Marine Vertebrates and Low Frequency Sound: Technical Report for LFA EIS

Over the past 50 years, economic and technological developments have dramatically increased the human contribution to ambient noise in the ocean. The dominant frequencies of most human-made noise in the ocean is in the low-frequency range (defined as sound energy below 1000Hz), and low-frequency sound (LFS) may travel great distances in the ocean due to the unique propagation characteristics of the deep ocean (Munk et al. 1989). For example, in the Northern Hemisphere oceans low-frequency ambient noise levels have increased by as much as 10 dB during the period from 1950 to 1975 (Urick 1986; review by NRC 1994). Shipping is the overwhelmingly dominant source of low-frequency manmade noise in the ocean, but other sources of manmade LFS including sounds from oil and gas industrial development and production activities (seismic exploration, construction work, drilling, production platforms), and scientific research (e.g., acoustic tomography and thermography, underwater communication). The SURTASS LFA system is an additional source of human-produced LFS in the ocean, contributing sound energy in the 100-500 Hz band. When considering a document that addresses the potential effects of a low-frequency sound source on the marine environment, it is important to focus upon those species that are the most likely to be affected. Important criteria are: 1) the physics of sound as it relates to biological organisms; 2) the nature of the exposure (i.e. duration, frequency, and intensity); and 3) the geographic region in which the sound source will be operated (which, when considered with the distribution of the organisms will determine which species will be exposed). The goal in this section of the LFA/EIS is to examine the status, distribution, abundance, reproduction, foraging behavior, vocal behavior, and known impacts of human activity of those species may be impacted by LFA operations. To focus our efforts, we have examined species that may be physically affected and are found in the region where the LFA source will be operated. The large-scale geographic location of species in relation to the sound source can be determined from the distribution of each species. However, the physical ability for the organism to be impacted depends upon the nature of the sound source (i.e. explosive, impulsive, or non-impulsive); and the acoustic properties of the medium (i.e. seawater) and the organism. Non-impulsive sound is comprised of the movement of particles in a medium. Motion is imparted by a vibrating object (diaphragm of a speaker, vocal chords, etc.). Due to the proximity of the particles in the medium, this motion is transmitted from particle to particle in waves away from the sound source. Because the particle motion is along the same axis as the propagating wave, the waves are longitudinal. Particles move away from then back towards the vibrating source, creating areas of compression (high pressure) and areas of rarefaction (low pressure). As the motion is transferred from one particle to the next, the sound propagates away from the sound source. Wavelength is the distance from one pressure peak to the next. Frequency is the number of waves passing per unit time (Hz). Sound velocity (not to be confused with particle velocity) is the impedance is loosely equivalent to the resistance of a medium to the passage of sound waves (technically it is the ratio of acoustic pressure to particle velocity). A high impedance means that acoustic particle velocity is small for a given pressure (low impedance the opposite). When a sound strikes a boundary between media of different impedances, both reflection and refraction, and a transfer of energy can occur. The intensity of the reflection is a function of the intensity of the sound wave and the impedances of the two media. Two key factors in determining the potential for damage due to a sound source are the intensity of the sound wave and the impedance difference between the two media (impedance mis-match). The bodies of the vast majority of organisms in the ocean (particularly phytoplankton and zooplankton) have similar sound impedence values to that of seawater. As a result, the potential for sound damage is low; organisms are effectively transparent to the sound – it passes through them without transferring damage-causing energy. Due to the considerations above, we have undertaken a detailed analysis of species which met the following criteria: 1) Is the species capable of being physically affected by LFS? Are acoustic impedence mis-matches large enough to enable LFS to have a physical affect or allow the species to sense LFS? 2) Does the proposed SURTASS LFA geographical sphere of acoustic influence overlap the distribution of the species? Species that did not meet the above criteria were excluded from consideration. For example, phytoplankton and zooplankton species lack acoustic impedance mis-matches at low frequencies to expect them to be physically affected SURTASS LFA. Vertebrates are the organisms that fit these criteria and we have accordingly focused our analysis of the affected environment on these vertebrate groups in the world’s oceans: fishes, reptiles, seabirds, pinnipeds, cetaceans, pinnipeds, mustelids, sirenians (Table 1).

