浅谈网络分析法及其在古生物学中的应用

网络分析作为一种新的数据可视化途径和定量方法, 能简化复杂系统而发现元素间的关系模式。它在定量社会科学、计算机科学与机器学习等领域均有众多应用实例。近年来, 在古生物学, 特别是古生物地理学相关研究中逐渐受到关注。本文介绍了网络的基本构成、常见网络类型及其数据储存方式、以及网络分析中的重要参数及其定义, 同时给出了两种实现网络分析的方法及相关工具, 即Gephi软件与R语言平台。通过分析比较两种方法的步骤及结果, 发现Gephi虽成图简洁美观, 但算法功能有限, 且无法完成成图前的数据处理以及成图后的多元分析, 因而最终推荐使用R语言编程进行网络分析。本文以奥陶纪末大灭绝后复苏期全球腕足动物数据为例, 详细展现了利用R语言及其应用包“igraph”编程进行网络分析的过程, 并实现了古生物地理学数据资料的处理以及网络分析图件的绘制。希望对即将接触此类工具的古生物学科研人员在进行网络分析时提供借鉴与参考。     

Improving drought stress tolerance in fenugreek (Trigonella foenum-graecum) by exogenous melatonin

Abstract

The present study was conducted to determine the changes which occurred in the water-stressed fenugreek (Trigonella foenum-gracum L.) in response to melatonin treatment. Fenugreek is a valuable medicinal plant which contains trigonelline that plays an osmoregulatory role in abiotic stress. To this end, the effects of three levels of water deficit in the first experiment and four concentrations of melatonin in the second experiment were investigated on the physiological and biochemical responses. The findings of the first experiment demonstrated that water deficit decreased the weight and length of fenugreek shoots as well as pigments contents, and catalase activity. In addition, such a deficit led to an increase in proline, trigonelline, melatonin and enhanced the activity of other antioxidant enzymes. Finally, the hydrogen peroxide and malondialdehyde concentrations increased under severe stress. The results of the second experiment indicated that melatonin treatment significantly reduced chlorophyll degradation. Furthermore, the activities of the ROS scavenging enzymes were increased by melatonin. Moreover, exogenous melatonin led to an increase in endogenous melatonin and trigonelline whereas it led to a decrease in proline content. These results revealed that fenugreek tolerated water deficit by increasing the endogenous melatonin and trigonelline, as well as the general physiological responses.     

Concordance between ecotypes and macroinvertebrate assemblages in Mediterranean streams

1. According to the guidelines of the European Water Framework Directive, assessment of the ecological quality of streams and rivers should be based on ecotype-specific reference conditions. Here, we assess two approaches for establishing a typology for Mediterranean streams: a top-down approach using environmental variables and bottom-up approach using macroinvertebrate assemblages.
2. Classification of 162 sites using environmental variables resulted in five ecotypes: (i) temporary streams; (ii) evaporite calcareous streams at medium altitude; (iii) siliceous headwater streams at high altitude; (iv) calcareous headwater streams at medium to high altitude and (v) large watercourses.
3. Macroinvertebrate communities of minimally disturbed sites ( n  = 105), grouped using UPGMA (unweighted pair-group method using arithmetic averages) on Bray–Curtis similarities, were used to validate four of the five ecotypes obtained using environmental variables; ecotype 5, large watercourses, was not included as this group had no reference sites.
4. Analysis of similarities ( anosim ) showed that macroinvertebrate assemblage composition differed among three of the four ecotypes, resulting in differences between the bottom-up and top-down classification approaches. Siliceous streams were clearly different from the other three ecotypes, evaporite and calcareous ecotypes did not show large differences in macroinvertebrate assemblages and temporary streams formed a very heterogeneous group because of large variability in salinity and hydrology.
5. This study showed that stream classification schemes based on environmental variables need to be validated using biological variables. Furthermore, our findings indicate that special attention should be given to the classification of temporary streams.     

