葛属(豆科)的分类学修订

本论文对葛属（Pueraria DC.）进行了形态学、解剖学及植物地理学研究，重点分析了小叶、托叶、花序及花的形态变异规律。首次发现葛属生长习性和种皮纹饰特征在组的划分上具有重要的分类学意义，支持前人运用托叶着生方式、花序类型及每节簇生花的数目等特征划分组的观点。首次在光学显微镜下对葛属植物14种1变种叶表皮性状做了较为全面、深入的观察，发现葛属叶表皮细胞的形状、垂周壁的式样以及气孔大小有一定分类学意义，为葛属的分类修订提供了新资料。首次应用电子扫描显微镜观察了葛属10种1变种和2个外类群广西土黄芪Nogra guangxiensis C. F. Wei和琼豆Teyleria koordersii (Backer ex Koord.-Schum.) Backer的种皮纹饰特征，发现葛属的种皮纹饰有网纹型、断棱型、复网纹型和锐棱型等4种类型，他们与托叶的着生方式具有一定的关联性。托叶背着的类群为网纹型，其中采自中国和越南不同居群的山野葛Pueraria montana (Lour.) Merr.种皮次级纹饰有差别，这显示山野葛分化比较活跃。托叶基着的三裂叶野葛P. phaseoloides (Roxb.) Benth.、大花三裂叶野葛P. phaseoloides (Roxb.) Benth. var. javanica (Benth.) Baker、苦葛P. peduncularis (Graham ex Benth.) Benth.以及云南野葛P. yunnanensis Franch.的种皮纹饰为断棱形，小花野葛P. stricta Kurz种皮纹饰为复网纹型，喜玛拉雅葛藤P. wallichii DC.种皮纹饰为锐棱型。依据种皮纹饰推断，喜玛拉雅葛藤最原始，黄毛葛藤P. calycina Franch.最进化，与形态学特征演化方向相吻合。广西土黄芪种皮纹饰为网纹型，琼豆种皮纹饰为复网纹型，表明它们与葛属亲缘关系较近。这与形态学和分子证据相吻合。本文首次运用广义线形模型（GLM）结合地理信息系统（GIS）对葛属现有地理分布、潜在分布及50年后潜在分布进行了分析。所预测的潜在分布范围与观察到的地理分布范围一致，说明对特化的气候忍耐性是限制葛属物种地理分布的主要因素。温度、降水和海拔高度对葛属地理分布限制作用比较大。未来潜在分布预测显示葛属有向南、北扩散的趋势。 作者在研究了四千余份腊叶标本及野外形态考察的基础上，结合叶表皮及种皮纹饰资料，确认葛属分为3组，共19种3变种。其中，对Sect. Breviramulae Maesen ex Z. F. Le & X. Y. Zhu进行了合格发表，运用形态学、解剖学及种皮纹饰资料恢复了云南野葛种的地位，并为其指定了后选模式，P. pulcherrima (Koord.-Schum.) Merr. ex Koord.-Schum.正确的学名为P. sericans Schum.，对4个名称进行了归并。本文还给出了组和种的检索表、葛属各个种的形态描述、地理分布图及模式标本照片。