Relationships between Testate Amoebae Assemblages (Protozoa) and Geographic Factors in Yunnan Plateau Lakes, China

Knowledge of the effect of geographic factors on the assemblages of protozoan testate amoebae is still limited, despite there having been a number of studies on this fauna. We applied statistical analyses to data on the distribution of testate amoebae from nine major lakes in the Yunnan Plateau, southwest China. Cluster analysis, based on community structure, separated the lakes into two groups - the oligotrophic/mesotrophic lakes and the hypercutrophic lakes - confirming the idea that the testate amoebae assemblages in lakes are closely related to the trophic status. Additionally, within the oligotrophic/mesotrophic lakes, there was distinct geographic clustering. Linear regression analysis and the Mantel test both revealed that similarity of species composition decreased with increasing geographic distance among the oligotrophic/mesotrophic lakes.

Geographic distribution of Pelteobagrus fulvidraco and Pelteobagrus vachelli in the Yangtze River based on mitochondrial DNA markers

Three populations of Pelteobagrus vachelli and Pelteobagrus fulvidraco of the Yangtze River were examined by PCR-RFLP analysis of mitochondrial DNA fragments. ND5/6 and D-loop fragments were digested by 10 restriction endonucleases. Significant geographic variations between upstream and mid-downstream populations in the haplotype frequencies and restriction patterns were revealed. This suggested that the diversity of P. vachelli was high; 11 haplotypes were obtained from all the samples. The upstream population shared seven haplotypes and the middle and downstream populations shared another four haplotypes. Among all of the haplotypes, one haplotype was shared in 30 samples of the populations from middle and downstream, but it was not found in the upstream population. Any haplotype found in the upstream population was not detected in the middle and downstream populations. Genetic diversity of P. fulvidraco was low and only five haplotyes were detected from all 60 samples. Phylogenic relationships also indicated that the fishes from upstream and mid-downstream were apparently divided into two populations.

