古代DNA研究中污染的控制和识别

现代分子生物学中PCR技术的发展使得直接分析古代动植物和人类材料中的DNA成为可能,这为考古学、人类学和古生物学提供了一种新的研究手段。但由于PCR技术的高度敏感性和古代DNA含量的极其微量性,古代DNA研究也极易受现代DNA污染。如何甄别所获得的DNA是真实的古代DNA而不是污染的现代DNA是所有古代DNA研究工作者都要面临的挑战,污染的控制和识别也因此成为古代DNA研究中一个至关重要的问题。本文将着重讨论在古代DNA研究的各个步骤中应如何进行有效的污染控制和识别。     

Evidence for Megalake Chad, north-central Africa, during the late Quaternary from satellite data

The existence of a very large Lake Chad during the late Quaternary, Megalake Chad, has long been questioned. A Megalake Chad would present strong evidence for climatic fluctuations of great magnitude during the Holocene in tropical Africa. In this paper we used satellite data from Landsat and Modis sensors to collect and analyse new information on landforms in a 2 000 000 km² region of the Lake Chad Basin. We detected 2300 km of remains marking the ancient shoreline of Megalake Chad. The satellite data also indicated many Saharan rivers and relict deltas leading to the long paleoshoreline. Large dunefield flattenings were observed and interpreted as the result of wave-cut erosion by the paleolake. Similarities were noticed between the landforms observed along the paleoshoreline of Megalake Chad and that of the former Aral Sea. This finding has significant consequences for reconstructing paleohydrology and paleoenvironments through the Lake Chad basin, and continental climate change.     

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: A problem of ancient DNA and molecular phylogenies

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.Correspondence to: A.C. van der Kuyl     

Studies on the Nucleic Acid and Protein Content in the Cotyledon Cells of Lotus Using Fluorescent Imaging System with a Scientific grade Charge Coupled Device

Enzyme dissociated cotyledon cells were obtained from red lotus ( Nelumbo sp. ) on the 5th day and 20th day after fertilization respectively. DNA, RNA and total protein content of individual 5 d and 20 d cell were measured correlatively by microfiuorescent imaging system with a cooled scientific-grade Charge coupled deviced (CCD) camera. The results showed that DNA content of the 20 day cell has become polyploidized from 4C to 8C approximately. The window analysis indicated that relative content of RNA and total protein of the 20 day cell was more than 11 times that of the 5 day cell in the same 4C DNA window respectively. The multiple in-creased of RNA and total protein content was about the same as that of DNA in 2 DNA windows (4C and 8C) of the 20 day cell. These data showed that the enormous accumulation of storage proteins in the cotyledon cells of red lotus depends on both DNA ploidy and selective expression of the subunit genes of the storage proteins during the developmental process.     

Local versus landscape-scale effects of anthropogenic land-use on forest species richness

The study investigated the effects of human-induced landscape patterns on species richness in forests. For 80 plots of fixed size, we measured human disturbance (categorized as urban/industrial and agricultural land areas), at ‘local’ and ‘landscape’ scale (500 m and 2500 m radius from each plot, respectively), the distance from the forest edge, and the size and shape of the woody patch. By using GLM, we analyzed the effects of disturbance and patch-based measures on both total species richness and the richness of a group of specialist species (i.e. the ‘ancient forest species’), representing more specific forest features. Patterns of local species richness were sensitive to the structure and composition of the surrounding landscape. Among the landscape components taken into account, urban/industrial land areas turned out as the most threatening factor for both total species richness and the richness of the ancient forest species. However, the best models evidenced a different intensity of the response to the same disturbance category as well as a different pool of significant variables for the two groups of species. The use of groups of species, such as the ancient forest species pool, that are functionally related and have similar ecological requirements, may represent an effective solution for monitoring forest dynamics under the effects of external factors. The approach of relating local assessment of species richness, and in particular of the ancient forest species pool, to land-use patterns may play an important role for the science-policy interface by supporting and strengthening conservation and regional planning decision making.     

