Marine Life Research Tools & Methods

The Oceans / NEXT: Relevant Journals »

Studying life in the ocean involves many different tools and methods. Here we will attempt to describe many of the resources for further study or use.

Ocean Instruments (WHOI)

All about different ocean instruments, how they work, what they do and why they do it. Written and/or edited by experts in ocean science and engineering, in addition to links to glossaries and multimedia technologies including video streaming, audio packages, and searchable databases. The site is updated as new information arrives from contributing ocean scientists and engineers. Check it out: http://www.whoi.edu/science/instruments/

Relevant Journals - we have collected what we believe to be a full list of scientific journals that are relevant to the study of marine life. Each is briefly described and many require a subscription but abstracts are usually available (and searchable) and many offer the choice to buy single papers or review sample copies. We are convinced that most effective research is that which is done in a meta-context with all relevant issues and fields. Also, the chances to blend traditional field boundaries has never been more possible or necessary considering the state of worldwide marine ecosystems.

Reference Books - depending upon which branch of Marine Biology you study, reference books are still vital to most research efforts. We list the reference texts we use on our Amazon Book Shop but your local library and online book sources can also be very helpful.

Online Research Tools

In our research efforts involving both online and offline species data we have combined what we learn in the resulting pages of this site. There are a myriad of online databases and meta-searches and it can be quite overwhelming. This is one of the reasons we created this site, by combining all useful available information for each species (including the best photographs, video, etc.) on each species' home page we found that only then could we get a relatively complete picture of that species as is currently known. Each species has the following information available: taxonomic data (WoRMS, ITIS), photo/video/sound ID data, general physical attributes, unique characteristics, world range & habitat information (including direct access to Ocean Biogeographic Information System (OBIS) data), feeding and reproductive behavior, warnings and comments, IUCN RedList and CITES listing data, GBIF Global Biodiversity Data, SIRIS biblio search, Molecular/genetic data database searches, references, etc. Each species home page is also dynamic and new online resources are easily added as they arise and evolve. By combining the above as well as conservation information and resources, marine life news and our forums, we hope that one can get a complete sense of any completed marine species.

AlgaeBase - database listing species data on the world's algae.

ARKive - The ARKive Project is a gathering together the very best films and photographs of the world's species into one centralized digital library, to create a unique audio-visual record of life on Earth.

Articles@PubMed - PubMed Central is a digital archive of life sciences journal literature, developed and managed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine.

BioOne - bioscience research journals: "For its users—students, researchers, and unaffiliated individuals—BioOne provides a unique aggregation of high-impact bioscience research journals, featuring timely content on a wide-array of today's most pressing topics, including global warming, stem cell research, ecological and biodiversity conservation. Complementing this content is an agile new platform launched in January 2009 that allows for easy navigation to content both within and outside the BioOne aggregation, as well as researcher-designed toolbars with valuable title, article, and reference-linking tools."

BioResearch - offers free access to a searchable catalogue of quality reviewed Internet resources covering the biological and biomedical sciences; including genetics, biotechnology, virology, biochemistry and molecular biology.

BIOSIS:BioBrowser - produced by BIOSIS, is a free web site offering resources for the life sciences information community.

CITES-listed species database - CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) is an international agreement between Governments. Its aim is to ensure that international trade in specimens of wild animals and plants does not threaten their survival. Around 25,000 plant species and 5,000 animal species listed, in the following proportions: 1) Appendix I: about 600 animal species and 300 plant species; 2) Appendix II: about 1,400 animal species and 25,000 plant species; and 3) Appendix III: about 270 animal species and 30 plant species.

Crustacean Society - to advance the study of all aspects of the biology of the Crustacea by promoting the exchange and dissemination of information throughout the world.

Encyclopedia of Life - "Our knowledge of the many life-forms on Earth - of animals, plants, fungi, protists and bacteria - is scattered around the world in books, journals, databases, websites, specimen collections, and in the minds of people everywhere. Imagine what it would mean if this information could be gathered together and made available to everyone – anywhere – at a moment's notice. This dream is becoming a reality through the Encyclopedia of Life. Our Vision: Global access to knowledge about life on Earth. Our Mission: To increase awareness and understanding of living nature through an Encyclopedia of Life that gathers, generates, and shares knowledge in an open, freely accessible and trusted digital resource."

ESA Online Journals - Ecological Society of America Journals. ESA publishes a suite of publications, from peer-reviewed journals to newsletters, fact sheets and teaching resources.

FishBase - 32,200 Fish Species, 295,600 Common names, 51,100 Pictures, 45,500 References, 1,900 Collaborators.

GBIF - The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of 57 countries and 47 organizations, GBIF promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet.

Genome Browser (Ensembl) - Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes.

