It is clear that the above can lead to confusion when scientists of different countries are trying to communicate with each other. Another example is the burrowing rodent called a gopher found throughout the western United States. In the southeastern United States the term gopher refers to a burrowing turtle very similar to the desert tortoise found in the American southwest. One final example; two North American mammals known as the elk and the caribou are known in Europe as the reindeer and the elk. We never sing “Rudolph the Red-nosed elk”! Confused? This was the reason for creating an internationally recognized system of naming organisms. To avoid confusion, living organisms are assigned a scientific name based on Latin or Latinized words. The English sparrow is Passer domesticus or Passer domesticus (italics or underlining these two names is the official written representation of a scientific name). Using a uniform naming system allows scientists from all over the world to recognize exactly which life form a scientist is referring to. The naming process is called the binomial system of nomenclature. Passer is comparable to a surname and is called the genus, while domesticus is the specific or species name (like your given name) of the English sparrow. Now scientists can give all sparrow-like birds the genus Passer but the species name will vary. All similar genera (plural for genus) can be grouped into another, “higher” category (see below). Study the following for a more through understanding of taxonomy. Taxonomy Analogy Kingdom: Animalia Country

Diversity of life

Diel vertical migration (DVM) by zooplankton is a universal feature in all the World’s oceans, as well as being common in freshwater environments. The normal pattern involves movement from shallow depths at night to greater depths during the day. For many herbivorous and omnivorous mesozooplankton that feed predominantly near the surface on phytoplankton and microzooplankton, minimising the risk of predation from fish seems to be the ultimate factor behind DVM. These migrants appear to use deep water as a dark daytime refuge where their probability of being detected and eaten is lower than if they remained near the surface. Associated with these vertical movements of mesozooplankton, predators at higher trophic levels, including invertebrates, fish, marine mammals, birds and reptiles, may modify their behaviour to optimise the exploitation of their vertically migrating prey. Recent advances in biotelemetry promise to allow the interaction between migrating zooplankton and diving air-breathing vertebrates to be explored in far more detail than hitherto.

http://www.swansea.ac.uk/bs/turtle/reprints/hays_Hydrobiologia2003.pdf

A review of the adaptive significance and ecosystem consequences of zooplankton diel vertical migrations

. The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller – indeed, minimal – proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased productivity through specific physical processes, such as topographic modification of currents and enhanced transport of particles and detrital matter. Because of its unique abiotic attributes, the deep sea hosts a specialized fauna. Although there are no phyla unique to deep waters, at lower taxonomic levels the composition of the fauna is distinct from that found in the upper ocean. Amongst other characteristic patterns, deep-sea species may exhibit either gigantism or dwarfism, related to the decrease in food availability with depth. Food limitation on the seafloor and water column is also reflected in the trophic structure of heterotrophic deep-sea communities, which are adapted to low energy availability. In most of these heterotrophic habitats, the dominant megafauna is composed of detritivores, while filter feeders are abundant in habitats with hard substrata (e.g. mid-ocean ridges, seamounts, canyon walls and coral reefs). Chemoautotrophy through symbiotic relationships is dominant in reducing habitats. Deep-sea biodiversity is among of the highest on the planet, mainly composed of macro and meiofauna, with high evenness. This is true for most of the continental margins and abyssal plains with hot spots of diversity such as seamounts or cold-water corals. However, in some ecosystems with particularly "extreme" physicochemical processes (e.g. hydrothermal vents), biodiversity is low but abundance and biomass are high and the communities are dominated by a few species. Two large-scale diversity patterns have been discussed for deep-sea benthic communities. First, a unimodal relationship between diversity and depth is observed, with a peak at intermediate depths (2000–3000 m), although this is not universal and particular abiotic processes can modify the trend. Secondly, a poleward trend of decreasing diversity has been discussed, but this remains controversial and studies with larger and more robust data sets are needed. Because of the paucity in our knowledge of habitat coverage and species composition, biogeographic studies are mostly based on regional data or on specific taxonomic groups. Recently, global biogeographic provinces for the pelagic and benthic deep ocean have been described, using environmental and, where data were available, taxonomic information. This classification described 30 pelagic provinces and 38 benthic provinces divided into 4 depth ranges, as well as 10 hydrothermal vent provinces. One of the major issues faced by deep-sea biodiversity and biogeographical studies is related to the high number of species new to science that are collected regularly, together with the slow description rates for these new species. Taxonomic coordination at the global scale is particularly difficult, but is essential if we are to analyse large diversity and biogeographic trends. Because of their remoteness, anthropogenic impacts on deep-sea ecosystems have not been addressed very thoroughly until recently. The depletion of biological and mineral resources on land and in shallow waters, coupled with technological developments, are promoting the increased interest in services provided by deep-water resources. Although often largely unknown, evidence for the effects of human activities in deep-water ecosystems – such as deep-sea mining, hydrocarbon exploration and exploitation, fishing, dumping and littering – is already accumulating. Because of our limited knowledge of deep-sea biodiversity and ecosystem functioning and because of the specific life-history adaptations of many deep-sea species (e.g. slow growth and delayed maturity), it is essential that the scientific community works closely with industry, conservation organisations and policy makers to develop robust and efficient conservation and management options.