伞形科囊瓣芹属的系统学研究

囊瓣芹属Pternopetalum Franchet是伞形科Apiaceae/Umbelliferae芹亚科Apioideae芹族Apieae重要成员。全属包括约32个分类群（包括变种），分布于南朝鲜、日本、中国的西南部和邻近的喜马拉雅地区，中国西南部的横断山区是其多样性中心。典型的东亚特有格局和对东亚亚热带森林环境的偏爱是其东亚区系故有份子的特征。 基于19个标本馆标本材料、野外调查以及相应的实验证据，本博士论文从三个研究主题对囊瓣芹属展开了全面而系统的研究。一是通过标本观察和野外调查，利用标本管理系统BRAHMS和表型分析软件包DELTA系统，完成了囊瓣芹属的世界性分类修订；二是基于上述的分类方案，选择伞形科其它属的44个种作为参考性类群（Reference taxa），利用Winclada, NONA和MESQUITE软件包开展了分支系统学研究；三是基于坐标化的点分布数据，利用DIVA-GIS系统的生态位模型，进行潜在分布预测和生态地理分布特征的分析。研究的主要初步结论如下： 一、分类修订 根据对19个标本馆标本材料（包括85个模式采集）的考证，以及对云南、四川、贵州等地野外居群的观察，结合DELTA系统的表型分析，本研究确认囊瓣芹属包含14个种，提出了14个新异名，属下分为东亚囊瓣芹组Sect. I. Pteridophyllae H. Wolff和囊瓣芹组Sect. II. Pternopetalum H. Wolff两个组的分类方案。前者包括东亚囊瓣芹P. tanakae (Sav. & Franchet) Hand.-Mazz.、高山囊瓣芹P. subalpinum Hand.-Mazz.、洱源囊瓣芹P. molle (Franchet) Hand.-Mazz.等5个种；后者包括五匹青P. vulgare (Dunn) Hand.-Mazz.、囊瓣芹P. davidii Franchet和澜沧囊瓣芹P. delavayi (Franchet) Hand.-Mazz.等9个种。萼齿、花柱基、和花柱的形态是区别两个组比较好的形态学特征。叶的着生位置、最终末回裂片的形状（是否异形）、分裂回数以及伞形花序着生的位置和果棱表面的附属构造是种间识别有用的检索特征。 二、系统发育分析 根据如上的14个种的分类方案，另外选取了伞形科小芹属Sinocarum H. Wolff、丝瓣芹属Acronema Falc. ex Edgew.和鸭儿芹属Cryptotaenia L.等10个属共44种作为参考类群，基于63个广义形态学性状和58个种的形态学矩阵，利用最大简约法对囊瓣芹属进行了分支分析。结果表明，囊瓣芹属的14个种与日本特有单型的仙洞草Chamaele decumbens (Thunb.)Makino.形成一个单独分支，处于分支图的基部位置。表明囊瓣芹属与鸭儿芹属有较近的亲缘关系。长枝吸引可能是造成Chamaele Miq.与东亚囊瓣芹分支的非正常聚合的原因。囊瓣芹属可能是单系内群，但它与Chamaele Miq.属间关系需要进一步研究。属下形成以五匹青P. vulgare和东亚囊瓣芹P. tanakae为代表的两个主干演化线。分支进化（Cladogenesis）在两个主干演化线形成了形态和地理上对称分布的“种对”。根据形态特征的变异和地理分布，这些“种对”分为三种类型：1、形态上多变而地理上广布的类型，以东亚囊瓣芹P. tanakae和五匹青P. vulgare为代表；2、形态上稳定地理上狭域特有的类型，以薄叶囊瓣芹P. leptophyllum (Dunn)Hand.-Mazz. 和川鄂囊瓣芹P. rosthornii (Diels) Hand.-Mazz.为代表；3、形态上趋同而多变，地理分布上几乎完全重叠的类型，以洱源囊瓣芹P. molle和澜沧囊瓣芹P. delavayi为代表。 性状状态的分析显示，属下形态特征的趋异具有较强的同朔性。不等长的伞辐和花梗，以及囊状的花瓣基部三个形态学特征可以标识包括仙洞草在内的囊瓣芹分支。祖征状态的重建表明，东亚囊瓣芹分支相对保留了更多的祖征，是属下相对原始的类型；五匹青分支是后期生境需求的特化，适应潮湿和荫蔽环境的衍生类型。 三、生态地理分布 基于1128个坐标化的点分布数据和生态位模型，利用地理信息系统软件包DIVA-GIS对囊瓣芹属的物种多样性、现代地理分布、潜在分布进行了分析。结果表明，二郎山-峨眉山地区以及重庆金佛山及其临近地区是囊瓣芹属的两个主要的多样性中心。分布区内局部尺度上的异常性多样性（Diversity abnormalies）可能有两个来源：一是高的异质性生境条件下物种形成速率的差异；二是中国西南山地的“冰原岛峰效应”（Nunataks），比如峨眉山和金佛山，对属的早期演化线成员所起到的“避难所”（Refuge）的作用。 所预测的潜在分布范围与观察到的地理分布范围是一致的，说明对特化的气候忍耐性是限制囊瓣芹属物种地理分布的主要因素。温度和降水的季节性变化对囊瓣芹属代表中的地理分布限制作用比较大。亚热带-高山针阔常绿林是属下物种比较适宜的生境。属的地理分布可能形成于中新世以后，生态位的保守性是解释囊瓣芹属东亚本土就地分化和多样化的原因。属的分布范围的形成可能经历了一个早期南退西进的过程，后期分布范围变化可能主要是东西方向上的迁移和扩展。喜马拉雅—横断山—峨眉山/金佛山/神农架—日本、南朝鲜一线是囊瓣芹属多样化过程中分布范围东西延伸的重要通道。喜马拉雅—中国西南—日本朝鲜亚热带森林植被的完整性和连续性是囊瓣芹属演化和分布区形成的基本条件。

