species richness were positive. Precipitation had indirect and positive effect on seed bank density and species richness through soil nitrogen, a significantly indirect negative effect on seed bank species richness through soil pH and soil available phosphorus, and a significantly indirect negative effect on seed bank density through soil pH. The reduction of precipitation under furture climate change might alter the hedging strategies of plants. The persistent soil seed bank in the forest-steppeecotone had a potential buffering effect against future precipitation reduction.

Cloning, expression prolife, and immune characterization of a novel stat family member (stat5bl) in Chinese tongue sole (Cynoglossus semilaevis).

STAT plays important roles in innate immunity during JAK/STAT signaling pathway, and STAT5 is particularly focused due to the existence of duplicated forms in fish and mammal. In Chinese tongue sole, stat5bl was suggested to be a candidate related to Vibrio harveyi resistance based on previous QTL screening. In this study, the full length of stat5bl cDNA was cloned and its expression patterns were analyzed. stat5bl was predominantly expressed in immune tissues, where the highest level was observed in liver, followed by skin and gill. Time course expression patterns were examined in six tissues (liver, skin, gill, kidney, intestine, spleen) after V. harveyi infection. stat5bl could be up-regulated by V. harveyi infection in all tissues except liver, despite the timepoints of peak were different. In contrast, stat5bl was significantly downregulated in liver. To elucidate the role of stat5bl in liver, in vitro RNAi were performed using primary liver cell culture. Knockdown of stat5bl could regulate the expression of genes closely related to JAK/STAT pathway. This study would enlarge our understanding of stat5bl in fish immunity.

A novel approach to study the morphology and chemistry of pollen in a phylogenetic context, applied to the halophytic taxon Nitraria L.(Nitrariaceae).

Nitraria is a halophytic taxon (i.e., adapted to saline environments) that belongs to the plant family Nitrariaceae and is distributed from the Mediterranean, across Asia into the south-eastern tip of Australia. This taxon is thought to have originated in Asia during the Paleogene (66-23 Ma), alongside the proto-Paratethys epicontinental sea. The evolutionary history of Nitraria might hold important clues on the links between climatic and biotic evolution but limited taxonomic documentation of this taxon has thus far hindered this line of research. Here we investigate if the pollen morphology and the chemical composition of the pollen wall are informative of the evolutionary history of Nitraria and could explain if origination along the proto-Paratethys and dispersal to the Tibetan Plateau was simultaneous or a secondary process. To answer these questions, we applied a novel approach consisting of a combination of Fourier Transform Infrared spectroscopy (FTIR), to determine the chemical composition of the pollen wall, and pollen morphological analyses using Light Microscopy (LM) and Scanning Electron Microscopy (SEM). We analysed our data using ordinations (principal components analysis and non-metric multidimensional scaling), and directly mapped it on the Nitrariaceae phylogeny to produce a phylomorphospace and a phylochemospace. Our LM, SEM and FTIR analyses show clear morphological and chemical differences between the sister groups Peganum and Nitraria. Differences in the morphological and chemical characteristics of highland species (Nitraria schoberi, N. sphaerocarpa, N. sibirica and N. tangutorum) and lowland species (Nitraria billardierei and N. retusa) are very subtle, with phylogenetic history appearing to be a more important control on Nitraria pollen than local environmental conditions. Our approach shows a compelling consistency between the chemical and morphological characteristics of the eight studied Nitrariaceae species, and these traits are in agreement with the phylogenetic tree. Taken together, this demonstrates how novel methods for studying fossil pollen can facilitate the evolutionary investigation of living and extinct taxa, and the environments they represent.

Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia.

The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR) and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI) to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05); presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant communities on the Tianshan Mountains. This pattern of community phylogenetic structure could have resulted from shared ancestry and species pool among these sample plots.

Himalayan origin and evolution of Myricaria (Tamaricaeae) in the neogene.

