Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.     

Predation rate and numerical response of Aphidoletes aphidimyza feeding on different densities of Aphis craccivora

Predation rate and numerical response are basic to any investigation of predator–prey relationships and key components in the selection of predators for biological control. The density-dependent predation rate and numerical response of Aphidoletes aphidimyza (Rondani) (Diptera: Cecidomyiidae) to varying densities (5, 10, 20, 40, 60 and 80) of third-instar Aphis craccivora (Koch) (Hemiptera: Aphididae), were studied in laboratory conditions [23±1°C, 70 ± 5% relative humidity (RH), and a photoperiod of 16:8 h L:D. Predation rate data were analysed using the age-stage, two-sex consumption rate software. Net consumption rate (C₀) increased by increasing prey density. The lowest and highest net consumption rates were 20.75 and 190.8 prey nymphs at densities of 5 and 80 A. craccivora. The transformation rate from prey population to predator offspring (Q_p) increased by increasing prey density. The reproductive numerical response, in terms of eggs laid, increased curvilinearly with increasing prey density. Females laid 121.375 ± 4.301 eggs when exposed to the highest prey density (80) and 52.5 ± 1.544 eggs at lowest prey density (5). It can be concluded that different densities of A. craccivora influenced the reproductive performance of A. aphidimyza in terms of predation rate and numerical response.     

On-station comparative analysis of reproductive and survival performance between Red Maasai,Dorper, and Merino sheep breeds

The reproductive performance of ewes and the survivability of lambs to weaning have a critical economic impact on sheep farming worldwide. Further, knowledge of major mortality causes allows an opportunity for improved flock management to evade financial losses. The maximum likelihood estimates for generalised linear mixed models and chi-square test methods were used to examine 971 mating records, 839 and 763 lambs born and weaned (singles or twins) from the Naivasha Sheep and Goats station in Kenya for the years 2011 to 2020 consisting of Dorper, Red Maasai (RedM), and Merino breeds. The RedM (P < 0.05) outperformed Dorper and Merino in weaning rate, whereas reproductive performance between the three breeds was not significantly different (P > 0.05) in litter size and multiple lambings per ewe lambing. On the one hand, Dorper significantly (P < 0.05) outperformed the other two breeds only in weaning weight per lamb born. In addition, among all the major causes of death, pneumonia appeared to be the one to which Dorper breeds were most susceptible (chi-square test, P < 0.05). According to the findings of this study, neither the Dorper nor the Merino sheep breeds were reproductively superior to the RedM in an extensive semi-arid production environment. In addition, Dorper's susceptibility to the leading causes of mortality, particularly pneumonia and sheep pox, were relatively high compared to other breeds and could be a precursor to massive economic losses for Dorper sheep producers. In contrast to the indigenous RedM breed, imported sheep breeds appeared to be more susceptible to major mortality-related under an extensive production system. Therefore, regardless of weaning weight, RedM breed production appears to be a more viable investment for small-scale farmers, particularly in semi-arid regions.     

