The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family

Summary All modern mammals contain a distinctive, highly repeated (⩾50,000 members) family of long interspersed repeated DNA called the L1 (LINE 1) family. While the modern L1 families were derived from a common ancestor that predated the mammalian radiation ∼80 million years ago, most of the members of these families were generated within the last 5 million years. However, recently we demonstrated that modern murine (Old World rats and mice) genomes share an older long interspersed repeated DNA family that we called Lx. Here we report our analysis of the DNA sequence of Lx family members and the relationship of this family to the modern L1 families in mouse and rat. The extent of DNA sequence divergence between Lx members indicates that the Lx amplification occurred about 12 million years ago, around the time of the murine radiation. Parsimony analysis revealed that Lx elements were ancestral to both the modern rat and mouse L1 families. However, we found that few if any of the evolutionary intermediates between the Lx and the modern L1 families were extensively amplified. Because the modern L1 families have evolved under selective pressure, the evolutionary intermediates must have been capable of replication. Therefore, replicationcompetent L1 elements can reside in genomes without undergoing extensive amplification. We discuss the bearing of our findings on the evolution of L1 DNA elements and the mammalian genome.     

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     

子莲杂交优势的利用及新品种选育的研究

1981—1987年的试验证实,利用杂交优势是子莲新品种选育的重要途径。作者通过杂交选育和引种,筛选培育出13号(白花建莲×红千叶)和2号(百叶莲×红花建莲)杂交子莲,杂交优势明显而稳定,其产鼠比对照品种——红花建莲增加20%以上,经济效益十分显著。为了推广这两种杂交子莲,作者还提出了子莲良种繁育时防杂的技术措施。     

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。     

Maternal genetic history of southern East Asians over the past 12,000 years

Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000–6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time.     

Forest vascular plants as indicators of plant species richness: A data analysis of a flora atlas from northwestern Germany

Abstract

Our study had the objective to examine whether the number of forest vascular plants in a forest-poor region may be indicative of total plant species richness and of the number of threatened plant species. We also related forest plant species richness to geological and soil variables. The analysis was based on a regional flora atlas from the Weser-Elbe region in northwestern Germany including incidence data of species in a total of 1109 grid cells (each ca. 2.8 × 2.8 km²). All taxa were classified either as forest or non-forest species. Total species richness in the grid cells ranged from 65 to 597, with a mean value of 308. The number of forest species varied between 20 and 309 (mean 176). Grid cells with or without particular geological units differed in total and forest species richness, with those containing peatland and marshland being particularly species-poor. Indicator value analysis showed that both total and forest species richness in the grid cells were related to soil acidity and nitrogen in a hump-backed manner, with the highest number of species found at moderately low values for nitrogen and at intermediate values of pH. Forest species richness was highly positively correlated with the number of non-forest species and threatened non-forest species. Indicators for high species richness were primarily those species that are confined to closed semi-natural forests with a varied topography and relatively base- and nutrient-rich soils. Grid cells including historically ancient forest exhibited a higher species richness than grid cells lacking ancient forest, indicating the importance of a long habitat continuity for a high phytodiversity. The “habitat coincidence” of high species richness is best explained by similar responses of forest species and species of other habitats to the main environmental gradients. It is suggested that the regional patterns found for the Weser-Elbe region can be transferred also to other forest-poor regions in Central Europe.     

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.     

洪湖子莲开花结实习性及调控技术的研究

阐明了子莲开花结实习性与花期气候的关系,并以洪湖气候与子莲开花结实的关系,莲蓬大小和莲蓬心皮数目与荷花发育时所处季节地关系以及死蕾,死花,死果与开花时天气的关系等三方面,论证了在该区调控子莲开花结实的必要性。最后还提出了调控子莲开花结实的几项农业技术。