BACKGROUND: Myricaria consists of about twelve-thirteen species and occurs in Eurasian North Temperate zone, most species in the Qinghai-Tibet Plateau (QTP) and adjacent areas. METHODOLOGY/PRINCIPAL FINDINGS: Twelve species of Myricaria plus two other genera Tamarix and Reaumuria in Tamaricaceae, were sampled, and four markers, ITS, rps16, psbB-psbH, and trnL-trnF were sequenced. The relaxed Bayesian molecular clock BEAST method was used to perform phylogenetic analysis and molecular dating, and Diva, S-Diva, and maximum likelihood Lagrange were used to estimate the ancestral area. The results indicated that Myricaria could be divided into four phylogenetic clades, which correspond to four sections within the genus, of them two are newly described in this paper. The crown age of Myricaria was dated to early Miocene ca. 20 Ma, at the probable early uplifting time of the Himalayas. The Himalayas were also shown as the center of origin for Myricaria from the optimization of ancestral distribution. Migration and dispersal of Myricaria were indicated to have taken place along the Asian Mountains, including the Himalayas, Kunlun, Altun, Hendukosh, Tianshan, Altai, and Caucasus etc., westward to Europe, eastward to Central China, and northward to the Mongolian Plateau. CONCLUSIONS/SIGNIFICANCE: Myricaria spatiotemporal evolution presented here, especially the Himalayan origin at early Miocene ca. 20 Ma, and then migrated westward and eastward along the Asian mountains, offers a significant evolutionary case for QTP and Central Asian biogeography.

Retreating or standing: responses of forest species and steppe species to climate change in arid Eastern Central Asia.

BACKGROUND: The temperature in arid Eastern Central Asia is projected to increase in the future, accompanied by increased variability of precipitation. To investigate the impacts of climate change on plant species in this area, we selected two widespread species as candidates, Clematis sibirica and C. songorica, from montane coniferous forest and arid steppe habitats respectively. METHODOLOGY/PRINCIPAL FINDINGS: We employed a combined approach of molecular phylogeography and species distribution modelling (SDM) to predict the future responses of these two species to climate change, utilizing evidence of responses from the past. Genetic data for C. sibirica shows a significant phylogeographical signal (N ST > F ST, P<0.05) and demographic contraction during the glacial-interglacial cycles in the Pleistocene. This forest species would likely experience range reduction, though without genetic loss, in the face of future climate change. In contrast, SDMs predict that C. songorica, a steppe species, should maintain a consistently stable potential distribution under the Last Glacial Maximum (LGM) and the future climatic conditions referring to its existing potential distribution. Molecular results indicate that the presence of significant phylogeographical signal in this steppe species is rejected and this species contains a high level of genetic differentiation among populations in cpDNA, likely benefiting from stable habitats over a lengthy time period. CONCLUSIONS/SIGNIFICANCE: Evidence from the molecular phylogeography of these two species, the forest species is more sensitive to past climate changes than the steppe species. SDMs predict that the forest species will face the challenge of potential range contraction in the future more than the steppe species. This provides a perspective on ecological management in arid Eastern Central Asia, indicating that increased attention should be paid to montane forest species, due to their high sensitivity to disturbance.

Comparison of right ventricular apex and right ventricular outflow tract septum pacing in the elderly with normal left ventricular ejection fraction: long-term follow-up.