光周期和温度对虎斑蝶卵、幼虫及蛹存活的影响

通过在人工气候箱内设定不同光周期和温度梯度单虫饲养观察个体发育史,研究了光周期和温度对虎斑蝶Danaus genutia幼期存活的影响,研究结果可为该高观赏价值蝶种的规模化养殖提供依据。结果表明,在长光照(L∶D=15∶9)条件下,17.5、20.0、22.5、25.0、27.5、30.0℃时虎斑蝶卵的孵化率分别为63.72%、71.67%、65.75%、75.00%、67.12%、59.56%,幼虫的存活率分别为85.67%、85.96%、91.19%、89.20%、80.86%、68.78%,蛹的存活率分别为82.76%、100.00%、96.00%、97.06%、100.00%、100.00%;在短光照(L∶D=9∶15)条件下,17.5、20.0、25.0、30.0℃时虎斑蝶卵的孵化率分别为86.36%、67.06%、75.00%、77.50%,幼虫的存活率分别为85.05%、84.59%、85.74%、80.78%,蛹的存活率分别为93.30%、94.12%、100.00%、100.00%。结果表明,17.5℃和30.0℃均不利于虎斑蝶幼期的存活,20.0～27.5℃是其幼期生长发育适宜的温度范围。长光照利于幼虫的存活,短光照利于卵的孵化和蛹的羽化;在17.5～30.0℃内,较高的温度利于蛹的羽化,而较低的温度利于卵的孵化和幼虫的存活;温度对虎斑蝶卵的孵化、幼虫的存活及蛹的羽化影响大于光周期;在养殖生产上,建议将幼期养殖温度控制在20.0～27.5℃,幼虫期饲养在长光照下为宜,卵和蛹期置于短光照下为宜。     

吉粳88高效再生体系的建立

以吉粳88为材料,通过对不同培养基和激素的筛选,确定最佳的再生体系。结果表明:NMB培养基为吉粳88最适的愈伤组织诱导培养基。通过L₉(3³)正交实验研究最适激素浓度配比,筛选出吉粳88愈伤组织诱导的最佳激素配比为2.0 mg/L 2,4-D+0.2 mg/L 6-BA+0.10 mg/L NAA。在添加2.0 mg/L 6-BA+0.5 mg/L NAA的NMB基本培养基条件下,吉粳88的分化率最高,成培苗率也最高。     

Optimising a clearance index based on neutral red as an indicator of physiological stress for bivalves

Neutral red is a weakly cationic dye that is soluble in water, has a low toxicity for almost all classes of organisms, and has been used as a histological and vital stain since the early twentieth century. Estimating the volume of water cleared of indicator material by suspension feeding bivalves (clearance or filtration rate) was one of the earliest applications of neutral red; however, less than thirty studies have applied this methodology since it was first described in 1954. The feeding/clearance rate is used as a sensitive indicator of physiological stress and is therefore an early-warning tool that is suitable for monitoring the ecological status of water bodies. The aim of our study was to optimise a clearance index based on neutral red solution by addressing the effect of i) the acidifying pH; ii) the holding temperature before spectrophotometric reading; and the time iii) before and iv) after the acidification of solutions of neutral red used to carry out clearance assays. Furthermore, as a case study we fine-tuned the clearance assay for the edible estuarine bivalve, Cerastoderma edule. The results showed that there were no statistical differences as regards the absorbance of neutral red solutions holding at 4 or 20 °C or a solution acidified between the ranges of pH 4–5. However, the absorbance significantly decreased as the pH increased to pH 6. The time before acidification had no significant effect on absorbance. Once the neutral red solution is acidified, the absorbance decreases over time, signifying that the absorbance should be read in the first 24 h. The concentration of neutral red used in the experiences should be sufficient to allow final concentrations of over 0.5 mg/L after the clearance period, since we observed that the sensitivity of this protocol decreased at low concentrations. In the case of C. edule, the optimum clearance conditions per individual were found to be 100 ml of 4 mg/L of neutral red dye during a 30 min period in dark conditions. A bioassay using a clearance index of C. edule based on this simple colorimetric technique would appear to be a potential tool for implementation in environmental monitoring programmes for water quality assessment in accordance with European directives. We trust that the new harmonised protocol will become a widely used and cost-effective means to monitor the clearance index as an indicator of physiological stress for bivalves.     