/pdf/deep-diverse-and-definitely-different-unique-attributes-of-30cfoyr2tg.pdf

Deep, diverse and definitely different: unique attributes of the world's largest ecosystem

Density-dependent processes such as growth, survival, reproduction and movement are compensatory if their rates change in response to variation in population density (or numbers) such that they result in a slowed population growth rate at high densities and promote a numerical increase of the population at low densities. Compensatory density dependence is important to fisheries management because it operates to offset the losses of individuals. While the concept of compensation is straightforward, it remains one of the most controversial issues in population dynamics. The difficulties arise when going from general concepts to specific populations. Compensation is usually quantified using some combination of spawner–recruit analysis, long-term field monitoring or manipulative studies, and computer modelling. Problems arise because there are limitations to each of these approaches, and these limitations generally originate from the high uncertainty associated with field measurements. We offer a hierarchical approach to predicting and understanding compensation that ranges from the very general, using basic life-history theory, to the highly site-specific, using detailed population models. We analyse a spawner–recruit database to test the predictions about compensation and compensatory reserve that derive from a three-endpoint life-history framework designed for fish. We then summarise field examples of density dependence in specific processes. Selected long-term field monitoring studies, manipulative studies and computer modelling examples are then highlighted that illustrate how density-dependent processes led to compensatory responses at the population level. Some theoretical and empirical advances that offer hope for progress in the future on the compensation issue are discussed. We advocate an approach to compensation that involves process-level understanding of the underlying mechanisms, life-history theory, careful analysis of field data, and matrix and individual-based modelling. There will always be debate if the quantification of compensation does not include some degree of understanding of the underlying mechanisms.

/pdf/compensatory-density-dependence-in-fish-populations-1bounl0hxh.pdf

Compensatory density dependence in fish populations: importance, controversy, understanding and prognosis

The marine ecosystem of the West Antarctic Peninsula (WAP) extends from the Bellingshausen Sea to the northern tip of the peninsula and from the mostly glaciated coast across the continental shelf to the shelf break in the west. The glacially sculpted coastline along the peninsula is highly convoluted and characterized by deep embayments that are often interconnected by channels that facilitate transport of heatandnutrientsintotheshelfdomain.Theecosystemisdividedintothreesubregions,thecontinental slope, shelf and coastal regions, each with unique ocean dynamics, water mass and biological distributions. The WAP shelf lies within the Antarctic Sea Ice Zone (SIZ) and like other SIZs, the WAP system is very productive, supporting large stocks of marine mammals, birds and the Antarctic krill, Euphausia superba.Ecosystemdynamicsisdominatedbytheseasonalandinterannualvariationinseaice extent and retreat. The Antarctic Peninsula is one among the most rapidly warming regions on Earth, having experienced a 28C increase in the annual mean temperature and a 68C rise in the mean winter temperature since 1950. Delivery of heat from the Antarctic Circumpolar Current has increased significantly in the past decade, sufficient to drive to a 0.68C warming of the upper 300 m of shelf water. In the past 50 years and continuing in the twenty-first century, the warm, moist maritime climate of the northern WAP has been migrating south, displacing the once dominant cold, dry continental Antarctic climate and causing multi-levelresponses inthe marine ecosystem. Ecosystem responses tothe regional warming include increased heat transport, decreased sea ice extent and duration, local declines in ice