Effect of land use conversion on soil organic carbon sequestration in the loess hilly area, loess plateau of China

Changes in land use may alter land cover, which results in carbon stock changes in biomass as well as in the soil. In China’s loess plateau, vegetation restoration has been conducted since 1950s to control soil erosion and improve the ecosystem, with significant investment of money and manpower. Despite these efforts, soil erosion has still been severe. To reduce soil erosion and improve land quality, China initiated another state-funded project, Grain-for-Green, in 1999 in the loess plateau. However, it is not clear how effective this newly initiated project will be. In this study, we evaluated the effect of land-use conversion on soil organic carbon (SOC) and the potential effect of the current project on SOC sequestration in the Anjiapo catchment area of the loess hilly area of the loess plateau in China. This evaluation is based on SOC measurements in cropland versus in other converted land use types. We found that SOC sequestration mainly occurred in the surface soil after land use conversion took place. Land use conversion from cropland to shrubland or wild grassland (i.e. undisturbed land) was better for SOC sequestration than tree plantation in the semi-arid loess hilly area. By using the land use change in the study area as a scenario, the potential contribution of land use change on SOC sequestration due to the Grain-for-Green project was estimated. It was found that this project in the loess plateau of China would be helpful for SOC sequestration if successfully implemented.     

模拟放牧干扰对黄土丘陵区生物结皮坡面土壤水分入渗的影响

水分是黄土高原地区植被恢复的关键影响因子,该区广泛分布的生物结皮显著影响土壤水分入渗。干扰影响生物结皮土壤水分入渗,但目前不同强度的干扰对生物结皮土壤水分入渗的影响仍不明确。本研究以黄土丘陵区吴起县合沟小流域的生物结皮坡面为对象,模拟羊蹄踩踏干扰,研究10%、20%、30%和40%干扰强度(以生物结皮破损度表征)对生物结皮坡面地表覆被的影响,采用线源入流入渗法观测了不同强度干扰后土壤水分入渗特征,通过结构方程模型和相关性分析,探索了干扰对生物结皮坡面土壤水分入渗的影响机制。结果表明:与对照(不干扰)相比,10%干扰强度下藻结皮盖度显著增加33.6%,20%干扰强度对藻结皮盖度无显著影响,30%和40%干扰强度下藻结皮盖度分别显著降低了36.1%和75.0%;40%干扰强度显著增加了枯落物盖度(34.3%),其他处理无显著影响;10%、20%和30%干扰强度下地表粗糙度分别显著降低了22.3%、11.1%和5.6%,40%干扰强度下增加了8.2%;40%干扰强度下初始入渗率显著增加了77.1%,其他干扰强度无显著影响;不同干扰对土壤稳定入渗率和平均入渗率无显著影响。可见,干扰主要通过降低藻结皮盖度,增加枯落物盖度和改变地表粗糙度,进而促进了土壤水分初始入渗。本研究可为黄土高原退耕地生物结皮管理提供科学依据。     

鄱阳湖水利枢纽工程建设对草鱼江湖洄游潜在的影响

鄱阳湖是长江四大家鱼索饵、育肥的重要场所,近年来鄱阳湖出现了枯水季水位严重降低、枯水期延长、湿地面积缩小的现象。为解决鄱阳湖水资源、水文、水生态等问题,建议在鄱阳湖入江水道兴建控制闸水利枢纽。然而,拟建的水利枢纽工程将打破鄱阳湖与长江的天然连通性,可能会对四大鱼类洄游过程产生影响。通过构建二维和三维水动力模型,分析鄱阳湖水利枢纽建设后入江水道与枢纽洄游通道的水动力学特征,结合实验和文献获得的草鱼幼鱼和成鱼游泳能力参数,阐明了枢纽建设对草鱼洄游的影响。结果表明:在设计调度模式下,草鱼幼鱼入湖期间,湖口段适宜通过天数达到83.74%以上,说明湖口及入江水道的水动力条件对洄游的影响较小,同时,枢纽工程处在过鱼高峰期仍能保持较高的过闸效率;草鱼成鱼出湖期间,丰、平水年闸前水动力条件对洄游的影响较小,仅在枯水年闸前流速几乎静止,草鱼适宜出湖天数偏低。在该调度模式下,水利枢纽建设运行后鄱阳湖整体水动力条件能够满足草鱼洄游需求。目前设计的鱼道在高、低水位时期均出现局部流速过大的现象,不满足过鱼条件。从四大家鱼江湖洄游的角度为鄱阳湖水利枢纽工程设计和运行提供科学参考。     

