AnthropMMD: An R package with a graphical user interface for the mean measure of divergence

The mean measure of divergence is a dissimilarity measure between groups of individuals described by dichotomous variables. It is well suited to datasets with many missing values, and it is generally used to compute distance matrices and represent phenograms. Although often used in biological anthropology and archaeozoology, this method suffers from a lack of implementation in common statistical software. A package for the R statistical software, AnthropMMD, is presented here. Offering a dynamic graphical user interface, it is the first one dedicated to Smith's mean measure of divergence. The package also provides facilities for graphical representations and the crucial step of trait selection, so that the entire analysis can be performed through the graphical user interface. Its use is demonstrated using an artificial dataset, and the impact of trait selection is discussed. Finally, AnthropMMD is compared to three other free tools available for calculating the mean measure of divergence, and is proven to be consistent with them.     

Taxonomic and functional ant diversity along a secondary successional gradient in a tropical forest

The taxonomic diversity (TD) of tropical flora and fauna tends to increase during secondary succession. This increase may be accompanied by changes in functional diversity (FD), although the relationship between TD and FD is not well understood. To explore this relationship, we examined the correlations between the TD and FD of ants and forest age in secondary forests at the α‐ and β‐diversity levels using single‐ and multi‐trait‐based approaches. Our objectives were to understand ant diversity patterns and to evaluate the role of secondary forests in the conservation of biodiversity and in the resilience of tropical forests. Ant assemblages were sampled across a chronosequence in the Lacandon region, Mexico. All species were characterized according to 12 functional ecomorphological traits relevant to their feeding behavior. We found that TD and FD were related to forest age at the alpha level, but not at the beta level. α‐functional richness and divergence increased linearly with species richness and diversity, respectively. Also, the relationship between taxonomic and functional turnover was linear and positive. Our results indicated that functional traits were complementary across the chronosequence. The increase in FD was mainly driven by the addition of rare species with relevant traits. The older secondary forests did not recover all of the functions of old growth forest but did show a tendency to recovery. Because older successional stages support more TD and FD, we suggest developing agriculture and forestry management practices that facilitate rapid post‐agricultural succession and thereby better preserve the functionality of tropical forests.     

遮荫对油用牡丹植株生长和光合特性的影响

设置100%全光照(L0)、50%全光照(L1)、25%全光照(L2)和15%全光照(L3)4种光环境,分析不同遮荫环境对油用牡丹的生长、光合作用及叶绿素荧光参数的影响。结果表明:(1)油用牡丹的花朵数量、比叶重、气孔密度在L2和L3处理下显著低于L0处理,但L1较L0无显著变化;随着遮荫水平增加,油用牡丹种子数量、气孔器面积百分比逐渐下降,且在4个不同处理间差异显著。(2)油用牡丹叶片最大净光合速率(Pmax)、光补偿点(LCP)和光饱和点(LSP)在遮荫条件下均有不同程度降低,L2和L3处理的Pmax和LSP显著低于L0,但L1较L0无显著变化。(3)L3处理的光系统Ⅱ(PSⅡ)的最大量子效率(Fv/Fm)为0.76,显著低于其余3个光照处理;随光化光诱导时间的增加,开放的PSⅡ反应中心的激发能捕获效率(Fv′/Fm′)呈逐渐下降并趋于稳定的趋势,而PSⅡ的实际量子产量效率(ΦPSⅡ)、光化学猝灭系数(qP)、非光化学猝灭系数(NPQ)呈逐渐增加并趋于稳定的趋势,稳定后的Fv′/Fm′、ΦPSⅡ值表现为L0L1L2L3,NPQ大小顺序为L3L2L1L0,但不同处理间的qP无显著差异。研究发现:过度遮荫(15%~25%自然光强)严重抑制了油用牡丹的净光合速率,而且与产量直接相关的花朵数量和种子数量也显著下降,最终造成严重减产;在云南昆明地区50%~100%之间的自然光可能是油用牡丹较为合适的生长光强。     

