Filogeografia e evolução molecular de lagostas sapateiras (Scyllarides spp.) da América do Sul

Nos últimos anos, duas espécies de lagostas sapateiras, Scyllarides brasiliensis e S. deceptor, vêm se destacando nos desembarques pesqueiros de lagostas do Atlântico Sul Ocidental. Para espécies comercialmente importantes, o desenvolvimento de estudos que permitam conhecer a variabilidade e entender a dinâmica populacional é fundamental. Assim, o objetivo do primeiro capítulo desta tese foi avaliar a diversidade genética e a estrutura populacional dessas duas lagostas ao longo de aprox. 2.800 km da costa da América do Sul. Para as análises, foram empregados marcadores mitocondriais (citocromo oxidase I: COI; e a região controle: RC) e marcadores nucleares (13 loci de microssatélites desenvolvidos nesta tese). As duas espécies apresentaram altos níveis de variabilidade (S. deceptor: N = 200, mtDNA: h > 0,841, π > 0,005; microssatélites: He = 0,685; S. brasiliensis: N = 211, He = 0,554), distribuídos homogeneamente entre as localidades (S. deceptor: ΦST < -0,004, ΦCT < 0,016, FST global = 0,001, Dest global = 0,003, FCT < 0,002, P > 0,05, K = 1; S. brasiliensis: FST global = 0,004, Dest global = 0,001, FCT < 0,004, P > 0,05, K = 1). A ausência de estruturação nas duas espécies pode estar relacionada a características biológicas que promovem a conectividade entre localidades geograficamente distantes, como alta fecundidade e alto potencial de dispersão das larvas planctônicas. Além disso, os dados mitocondriais sugerem que a história demográfica de S. deceptor foi marcada por eventos de expansão populacionais e geográficos possivelmente relacionados às condições ambientais favoráveis dos episódios interglaciais do Pleistoceno Médio-Tardio. Diversos estudos têm mostrado que os fenômenos de inserção de regiões mitocondriais no DNA nuclear (NuMts) e heteroplasmia limitam a correta amplificação e identificação dos marcadores mitocondriais. Em estudos filogenéticos e de genética de populações, a presença inadvertida de sequências de diversas origens viola o principio de ortologia, o que pode resultar em inferências evolutivas erradas. Assim, o objetivo do segundo capítulo desta tese foi identificar e caracterizar os possíveis NuMts e sequências heteroplásmicas de três regiões mitocondriais (COI, RC e o gene da subunidade maior do RNA ribossomal: 16S) em quatro espécies do gênero Scyllarides (S. aequinoctialis, S. brasiliensis, S. deceptor e S. delfosi). A clonagem e sequenciamento de extratos de DNA genômico e DNA enriquecido com mtDNA revelaram que os genomas destas espécies podem exibir NuMts (que divergem entre 0,6 e 17,6% do mtDNA) e heteroplasmia (que divergem < 0,2% do mtDNA prevalente). Os NuMts surgiram possivelmente de vários eventos independentes de integração ao núcleo ao longo da história evolutiva do gênero Scyllarides. Dependendo do seu grau de similaridade com o mtDNA, a presença de NuMts nas análises filogenéticas no nível de gênero pode causar superestimativa do número de espécies e alterações nos comprimentos dos ramos e nas relações filogenéticas entre espécies.

Paleoenvironmental records from the Quelccaya ice cap, Peru and preliminary results from the Dunde ice cap, China [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): The 1000 year records of particulate deposition (soluble and insoluble), oxygen isotopic ratios, and net accumulation from the Quelccaya ice cap are presented. The net accumulation record from Quelccaya is shown to serve as a reasonable proxy for the water levels in Lake Titicaca. ... The ice core record from the Dunde ice cap offers the potential to reconstruct a very detailed history of environmental conditions on the Tibetan Plateau for the last 3000 years.