白豆杉的地理分布格局及潜在分布区估计

　　根据物种的分布信息结合环境因子估计物种的分布区对珍稀濒危物种的保护有着重要的意义。白豆杉Pseudotaxus chienii为第三纪孑遗植物，我国东南部地区特有，分布区狭窄。本文通过对白豆杉的标本记录研究它的地理分布，找出影响其分布的关键因子并对其潜在分布区进行估计，并解释其分布区形成的原因。全球升温将对物种分布造成重要影响，通过温度升高情况下2100年的气候数据模拟白豆杉未来的潜在分布区，估计温度升高对白豆杉的影响，将对白豆杉的保护有着重要的意义。 　　根据白豆杉的标本信息结合Diva-Gis软件对白豆杉的地理分布进行研究。以海拔图层和植被图层为底图对白豆杉的分布格局进行研究，并对白豆杉种群的多度进行统计分析。用Diva-Gis软件的气候数据提取功能提取白豆杉分布点的气候信息，并运用主成分分析对影响白豆杉分布的气候因子进行分析，找出影响白豆杉分布的主要环境因子。根据白豆杉的分布信息和气候数据，运用Diva-Gis内嵌的BIOCLIM模型和DOMAIN模型对白豆杉在不同气候条件下的潜在分布区进行估计，评价温度升高对白豆杉分布区的影响。 　　白豆杉分布格局研究结果表明，白豆杉分布在我国东南部地区中低海拔山区，白豆杉的分布和植被类型及海拔有着密切的关系。白豆杉的分布与海拔的关系表现为，由东到西，分布的最低海拔升高，海拔范围缩小。白豆杉分布地的植被类型为常绿灌木林，常绿阔叶林及针、阔叶混交林。白豆杉由东向西的海拔变化趋势与植被类型的由东向西的海拔变化趋势相一致。PCA分析结果表明白豆杉的分布与温度相关因子有着密切的关系。 　　现在气候对潜在分布区的估计表明,白豆杉的潜在分布区散布于浙、闽、粤、赣、湘，桂及黔几省各自交界之处即从浙江南部山区沿武夷山山系至南岭山系（向北到沿湘赣交界的罗宵山系）至大瑶山山系（向北沿雪峰山）。潜在分布区南部有三处分布的热点地区，即浙江南部、湖南南部和广西北部地区。三个主要分布区之间仅有有星散的潜在分布区存在，或没有潜在分布区出现，处在一种高度的隔离状态。造成这种潜在分布格局形成的原因可能有二，一是第四纪冰期的到来使白豆杉的分布区向南迁移，局部性气候的变化和地质变化可能导致了部分白豆杉的生境的消失，从而使得原来连续的分布区破碎化，形成了现在的星散分布；二是白豆杉的潜在分布区预测结果与中国东南部地区的山脉走势非常一致，山脉地带小生境多样化能够为白豆杉在垂直地带上的迁移提供更大的可能性。 　　未来气候数据对白都杉的潜在分布区估计表明，温度升高后白豆杉最适生分布区显著缩小。白豆杉的潜在分布区的地理分布格局发生了明显的变化，原来在南部的适生区明显缩小，星散程度更高。除已知的分布地外，在江西西南部武夷山、南岭山脉的湖南、广西、广东三省交界的地方都是白豆杉的适生区。江西和湖南交界的罗宵山山脉北部到井冈山都有白豆杉分布可能性较大，可以作为野外调查的重点地区。气候变化会使白豆杉在浙江、湖南南部的最适生境破碎化从而影响白豆杉的分布。生境保护对白豆杉的保护起着关键作用。