不同施肥水平对桢楠多胚苗生长及光合生理的影响

采用营养袋培育的方法,以苗龄45d(根茎初步木质化)的桢楠幼苗为试验材料,选取单胚苗(D)、双胚大苗(SD)和双胚小苗(SX)3种类型桢楠幼苗栽植于袋中,根据年施复合肥量标准设置对照(CK,每袋0g)、中(M,每袋0.2g)和高(H,每袋0.3g)3个施肥水平,于7月初开始施肥,每20d施1次共分4次(每次25%)施入,分别于8月、10月中旬测定幼苗生长指标和光合生理指标,探讨施肥对桢楠多胚苗生长和光合生理的影响。结果显示:(1)中量施肥(M)对3类幼苗的苗高和地径生长量有明显的促进作用,而高量施肥(H)在整个试验过程中对幼苗生长的影响表现为先促进后抑制的趋势。(2)中量施肥(M)可以促进3类幼苗叶片的叶绿素合成,延长叶片功能周期,增大净光合速率和气孔导度,进而提高幼苗在强光照、高CO_2环境下的光合作用能力。(3)中量施肥可以使幼苗的光补偿点(LCP)、CO_2补偿点(CCP)下降,光饱和点(LSP)、CO_2饱和点(CSP)上升,增强幼苗适应环境的能力,积累更多的有机物;高量施肥对幼苗的光合指标也表现为先促进后抑制的作用。研究表明,适量(每袋0.2g)施肥能促进各类桢楠幼苗光合色素合成、光合作用效率以及对环境的适应能力,从而促进幼苗的生长;适量施肥也使双胚大苗较快缩小与单胚苗生长指标间的差距,同时也对双胚小苗生长表现出一定的促进作用,这对于促进珍贵树种桢楠的种质资源保护、提高苗木出圃率和降低育苗成本有重要意义。     

长白落叶松冠层光合作用的空间异质性

以2014年黑龙江省帽儿山林场14年生人工长白落叶松为研究对象,对比分析了各项光合指标、环境因子及光合生理参数在冠层内的空间差异性,并探讨了净光合速率(P_n)与其他指标的关系.结果表明: 在树冠垂直方向,上层P_n、气孔导度(g_s)和蒸腾速率(T_r)显著高于中层和下层,胞间CO₂浓度(C_i)表现为下层>中层>上层;光合有效辐射(PAR)从上层外部到下层内部呈显著降低趋势,水汽压差(VPD)和叶片温度(T_l)表现为上层显著高于中层和下层,相对湿度(RH)则无显著差异;最大净光合速率(P_{n max})、暗呼吸速率(R_d)、光补偿点(LCP)和光饱和点(LSP)均表现为上层>中层>下层,下层比上层分别降低32.7%、55.8%、80.2%和51.6%,表观量子效率(AQY)表现为下层>中层>上层,下层分别是中层和上层的1.2和1.3倍.水平方向,光合指标和环境因子的差异性主要体现在树冠上层,P_n、g_s、T_r、PAR和VPD表现为树冠外部显著高于树冠内部,而C_i和RH差异不显著;P_{n max}、R_d、LCP和LSP表现为外部>内部,内部比外部分别降低0.4%、37.7%、42.0%和16.4%,而AQY在内部比外部高0.7%.C_i是限制P_n的主要生理因子,PAR是影响P_n的主要环境因子,尤其在弱光区域PAR对P_n的影响十分明显.因此,在模拟和预估树木冠层光合作用时,考虑空间异质性有一定的必要性.     

半干旱区膜上覆土穴播对春小麦旗叶光合作用和水分利用的影响

在甘肃定西大田定位试验的基础上,2012—2013年连续2年比较了全膜覆土穴播(PMS)、覆膜穴播(PM)和露地穴播(CK)春小麦旗叶的SPAD值、叶绿素荧光参数、光合气体交换参数以及叶面积指数(LAI)、产量、耗水量和水分利用效率.结果表明: PMS提高了小麦旗叶SPAD值,扬花后显著高于PM,增加了10.0%～21.5%,较CK增加了3.2%～21.6%.PMS的旗叶最大光化学效率(F_v/F_m)、PSⅡ实际光化学效率(Φ_PSⅡ)和光化学猝灭系数高于PM和CK,较PM最高分别提高了6.1%、9.6%和30.9%,并在灌浆期达到显著差异;而PMS的非光化学猝灭系数(q_N)值最低,并在抽穗期与PM达显著差异水平,2012和2013年分别降低了23.8%和15.4%.PMS的气孔导度(g_s)较PM和CK高,在灌浆期与PM达到显著差异,2012和2013年分别提高了17.1%和21.1%;PMS的蒸腾速率(T_r)较PM提高了5.4%～16.7%,光合速率(P_n)增加了11.2%～23.7%,旗叶瞬时水分利用效率(WUE_i)提高了5.6%～7.2%(除2013年抽穗期外),并在2012年扬花期达到显著差异.PMS的LAI高于PM和CK,尤其在季节性干旱的2013年达到显著差异.因此,PMS提高了叶片SPAD值,增强了旗叶对光合能量的同化能力和气体交换强度,使更多的光合能量进入光化学同化方向,降低了热耗散,使P_n增加,提高了旗叶WUE_i,基于较高的光合速率和群体LAI,最终提高小麦产量和水分利用效率.     

