分子系统学分析平台的建立和应用

分子系统学建立在实验和计算的基础之上。DNA快速测序技术的普及为分子系统学家提供了大量数据，而序列分析技术则是探索数据发现知识的重要工具。在基因组时代，随着大量模式生物完整基因组序列的获得，分子系统学正面临着前所未有的机遇和挑战。一方面，生命之树计划有助于确定新的模式生物和开展相应的基因组计划;另一方面，模式生物的基因组计划有助于阐明它们之间的进化关系和基因组的进化模式。更为重要的是，分子系统学序列分析技术已经发展成为探索与整合基因组数据的强有力工具，从而在生命科学中发挥重要作用。事实上，分子系统学和基因组学的相互渗透正在形成一门崭新的交叉学科——系统发育基因组学。 为了奠定分子系统学研究中信息管理和数据分析工作的坚实基础，我们建立了分子系统发育分析平台。该平台为研究人员提供专业数据库服务和数据分析技术支持，以及相关的网络资源。 分子系统发育分析平台包括了3个专业数据库。第一个是DNA凭证标本数据库。该数据库中的记录包括了7项字段：英文科名、中文科名、物种拉丁名、采集人、采集号、采集地和采集时间。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括3491条标本记录。第二个是引物数据库。PCR引物是分子系统学实验的重要条件之一。该数据库中的记录包括3项字段：引物名称、序列内容和退火温度。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括170条用于扩增植物细胞核、叶绿体和线粒体基因组DNA序列的引物记录。第三个是生物计算数据库。该数据库为研究人员提供传输和保存序列分析数据和结果文件的服务。 为了确保数据库的安全性和使用性，我们开发了数据库的接口和检索工具，以及系统管理员和用户资格认证程序。通过前者，使用者可以进行数据的上传、下载、管理和检索等操作。而后者则是对不同使用者身份和权限进行设定。管理员的权限高于用户，主要负责本系统的日常维护和管理工作，以及对新增管理员和用户进行资格认证。 分析技术支持旨在帮助用户快速掌握常用的系统发育分析方法，进行有效的数据分析，从复杂的统计学算法和计算机程序中解放出来，将精力集中于计算结果的生物学解释。在该部分中，我们首先简要介绍了常用的分析方法，并且针对分子系统学中的不同问题提供了相应的解决方案。这些问题包括：系统发育重建、替代速率和分歧时间的估计、祖先分布区的重建、性状进化假说的检验、以及密码子水平适应性进化的检测。我们特别强调了似然比检验和贝叶斯推测作为方法论上的重要进展在分子系统学中所发挥的关键作用。本部分还包括大量常用的分子系统学程序或软件包及其快速使用说明和命令模块。下载安装之后，用户即可按照说明使用命令模块进行数据分析。 此外，该平台还提供了一些常用的网络资源地址，如生物信息中心、分子进化和系统发育实验室、专业期刊和相关数据库等。 最后还给出了4个应用实例，即针对特定分子系统学问题的解决方案和初步的分析结果。 第一个例子说明系统发育重建方法的应用。为了确定杨梅科的系统学位置，对6种DNA序列和叶绿体trnL-F区内的间隔性状进行了分析。单个分析表明这6种序列之间在系统学信息上存在显著差异。叶绿体基因组序列的合并分析强烈支持杨梅科和（木麻黄科，（桦木科，核果桦科））的姐妹群关系，而间隔性状的存在能够充分提高其分辨率和支持率。 第二个例子说明如何推测历史生物地理学过程。我们对壳斗目8科25属植物叶绿体基因组的trnL-F、matK、rbcL和atpB的合并序列进行了最大简约分析，得到唯一的最大简约树。基于该系统树和25属植物的地理分布数据，采用扩散－替代分析方法重建了系统树每个节点上的祖先分布区，推测了壳斗目的分布历史。结果表明，壳斗目的历史生物地理学过程由3次替代事件和20次扩散事件组成。其中最重要的替代事件是由于冈瓦纳大陆和劳亚大陆分离所导致的南青冈科及其姐妹群之间的分化。另外，在壳斗科和核心高等金缕梅类中多次发生从欧亚大陆到北美洲、甚至南美洲的平行扩散事件。 第三个例子说明如何估计分歧时间。我们仍然使用扩散－替代分析中所用的最大简约树作为分析的依据，并根据等级制似然比检验确定的最优替代模型对该系统树的支长进行了最大似然优化。似然比检验表明，该系统树不服从分子钟假说。我们以冈瓦纳大陆和劳亚大陆分离的地质事件和5个属的最早化石记录作为标定点，采用罚分似然法在没有分子钟的条件下估计了壳斗目的科间分歧时间。结果表明，绝大多数科间分歧事件都发生在白垩纪。 第四个例子说明如何检测密码子水平的适应性进化。分支间可变选择压力模型的似然比检验表明SARS冠状病毒的S基因在跨种传播过程中发生了正选择。