Spatial and temporal analysis of bottlenose dolphin strandings in South Carolina, 1992-2005

This CD contains summary data of bottlenose dolphins stranded in South Carolina using a Geographical Information System (GIS) and contains two published manuscripts in .pdf files. The intent of this CD is to provide data on bottlenose dolphin strandings in South Carolina to marine mammal researchers and managers. This CD is an accumulation of 14 years of stranding data collected through the collaborations of the National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research (CCEHBR), the South Carolina Department of Natural Resources, and numerous volunteers and veterinarians that comprised the South Carolina Marine Mammal Stranding Network. Spatial and temporal information can be visually represented on maps using GIS. For this CD, maps were created to show relationships of stranding densities with land use, human population density, human interaction with dolphins, high geographical regions of live strandings, and seasonal changes. Point maps were also created to show individual strandings within South Carolina. In summary, spatial analysis revealed higher densities of bottlenose dolphin strandings in Charleston and Beaufort Counties, which consist of urban land with agricultural input. This trend was positively correlated with higher human population levels in these coastal counties as compared with other coastal counties. However, spatial analysis revealed that certain areas within a county may have low human population levels but high stranding density, suggesting that the level of effort to respond to strandings is not necessarily positively correlated with the density of strandings in South Carolina. Temporal analysis revealed a significantly higher density of bottlenose dolphin strandings in the northern portion of the State in the fall, mostly due to an increase of neonate strandings. On a finer geographic scale, seasonal stranding densities may fluctuate depending on the region of interest. Charleston Harbor had the highest density of live bottlenose dolphin strandings compared to the rest of the State. This was due in large part to the number of live dolphin entanglements in the crab pot fishery, the largest source of fishery-related mortality for bottlenose dolphins in South Carolina (Burdett and McFee 2004). Spatial density calculations also revealed that Charleston and Beaufort accounted for the majority of dolphins that were involved with human activities. 1

A marine biogeographic assessment of the northwestern Hawaiian Islands

The mission of NOAA’s Office of National Marine Sanctuaries (ONMS) is to serve as the trustee for a system of marine protected areas, to conserve, protect and enhance biodiversity. To assist in accomplishing this mission, the ONMS has developed a partnership with NOAA’s Center for Coastal Monitoring and Assessment’s Biogeography Branch (CCMA-BB) to conduct biogeographic assessments of marine resources within and adjacent to the marine waters of NOAA’s National Marine Sanctuaries (Kendall and Monaco, 2003). Biogeography is the study of spatial and temporal distributions of organisms, their associated habitats, and the historical and biological factors that influence species’ distributions. Biogeography provides a framework to integrate species distributions and life history data with information on the habitats of a region to characterize and assess living marine resources within a sanctuary. The biogeographic data are integrated in a Geographical Information System (GIS) to enable visualization of species’ spatial and temporal patterns, and to predict changes in abundance that may result from a variety of natural and anthropogenic perturbations or management strategies (Monaco et al., 2005; Battista and Monaco, 2004). Defining biogeographic patterns of living marine resources found throughout the Northwestern Hawaiian Islands (NWHI) was identified as a priority activity at a May 2003 workshop designed to outline scientifi c and management information needs for the NWHI (Alexander et al., 2004). NOAA’s Biogeography Branch and the Papahanaumokuakea Marine National Monument (PMNM) under the direction of the ONMS designed and implemented this biogeographic assessment to directly support the research and management needs of the PMNM by providing a suite of spatially-articulated products in map and tabular formats. The major fi ndings of the biogeographic assessment are organized by chapter and listed below.