施钾对甘薯氮素转移分配及氮代谢酶活性的影响

利用¹⁵N示踪技术,研究了施钾对甘薯发根结薯期、薯块膨大期地上和地下部氮素转移分配、光合特性及氮代谢酶活性的影响.结果表明: 在发根结薯期,施钾显著提高¹⁵N向地上部的转移分配,其中K₃(K₂O, 300 mg·kg^-1)处理与对照相比¹⁵N向叶片转移速率提高了76.2%,¹⁵N积累量提高了92.1%.在薯块膨大期,随施钾量增加地上部叶片¹⁵N总分配率由33.7%降低至24.4%,块根¹⁵N分配率由5.8%升高至17%,其中K₃处理块根¹⁵N积累量是对照的3倍.两个关键生长期硝酸还原酶、谷氨酸脱氢酶、谷氨酰胺合酶、谷氨酸合酶和净光合速率(P_n)均随施钾量的增加而提高.逐步回归分析表明,氮代谢酶活性和P_n是影响甘薯¹⁵N转移和分配的主要因素(R分别为0.965和0.942),通径分析表明,在发根结薯期主要通过促进硝酸还原酶和谷氨酸脱氢酶介导的氮素催化能力促进氮素向地上部分配;在薯块膨大期主要通过提高谷氨酰胺合酶/谷氨酸合酶循环介导的氮素同化能力促进氮素向地下部分配.     

Population genetic evidence for cold adaptation in European Drosophila melanogaster populations

We studied Drosophila melanogaster populations from Europe (the Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic evidence of adaptation to cold. We present here four lines of evidence for genes involved in cold adaptation from four perspectives: (i) the frequency of SNPs at genes previously known to be associated with chill‐coma recovery time (CCRT), startle reflex (SR) and resistance to starvation stress (RSS) vary along environmental gradients and therefore among populations; (ii) SNPs of genes that correlate significantly with latitude and altitude in African and European populations overlap with SNPs that correlate with a latitudinal cline from North America; (iii) at the genomewide level, the top candidate genes are enriched in gene ontology (GO) terms that are related to cold tolerance; (iv) GO enriched terms from North American clinal genes overlap significantly with those from Africa and Europe. Each SNP was tested in 10 independent runs of Bayenv2, using the median Bayes factors to ascertain candidate genes. None of the candidate genes were found close to the breakpoints of cosmopolitan inversions, and only four candidate genes were linked to QTLs related to CCRT. To overcome the limitation that we used only four populations to test correlations with environmental gradients, we performed simulations to estimate the power of our approach for detecting selection. Based on our results, we propose a novel network of genes that is involved in cold adaptation.     

Why are many anthropogenic agroecosystems particularly species-rich?

Species-rich meadow and pasture habitats are recognised by the European Union Habitats Directive as targets for biodiversity conservation. High species richness is hypothesised to be associated with diversity in plant functional traits and life-history strategies, which are potentially restricted in situations of extremely high and low biomass production. However, variability in functional traits has yet to be investigated across a broad biomass range in nature. We measured variability in a range of functional traits and Grime's competitor, stress-tolerator, ruderal (CSR) strategies for species comprising lowland meadows, subalpine pastures, abandoned grassland and field margins at sites in northern Italy, alongside peak above-ground biomass. The factor most highly and positively correlated with species richness was strategy richness (the number of CSR strategies; Pearson's r = 0.864, P < 0.0001, n = 39), followed by variance in traits involved in leaf resource economics and the timing of flowering. Species richness, trait variance and strategy richness were greatest at intermediate biomass. Thus whilst extremes of biomass production were associated with relatively few taxa exhibiting similar trait values and specialised strategies, greater species richness was apparent in meadows and pastures in which species exhibited divergence in resource economics trait values, reproductive timing and strategy richness.