Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA

The distribution of selection coefficients of new mutations is of key interest in population genetics. In this paper we explore how codon-based likelihood models can be used to estimate the distribution of selection coefficients of new amino acid replacement mutations from phylogenetic data. To obtain such estimates we assume that all mutations at the same site have the same selection coefficient. We first estimate the distribution of selection coefficients from two large viral data sets under the assumption that the viral population size is the same along all lineages of the phylogeny and that the selection coefficients vary among sites. We then implement several new models in which the lineages of the phylogeny may have different population sizes. We apply the new models to a data set consisting of the coding regions from eight primate mitochondrial genomes. The results suggest that there might be little power to determine the exact shape of the distribution of selection coefficient but that the normal and gamma distributions fit the data significantly better than the exponential distribution.     

The distribution of aquaporin subtypes (PIP1, PIP2 and gamma-TIP) is tissue dependent in soybean (Glycine max) root nodules

BACKGROUND AND AIMS The inner cortical cells (IC-cells) of legume root nodules have been previously shown to regulate the resistance to nodule O2 diffusion by a rapid contraction/expansion mechanism, which controls the volume of intercellular spaces and their occlusion by a liquid phase. The expression of aquaporins in IC-cells was also found to be involved in this nodule O2 diffusion mechanism. The aim of this study was to compare the expression of plasma membrane intrinsic proteins (PIP) aquaporin isoforms with tonoplast intrinsic protein (gamma-TIP) in both IC-cells and adjacent cell types. METHODS: Using immunogold labelling in ultra-thin sections of Glycine max nodules, the expression of two PIP isoforms was observed and compared with the gamma-TIP pattern. KEY RESULTS: The plasma membrane aquaporins PIP1 and PIP2 were expressed more in IC-cells and endodermis than in pericycle and infected cells. The tonoplast aquaporin gamma-TIP has shown a distribution pattern similar to that of the PIPs. CONCLUSIONS: PIPs and gamma-TIP aquaporins are highly expressed in both plasmalemma and tonoplast of nodule IC-cells. This distribution is consistent with the putative role of water fluxes associated with the regulation of nodule conductance to O2 diffusion and the subsequent ATP-dependent nitrogenase activity. In the endodermis, these aquaporins might also be involved in nutrient transport between the infected zone and vascular traces.     

Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes

Vitamin B(6) (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5'-phosphate (PLP; the active form of VB6) are known: the de novo pathway, the salvage pathway, and the fungal type pathway. Most unicellular organisms and plants biosynthesize VB6 using one or two of these three biosynthetic pathways. However, animals such as insects and mammals do not possess any of the pathways and, thus, need to intake VB6 in their diet to survive. It is conceivable that breakdowns of these pathways occurred in the evolutionary lineages of insects and mammals, and one of the major reasons for this would be the loss of pertinent genes. We studied the evolution of VB6 biosynthesis from the view of the gain and loss of 10 pertinent genes in 122 species whose genome sequences were completely determined. The results revealed that each gene in the pathways was lost more than once in the entire evolutionary lineages of the 122 species. We also found the following three points regarding the evolution of PLP biosynthesis: (1) the breakdown of the PLP biosynthetic pathways occurred independently at least three times in animal lineages, (2) the de novo pathway was formed by the generation of pdxB in gamma-proteobacteria, and (3) the order of the gene loss in VB6 metabolism was conserved among different evolutionary lineages. These results suggest that the evolution of VB6 metabolism was subject to gains and frequent losses of related genes in the 122 species examined. This dynamic nature of the evolutionary changes must have been responsible for the breakdowns of the pathways, resulting in profound differentiation of heterotrophy among the species.     