A Biogeographic assessment off North/Central California: In support of the National Marine Sanctuaries of Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase II - Environmental setting and update to marine birds and animals

NOAA’s National Centers for Coastal Ocean Science (NCCOS) conducts and supports research, monitoring, assessments, and technical assistance to meet NOAA’s coastal stewardship and management responsibilities. In 2001 the Biogeography Branch of NCCOS partnered with NOAA’s National Marine Sanctuary Program (NMSP) to conduct biogeographic assessments to support the management plan updates for the sanctuaries. The first biogeographic assessment conducted in this partnership focused on three sanctuaries off north/ central California: Cordell Bank, Gulf of the Farallones and Monterey Bay. Phase I of this assessment was conducted from 2001 to 2004, with the primary goal to identify and gather the best available data and information to characterize and identify important biological areas and time periods within the study area. The study area encompasses the three sanctuaries and extends along the coastal ocean off California from Pt. Arena to Pt. Sal (35°-39°N). This partnership project was lead by the NCCOS Biogeography Branch, but included over 90 contributors and 25 collaborating institutions. Phase I results include: 1) a report on the overall assessment that includes hundreds of maps, tables and analyses; 2) an ecological linkage report on the marine and estuarine ecosystems along the coast of north/central California, and 3) related geographic information system (GIS) data and other summary data files, which are available for viewing and download in several formats at the following website: http://ccma.nos.noaa.gov/products/biogeography/canms_cd/welcome.html Phase II (this report) was initiated in the Fall of 2004 to complete the analyses of marine mammals and update the marine bird colony information. Phase II resulted in significant updates to the bird and mammal chapters, as well as adding an environmental settings chapter, which contains new and existing data and maps on the study area. Specifically, the following Phase II topics and items were either revised or developed new for Phase II: •environmental, ecological settings – new maps on marine physiographic features, sea surface temperature and fronts, chlorophyll and productivity •all bird colony or roost maps, including a summary of marine bird colonies •updated at-sea data CDAS data set (1980-2003) •all mammal maps and descriptions •new overall density maps for eight mammal species •new summary pinniped rookery/haulout map •new maps on at-sea richness for cetaceans and pinnipeds •most text in the mammal chapter •new summary tables for mammals on population status and spatial and temporal patterns

Literature review for a resource characterization of Cape Romain National Wildlife Refuge

Through research aimed at understanding the coastal environment, surveys designed to help manage the resource, and national programs to monitor environmental condition, we see a picture of a dynamic ecosystem that is Cape Romain National Wildlife Refuge (CRNWR). Currently, there are efforts underway to protect threatened species; monitor fish populations; and quantify the biological, physical, and chemical characteristics of this environment. The potential impacts to this system are just now being understood as ecological responses to human modification are observed and explained. As a starting point, this document compiles existing information about Cape Romain NWR in five topic areas and addresses the potential impacts to the Refuge. This review is intended to serve as a stepping stone to developing a research agenda in support of management of the Refuge. There are various sources of information on which to build a framework for monitoring conditions and detecting change to this environment. For instance, information on basic ecological function in estuarine environments has evolved over several decades. Long-term surveys of Southeast fisheries exist, as well as shellfish and sediment contaminants data from estuaries. Environmental monitoring and biological surveys at the Refuge continue. Recently, studies that examine the impacts to similar coastal habitats have been undertaken. This document puts past studies and ongoing work in context for Refuge managers and researchers. This report recommends that the next phase of this resource characterization focus on: • compiling relevant tabular and spatial data, as identified here, into a Geographic Information System (GIS) framework • assessing the abundance and diversity of fisheries utilizing CRNWR • delineating additional data layers, such as intertidal habitats and subtidal clam beds, from low-level aerial photography, hard copy maps, and other sources • continued inventories of plant and animal species dependent on the Refuge • monitoring physical and chemical environmental parameters using the methodology employed at National Estuarine Research Reserve System (NERRS) and other coastal sites, where appropriate • further definition of the potential risks to the Refuge and preparing responses to likely impacts.