Protocols for conducting dolphin capture-release health assessment studies

Marine mammals, such as dolphins, can serve as key indicator species in coastal areas by reflecting the effects of natural and anthropogenic stressors. As such they are often considered sentinels of environmental and ecosystem health (Bossart 2006; Wells et al. 2004; Fair and Becker 2000). The bottlenose dolphin is an apex predator and a key component of many estuarine environments in the southeastern United States (Woodward-Clyde Consultants 1994; SCDNR 2005). Health assessments of dolphins are especially critical in areas where populations are depleted, show signs of epidemic disease and/or high mortality and/or where habitat is being altered or impacted by human activities. Recent assessments of environmental conditions in the Indian River Lagoon, Florida (IRL) and the estuarine waters surrounding Charleston, South Carolina (CHS) highlight the need for studies of the health of local bottlenose dolphins. While the condition of southeastern estuaries was rated as fair in the National Coastal Condition Report (U.S. EPA 2001), it was noted that the IRL was characterized by poorer than expected benthic communities, significant sediment toxicity and increased nutrient concentrations. Similarly, portions of the CHS estuary have sediment concentrations of aliphatic aromatic hydrocarbons, select inorganic metals, and some persistent pesticides far in excess of reported bioeffect levels (Hyland et al. 1998). Long-term trends in water quality monitoring and recent scientific research suggest that waste load assimilation, non-point source runoff impacts, contaminated sediments, and toxic pollutants are key issues in the CHS estuary system. Several ‘hot spots’ with high levels of heavy metals and organic compounds have been identified (Van Dolah et al. 2004). High concentrations of anthropogenic trace metals, polychlorinated biphenyls (PCB’s) and pesticides have been found in the sediments of Charleston Harbor, as well as the Ashley and Cooper Rivers (Long et al. 1998). Two superfund sites are located within the CHS estuary and the key contaminants of concern associated with these sites are: polycyclic aromatic hydrocarbons (PAH), lead, chromium, copper, arsenic, zinc and dioxin. Concerns related to the overall health of IRL dolphins and dermatologic disease observed in many dolphins in the area (Bossart et al. 2003) initiated an investigation of potential factors which may have impacted dolphin health. From May-August 2001, 35 bottlenose dolphins died in the IRL during an unusual mortality event (MMC 2003). Many of these dolphins were diagnosed with a variety of skin lesions including proliferative ulcerative dermatitis due to protozoa and fungi, dolphin pox and a vesicular dermatopathy of unknown etiology (Bossart et al. 2003). Multiple species from fish to dolphins in the IRL system have exhibited skin lesions of various known and unknown etiologies (Kane et al. 2000; Bossart et al. 2003; Reif et al. 2006). On-going photo-identification (photo-ID) studies have documented skin diseases in IRL dolphins (Mazzoil et al. 2005). In addition, up to 70% of green sea turtles in the IRL exhibit fibropapillomas, with the highest rates of occurrence being seen in turtles from the southern IRL (Hirama 2001).

Change in Pacific Northwest coastal ecosystems. Proceedings of the Pacific Northwest Coastal Ecosystems Regional Study Workshop, August 73-14, 1996, Troutdale, Oregon

Over the past one hundred and fifty years, the landscape and ecosystems of the Pacific Northwest coastal region, already subject to many variable natural forces, have been profoundly affected by human activities. In virtually every coastal watershed from the Strait of Juan de Fuca to Cape Mendocino, settlement, exploitation and development of resou?-ces have altered natural ecosystems. Vast, complex forests that once covered the region have been largely replaced by tree plantations or converted to non-forest conditions. Narrow coastal valleys, once filled with wetlands and braided streams that tempered storm runoff and provided salmon habitat, were drained, filled, or have otherwise been altered to create land for agriculture and other uses. Tideflats and saltmarshes in both large and small estuaries were filled for industrial, commercial, and other urban uses. Many estuaries, including that of the Columbia River, have been channeled, deepened, and jettied to provide for safe, reliable navigation. The prodigious rainfall in the region, once buffered by dense vegetation and complex river and stream habitat, now surges down sirfiplified stream channels laden with increased burdens of sediment and debris. Although these and many other changes have occurred incrementally over time and in widely separated areas, their sum can now be seen to have significantly affected the natural productivity of the region and, as a consequence, changed the economic structure of its human communities. This activity has taken place in a region already shaped by many interacting and dynamic natural forces. Large-scale ocean circulation patterns, which vary over long time periods, determine the strength and location of currents along the coast, and thus affect conditions in the nearshore ocean and estuaries throughout the region. Periodic seasonal differences in the weather and ocean act on shorter time scales; winters are typically wet with storms from the southwest while summers tend to be dry with winds from the northwest. Some phenomena are episodic, such as El Nifio events, which alter weather, marine habitats, and the distribution and survival of marine organisms. Other oceanic and atmospheric changes operate more slowly; over time scales of decades, centuries, and longer. Episodic geologic events also punctuate the region, such as volcanic eruptions that discharge widespread blankets of ash, frequent minor earthquakes, and major subduction zone earthquakes each 300 to 500 years that release accumulated tectonic strain, dropping stretches of ocean shoreline, inundating estuaries and coastal valleys, and triggering landslides that reshape stream profiles. While these many natural processes have altered, sometimes dramatically, the Pacific Northwest coastal region, these same processes have formed productive marine and coastal ecosystems, and many of the species in these systems have adapted to the variable environmental conditions of the region to ensure their long-term survival.

