A procedure for the extraction of chloroplast DNA from broad-leaved tree species

A method for the extraction of ctDNA from isolated chloroplast was developed. This method is simple and adapted particularly to broad-leaved trees, including sclerophyllous species with high phenolic and polysaccharide contents. This method includes two major steps: first, chloroplasts are isolated in non-aqueous solutions to avoid oxidation and phenolic problems; second, ctDNA is extracted from the chloroplasts using aqueous solutions and specific methods to provide highly purified ctDNA.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

进化距离与相对替代率的比较研究

系统树是描述物种、人种甚至基因间亲缘关系和演化的重要工具,必须以进化距离或(相对)替代率作为重要的参数。但以哪一个参数构建的树更能反映真实的系统树呢?事实上迄今并无人对此作过认真的研究。本文以模拟数据并用方差分析法检验两个参数的异同并讨论其包含的生物学意义。研究结果表明,当氨基酸的替代率和核苷酸的替代率分别为0.18和0.13时,它们的进化距离分别为0.199和0.143。经方差分析证实,若检验的氨基酸和核苷酸最大数目均为75只时,不论以替代率或进化距离中那一个作为构树参数,拓扑树事实上几乎只有一个。这就是说,该时拓扑树可靠性很大,而且随着它们替代率的减少,则检验的氨基酸和核苷酸的数目会随之增加。但是一旦氨基酸的替代率和核苷酸的替代率超过上述数字,则两个参数构建的树在拓扑长度上是不等价的。经分析,若进化距离大致上与进化时间成线性关系的话,则应选用进化距离。用进化距离重建的系统树事实上支持中性学说;若进化距离与进化时间显著地不存在线性关系的话,则可选用替代率,该情况表明中性学说不适用,似更倾向于新达尔文主义。     

Relations between water content, potential and permeability in stems of conifers

Abstract. The influence of sapwood water content on the conductivity of sapwood to water was measured on stem sections of Pinus contorta. A reduction in relative water content from 100 to 90% caused permeability to fall to about 10% of the saturated value.
Pressure–volume curves of branchwood and stem sapwood of Pinus contorta and Picea sitchensis have been analysed to definè the tissue capacitance and the time constant and resistance for water movement between stored water and the functional xylem as functions of tissue water potential. Three phases in water loss were discernible. In the initial phase at high water potentials (> –0.5 MPa), the capacitance was large, the time constant long and the resistance to flow large in comparison with intermediate water potentials (−0.5 to −1.5 MPa). At still lower water potentials (−1.5 to −3.0 MPa), the time constant and resistance declined still further but the capacitance had a tendency to increase again, especially in the stemwood of Sitka spruce. Typical values in the second phase were for the time constant 5 s, for the resistance 4 × 10⁻¹³ N s m⁻⁵ and for the capacitance (change in relative water content per unit change in potential) 1×10⁻¹¹ m³ Pa⁻¹. These parameters define the availability of stored water and are being used in a dynamic model of water transport in trees.     

Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera,Kalotermitidae)

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75–93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at <50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.     

滇西北玉龙雪山不同海拔云南松(Pinus yunnanensis)径向生长对气候因子的响应

云南松(Pinus yunnanensis)是重要的造林树种,在我国西南地区广泛分布。研究不同海拔云南松径向生长对气候变化的响应,有助于了解气候变化背景下云南松的敏感性和适应性。在滇西北丽江玉龙雪山不同海拔采集了云南松树木年轮样品,采用传统的树木年轮方法制作了不同海拔云南松树轮宽度标准化年表,并分析了不同海拔云南松径向生长与气候因子的相关性。结果表明:1)低海拔样点云南松具有较快的年平均生长速率。2)不同海拔云南松对气候因子的响应模式一致,树轮宽度与当年5—6月的降水量、帕尔默干旱指数(PDSI)和相对湿度呈正相关,与同期温度呈负相关。3)不同海拔的云南松径向生长对气象因子的响应程度不一样,即低海拔样点云南松树轮宽度与当年5月份的干旱指数、相对湿度、降水量相关系数较高;而高海拔样点的云南松树轮宽度与5—6月的降水、相对湿度、干旱指数的相关系数较低。研究表明春末夏初的水分条件是玉龙雪山云南松径向生长的主要限制因子,且低海拔地区云南松生长受水分限制更为严重,区域气候变暖和干旱化趋势可能对低海拔地区云南松的生长产生持续的负面效应。研究结果可为探讨气候变化下云南松的适宜分布区、以及云南松人工林的经营和可持续管理提供参考。     

植物乳杆菌编码复制起始蛋白天然质粒的系统进化分析

【目的】探究复制起始蛋白(Replication initiation protein,Rep)是否可以作为天然质粒系统进化关系研究的分子标记。【方法】以植物乳杆菌天然质粒编码的Rep为研究对象,通过构建Rep系统进化树详细分析和讨论这些质粒的系统进化关系。【结果】植物乳杆菌45个编码Rep天然质粒可以划分为5个进化关系紧密的家族和1个独立进化质粒p G6302,家族1-4质粒可以进一步划分为10个进化关系更近的亚家族类群,因此这些质粒可能起源于6个祖先质粒。【结论】Rep氨基酸序列显示了适度的保守性和变异性,是植物乳杆菌编码Rep质粒进化研究理想的分子标记,为植物乳杆菌天然质粒系统进化研究提供了一种简单、有效的分析方法和标准,并为植物乳杆菌或其他乳酸菌天然质粒系统进化研究提供了分子水平的佐证和依据。     

基于相邻木排列关系的混交度研究

混交度是反映森林群落中树种相互隔离状况的一个重要指标,目前已提出多种混交度指数.Mg考虑了对象木与最近相邻木的树种异同,Mv和Ms进一步考虑了最近相邻木(空间结构单元)树种数,但仍不能准确描述树种隔离程度.基于相邻木排列关系的混交度Mp,利用“1+4”结构的17个不同空间结构单元和天目山常绿阔叶林数据对Mg、Mv、Ms和Mp4个混交度进行了比较分析.结果表明:Mp的区分能力最强,Mv和Ms次之,Mg最差.Mp最适用于分析混交结构复杂的林分.在天目山常绿阔叶林分析中,混交度水平为中度,4个最近邻体中有2个相同种顺序排列的空间结构单元个数明显多于交错排列的个数.基于相邻木排列关系的混交度Mp能准确区分树种隔离程度,提高了混交度的区分度,可反映森林实际混交状况.     

山桐子实生优树选择研究初报

以四川等8个省份的山桐子野生资源为研究对象,通过实地走访和调查,了解山桐子资源分布状况和生态环境,利用产量、含油率等经济性状对山桐子野生群体进行优株选择。结果表明:安徽、江苏、浙江、江西各地主要以山桐子分布,而湖北、湖南、陕西、四川等地主要以山桐子的变异类型——毛叶山桐子为主,其中四川省毛叶山桐子分布较为密集;通过对各地点气候条件和土壤条件分析得出,山桐子适应性强,对气候要求不严,适合在微酸性土壤生长,尤喜肥沃土壤;根据能源油料植物原则对山桐子提出选优标准,从234株山桐子实生树中初步选择43个单株;主成分分析和聚类分析结果将43个单株划分为最高产量、较高产量和中产量3大类,且所有单株的单株产量、单位面积产量和全果含油率3个主要经济指标均高出群体平均值20%以上。本研究为山桐子种质资源收集与评价、优良种质或品种的选育奠定了重要基础。