Global Invasive Species databse - The Global Invasive Species Database was developed by the IUCN/SSC Invasive Species Specialist Group (ISSG) as part of the global initiative on invasive species led by the Global Invasive Species Programme (GISP). It provides global information on invasive alien species to agencies, resource managers, decision-makers, and interested individuals. The database focuses on invasive species that threaten biodiversity and covers all taxonomic groups from micro-organisms to animals and plants. Species information is supplied by expert contributors from around the world and includes; species' biology, ecology, native and alien range, references, contacts, links and images.

Google Scholar - Google Scholar enables you to search specifically for scholarly literature, including peer-reviewed papers, theses, books, preprints, abstracts and technical reports from all broad areas of research. Use Google Scholar to find articles from a wide variety of academic publishers, professional societies, preprint repositories and universities, as well as scholarly articles available across the web.

Hexacorals - Biogeoinformatics of hexacorallia (corals, sea anemones, and their allies): interfacing geospatial, taxonomic, and environmental data for a group of marine invertebrates.

IOC OceanPortal - Ocean Portal is a high-level directory of Ocean Data and Information related web sites produced by the IOC/IODE Marine Data Training Team. Its objective is to help scientists and other ocean experts in locating such data & information.

IUCN Red List - The IUCN Red List of Threatened Species provides taxonomic, conservation status and distribution information on taxa that have been evaluated using the IUCN Red List Categories and Criteria. This system is designed to determine the relative risk of extinction, and the main purpose of the IUCN Red List is to catalogue and highlight those taxa that are facing a higher risk of global extinction (i.e. those listed as Critically Endangered, Endangered and Vulnerable). The IUCN Red List also includes information on taxa that are categorized as Extinct or Extinct in the Wild; on taxa that cannot be evaluated because of insufficient information (i.e. are Data Deficient); and on taxa that are either close to meeting the threatened thresholds or that would be threatened were it not for an ongoing taxon-specific conservation programme (i.e. Near Threatened).

Marine Genomics Project - the web-based interface to bioinformatics data management and data analysis tools. The site has been developed by the bioinformatics group at the DB2E dept. of the Medical University of South Carolina for the Marine Genomics Consortium at the Hollings Marine Lab in Charleston, SC. Both public and species-curators can browse all data within the Marine Genomics website. All species-specific data is accessible via the species links to the right of the page. Curators have permissions to curate and edit their species data, resume/CV information, publications they wish to make available on MG as well as addition/deletion of related projects that might have significance to the community.

Marine Species Identification Portal - The Marine Species Identification Portal is an initiative of ETI BioInformatics in the KeyToNature programme (a project in the EC e-contentPlus Programme). This website provides open access to scientific information on marine species including identification keys to support the scientific community in activities such bio-monitoring programs, and to provide students and other interested parties with general information on marine biodiversity. This portal unlocks information on 9900 marine species and 5553 higher taxa, most of which with a description and one or more illustrations. A total of 7941 taxa are keyed out in 52 identification keys. Furthermore, 18850 synonyms plus 2782 vernacular names in English and 8389 names in 25 other languages facilitate searching.

Molecular Biology - a comprehensive package for the hands-on teaching of Molecular Biology.

NCBI - National Center for Biotechnology Information: "As a national resource for molecular biology information, NCBI's mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules."

Ocean Biogeographic Information System (OBIS) - "OBIS is an evolving strategic alliance of people and organizations sharing a vision to make marine biogeographic data, from all over the world, freely available over the World Wide Web. OBIS is tailored towards global awareness of our oceans and global contribution to knowledge about our oceans. Thus, it is extremely important that OBIS maintains its status as an 'open-access' database. OBIS plans to make all tools on the website available for everyone to use: the database exclusively uses open source software, so all of the programming code is available to the public."

ReefBase - world's premier online information system on coral reefs, and provides information services to coral reef professionals involved in management, research, monitoring, conservation and education.

sciBASE - aggregates and integrates major bibliographic databases from third party publishers to give its subscribers convenient, digital access to the world's scientific information.

ScienceDirect - world's largest electronic collection of science, technology and medicine full text and bibliographic information.

SCIRIS - "the most comprehensive scientific research tool on the web. With over 440 million scientific items indexed at last count, it allows researchers to search for not only journal content but also scientists' homepages, courseware, pre-print server material, patents and institutional repository and website information."

Scripps Institution of Oceanography Library - databases, journals, resources and collections, etc. of the Scripps Institute of Oceanography.

Sea Slug Forum - everything you ever wanted to know about sea slugs (nudibranchs, bubble-shells, sea hares, and others) including behavior, anatomy, aquarium FAQs and associated marine animals and plants.

SIRIS - Smithsonian Institution Research Information System: "Search over 7.4 million records with 568,100 images, video and sound files, electronic journals and other resources from the Smithsonian's museums, archives & libraries."

SpringerLink - one of the world's leading online information services for scientific, technical, and medical (STM) books and journals. SpringerLink is a preferred data source for researchers in academic and corporate institutions and other vital knowledge centers.