Baseline assessment of Guánica Bay, Puerto Rico in support of watershed restoration

Guánica Bay is a major estuary on the southwest coast of Puerto Rico. Significant coral reef ecosystems are present outside the bay. These valuable habitats may be impacted by transport of sediments, nutrients and contaminants from the watershed, through the bay and into the offshore waters. The National Oceanic and Atmospheric Administration’s (NOAA) National Centers for Coastal Ocean Science (NCCOS), in consultation with local and regional experts, conducted an interdisciplinary assessment of coral reef ecosystems, contaminants, sedimentation rates and nutrient distribution patterns in and around Guánica Bay. This work was conducted using many of the same protocols as ongoing monitoring work underway elsewhere in the U.S. Caribbean and has enabled comparisons among coral reef ecosystems between this study and other locations in the region. This characterization of Guánica marine ecosystems establishes benchmark conditions that can be used for comparative documentation of future change, including possible negative outcomes due to future land use change, or improvement in environmental conditions arising from management actions. This report is organized into six chapters that represent a suite of interrelated studies. Chapter 1 provides a short introduction to the study area. Chapter 2 is focused on biogeographic assessments and benthic mapping of the study area, including new surveys of fish, marine debris and reef communities on hardbottom habitats in the study area. Chapter 3 quantifies the distribution and magnitude of a suite of contaminants (e.g., heavy metals, PAHs, PCBs, pesticides) in both surface sediments and coral tissues. Chapter 4 presents results of sedimentation measurements in and outside of the bay. Chapter 5 examines the distribution of nutrients in in the bay, offshore from the bay and in the watershed. Chapter 6 is a brief summary discussion that highlights key findings of the entire suite of studies.

Synthesis of marine ecosystem monitoring activities for the United States Virgin Islands: 1990-2009

The ecological integrity of coral reef ecosystems in the U.S. Caribbean is widely considered to have deteriorated in the last three decades due to a range of threats and stressors from both human and non-human processes Rothenberger 2008, Wilkinson 2008). In response to the threats to Caribbean coral reef ecosystems and other regions around the world, the United States Government authorized the Coral Reef Conservation Act of 2000 to: (1) preserve, sustain, and restore the condition of coral reef ecosystems; (2) promote the wise management and sustainable use of coral reef ecosystems to benefit local communities and the Nation; and (3) develop sound scientific information on the condition of coral reef ecosystems and the threats to such ecosystems. The Act also resulted in the formation of a National Coral Reef Action Strategy and a Coral Reef Conservation Program. The Action Strategy (Goal 2 of Action Theme 1) outlined the importance of monitoring and assessing coral reef health as a mechanism toward reducing many threats to these ecosystems. Monitoring was considered of high importance in addressing impacts from climate change; disease; overfishing; destructive fishing practices; habitat destruction; invasive species; coastal development; coastal pollution; sedimentation/runoff and overuse from tourism. The strategy states that successful coral reef ecosystem conservation requires adaptive management that responds quickly to changing environmental conditions. This, in turn, depends on monitoring programs that track trends in coral reef ecosystem health and reveal patterns in their condition before irreparable harm occurs. As such, monitoring plays a vital role in guiding and supporting the establishment of complex or potentially controversial management strategies such as no-take ecological reserves, fishing gear restrictions, or habitat restoration, by documenting the impacts of gaps in existing management schemes and illustrating the effectiveness of new measures over time. Long-term monitoring is also required to determine the effectiveness of various management strategies to conserve and enhance coral reef ecosystems.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

Threatened corals provide underexplored microbial habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

Physiological ecology of juvenile chinook salmon (Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary and Gulf of the Farallones, California

Juvenile chinook salmon, Oncorhynchus tshawytscha, from natal streams in California’s Central Valley demonstrated little estuarine dependency but grew rapidly once in coastal waters. We collected juvenile chinook salmon at locations spanning the San Francisco Estuary from the western side of the freshwater delta—at the confluence of the Sacramento and San Joaquin Rivers—to the estuary exit at the Golden Gate and in the coastal waters of the Gulf of the Farallones. Juveniles spent about 40 d migrating through the estuary at an estimated rate of 1.6 km/d or faster during their migration season (May and June 1997) toward the ocean. Mean growth in length (0.18 mm/d) and weight (0.02 g/d) was insignificant in young chinook salmon while in the estuary, but estimated daily growth of 0.6 mm/d and 0.5 g/d in the ocean was rapid (P≤0.001). Condition (K factor) declined in the estuary, but improved markedly in ocean fish. Total body protein, total lipid, triacylglycerols (TAG), polar lipids, cholesterol, and nonesterified fatty acids concentrations did not change in juveniles in the estuary, but total lipid and TAG were depleted in ocean juveniles. As young chinook migrated from freshwater to the ocean, their prey changed progressively in importance from invertebrates to fish larvae. Once in coastal waters, juvenile salmon appear to employ a strategy of rapid growth at the expense of energy reserves to increase survival potential. In 1997, environmental conditions did not impede development: freshwater discharge was above average and water temperatures were only slightly elevated, within the species’ tolerance. Data suggest that chinook salmon from California’s Central Valley have evolved a strong ecological propensity for a ocean-type life history. But unlike populations in the Pacific Northwest, they show little estuarine dependency and proceed to the ocean to benefit from the upwelling-driven, biologically productive coastal waters.