Sampling design tool for ArcGIS: Instruction manual.[for ESRI ArcGIS 10.0 Service Pack 3 or higher]

The Biogeography Branch’s Sampling Design Tool for ArcGIS provides a means to effectively develop sampling strategies in a geographic information system (GIS) environment. The tool was produced as part of an iterative process of sampling design development, whereby existing data informs new design decisions. The objective of this process, and hence a product of this tool, is an optimal sampling design which can be used to achieve accurate, highprecision estimates of population metrics at a minimum of cost. Although NOAA’s Biogeography Branch focuses on marine habitats and some examples reflects this, the tool can be used to sample any type of population defined in space, be it coral reefs or corn fields.

Majuro Atoll, Republic of the Marshall Islands coral reef ecosystems mapping report

Digital maps of the coral reef ecosystem (<~30m deep) of Majuro Atoll, Republic of the Marshall Islands, were created through visual interpretation of remote sensing imagery. Digital Globe’s Quickbird II satellite images were acquired between 2004 and 2006 and georeferenced to within 1.6 m of their true positions. Reef ecosystem features were digitized directly into a GIS at a display scale of 1:4000 using a minimum feature size of 1000 square meters. Benthic features were categorized according to a classification scheme with attributes including zone (location, such as lagoon or forereef, etc.), structure (bottom type, such as sand or patch reef, etc.) and percent hard bottom. Ground validation of habitat features was conducted at 311 sites in 2009. Resulting maps consisted of 1829 features covering 366 square kilometers. Results demonstrate that reef zones occurred in a typical progression of narrow bands from offshore, though forereef, reef flat, shoreline, land, backreef, and lagoon habitats. Lagoon was the largest zone mapped and covered nearly 80% of the atoll, although much of it was too deep to have structures identified from the satellite imagery. Dominant habitat structures by area were pavement and aggregate reef, which covered 29% and 18% of the mapped structures, respectively. Based on the number of features, individual and aggregated patch reefs comprised over 40% of the features mapped. Products include GIS based maps, field videos and pictures, satellite imagery, PDF atlas, and this summary report. Maps and associated data can be used to support science and management activities on Majuro reef ecosystems including inventory, monitoring, conservation, and sustainable development applications.

Prioritizing seagrass restoration sites: study examines predictors of seagrass bed recovery

Ecologic researchers are modeling the impact of vessel grounding to seagrass beds using GIS in the Florida Keys National Marine Sanctuary. The surface creation tools in the ArcGIS 3D Analyst extension help assess both the damage and recovery of these seagrass beds.

Diel movements of fishes linked to benthic seascape structure in a Caribbean coral reef ecosystem

Many common fishes associated with Caribbean coral reef ecosystems use resources from more than 1 patch type during routine daily foraging activities. Few studies have provided direct evidence of connectivity across seascapes, and the importance of benthic seascape structure on movement behavior is poorly known. To address this knowledge gap, we coupled hydro-acoustic technology to track fish with seafloor mapping and pattern analysis techniques from landscape ecology to quantify seascape structure. Bluestriped grunts Haemulon sciurus and schoolmaster snapper Lutjanus apodus were tracked over 24 h periods using boat-based acoustic telemetry. Movement pathways, and day and night activity spaces were mapped using geographical information system (GIS) tools, and seafloor structure within activity spaces was mapped from high-resolution aerial photography and quantified using spatial pattern metrics. For both fish species, night activity spaces were significantly larger than day activity spaces. Fish exhibited a daytime preference for seascapes with aggregate coral reef and colonized bedrock, then shifted to night activity spaces with lower complexity soft sediment including sand, seagrass, and scattered coral/rock. Movement path complexity was negatively correlated with seascape complexity. This demonstrates direct connectivity across multiple patch types and represents the first study to apply quantitative landscape ecology techniques to examine the movement ecology of marine fish. The spatially explicit approach facilitates understanding to the linkages between biological processes and the heterogeneity of the landscape. Such studies are essential for identifying ecologically relevant spatial scales, delineating essential fish habitat and designing marine protected areas.