中国沙棘(Hippophae rhamnoides subsp. sinensis)天然群体的遗传变异分析

近十年，植物群体遗传学的研究飞速发展，然而与海拔相关的植物群体遗传结构和遗传变异研究却相对较少。到目前为止，还不清楚遗传变异与海拔之间是否有一个通用的格局。在山区，各种生态因子，如温度、降水、降雪、紫外线辐射强度以及土壤成分都随海拔梯度急剧变化，造成了即使在一个小的空间区域，植被类型变化显著，这种高山环境的异质性和复杂性为我们研究植物群体遗传结构和分化提供了方便。沙棘(Hippophea)属于胡颓子科(Elaeagnaceae)为多年生落叶灌木或乔木，雌雄异株，天然种群分布极为广泛。中国沙棘(H. rhamnoides subsp. sinensis)是沙棘属植物中分布较广的一个亚种，种内形态变异非常丰富，加之其具有独特的繁育系统和广泛的生态地理分布，是研究沙棘属植物遗传变异和系统分化的理想材料。本文从1,800 m 到3,400 m 分5 个海拔梯度进行取样，用RAPD 和cpSSR 分子标记研究了卧龙自然保护区中国沙棘天然群体的遗传结构和遗传变异。5 个取样群体依次标记为A、B、C、D 和E，它们分别代表分布在海拔1,800，2,200，2,600，3,000 和3,400 m 的5 个天然群体。RAPD实验用11 条寡核苷酸引物，扩增得到151 个重复性好的位点，其中143 个多态位点，多态率达94.7%。在5 个沙棘群体中，总遗传多样性值(HT)为0.289，B群体内的遗传多样性值为0.315，这完全符合沙棘这种多年生、远交的木本植物具有高遗传变异的特性。5 个群体内遗传多样性随海拔升高呈低－高－低变异趋势，在2,200 m海拔处的B群体遗传多样性达最大值0.315，3,400 m海拔处的E群体则表现最小仅0.098。5 个群体间的遗传分化值GST＝0.406，也即是说有40.6%的遗传变异存在于群体间，1,800 m海拔处的A群体与其它群体的明显分离是造成群体间遗传分化大的原因。UPGMA聚类图和PCoA散点图进一步确证了5 个群体间的关系和所有个体间的关系。最后，经过Mantel检测，遗传距离与海拔表现了明显的相关性(r = 0.646, P = 0.011)。cpSSR 实验中，经过对24 对cpSSR 通用引物筛选，11 对引物能扩增出特异性条带，只有2 对引物(ccmp2 和ARCP4)呈现多态性。4 个等位基因共组合出4 种单倍型，单倍型Ⅰ出现在A 群体的所有个体和B 群体的8 个个体中，C、D、E 三个群体均不含有，而单倍型Ⅱ出现在C、D、E 三个群体的所有个体及B 群体的18 个个体中，A 群体不含有。另外两种单倍型Ⅲ和Ⅳ为稀有类型，仅B 群体中的4 个个体拥有。这种单倍型分布模式和TFPGA 群体聚类图揭示了，C、D、E 群体可能来源于同一祖先种，而A 群体却是由另一祖先种发展起来的，B 群体则兼具了这两种起源种的信息，这可能是因为在历史上的某一时期，在中国沙棘群体高山分化的过程中，B 群体处某个或者某些个体发生了基因突变，具备了适应高海拔环境的能力，产生了高海拔沙棘群体的祖先种。 In recent ten years, studies about population genetics of plants developed rapidly,whereas their genetic structure and genetic variation along altitudinal gradients have beenstudied relatively little. So far, it is uncleared whether there is a common pattern betweengenetic variation and altitudinal gradients. In the mountain environments, importantecological factors, e.g., temperature, rainfall, snowfall, ultraviolet radiation and soil substratesetc., change rapidly with altitudes, which cause the vegetation distribution varying typically,even on a small spatial scale. The mountain environments, which are heterogeneous andcomplex, facilitate and offer a good opportunity to characterize population genetic structureand population differentiation.The species of the genus Hippophae L. (Elaeagnaceae) are perennial deciduous shrubs ortrees, which are dioecious, wind-pollinated pioneer plants. The natural genus has a widedistribution extending from Northern Europe through Central Europe and Central Asia toChina. According to the latest taxonomy, the genus Hippophae is divided into six species and12 subspecies. The subspecies H. rhamnoides ssp. sinensis shows significant morphologicalvariations, large geographic range and dominantly outcrossing mating system. Thesecharacteristics of the subspecies are favourable to elucidate genetic variation and systemevolution. To estimate genetic variation and genetic structure of H. rhamnoides ssp. sinensisat different altitudes, we surveyed five natural populations in the Wolong Natural Reserve at altitudes ranging from 1,800 to 3,400 m above sea level (a.s.l.) using random amplifiedpolymorphic DNA markers (RAPDs) and cpSSR molecular methods. The five populations A,B, C, D, and E correspond to the altitudes 1,800, 2,200, 2,600, 3,000 and 3,400 m,respectively.Based on 11 decamer primers, a total of 151 reproducible DNA loci were yielded, ofwhich 143 were polymorphic and the percentage of polymorphic loci equaled 94.7%. Amongthe five populations investigated, the total gene diversity (HT) and gene diversity within population B equaled 0.289 and 0.315, respectively, which are modest for a subspecies of H.rhamnoides, which is an outcrossing, long-lived, woody plant. The amount of geneticvariation within populations varied from 0.098 within population E (3,400 m a.s.l.) to 0.315within population B (2,200 m a.s.l.). The coefficient of gene differentiation (GST) amongpopulations equaled 0.406 and revealed that 40.6% of the genetic variance existed amongpopulations and 59.4% within populations. The population A (1,800 m a.s.l.) differed greatlyfrom the other four populations, which contributes to high genetic differentiation. A UPGMAcluster analysis and principal coordinate analyses based on Nei's genetic distances furthercorroborated the relationships among the five populations and all the sampling individuals,respectively. Mantel tests detected a significant correlation between genetic distances andaltitudinal gradients (r = 0.646, P = 0.011).Eleven of the original 24 cpSSR primer pairs tested produced good PCR products, onlytwo (ccmp2 and ARCP4) of which were polymorphic. Four total length variants (alleles) werecombined resulting in 4 haplotypes. The haplotype was present in all individuals of Ⅰpopulation A and 8 individuals of populations B, the other three populations (C, D and Epopulations) did not share. The haplotype was present in all individuals of populations C, D Ⅱand E and 18 individuals of populations B, population A did not share. The other twohaplotypes and were rare haplotypes, which were only shared in 4 individuals of Ⅲ Ⅳpopulation B. The distribution of haplotypes and TFPGA population clustering map showedthat the populations C, D and E might be origined from one ancestor seed and population Amight be from another, whereas population B owned information of the two ancestor seeds. Itwas because that gene mutation within some individual or seed in the location of population Bwas likely to happen in the history of H. rhamnoides, which was the original ancestor of thehigh-altitude populations.