Current velocity and catch efficiency in sampling settlement-stage larvae of coral-reef fishes

Light traps and channel nets are fixed-position devices that involve active and passive sampling, respectively, in the collection of settlement-stage larvae of coral-reef fishes. We compared the abundance, taxonomic composition, and size of such larvae caught by each device deployed simultaneously near two sites that differed substantially in current velocity. Light traps were more selective taxonomically, and the two sampling devices differed significantly in the abundance but not size of taxa caught. Most importantly, light traps and channel nets differed greatly in their catch efficiency between sites: light traps were ineffective in collecting larvae at the relatively high-current site, and channel nets were less efficient in collecting larvae at the low-current site. Use of only one of these sampling methods would clearly result in biased and inaccurate estimates of the spatial variation in larval abundance among locations that differ in current velocity. When selecting a larval sampling device, one must consider not only how well a particular taxon may be represented, but also the environmental conditions under which the device will be deployed.

The activity pattern of Tegula funebralis

The activity pattern of the black turban snail, Tegula funebralis (A. Adams, 1854) at Pacific Grove, California, is the subject of this article. Field studies were carried out to follow the locomotory and feeding activities of individuals of T. funebralis, to determine how much of each animal's time was spent in each of these activities, and when and under what environmental conditions they occurred.

Reconstruction of aridity for the Sierra de la Laguna, Baja California Sur, Mexico

A well-documented history of past climatic conditions is needed to understand and resolve some ecological problems, but the existing climatological records are too short to detect long-term climatic variability and changes. Some trees, such as pines, produce annual tree rings with different widths depending on prevailing environmental conditions, such as climate. Tree-ring analysis of long-lived trees can be used to estimate past variations in climate. The principal aim of this study is to reconstruct aridity for the southern portion of the Baja California Peninsula, by means of dendroclimatologic techniques.

The influence of climate on phytoplankton communities in the upper San Francisco estuary

EXTRACT (SEE PDF FOR FULL ABSTRACT): The 1977 climate shift was characterized by low chlorophyll a concentrations and a shift in phytoplankton community composition throughout the upper San Francisco Bay estuary. ... For climate to be a driving force in phytoplankton communities, it must affect mechanisms that control biomass and community composition. The influence of climate on environmental conditions and phytoplankton community composition among water-year types was examined using 19 years of physical, chemical, and phytoplankton data collected monthly at 15 stations throughout the estuary.

A comparative study on the hatching of common carp eggs in hapa and hatchery (model CIFE D-80)

Common carp (Cyprinus carpio) eggs were incubated to study the efficiency of hatching in hapa and hatchery. During incubation the recorded temperature was 21-28 degree C and 20-31 degree C, dissolved oxygen 6-9 ppm. and 3-5 ppm., total alkalinity 180-250 ppm. and 28-62 ppm. respectively in the hatchery (model C.I.F.E. D-80) and hapa. CO sub(2) was totally absent in the hatchery, but recorded 3-10 ppm. in the hapa. The flow of water was maintained at 1.25 l/minute/jar in the hatchery. Under the above environmental conditions the eggs hatched in 42-51 hrs. in the hatchery and 61-81 hrs. in the hapa from egg to spawn thereby establishing the hatchery to be a better hatching system for carp eggs.

Variability in the distribution of planktonic fish eggs and larvae in the nearshore waters off Bombay

Distribution of planktonic fish eggs and larvae in the nearshore waters off Bombay was studied during November 1979 to December 1980. Monthly samples were collected along three transects (Versova, Mahim and Thana) covering eleven stations which represented different environmental conditions. Fish eggs and larvae were common in the area of study with maximum abundance in December 1979 and April/August 1980. Mean density of fish eggs was maximum along the Mahim transect while population of larvae was more in the Versova transect. Total number of families of fish larvae represented in the collections increased from nearshore to offshore area.