Nocturnal migration patterns of two Caribbean reef fishes, Haemulon sciurus and Lutjanus apodus [Poster]

In the Caribbean, many coral reef associated fishes have been observed making diel migrations, yet little is known about the detailed movement pathways and space use patterns of individual fish. Often these migrations occur along temporally or spatially consistent corridors that connect preferred resting and foraging habitats. Recent analysis of gut contents from Haemulids and Lutjanids, has provided evidence that these species forage in seagrass beds and other habitats near their coral reef refuges. Few studies have provided direct and spatially explicit evidence of nocturnal migrations and detailed day and night space use patterns for individual fish. This study integrated manual acoustic telemetry to track two common reef species, the bluestriped grunt (Haemulon sciurus) and schoolmaster snapper (Lutjanus apodus) throughout their daily home range. Space use patterns of these species were then examined using Geographical Information System (GIS) tools to link movement behavior to seascape structure derived in a benthic habitat map. This study represents a novel integration of spatial technologies to enhance our understanding of the movement ecology of adult H. sciurus and L. apodus.

Assessment of existing information on Atlantic coastal fish habitats: development of a web-based spatial bibliography, query tools, and data summaries

The primary objective of this project, “the Assessment of Existing Information on Atlantic Coastal Fish Habitat”, is to inform conservation planning for the Atlantic Coastal Fish Habitat Partnership (ACFHP). ACFHP is recognized as a Partnership by the National Fish Habitat Action Plan (NFHAP), whose overall mission is to protect, restore, and enhance the nation’s fish and aquatic communities through partnerships that foster fish habitat conservation. This project is a cooperative effort of NOAA/NOS Center for Coastal Monitoring and Assessment (CCMA) Biogeography Branch and ACFHP. The Assessment includes three components; 1. a representative bibliographic and assessment database, 2. a Geographical Information System (GIS) spatial framework, and 3. a summary document with description of methods, analyses of habitat assessment information, and recommendations for further work. The spatial bibliography was created by linking the bibliographic table developed in Microsoft Excel and exported to SQL Server, with the spatial framework developed in ArcGIS and exported to GoogleMaps. The bibliography is a comprehensive, searchable database of over 500 selected documents and data sources on Atlantic coastal fish species and habitats. Key information captured for each entry includes basic bibliographic data, spatial footprint (e.g. waterbody or watershed), species and habitats covered, and electronic availability. Information on habitat condition indicators, threats, and conservation recommendations are extracted from each entry and recorded in a separate linked table. The spatial framework is a functional digital map based on polygon layers of watersheds, estuarine and marine waterbodies derived from NOAA’s Coastal Assessment Framework, MMS/NOAA’s Multipurpose Marine Cadastre, and other sources, providing spatial reference for all of the documents cited in the bibliography. Together, the bibliography and assessment tables and their spatial framework provide a powerful tool to query and assess available information through a publicly available web interface. They were designed to support the development of priorities for ACFHP’s conservation efforts within a geographic area extending from Maine to Florida, and from coastal watersheds seaward to the edge of the continental shelf. The Atlantic Coastal Fish Habitat Partnership has made initial use of the Assessment of Existing Information. Though it has not yet applied the AEI in a systematic or structured manner, it expects to find further uses as the draft conservation strategic plan is refined, and as regional action plans are developed. It also provides a means to move beyond an “assessment of existing information” towards an “assessment of fish habitat”, and is being applied towards the National Fish Habitat Action Plan (NFHAP) 2010 Assessment. Beyond the scope of the current project, there may be application to broader initiatives such as Integrated Ecosystem Assessments (IEAs), Ecosystem Based Management (EBM), and Marine Spatial Planning (MSP).