On the interpretation of some planktonology equations

Summary The concept of the mean value of a function is used to interpret some population-dynamics equations. The well-known formula for the per capita growth rate r gives a precise mean value for any (not only exponentially growing) populations. This result is used to derive the birth and death rate equations of Paloheimo (1974) with minimal initial limitations.Abbreviations t time - N number of animals - E number of eggs - r specific (i.e. per capita) population growth rate - b specific birth rate - d specific death rate - D duration of embryonic development     

Ingestion Rates of Some Daphnia Species in a Shallow Lake (Lake Balaton,Hungary)

Filtering rates of three species of Daphnia were studied in situ by the ¹⁴C technique during the summer in a lake with a water temperature of 20-25°C (Lake Balaton, Hungary). The renewal time of gut contents proved to be 3-5 min in each of the three species whether fed on natural or artificial food. From May to September, filtering rates of D. cucullata, D. hyalina and D. galeata averaged 7.8, 10.3 and 9.2 ml ind.⁻¹ day⁻¹, respectively. Identically long individuals of all three species had almost the same filtering rates in spring, whereas in summer animals of identical weights had similar filtering rates regardless of species because of the length variability of the helmets. The grazing rate of adult filter-feeding crustaceans is suggested to be approximately 7 % per day.     

转基因鱼构建模式的研究II.构建转基因鱼的几个影响因素(英文)

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光合单位的周转率与叶片光合速率的关系

利用闪光技术,测得若干高等植物叶片的光合单位为 1450～2050 Chl/CO_2。在含O_2 2％及CO_2浓度和光通量密度都饱和的条件下,测得叶片的连续光合速率为25～70μmol CO_2 m~(-2) s~(-1)。从上述数据及叶片叶绿素含量计算,得叶片光合单位的周转率已达80～160次/s。这样的周转速率与Emerson当初用改变闪光间暗间隔而测到的光合单位周转时间相似(即<10 ms/次,或>100次/s),从而证实了光合单位的周转与光合速率直接有关。这样的速率可称之为叶片光合的理论速率。     

沙埋对两种一年生藜科植物存活及光合生理的影响

为了解沙埋对沙生植物存活的影响及其光合生理响应特征,比较不同藜科沙生植物耐沙埋能力及其光合响应,在内蒙古科尔沁沙地研究了沙米(Agriophyllum squarrosum)和大果虫实(Corispermum marocarpum)在不同沙埋深度下第5、10、15天的净光合速率、气孔导度、蒸腾速率、水分利用效率的变化,并于植物生长末期对存活率进行了测定。结果表明:沙米较大果虫实具有较强的耐沙埋能力,其中沙米幼苗最大耐沙埋深度超过苗高10 cm,大果虫实在埋深等于其苗高时全部死亡;随沙埋深度增加,沙米和大果虫实的存活率均显著下降,但沙米的下降幅度明显小于大果虫实;沙埋后,2种植物的气孔关闭或开放程度减小,通过降低蒸腾速率和提高水分利用效率来适应沙埋胁迫;随着沙埋胁迫的加剧,2种植物的净光合速率下降,表明沙埋胁迫对植物的光合作用破坏较大;相比于大果虫实,沙米对于沙埋胁迫有着更好的光合适应,随着胁迫的时间增加,其净光合速率有所恢复。     

新疆野生郁金香与栽培品种的杂交性状

为研制具有自主知识产权的郁金香（Tulipa gesneriana）新种质,本实验选择6种栽培郁金香品种为母本,5种野生郁金香为父本进行杂交试验。结果显示,平均受精率为（84．8±3．5）％,母本受精率最高的是克斯奈丽斯,平均为（94．0±2．3）％,受精率最低的是蒙特卡罗,平均为（71．0±3．8）％。果实发育1个月最高坐果率为100．0％,平均为（75．2±4．1）％,2个月最高坐果率为（90．0±3．6）％,平均为（47．0±3．4）％;杂交种子平均结实率为24．3％。研究结果表明,母本与杂交组合对受精率、坐果率和结实率有显著影响,父本则没有显著影响：杂交组合小黑人×伊犁郁金香、小黑人×柔毛郁金香及小黑人X天山郁金香亲合性较好,其杂交种子结实率分别为78．2％、68．4％和57．5％。     

Invariance of demographic parameters using total or viable eggs

Recently Mou et al. (J. Appl. Entomol., 139, 2015 and 00) recommended that in population studies in which hatch rates vary with maternal age, demographic parameters should be calculated excluding unhatched eggs. A mathematical proof was provided to support this. In this note, we expose a flaw in their proof and show that the demographic parameters do not differ by considering either all eggs or only viable ones, as long as the beginning and end of a generation are defined accordingly.     