/pdf/marine-pelagic-ecosystems-the-west-antarctic-peninsula-42mrovubq2.pdf

Marine pelagic ecosystems: the West Antarctic Peninsula

DNA sequences for a 639 bp region of mitochondrial cytochrome oxidase I (mtCOI) were determined for 34 species of ten genera in two families of calanoid copepods, including: Calanoides, Cosmocalanus, Meoscalanus, Nannocalanus, Neocalanus, and Undinula (family Calanidae); and Clausocalanus, Ctenocalanus, Drepanopus, and Pseudocalanus (family Clausocalanidae). MtCOI gene sequences proved to be diagnostic molecular systematic characters for accurate identification and discrimination of the species. Levels of mtCOI variation within species (range: 1–4%) were significantly less than those between species (9–25%). Higher levels of intraspecific variation (>2%) usually resulted from comparisons between ecologically distinct or geographically isolated populations. MtCOI sequence variation resolved evolutionary relationships among species of Clausocalanus, Neocalanus, and Pseudocalanus, although there was evidence of saturation at some variable sites. Phylogenetic relationships among 11 copepod genera (adding Calanus to the list above) were reconstructed using a 660 bp region of nuclear small-subunit 18S rRNA, a slowly evolving gene that showed no variability within a species and differed by <1–6% among the genera. The 18S rRNA molecular phylogeny was consistent with the accepted limits of the Calanidae and Clausocalanidae and clearly resolved relationships among genera within each family. This molecular systematic and phylogenetic study was part of the ZooGene project, an international partnership to create a DNA sequence database as a tool for uniform, molecularly based species identification of planktonic calanoid copepods and euphausiids.

Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae

High-frequency acoustic scattering techniques have been used to investigate dominant scatterers in mixed zooplankton populations. Volume backscattering was measured in the Gulf of Maine at 43, 120, 200, and 420 kHz. Zooplankton composition and size were determined using net and video sampling techniques, and water properties were determined using conductivity, temperature, and depth sensors. Dominant scatterers have been identified using recently developed scattering models for zooplankton and microstructure. Microstructure generally did not contribute to the scattering. At certain locations, gas-bearing zooplankton, that account for a small fraction of the total abundance and biomass, dominated the scattering at all frequencies. At these locations, acoustically inferred size agreed well with size determined from the net samples. Significant differences between the acoustic, net, and video estimates of abundance for these zooplankton are most likely due to limitations of the net and video techniques. No other type of biological scatterer ever dominated the scattering at all frequencies. Copepods, fluid-like zooplankton that account for most of the abundance and biomass, dominated at select locations only at the highest frequencies. At these locations, acoustically inferred abundance agreed well with net and video estimates. A general approach for the difficult problem of interpreting high-frequency acoustic scattering in mixed zooplankton populations is described.