The law of payoff consistency: Games with continuous differences on resource values

We analyzed general continuous games in which two players compete for a resource with a different value. There is a pure ESS function in which an increase in the resource value increases the cost which players are willing to pay to obtain the resource. We also found that the expected payoff of the player does not change at all, even if the rules of the game were changed. If the rules of a contest become more costly and more vain, the cost equilibrium of the contest would become lower and perfectly cancel the effect of the change in the rules. The payoff is affected only by the distribution of resource value. This implies that however costly and however vain a contest in nature appears, it would not immediately relate with the individual’s loss and species benefit. We name this phenomenon “the law of payoff consistency”.     

不同氮素形态比例对五味子幼苗生长特性的影响

以2年生五味子苗木为试验材料,在田间条件下,施以铵态氮(NH4+-N)和硝态氮(NO3--N)不同比例,分析了叶片可溶性蛋白、叶绿素含量、根系及茎叶中全氮含量、生物量等季节的动态变化规律,探讨了不同氮素形态比例对五味子苗木生长的影响。结果表明,五味子苗木在不同生长时期对不同氮素形态的吸收和利用存在明显差异,NH4+-N和NO3--N对五味子幼苗生长有显著的联合效应。在五味子生长前期,五味子主要以吸收和同化NH4+-N为主,并以铵态氮和硝态氮比例为75∶25时地上部生物量积累较多;而在五味子生长的中后期,五味子主要以NO3--N吸收和同化为主,并以铵态氮和硝态氮比例为25∶75时地上部生物量积累较多。     

Leaf vascular systems in C(3) and C(4) grasses: a two-dimensional analysis

BACKGROUND AND AIMS: It is well documented that C(4) grasses have a shorter distance between longitudinal veins in the leaves than C(3) grasses. In grass leaves, however, veins with different structures and functions are differentiated: large longitudinal veins, small longitudinal veins and transverse veins. Thus, the densities of the three types of vein in leaves of C(3) and C(4) grasses were investigated from a two-dimensional perspective. METHODS: Vein densities in cleared leaves of 15 C(3) and 26 C(4) grasses representing different taxonomic groups and photosynthetic subtypes were analysed. KEY RESULTS: The C(4) grasses had denser transverse veins and denser small longitudinal veins than the C(3) grasses (1.9 and 2.1 times in interveinal distance), but there was no significant difference in large longitudinal veins. The total length of the three vein types per unit area in the C(4) grasses was 2.1 times that in the C(3) grasses. The ratio of transverse vein length to total vein length was 14.3 % in C(3) grasses and 9.9 % in C(4) grasses. The C(3) grasses generally had greater species variation in the vascular distances than the C(4) grasses. The bambusoid and panicoid C(3) grasses tended to have a denser vascular system than the festucoid C(3) grasses. There were no significant differences in the interveinal distances of the three vein types between C(4) subtypes, although the NADP-malic enzyme grasses tended to have a shorter distance between small longitudinal veins than the NAD-malic enzyme and phosphoenolpyruvate carboxykinase grasses. CONCLUSIONS: It seems that C(4) grasses have structurally a superior photosynthate translocation and water distribution system by developing denser networks of small longitudinal and transverse veins, while keeping a constant density of large longitudinal veins. The bambusoid and panicoid C(3) grasses have a vascular system that is more similar to that in C(4) grasses than to that in the festucoid C(3) grasses.     

The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy

Methanogenesis and methane oxidation are the major biological processes affecting the global cycling of the powerful greenhouse gas methane. To carry out the two alternative bioconversions, Nature has cleverly recycled key reactions for the C1 transfers between the oxidation levels of formaldehyde and formate, and these involve analogous enzyme systems and common specialized cofactors, methanopterin and methanofuran. Until recently, the distribution of these functions has been limited to methanogenic archaea and methylotrophic proteobacteria, and their evolutionary history remained obscure. Single interdomain lateral transfer of the respective genes has been suggested to play a role. Here we show that genes for C1 transfer reactions linked to methanopterin and methanofuran are also present in diverse representatives of the enigmatic bacterial clade, the Planctomycetes. Phylogenetic analysis places the planctomycete sequences as distantly from their archaeal counterparts as from their proteobacterial counterparts, suggesting novel scenarios for the evolution of the C1 transfer functions in both methanogens and methylotrophs. This finding suggests a possible role for Planctomycetes in the evolution of the methane cycle on Earth.     