Growth, protein-turnover rates and nucleic-acid concentrations in the white muscle of rainbow trout during development

We have studied the growth rate, nucleic-acid concentration, protein-accumulation rate (K_G), and several other parameters relating to protein turnover, such as the protein-synthesis (K_S), and protein-degradation rates (K_D), protein-synthesis capacity (C_S), protein-synthesis efficiency (K_RNA), protein-synthesis rate per DNA unit (K_DNA) and protein-retention efficiency (PRE), in the white muscle of rainbow trout during development. Both growth rate and relative food intake decreased significantly with age and weight, as did the food-efficiency ratio (FER) and protein-efficiency ratio (PER). Although absolute RNA and DNA contents increased with age, their relative concentrations decreased. The RNA/DNA ratio increased sharply from 14 to 28 weeks but afterwards decreased towards initial values. Hypertrophy increased rapidly to the 28-week stage but thenceforth increased much more slowly. Hyperplasia, on the other hand, continued to increase linearly, resulting in a significant four- to fivefold predominance in this type of growth at the end of the 96-week experimental period. K_G decreased significantly with age, as did K_S, and C_S, whereas at the 14-week stage, K_D was significantly lower than at other ages. K_RNA increased until 28 weeks. K_DNA increased significantly in juvenile fish compared to both fingerlings and adults, where it showed similar lower values. PRE remained high at all ages.     

除草剂草甘膦对中华大蟾蜍的慢性毒性

为揭示除草剂对农林生态系统中脊椎动物天敌潜在的、长期的慢性毒性,测定了草甘膦对中华大蟾蜍（Bufo gargarizans Cantor）蝌蚪生长发育和运动频率的影响以及对中华大蟾蜍成体空胃率的影响。结果表明,亚致死剂量的草甘膦溶液对中华大蟾蜍蝌蚪的生长发育和运动频率具有明显的抑制作用,蝌蚪体长、体宽、尾长、尾宽和体质量的增长率均与草甘膦浓度呈极显著负相关;蝌蚪的运动频率亦与草甘膦浓度显著负相关。同时,草甘膦的喷施对中华大蟾蜍成体的捕食造成负面影响,其空胃率与草甘膦浓度呈极显著正相关,即使在草甘膦的推荐使用浓度范围之内．中华大蟾蜍（成体）处理组亦出现30％～60％的空胃率。     

In vivo temperature limitations of photosynthesis in Phaseolus vulgaris L

The purpose of this study was to evaluate the temperature response of photosynthesis in two common bean genotypes differing in crop yield when grown under warm conditions. The cultivar Nobre is sensitive to high temperatures, whereas Diplomata shows better crop yield under high temperatures. Plants were grown in a greenhouse prior to transferring to a controlled environment cabinet for the temperature treatments. In a first experiment, 30 days-old plants were subjected to a short exposure (1 day) at temperatures that varied from 9 °C to 39 °C. Diplomata had lower net CO₂ assimilation rate (A) at 15 °C and 21 °C, but higher from 27 °C to 39 °C. Photosynthetic parameters calculated from modeling the response of A to the intercellular CO₂ concentration suggested that the different temperature responses of the two genotypes are caused by different rates of diffusion of CO₂ to the assimilation site, not by differences in biochemical limitations of photosynthesis. While stomatal conductance (g_s) did not differ between the genotypes, mesophyll conductance (g_m) was slightly greater for Nobre at 15 °C, but much higher in Diplomata from 21 °C to 39 °C. In a second experiment, no difference was observed in biomass accumulation between the two genotypes after growth for 24 days under a 35/20 °C (day/night) regime. Hence, the differences in photosynthesis did not cause variation in plant growth at the vegetative stage. The differential genotypic response of g_m to temperature suggests that g_m might be an important limitation to photosynthesis in Nobre, the common bean genotype sensitive to elevated temperature. However, more studies are needed employing other methods for g_m evaluation to validate these results.     