Studies on hybridization effects of different geographic populations of Chlamys farreri - II. The medium-term growth and development of Chlamys farreri populations from China and Russia and their reciprocal crosses

Based on the research of juvenile (2, 3, 4 months) growth and survival of three populations of two different geographic areas in Chlamys farreri from Russian and China and their F, hybrids derived from Chinese cultural population (CC) female x Russian population (RW) male, Chinese wild population (CW) female x Russian population (RW) male, Russian population (RW) female x Chinese wild population (CW) the study of the medium-term (6, 8, 10, 12 months) growth and development of Chlamys farreri was carried out. The four determined results indicated that there existed different extent heterosis (3% similar to 52 %) for the growth in three types of F-1 hybrids, and the offspring derived from CC female X Rmale had a stronger heterosis among the crosses at the medium-term; the uptrend among traits are wet weight > shell width > shell length > shell height, Chinese cultural population could be recognized as excellent parent, and seasonal variations influence very much on the daily increment and growth rate of each trait of Chlamys farreri and it is only able to survive and could barely grow in winter (6 similar to 8 months), but grows fast in temperate season (10similar to12 months).

Microsatellite-centromere distances and microsatellite diversity in different ploidy classes of Chinese shrimp (Fenneropenaeus Chinensis)

This is the first report of microsatellite-centromere mapping in this commercial species Fenneropenaeus Chinensis, and will be important for providing fixed points in the linkage groups of genetic maps. Triploid Chinese shrimp was induced by heat shock. The fertilized eggs were treated either by retention of the first polar body or the second polar body to produce Meiosis I (MI) or Meiosis II (MII) triploid. The triploidy status in each Chinese shrimp could be confirmed by nine polymorphic microsatellite loci, in which the parents with different alleles and the female parents were each heterozygous. The nine loci were mapped in relation to their centromeres in three MII triploid families, which were induced by retention of the second polar bodies after fertilization with sperm. Microsatellite-centromere (M-C) distances ranged from 9.6 cM to 37 cM under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards assembly of genetic maps in F. chinensis. Twelve polymorphic microsatellites were used to assess the heterozygosity and allelic diversity in different ploidy classes. As expected, triploids were significantly more polymorphic than diploids. The diploids had an average heterozygosity and allelic diversity value of 0.86, whereas the triploids heterozygosity averaged 0.93 and had allelic diversity value of 1.29. However, MI triploids were not significantly more polymorphic than MII in the microsatellite loci.

Geographic variation in the leaf essential oils of Juniperus sabina L. and J-sablina var. arenaria (E.H. Wilson) Farjon

The composition of the leaf oils from seven populations of J. sabina L., one population of Juniperus sabina var. arenaria (E. H. Wilson) Farjon were examined for their geographic variation. In addition, the leaf oils of J. chinensis L. and J. davurica Pall. were compared to J. sabina. Juniperus sabina var. arenarla, the sand loving juniper, oil was found to be very similar to that of J. davurica, Mongolia, and J. sabina, on sand dunes in Mongolia. This suggests that J. sabina var. arenaria might be conspecific with J. davurica. Farjon's move (2001) of J. sabina var. arenaria out of J. chinensis is supported. Considerable differentiation was found in populations of J. sabina from the Iberian peninsula. Cedrol, citronellol, safrole, trans-sabinyl acetate, terpinen-4-ol and beta-thujone were found to be polymorphic in several populations.

On the Geographic Location of Internet Resources

One relatively unexplored question about the Internet's physical structure concerns the geographical location of its components: routers, links and autonomous systems (ASes). We study this question using two large inventories of Internet routers and links, collected by different methods and about two years apart. We first map each router to its geographical location using two different state-of-the-art tools. We then study the relationship between router location and population density; between geographic distance and link density; and between the size and geographic extent of ASes. Our findings are consistent across the two datasets and both mapping methods. First, as expected, router density per person varies widely over different economic regions; however, in economically homogeneous regions, router density shows a strong superlinear relationship to population density. Second, the probability that two routers are directly connected is strongly dependent on distance; our data is consistent with a model in which a majority (up to 75-95%) of link formation is based on geographical distance (as in the Waxman topology generation method). Finally, we find that ASes show high variability in geographic size, which is correlated with other measures of AS size (degree and number of interfaces). Among small to medium ASes, ASes show wide variability in their geographic dispersal; however, all ASes exceeding a certain threshold in size are maximally dispersed geographically. These findings have many implications for the next generation of topology generators, which we envisage as producing router-level graphs annotated with attributes such as link latencies, AS identifiers and geographical locations.