Plant nitrogen dynamics and nitrogen-use strategies under altered nitrogen seasonality and competition

BACKGROUND AND AIMS: Numerous studies have examined the effects of climatic factors on the distribution of C(3) and C(4) grasses in various regions throughout the world, but the role of seasonal fluctuations in temperature, precipitation and soil N availability in regulating growth and competition of these two functional types is still not well understood. This report is about the effects of seasonality of soil N availability and competition on plant N dynamics and N-use strategies of one C(3) (Leymus chinensis) and one C(4) (Chloris virgata) grass species. METHODS: Leymus chinensis and C. virgata, two grass species native to the temperate steppe in northern China, were planted in a monoculture and a mixture under three different N seasonal availabilities: an average model (AM) with N evenly distributed over the growing season; a one-peak model (OM) with more N in summer than in spring and autumn; and a two-peak model (TM) with more N in spring and autumn than in summer. KEY RESULTS: The results showed that the altered N seasonality changed plant N concentration, with the highest value of L. chinensis under the OM treatment and C. virgata under the TM treatment, respectively. N seasonality also affected plant N content, N productivity and N-resorption efficiency and proficiency in both the C(3) and C(4) species. Interspecific competition influenced N-use and resorption efficiency in both the C(3) and C(4) species, with higher N-use and resorption efficiency in the mixture than in monoculture. The C(4) grass had higher N-use efficiency than the C(3) grass due to its higher N productivity, irrespective of the N treatment or competition. CONCLUSIONS: The observations suggest that N-use strategies in the C(3) and C(4) species used in the study were closely related to seasonal dynamics of N supply and competition. N seasonality might be involved in the growth and temporal niche separation between C(3) and C(4) species observed in the natural ecosystems.     

中国森林生态系统土壤CO2释放分布规律及其影响因素

联合国气候框架公约的签署提升了人们对全球变暖、碳循环变化的关注。陆地生态系统在全球变暖格局下的地位与作用,尤其是土壤碳库对全球变暖格局的响应是全球变化研究的焦点。土壤CO₂释放作为土壤-大气CO₂交换的主要途径之一,也就成为各国生态学家研究的重点内容。在对我国森林生态系统CO₂释放通量以及相关气候、生物等因子的资料进行收集、整理和分析的基础上,探讨了我国森林生态系统土壤CO₂释放的分布规律,以及这种规律性分布的气候、生物影响因素。对于我国这样一个南北跨度大的国家,不同区域的森林生态系统土壤CO₂释放通量间存在较大的差异,在全国尺度上,森林生态系统土壤CO₂释放通量平均值为(1.79 ± 0.86) g C m^-2 d^-1,而且土壤CO₂释放通量随着纬度增加逐渐降低。作为一个复杂的生态过程,土壤CO2释放受到生物、非生物因子或独立、或综合的影响。通过分析指出,在全国尺度上,年均温、降雨量、群落净生产力及凋落物量显著地影响森林土壤CO₂释放通量。同时,也正是这些影响因子的纬度分布,导致了我国森林生态系统土壤CO₂释放通量的纬度分布规律。作为衡量土壤CO₂释放对温度敏感性的重要指标,计算了我国森林生态系统土壤CO2释放温度敏感性系数-Q₁₀值,约为1.5,该值显著低于全球平均水平,2.0。     

Optimal spending functions for asymmetric group sequential designs

We present optimized group sequential designs where testing of a single parameter theta is of interest. We require specification of a loss function and of a prior distribution for theta. For the examples presented, we pre-specify Type I and II error rates and minimize the expected sample size over the prior distribution for theta. Minimizing the square of sample size rather than the sample size is found to produce designs with slightly less aggressive interim stopping rules and smaller maximum sample sizes with essentially identical expected sample size. We compare optimal designs using Hwang-Shih-DeCani and Kim-DeMets spending functions to fully optimized designs not restricted by a spending function family. In the examples selected, we also examine when there might be substantial benefit gained by adding an interim analysis. Finally, we provide specific optimal asymmetric spending function designs that should be generally useful and simply applied when a design with minimal expected sample size is desired.     