BACKGROUND: Whether right ventricular outfow tract septum (RVOTS) pacing is superior to right ventricular apex (RVA) pacing with respect to left ventricular synchrony, cardiac function, and remodelling in the elderly with normal left ventricular ejection fraction (LVEF), is still unknown. AIM: To assess the impact of RVOTS vs. RVA pacing on the cardiac performance of the elderly with normal LVEF during a long-term observation. METHODS: From 2007 to 2010, 65 patients with standard pacing indications for permanent pacing were recruited and randomised to receive RVA (32 patients) or RVOTS pacing (33 patients). Over a median 28 months' follow-up, available data was summarised, including New York Heart Association (NYHA) functional class, echocardiographic and pacing parameters, axis, QRS duration and plasma B-type natriuretic peptide (BNP) level. Then these values were compared between the RVA group and the RVOTS group, as well as between pacemaker pre- and post-implantation in the RVA group and in the RVOTS group, respectively. RESULTS: There were no significant differences in baseline characteristics between the RVA group and the RVOTS group. The median pacing durations did not differ significantly between the groups (31.5 months in the RVA group vs. 28 months in the RVOTS group, p = 0.728). Compared to the baseline values, LVEF decreased with RVA pacing (from 59.5 ± 6.21 to 54.22 ± 8.73, p = 0.001), but LVEF did not markedly vary in the RVOTS group (57.82 ± 6.06 and 56.94 ± 5.54, p = 0.152). The number of patients with moderate tricuspid valve regurgitation remarkably increased in the RVA group, from six (18.75%) patients to 10 (31.3%) patients, preoperatively to postoperatively (p = 0.046), but this change was not statistically significant in the RVOTS group. Compared to the RVOTS group, NYHA functional class had a deteriorated tendency in the RVA group (p = 0.071). After the implantation, the increase of median BNP level was observed in the RVA group (35 pg/mL at preimplantation and 50 pg/mL at the end of follow-up, p = 0.007); No significant change was obtained in the RVOTS group (36.4 pg/mL at pre-implantation vs. 38 pg/ml at the end of follow-up, p = 0.102). Compared to the RVA pacing group, the mean QRS width narrowed substantially in the RVOTS pacing group (from 143.56 ± 12.90 to 105.52 ± 15.21, p = 0.000). In terms of the end diastolic and systolic diameters of the left ventricular, there were no statistical variations observed during the follow-up. CONCLUSIONS: Permanent RVA pacing in elderly patients with normal LVEF led to left ventricular systolic function deterioration denoted by lower LVEF and higher BNP level. When compared to RVA pacing, RVOTS pacing had no remarkable benefit in terms of preventing cardiac remodelling.

Safety and bioactivity of intracoronary delivery of naked plasmid DNA encoding human atrial natriuretic factor.

AIM: To evaluate the safety and bioactivity of catheter-mediated intracoronary gene delivery of naked plasmid DNA encoding human atrial natriuretic factor (hANF). METHODS: hANF gene delivery was performed in 12 canines. For each canine, 4 mg of reconstructed naked plasmid DNA encoding hANF (pCR3*hANF, n=6) or pCR3 (n=6, control) in 2 mL normal saline was injected into left coronary artery via a coronary angiographic catheter. The expression of hANF mRNA in left ventricular myocardium, liver, lung, and kidney was identified by reverse transcription polymerase chain reaction and Southern blot analysis 40 d after gene delivery. Plasma ANF levels were determined by radioimmunoassay. RESULTS: The naked pCR3*hANF caused significant expression of hANF mRNA in ventricular myocardium (P <0.01). No hANF mRNA was detected in distal tissues, including liver, lung, and kidney (P >0.05). ANF levels were significantly higher in pCR3*hANF group than those in control group. CONCLUSION: These facts firstly demonstrate that intracoronary delivery of naked pCR3*hANF is probably a safe and feasible method for gene delivery by which hANF gene can be expressed in ventricular myocardium effectively.

Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations.

Mutations in BRCA1 and BRCA2 confer a high risk of breast and ovarian cancer, but account for only a small fraction of breast cancer susceptibility. To find additional genes conferring susceptibility to breast cancer, we analyzed CHEK2 (also known as CHK2), which encodes a cell-cycle checkpoint kinase that is implicated in DNA repair processes involving BRCA1 and p53 (refs 3,4,5). We show that CHEK2(*)1100delC, a truncating variant that abrogates the kinase activity, has a frequency of 1.1% in healthy individuals. However, this variant is present in 5.1% of individuals with breast cancer from 718 families that do not carry mutations in BRCA1 or BRCA2 (P = 0.00000003), including 13.5% of individuals from families with male breast cancer (P = 0.00015). We estimate that the CHEK2(*)1100delC variant results in an approximately twofold increase of breast cancer risk in women and a tenfold increase of risk in men. By contrast, the variant confers no increased cancer risk in carriers of BRCA1 or BRCA2 mutations. This suggests that the biological mechanisms underlying the elevated risk of breast cancer in CHEK2 mutation carriers are already subverted in carriers of BRCA1 or BRCA2 mutations, which is consistent with participation of the encoded proteins in the same pathway.