Indexing Distances in Large Graphs and Applications in Search Tasks

This thesis elaborates on the problem of preprocessing a large graph so that single-pair shortest-path queries can be answered quickly at runtime. Computing shortest paths is a well studied problem, but exact algorithms do not scale well to real-world huge graphs in applications that require very short response time. The focus is on approximate methods for distance estimation, in particular in landmarks-based distance indexing. This approach involves choosing some nodes as landmarks and computing (offline), for each node in the graph its embedding, i.e., the vector of its distances from all the landmarks. At runtime, when the distance between a pair of nodes is queried, it can be quickly estimated by combining the embeddings of the two nodes. Choosing optimal landmarks is shown to be hard and thus heuristic solutions are employed. Given a budget of memory for the index, which translates directly into a budget of landmarks, different landmark selection strategies can yield dramatically different results in terms of accuracy. A number of simple methods that scale well to large graphs are therefore developed and experimentally compared. The simplest methods choose central nodes of the graph, while the more elaborate ones select central nodes that are also far away from one another. The efficiency of the techniques presented in this thesis is tested experimentally using five different real world graphs with millions of edges; for a given accuracy, they require as much as 250 times less space than the current approach which considers selecting landmarks at random. Finally, they are applied in two important problems arising naturally in large-scale graphs, namely social search and community detection.

Contemporary pilgrimage in Ireland: a cultural geographic perspective

Using the lenses of contemporary cultural geography, this research develops an understanding of pilgrimage as a relational and reciprocal process that co-produces self and world. Drawing on the phenomenology of Merleau-Ponty, I argue that through the performances and experiences of contemporary pilgrimage in Ireland, participants and locations emerge as pilgrims and pilgrimage places. This approach unites different strands of cultural geography, including the mobilities field, more-than representational concerns, discussions of embodiment and practice, emotional and affective geographies, and religious and spiritual geographies. I explore how pilgrimage is an active process in which self and world, belief and practice, and the numinous and material entwine and merge. An autoethnographic methodology is enacted as an embodied, intersubjective, and reflexive research approach that incorporates the motivations, experiences, and beliefs of research participants, alongside my own descriptions and reflections. The methodology is focused on encountering and documenting pilgrimage practices as they occur in place and relating these embodied spatial practices to the accounts of pilgrims. The insights generated by engagements with research participants and through my own pilgrimages, offer new appreciations of the enduring appeal of pilgrimage in Ireland as a religious-spiritual and cultural activity that allows people to express personal intentions, to develop their faith, and to seek numinous encounters. Through the pilgrimages at Lough Derg, Croagh Patrick, and three holy wells, I produce a layered account of the empirical circumstances of the practices. The presentation of these places and events is enhanced by the use of evocative images and audiovisual recordings. By centring my study on the practices and experiences of different pilgrimages in present-day Ireland, and critically deploying strands of cultural geography and pilgrimage studies, this research produces new qualitative understandings of pilgrimage and contributes to discussions concerned with the relationships between self and world.

Placement of Small Vertical Axis Wind Turbine to Maximize Power Generation Influenced by Architectural and Geographic Interfaces in Urban Areas

Current methods for large-scale wind collection are unviable in urban areas. In order to investigate the feasibility of generating power from winds in these environments, we sought to optimize placements of small vertical-axis wind turbines in areas of artificially-generated winds. We explored both vehicular transportation and architecture as sources of artificial wind, using a combination of anemometer arrays, global positioning system (GPS), and weather report data. We determined that transportation-generated winds were not significant enough for turbine implementation. In addition, safety and administrative concerns restricted the implementation of said wind turbines along roadways for transportation-generated wind collection. Wind measurements from our architecture collection were applied in models that can help predict other similar areas with artificial wind, as well as the optimal placement of a wind turbine in those areas.

Experimental study and theoretical analysis of signage legibility distances as a function of observation angle

Signage systems are widely used in buildings to provide information for wayfinding, thereby assisting in navigation during normal circulation of pedestrians and, more importantly, exiting information during emergencies. An important consideration in determining the effectiveness of signs is establishing the region from which the sign is visible to occupants, the so-called Visibility Catchment Area (VCA). This paper attempts to factor into the determination of the VCA of signs, the observation angle of the observer using both experimental and theoretical analysis.

Signage legibility distances as a function of observation angle

Signage systems are widely used in buildings to provide information for wayfinding, thereby assisting in navigation during normal circulation of pedestrians and, more importantly, exiting information during emergencies. An important consideration in determining the effectiveness of signs is establishing the region from which the sign is visible to occupants, the so-called visibility catchment area (VCA). This study attempts to factor into the determination of the VCA of signs, the observation angle of the observer. In building regulations, it is implicitly assumed that the VCA is independent of the observation angle. A theoretical model is developed to explain the relationship between the VCA and observation angle and experimental trials are performed in order to assess the validity of this model. The experimental findings demonstrate a consistency with the theoretical model. Given this result, the functionality of a comprehensive evacuation model is extended in accordance with the assumptions on which the theoretical model is based and is then demonstrated using several examples