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn, allows evaluation of its importance in maintaining the structure/function of the protein. When using probabilistic methods for site-specific rate inference, few alternatives are possible. In this study we use simulations to compare the maximum-likelihood and Bayesian paradigms. We study the dependence of inference accuracy on such parameters as number of sequences, branch lengths, the shape of the rate distribution, and sequence length. We also study the possibility of simultaneously estimating branch lengths and site-specific rates. Our results show that a Bayesian approach is superior to maximum-likelihood under a wide range of conditions, indicating that the prior that is incorporated into the Bayesian computation significantly improves performance. We show that when branch lengths are unknown, it is better first to estimate branch lengths and then to estimate site-specific rates. This procedure was found to be superior to estimating both the branch lengths and site-specific rates simultaneously. Finally, we illustrate the difference between maximum-likelihood and Bayesian methods when analyzing site-conservation for the apoptosis regulator protein Bcl-x(L).     

Expression of the nuclear gene TaF(A)d is under mitochondrial retrograde regulation in anthers of male sterile wheat plants with timopheevii cytoplasm

Alterations of mitochondrial-encoded subunits of the F_oF₁-ATPsynthase are frequently associated with cytoplasmic male sterility(CMS) in plants; however, little is known about the relationshipof the nuclear encoded subunits of this enzyme with CMS. Inthe present study, the full cDNA of the gene TaF_Ad that encodesthe putative F_Ad subunit of the F_oF₁-ATP synthase was isolatedfrom the wheat (Triticum aestivum) fertility restorer ‘2114’for timopheevii cytoplasm-based CMS. The deduced 238 amino acidpolypeptide is highly similar to its counterparts in dicotsand other monocots but has low homology to its mammalian equivalents.TaF_Ad is a single copy gene in wheat and maps to the short armof the group 6 chromosomes. Transient expression of the TaF_Ad–GFPfusion in onion epidermal cells demonstrated TaF_Ad's mitochondriallocation. TaF_Ad was expressed abundantly in stem, leaf, anther,and ovary tissues of 2114. Nevertheless, its expression wasrepressed in anthers of CMS plants with timopheevii cytoplasm.Genic male sterility did not affect its expression in anthers.The expression of the nuclear gene encoding the 20 kDa subunitof F_o was down-regulated in a manner similar to TaF_Ad in theT-CMS anthers while that of genes encoding the 6 kDa subunitof F_o and the subunit of F₁ was unaffected. These observationsimplied that TaF_Ad is under mitochondrial retrograde regulationin the anthers of CMS plants with timopheevii cytoplasm. Key words: CMS, F_Ad subunit, F_oF₁-ATP synthase, retrograde regulation, wheat Received 8 October 2007; Revised 9 January 2008 Accepted 28 January 2008     

Use of cenograms in mammalian palaeoecology. A critical review

Cenograms are graphic representations of the size distribution of the mammalian species present in a community and are used in palaeoecological studies to obtain information about the environment. Three empirical rules are commonly applied in the interpretation of cenograms. This paper reviews the methodology of cenograms, special attention being paid to those rules. A database of 92 recent faunas and environmental data has been used to explore the relationships between the shape of the cenograms and the environment. A quantitative procedure has been developed to test the validity of the rules from a statistical point of view. The analyses carried out in this paper failed to confirm the alleged relationships between the size distribution of the large mammals and the aridity of the environment and between the size distribution of the small mammals and the temperature. The gap in medium-sized species is related to the vegetation structure, although only in tropical communities.     