An examination of phylogenetic models of substitution rate variation among lineages

Molecular evolutionary rates can show significant variation among lineages, complicating the task of estimating substitution rates and divergence times using phylogenetic methods. Accordingly, relaxed molecular clock models have been developed to accommodate such rate heterogeneity, but these often make the assumption of rate autocorrelation among lineages. In this paper, I examine the validity of this assumption.     

Surfacing frequency as an index of bioenergetics components of air breathing fishes

Surfacing frequency (Sf) in obligatory air-breathing fishes is a behavioural index of O₂ uptake; as both are interrelated, there is a possibility of predicting one from the other. From the point of cause and effect relationship, feeding (C) is regarded as the cause and Sf and O₂ uptake as its effects. Hence, the last two are predictable from the cause. A pathway for predicting the bioenergetics components, feeding (C), metabolism (M) and growth (P) from a behavioural index of surfacing frequency has been proposed. In this model, C occupies the focal point connecting on the horizontal plane Sf on one side and P on the other side and M vertically. The developed multiple regression models predict the bioenergetics components of the fishes,Macropodus cupanus andChanna striatus of different weight classes ex-posed to different rations and temperatures; the percentage of variation accounted for by the equations is over 90. The pathway can also be followed for predicting bioenergetics components of gill-breathing fishes, if feeding rate alone is known. On application of the relevant part of the pathway toSalmo trutta, the percentage of variation accounted by the equations is 95.     

Altitudinal and seasonal effects on aerobic metabolism of deer mice

Summary I compared the maximal aerobic metabolic rates ( ), field metabolic rates (FMR), aerobic reserves ( -FMR), and basal metabolic rates (BMR) of wild and recently captured deer mice from low (440 m) and high (3800 m) altitudes. To separate the effects of the thermal environment from other altitudinal effects, I examined mice from different altitudes, but similar thermal environments (i.e., summer mice from high altitude and winter mice from low altitude). When the thermal environment was similar, , FMR, and aerobic reserve of low and high altitude mice did not differ, but BMR was significantly higher at high altitude. Thus, in the absence of thermal differences, altitude had only minor effects on the aerobic metabolism of wild or recently captured deer mice.At low altitude, there was significant seasonal variation in , FMR, and aerobic reserve, but not BMR. BMR was correlated with , but not with FMR. The significant positive correlation of BMR with indicates a cost of high , because higher BMR increases food requirements and energy use during periods of thermoneutral conditions.Abbreviations BMR basal metabolic rate - FMR field metabolic rate - partial pressure of oxygen - T _a ambient temperature - T _b body temperature - T _e operative temperature - maximal aerobic metabolic rate     

高原鼠兔在不同植被覆盖的立地占据、局部灭绝和建群率研究

青藏高原的草地生态系统被野生动物和家畜广泛地利用。大型有蹄类动物的放牧和小型哺乳类动物的挖掘行为,会改变其栖息地的植物群落。基于拉萨市墨竹工卡县日多镇年村牦牛(Bos grunniens)放牧的实践,我们发现高原鼠兔(Ochotona curzoniae)立地占域率、建群和区域灭绝率与栖息地变量之间存在一定的格局关系。为了了解高原鼠兔立地占域率、建群和区域灭绝率与栖息地之间的关系,我们采用多季节性立地占据模型,利用Presence软件对相关数据进行分析。结果表明,高原鼠兔局部灭绝率与植被覆盖度之间存在正相关性,而与建群率之间则呈负相关性。