Land-sea characterization of the St. Croix East End Marine Park, U.S. Virgin Islands

The St. Croix East End Marine Park (STXEEMP) was established in 2003 as the first multi-use marine park managed by the U.S. Virgin Islands Department of Planning and Natural Resources. It encompasses an area of approximately 155 km2 and is entirely within Territorial waters which extend up to 3 nautical miles from shore. As stated in the 2002 management plan, the original goals were to: protect and maintain the biological diversity and other natural values of the area; promote sound management practices for sustainable production purposes; protect the natural resource base from being alienated for other land use purposes that would be detrimental to the area’s biological diversity; and to contribute to regional and national development (The Nature Conservancy, 2002). At the time of its establishment, there were substantial data gaps in knowledge about living marine resources in the St. Croix, and existing data were inadequate for establishing baselines from which to measure the future performance of the various management zones within the park. In response to these data gaps, National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment, Biogeography Branch (CCMA-BB) worked with territorial partners to characterize and assess the status of the marine environment in and around the STXEEMP and land-based stressors that affect them. This project collected and analyzed data on the distribution, diversity and landscape condition of marine communities across the STXEEMP. Specifically, this project characterized (1) landscape and adjacent seascape condition relevant to threats to coral reef ecosystem health, and (2) the marine communities within STXEEMP zones to increase local knowledge of resources exposed to different regulations and stressors.

Contrasting seasonal patterns in dimethylsulfide, dimethylsulfoniopropionate, and chlorophyll a in a shallow North Carolina estuary and the Sargasso Sea

Time series measurements of dimethylsulfide (DMS), particulate dimethylsulfoniopropionate (DMSPp), chlorophyll a (chl a), algal pigments, major nutrients, and the potential activity of DMSP lyase enzymes were made over a 2 yr period (6 March 2003 to 28 March 2005) near the mouth of the shallow, tidally mixed Newport River estuary, North Carolina, USA. DMSPp had a mean of 43 ± 20 nM (range = 10.5 to 141 nM, n = 85) and DMS a mean of 2.7 ± 1.2 nM (range = 0.9 to 7.0 nM). The mean DMS in Gallants Channel was not significantly different from that measured in the Sargasso Sea near Bermuda during a previous 3 yr time series study (2.4 ± 1.5 nM), despite there being a 43-fold higher mean chl a concentration (4.9 ± 2.4 µg l–1) at the coastal site. In winter, DMS was low and chl a was high in the surface waters of the Sargasso Sea, while the opposite was true at the coastal site. Consequently, DMS concentrations per unit algal chl a were on average 170 times higher in the Sargasso Sea than at the coastal site during the summer, but only 7 times higher during the winter. The much higher chl a-specific DMS concentrations at the oceanic site during the summer were linked to higher ratios of intracellular DMSP substrate and DMSP lyase enzyme per unit chl a. These differences in turn appear to be linked to large differences in nutrient concentrations and solar UV stress at the 2 sites and to associated differences in the composition of algal assemblages and physiological acclimation of algal cells.

Trade secrets: a ten year overview of the illegal import of sea turtle products into the United States

For more than 25 years all sea turtle products have been prohibited from international commerce by the 170-member nations of the Convention on International Trade in Endangered Species (CITES). Sea turtles continue to be threatened by direct take (including poaching) and illegal trade despite multi-national protection efforts. Although take may contribute significantly to sea turtle decline, illegal take is difficult to measure since there are few quantified records associated with legal fisheries and fewer still for illegal take (poaching). We can, however, quantify one portion of the illegal sea turtle trade by determining how many illegal products were seized at United States ports of entry over a recent 10-year period. The United States Fish and Wildlife Service (USFWS) oversees the import and export of wildlife and wildlife products, ensuring that wildlife trade complies with United States laws and international treaties. Additionally, the USFWS has legal authority to target suspected illegal wildlife activity through undercover and field investigations. In an effort to assess the scale of illegal sea turtle take and trade, we have conducted a 10-year (1994 – 2003) review of the law enforcement database maintained by the USFWS. This database tracks the number and type of wildlife cases, the quantity of seized products, and the penalties assessed against violators. These data are minimum estimates of the sea turtle products passing through the United States borders, as smuggled wildlife is oftentimes not detected.