/pdf/determining-dominant-scatterers-of-sound-in-mixed-twxl0nl0ie.pdf

Determining dominant scatterers of sound in mixed zooplankton populations

https://www.int-res.com/articles/meps/72/m072p079.pdf

Phenology in Calanus finmarchicus; hypotheses about control mechanisms

Species diversity of the metazoan holozooplankton assemblage of the Sargasso Sea, Northwest Atlantic Ocean, was examined through coordinated morphological taxonomic identification of species and DNA sequencing of a ∼650 base-pair region of mitochondrial cytochrome oxidase I (mtCOI) as a DNA barcode (i.e., short sequence for species recognition and discrimination). Zooplankton collections were made from the surface to 5,000 meters during April, 2006 on the R/V R.H. Brown. Samples were examined by a ship-board team of morphological taxonomists; DNA barcoding was carried out in both ship-board and land-based DNA sequencing laboratories. DNA barcodes were determined for a total of 297 individuals of 175 holozooplankton species in four phyla, including: Cnidaria (Hydromedusae, 4 species; Siphonophora, 47); Arthropoda (Amphipoda, 10; Copepoda, 34; Decapoda, 9; Euphausiacea, 10; Mysidacea, 1; Ostracoda, 27); and Mollusca (Cephalopoda, 8; Heteropoda, 6; Pteropoda, 15); and Chaetognatha (4). Thirty species of fish (Teleostei) were also barcoded. For all seven zooplankton groups for which sufficient data were available, Kimura-2-Parameter genetic distances were significantly lower between individuals of the same species (mean=0.0114; S.D. 0.0117) than between individuals of different species within the same group (mean=0.3166; S.D. 0.0378). This difference, known as the barcode gap, ensures that mtCOI sequences are reliable characters for species identification for the oceanic holozooplankton assemblage. In addition, DNA barcodes allow recognition of new or undescribed species, reveal cryptic species within known taxa, and inform phylogeographic and population genetic studies of geographic variation. The growing database of “gold standard” DNA barcodes serves as a Rosetta Stone for marine zooplankton, providing the key for decoding species diversity by linking species names, morphology, and DNA sequence variation. In light of the pivotal position of zooplankton in ocean food webs, their usefulness as rapid responders to environmental change, and the increasing scarcity of taxonomists, the use of DNA barcodes is an important and useful approach for rapid analysis of species diversity and distribution in the pelagic community.

A “Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)

Many species of euphausiids (Euphausiacea, Crustacea) are distinguished by subtle or geographically variable morphological characters, and erroneous identification of euphausiid species may be more frequent than currently acknowledged. DNA barcodes (short DNA sequences that discriminate species and aid in recognition of unknown species) are of use for this group. A � 650 bp region of mitochondrial cytochrome oxidase I (mtCOI) was sequenced for 40 species of 10 euphausiid genera: Bentheuphausia, Euphausia, Meganyctiphanes, Nematobrachion, Nematoscelis, Nyctiphanes, Stylocheiron, Tessarabrachion, Thyssanoessa and Thysanopoda. mtCOI sequence variation discriminated all species; pairwise differences averaged 16.4% (range 7‐24%); mean generalized time reversible (GTR) genetic distance was 26.7%. mtCOI reliably identified euphausiid species: variation within species was typically ,1% and GTR distance was typically ,2%. Atlantic and Pacific Ocean populations of Euphausia brevis differed by 13% (GTR genetic distance ¼ 28%) and may deserve status as distinct species. mtCOI gene trees were reconstructed for five genera using maximum parsimony, maximum likelihood and Bayesian algorithms; best-fit models of nucleotide evolution were determined for each genus. The mtCOI gene tree for 20 species of Euphausia reproduced one of three morphologically defined species groups. mtCOI resolved relationships among closely related species of most genera, usually in accord with morphological groupings. A comprehensive DNA barcode database for euphausiids will help ensure accurate species identification, recognition of cryptic species and evaluation of taxonomically meaningful geographic variation.

Nancy J. Copley

Papers

Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae

Determining dominant scatterers of sound in mixed zooplankton populations

Phenology in Calanus finmarchicus; hypotheses about control mechanisms

A “Rosetta Stone” for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)

DNA barcodes for species identification of euphausiids (Euphausiacea, Crustacea)