根系温度对光核桃幼苗光合机构热稳定性的影响

以光核桃(Prunus mira)幼苗为材料, 通过控制根系温度研究了根系温度变化与叶片脱落酸(ABA)的关系及其对光合机构热稳定性的影响。结果表明: 1)环境高温(37和40 ℃)胁迫下保持根系温度适宜((25±2) ℃)时, 幼苗叶片相对含水量(Relative water content, RWC)下降较少, 但叶片ABA含量低, 超氧化物歧化酶(SOD)、抗坏血酸过氧化物酶(APX)、过氧化物酶(POD)和过氧化氢酶(CAT)活性低, 过氧化氢(H₂O₂)含量和膜质过氧化水平(丙二醛(Malondialdehyde, MDA)浓度)提高, 最大光化学效率(F_v/F_m)下降程度较大; 2)而同等环境高温(37和40 ℃)条件下根系温度逐步升高时, 幼苗叶片RWC降低, 叶片ABA含量增加, SOD、APX、POD、CAT活性高, H₂O₂含量高, MDA生成量低, F_v/F_m降低程度较小。与37 ℃相比, 40 ℃处理条件下各生理指标变化趋势相似, 但差异加大。因此认为: 高温胁迫条件下, 根系温度适宜时RWC高, 但导致光合机构伤害较重; 根系感受高温胁迫能够增加叶片ABA含量, 有助于保护光合机构、提高光合机构的抗热性。     

Young daughter cladodes affect CO2 uptake by mother cladodes of Opuntia ficus-indica

BACKGROUND AND AIMS: Drought damages cultivated C3, C4 and CAM plants in the semi-arid lands of central Mexico. Drought damage to Opuntia is common when mother cladodes, planted during the dry spring season, develop young daughter cladodes that behave like C3 plants, with daytime stomatal opening and water loss. In contrast, wild Opuntia are less affected because daughter cladodes do not develop on them under extreme drought conditions. The main objective of this work is to evaluate the effects of the number of daughter cladodes on gas exchange parameters of mother cladodes of Opuntia ficus-indica exposed to varying soil water contents. METHODS: Rates of net CO2 uptake, stomatal conductance, intercellular CO2 concentration, chlorophyll content and relative water content were measured in mature mother cladodes with a variable number of daughter cladodes growing in spring under dry and wet conditions. KEY RESULTS: Daily carbon gain by mother cladodes was reduced as the number of daughter cladodes increased to eight, especially during drought. This was accompanied by decreased mother cladode relative water content, suggesting movement of water from mother to daughter cladodes. CO2 assimilation was most affected in phase IV of CAM (late afternoon net CO2 uptake) by the combined effects of daughter cladodes and drought. Rainfall raised the soil water content, decreasing the effects of daughter cladodes on net CO2 uptake by mother cladodes. CONCLUSIONS: Daughter cladodes significantly hasten the effects of drought on mother cladodes by competition for the water supply and thus decrease daily carbon gain by mother cladodes, mainly by inhibiting phase IV of CAM.     

Changes in CH4 and CO2 emissions from soils under flooded conditions after being exposed to FACE (free-air CO2 enrichment) for three years

To evaluate the variations of CO₂ and CH₄ emissions from FACE (free-air CO₂ enrichment, F) soils three years after rice-wheat rotation FACE treatment, incubation experiments in the laboratory with laboratory and elevated CO₂ concentration (1000 μl L?1) were carried out under flooded conditions at 25°C. Results show that soil organic carbon is increased by 11% after exposure to FACE treatment for three years. The results indicate that at laboratory and elevated CO₂, the cumulative CO₂ emissions from FACE soils are 35% and 22% higher than those from the ambient soils, whereas the cumulative CH₄ emissions from FACE soils are 2.6 and 2.3 times that of ambient soils. Thus, there is a larger ratio of cumulative emissions of CH₄ to CO₂ in the soil F. The elevated CO₂ concentration during the incubation stimulates the cumulative CO₂ emission significantly, but its stimulation on CH₄ emission is not statistically significant. The results indicate that the elevated atmospheric CO₂ concentration stimulates the turnover rates of soil organic matter, with a net increase in soil organic matter content, and alters the CH₄/CO₂ ratio.     