2000-2019年京津冀地区植被覆盖状况变化及驱动因素

近20年来中国和印度通过土地利用活动改变地表覆盖使植被变得更绿,京津冀地区是植被变得更绿的典型地区。收集京津冀地区2000-2019年MODIS增强型植被指数（EVI）、植被覆盖百分比数据,以及年平均温度和降水量等数据,分析该区近20年来自然植被和农田植被EVI变化过程和趋势,揭示其变化的驱动因素,结果显示2000-2019年京津冀地区自然植被和农田植被EVI显著增加,自然植被EVI增加速率是农田植被的1.8倍。99.51%的自然植被和96.95%的农田植被生长状况改善。2000-2019年京津冀地区自然植被EVI与年平均温度和年降水量相关性不显著。农田植被EVI与年平均温度显著相关,与年降水量相关性不显著。农田灌溉和年平均温度变化是农田植被EVI显著增加的主要驱动因素。近20年京津冀地区通过实施以造林为主的生态建设工程,自然植被生长覆盖状况呈现极显著变好。同时森林植被比非森林植被覆盖百分比增加趋势更明显。以造林为主的生态建设工程是京津冀地区自然植被生长覆盖状况显著变好的主要驱动因素。     

阿根廷文化景观研究、项目和表现

旨在促进应用“文化景观”概念作为分析和开发阿根廷地域项目的工具。第1部分,力图总结有关文化景观的概念,术语名词的起源、传播以及其所暗含的可能性和矛盾性。第2部分,讨论这个概念成为项目工具的方式。第3部分中,强调了绘图在分析和项目中的核心作用。第4部分,以2个案例研究表明在前3个部分中阐述的问题。结论提出了这种开展项目的方式的潜能、挑战和矛盾。而只有针对地域特性的详细研究才能使找到一种回馈当地发展的管理方式成为可能。     

Oral health of the Paleoamericans of Lagoa Santa,central Brazil

The peopling, origins, and early prehistory of the Americas are topics of intense debate. However, few studies have used human remains to document and interpret patterns of health and lifestyle of Paleoamericans. This study provides the first investigation to characterize oral health in a series of early Holocene skeletal remains from Lagoa Santa, Brazil, a locality containing the remains of some of the earliest inhabitants of South America (10,000–7,000 BP). The sample is composed of 949 teeth and 1925 alveoli from an estimated 113 individuals excavated from 17 archaeological sites located in the State of Minas Gerais. We compare dental caries and abscess prevalence at Lagoa Santa to a large sample of human skeletons from the Western Hemisphere Project (WHP) database using both individual and tooth/alveolus count methods. In addition, antemortem tooth loss and tooth wear were analyzed in Lagoa Santa by sex and age. The results show that Lagoa Santa dental caries and abscess prevalence are significantly higher than observed among other hunter–gatherers included in the WHP database, except when abscess prevalence is considered by individual count. Adult females have less tooth wear coupled with higher prevalence of dental caries and antemortem tooth loss than adult males. These results point to an unexpected record of poor oral health at Lagoa Santa, especially among females. A diet based on a highly cariogenic combination of wild tubers and fruits is suggested as an explanation for the elevated rate, characterizing an early adaptation to a tropical environment in South America. Am J Phys Anthropol 154:11–26, 2014. © 2014 Wiley Periodicals, Inc.     

国家自然科学基金委重大项目“禾本科植物的适应性辐射及其进化机制”结题综述

国家自然科学基金委重大项目"禾本科植物的适应性辐射及其进化机制"利用比较形态学、分子系统学、进化发育生物学、古生物学等多方面证据,通过多学科交叉的方法探讨了禾本科植物中出现的适应性辐射现象及其机制,在禾本科的系统发育关系以及适应性辐射的基本式样、生物和非生物环境因素在物种适应和分化以及物种快速形成中的作用、基因组大小及其结构变异以及突变、重复和调控模式变化对适应性辐射过程中关键性状(功能)的影响等方面取得了重要进展,在人才培养、国际合作和实验体系建立等方面极具特点。该项目的顺利完成为更好地阐明植物多样性形成的原因与机理奠定了良好的基础。