古DNA捕获新技术与中国南方早期人群遗传研究新格局

古DNA捕获技术目前已获得极大的发展,能够从骨骼和环境沉积物等多种材料中获取到目的DNA片段,而且对于保存环境较差的低纬度地区,同样能够获取有效的内源DNA片段,极大地丰富了古DNA研究的材料来源。本文围绕这一新技术开展总结和讨论,主要分为两个方面：1）总结并介绍该技术应用前景;2）应用这一技术打开了中国南方早期人群研究的新局面,梳理该新技术的应用对史前中国南方人群古基因组研究所获得的新认识,并对中国南方早期人群古基因组深入分析;另外,利用古DNA捕获技术成功获取云南3446~3180 BP的大阴洞遗址4例高质量线粒体基因组信息,并开展了人群遗传历史的研究。     

Footprints of ancient‐balanced polymorphisms in genetic variation data from closely related species

When long‐lasting, balancing selection can lead to “trans‐species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa.     

土家族源流的遗传学初探

通过分析湖北恩施、湖南吉首地区土家族两个人群样本,利用14个Y染色体非重组区(NRY)单倍群分型技术对土家族的遗传结构进行了研究。分型结果结合其他地区土家族两个人群和相关民族群体进行主成分分析,并将分析结果根据不同人群的地理分布展示在地图上。然后对各主成分和单倍群进行偏相关分析来探讨它们之间的相关性。结果显示土家族主体与汉族在父系结构上比较接近,但依然有一定的区别。同时还发现龙山地区唯一保留土家语的土家族与氐羌族群有很明显的相关性,这说明土家族最早的起源可能正是氐羌民族。实验结果表明,恩施和吉首地区的大部分土家族与周边民族群体间的血缘交流频繁;而龙山和永顺的土家族更能代表土家先民的遗传结构,他们与西部氐羌族群密切相关。     

Treatment and utilization of wastewater in the Beijing Zoo by an aquatic macrophyte system

This paper deals with a nutrient cycling experiment in the Beijing Zoo that uses macrophytes as the added link to make a purification system. The whole system consisted of macrophyte cultivating area and no macrophyte area. By making up the different functional groups of aquatic plants, a multilevel cycling network is formed, which has a rather high purification capability. During the experimental period, the water quality of the Waterfowl Lake and the Peony Pavilion Lake improved significantly, with total nitrogen and total phosphorus reductions of up to 58 and 38%, respectively. Other parameters also confirmed the good purification effect of this system. The economic and social benefits met the requirement of the original design.     

鄱阳湖围垦区藕塘越冬白鹤的时间分配与行为节律

2016年12月—2017年3月,采用瞬时扫描法研究了鄱阳湖围垦区藕塘生境中白鹤Grus leucogeranus越冬期的行为,共扫描2560次,23219只次,包括18031只次成鹤和5188只次幼鹤。结果表明,觅食(41.78%)、警戒(25.02%)、修整(15.00%)和休息(10.84%)是白鹤越冬期的主要行为。与自然生境相比,藕塘生境中白鹤主要采取多休息和修整的策略来节省能量支出。成鹤的觅食行为(35.29%)显著低于幼鹤(62.42%)(F_(1,12)=45.977,P0.01),警戒行为(28.66%)则显著高于幼鹤(10.26%)(F_(1,12)=38.975,P0.01)。家庭群成鹤觅食行为(43.96%)极显著高于非家庭群成鹤(27.04%)(F_(1,12)=60.169,P0.01)。家庭群成鹤需要喂食幼鹤,它们花费更多的时间觅食弥补能量的消耗。行为节律上,白鹤各时段觅食行为占总行为的比例均较高,11:00—11:59出现明显高峰,占总行为的48.64%。警戒行为无明显的低谷和高峰。成鹤在各时段的觅食行为比例均明显低于幼鹤,成鹤和幼鹤的觅食曲线变化趋势相似,即觅食比例的升高和降低比较同步。成鹤在各时段的警戒行为和修整行为比例均明显高于幼鹤,成幼鹤的休息行为比例在各时段差别不大,均在14:00—14:59有个明显的高峰。家庭群成鹤的觅食行为比例几乎在各时段均明显高于非家庭群,家庭群成鹤的修整行为和休息行为在大部分时段均低于非家庭群成鹤。因此家庭群成鹤采取多取食,少休息和修整的策略提高自身的适合度,同时保证对后代的抚育。