An investigation of genomic base distribution

While veritable oceans of ink have been spilled over the base distributions within genes, the literature is virtually silent on large scale intra genomic base distribution. To address this issue, we have examined approximately 3400 chromosomal sequences from approximately 2000 entire genomes-including DNA and RNA, single- and double-stranded, coding and non-coding genomes. For each sequence the mean, variance, skewness, and kurtosis for each base were computed along with the genome base composition. The main findings are: (1) there is no simple relationship between these statistics and the base composition of the genome, (2) in non-viral genomes, base distribution is non-uniform, (3) base distribution in non-eukaryotic genomes obeys a number of simple rules, (4) these rules are not dependent on the presence of coding sequences, (5) bacterial genomes in particular are unusually compliant with these rules, and (6) eukaryotes have a unique pattern of base distribution.     

Process-based approach reveals directional effects of environmental factors on movement between habitats

1.?Understanding the effects of environmental factors on animal distributions is a central issue in ecology. However, movement rules inferred from distribution patterns do not reveal the processes through which animal distribution is realized. 2.?We investigated individual movement rules using a process-based approach. In experiments, coastal fish larvae (red drum, Sciaenops ocellatus) were matched with an intraspecific competitor of different sizes, and time series of habitat transition of individuals were fitted with a continuous-time Markov chain model to evaluate the effects of the presence of a competitor, behavioural interactions and habitat quality on the likelihoods of habitat transition. 3.?The process-based approach revealed that these factors did not simply act as a 'slope' between habitats that makes it easier to go in one direction and more difficult to return. Rather, these factors modify the movement rules differently depending on the directions of the movement. 4.?Individuals were less likely to enter a better habitat in the presence of a larger conspecific, more likely to shift to a poorer habitat when they received aggressive behaviour and more likely to stay in a better habitat in the presence of food. However, no effect was found on the transition intensity for moving in the opposite direction. 5.?The process-based approach to evaluating movement rules of animals allowed us to see the contrasting directional effects of different factors on the underlying movement rules used by animals, as opposed to pattern-based fitting of observed distributions. Consideration of these rules would improve the existing habitat-choice models.     

Pseudoviviparous reproduction of Poa alpina var. vivipara L. (Poaceae) during long-term exposure to elevated atmospheric CO2

Pseudovivipary is an asexual reproductive strategy exhibited by some arctic/alpine grasses in which leafy plantlets are produced in place of seeds, with genetic conservation an advantage for stress tolerators in these nutrient-poor habitats. Photosynthetic metabolism and the development of this reproductive system were investigated under varying nutrient availability and predicted future CO(2) partial pressure (pCO(2)). Poa alpina var. vivipara L., grown at present ambient pCO(2) or ambient plus 340 micro mol mol(-1) CO(2) (elevated pCO(2)), was supplied with either 0.05 mol m(-3) phosphorus and 0.2 mol m(-3) nitrogen, or 0.2 mol m(-3) phosphorus and 1.0 mol m(-3) nitrogen. Gas exchange measurements and determination of total non-structural carbohydrate (TNC), nitrogen and phosphorus contents revealed that parent plant leaf blade tissues experienced acclimatory loss of photosynthetic capacity after long-term growth at elevated pCO(2) (particularly so when nutrient availability was low); there were associated reductions in photosynthetic nitrogen and phosphorus use efficiencies (PNUE and PPUE). In addition, decreased PNUE and PPUE were exhibited by plantlets grown at elevated pCO(2) with low nutrient availability. Decreased reproductive dry matter in this treatment also resulted from a lack of reproductive initiation in daughter tillers, and altered phenology. Pseudoviviparous P. alpina is likely to be at a disadvantage in both vegetative and reproductive phases at predicted future elevated atmospheric CO(2) concentrations, particularly where nutrients are scarce and when in competition with species experiencing less acclimatory loss of photosynthetic capacity.