Biogeographic characterization of essential fish habitats affected by human activities in the coastal zone of Puerto Rico

The overall purpose of this project was to collect available information on the characteristics of essential fish habitats in protected and non-protected marine areas around the islands of Puerto Rico. Specifically, this project compiled historical information on benthic habitats and the status of marine resources into a Geographic Information System (GIS) by digitizing paper copies of existing marine geologic maps that were developed for the Caribbean Fishery Management Council (CFMC) for areas around the Commonwealth of Puerto Rico. In addition, information on benthic habitat types, Essential Fish Habitat (EFH) requirements, and fishing and non-fishing impacts to marine resources were compiled for two priority areas: La Parguera and Vieques. The information obtained will help to characterize and select habitats for future monitoring of impacts of fishing and non-fishing activities and to develop management recommendations for conservation of important marine habitats. The project focused specifically on areas identified as priorities for conservation by the Puerto Rico Department of Natural and Environmental Resources (DNER) and the Local Action Strategy Overfishing Group.

Shallow-water benthic habitats of St. John, U.S. Virgin Islands

Coral reef ecosystems of the Virgin Islands Coral Reef National Monument, Virgin Islands National Park and the surrounding waters of St. John, U.S. Virgin Islands are a precious natural resource worthy of special protection and conservation. The mosaic of habitats including coral reefs, seagrasses and mangroves, are home to a diversity of marine organisms. These benthic habitats and their associated inhabitants provide many important ecosystem services to the community of St. John, such as fishing, tourism and shoreline protection. However, coral reef ecosystems throughout the U.S. Caribbean are under increasing pressure from environmental and anthropogenic stressors that threaten to destroy the natural heritage of these marine habitats. Mapping of benthic habitats is an integral component of any effective ecosystem-based management approach. Through the implementation of a multi-year interagency agreement, NOAA’s Center for Coastal Monitoring and Assessment - Biogeography Branch and the U.S. National Park Service (NPS) have completed benthic habitat mapping, field validation and accuracy assessment of maps for the nearshore marine environment of St. John. This work is an expansion of ongoing mapping and monitoring efforts conducted by NOAA and NPS in the U.S. Caribbean and replaces previous NOAA maps generated by Kendall et al. (2001) for the waters around St. John. The use of standardized protocols enables the condition of the coral reef ecosystems around St. John to be evaluated in context to the rest of the Virgin Island Territories and other U.S. coral ecosystems. The products from this effort provide an accurate assessment of the abundance and distribution of marine habitats surrounding St. John to support more effective management and conservation of ocean resources within the National Park system. This report documents the entire process of benthic habitat mapping in St. John. Chapter 1 provides a description of the benthic habitat classification scheme used to categorize the different habitats existing in the nearshore environment. Chapter 2 describes the steps required to create a benthic habitat map from visual interpretation of remotely sensed imagery. Chapter 3 details the process of accuracy assessment and reports on the thematic accuracy of the final maps. Finally, Chapter 4 is a summary of the basic map content and compares the new maps to a previous NOAA effort. Benthic habitat maps of the nearshore marine environment of St. John, U.S. Virgin Islands were created by visual interpretation of remotely sensed imagery. Overhead imagery, including color orthophotography and IKONOS satellite imagery, proved to be an excellent source from which to visually interpret the location, extent and attributes of marine habitats. NOAA scientists were able to accurately and reliably delineate the boundaries of features on digital imagery using a Geographic Information System (GIS) and fi eld investigations. The St. John habitat classification scheme defined benthic communities on the basis of four primary coral reef ecosystem attributes: 1) broad geographic zone, 2) geomorphological structure type, 3) dominant biological cover, and 4) degree of live coral cover. Every feature in the benthic habitat map was assigned a designation at each level of the scheme. The ability to apply any component of this scheme was dependent on being able to identify and delineate a given feature in remotely sensed imagery.