Tree of Life Web Project - a collaborative effort of biologists from around the world. On more than 3000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics.

UCSB Resources - marine and aquatic science reference guide and resources at the University of California in Santa Barbara.

Undersea Research - NOAA's Undersea Research Center at UNCW.

USGS:MRIB - Marine Realms Information Bank; an online distributed digital geolibrary for the USGS Coastal and marine Geology Program.

Wikipedia - the online encyclopedia written collaboratively by contributors from around the world. The site is a wiki, which means that anyone can edit articles, simply by clicking on the edit this page link.

WoRMS - World Register of Marine Species: "The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them."

Zetoc - provides access to the British Library's Electronic Table of Contents of around 20,000 current journals and around 16,000 conference proceedings published per year. The database covers 1993 to date, and is updated on a daily basis.

We hope you find MarineBio as useful as we do and if you find we are missing useful online research tools, please let us know.

The Oceans / NEXT: Relevant Journals »

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Marine Biology News   :: ScienceDaily

Lessons in coral reef survival from deep time

Lessons from tens of millions of years ago are pointing to new ways to save and protect today's coral reefs and their myriad of beautiful and many-hued fishes at a time of huge change in the Earth's systems. Today's complex relationship between fishes and corals developed relatively recently in geological terms -- and is a major factor in shielding reef species from extinction, say experts.

Carbon dioxide is 'driving fish crazy'

Rising human carbon dioxide emissions may be affecting the brains and central nervous system of sea fishes with serious consequences for their survival, an international scientific team has found. Carbon dioxide concentrations predicted to occur in the ocean by the end of this century will interfere with fishes' ability to hear, smell, turn and evade predators, says a professor.

Multiple partners not the only way for corals to stay cool

For the first time scientists have shown that corals hosting a single type of zooxanthellae can have different levels of thermal tolerance -– a feature that was only known previously for corals with a mix of zooxanthellae. This finding is important because many species of coral are dominated by a single type of zooxanthellae.

Inventory lists 19,232 newly discovered species during latest count

More than half of the 19,232 species newly known to science in 2009, the most recent calendar year of compilation, were insects -- 9,738 or 50.6 percent -- according to the 2011 State of Observed Species.

Breakthrough model reveals evolution of ancient nervous systems through seashell colors

Determining the evolution of pigmentation patterns on mollusk seashells -- which could aid in the understanding of ancient nervous systems -- has proved to be a challenging feat for researchers. Now, however, through mathematical equations and simulations, researchers have used 19 different species of the predatory sea snail Conus to generate a model of the pigmentation patterns of mollusk shells.

Wandering albatross alters its foraging due to climate change

Wandering albatrosses have altered their foraging due to changes in wind fields in the southern hemisphere during the last decades. Since winds have increased in intensity and moved to the south, the flight speed of albatrosses increased and they spend less time foraging. As a consequence, breeding success has improved and birds have gained 1 kilogram.

Can we save the whales by putting a price on them?

Every year, anti-whaling groups spend millions of dollars on activities intended to end commercial whaling. And every year, commercial whaling not only continues, but grows. While protests, education, lobbying and dangerous confrontations on the high seas have saved some whales, the whaling industry shows no sign of shutting down -- or slowing down. Now, an economist and two marine scientists suggest a new strategy that they believe could save whales by putting a price on them.

Fish offspring grow best at same temperature as parents

Fish parents can pre-condition their offspring to grow fastest at the temperature they experienced, according to new research.

World's most extreme deep-sea vents revealed: Deeper than any seen before, and teeming with new creatures

Scientists have revealed details of the world's most extreme deep-sea volcanic vents, five kilometers down in a rift in the Caribbean seafloor. The undersea hot springs, which lie 0.8 kilometers deeper than any seen before, may be hotter than 450 °C and are shooting a jet of mineral-laden water more than a kilometer into the ocean above.

Bycatch-22: Protecting Butterfish

Scientists work to assist fishermen in ways to avoid accidentally hauling in butterfish, a species protected by fishing limits. The researchers develop models to predict where the fish will be.

Paddlefish sensors tuned to detect signals from zooplankton prey

Neurons fire in a synchronized bursting pattern in response to robust signals indicating nearby food.

Harp seals on thin ice after 32 years of warming

Warming in the North Atlantic over the last 32 years has significantly reduced winter sea ice cover in harp seal breeding grounds, resulting in sharply higher death rates among seal pups in recent years, according to a new study.

Fish mimics octopus that mimics fish

Nature's game of intimidation and imitation comes full circle in the waters of Indonesia, where scientists have recorded for the first time an association between the black-marble jawfish and the mimic octopus.

Salt water alone unlikely to halt Burmese python invasion

Invasive Burmese python hatchlings from the Florida Everglades can withstand exposure to salt water long enough to potentially expand their range through ocean and estuarine environments.

'Lost world' discovered around Antarctic vents

Communities of species previously unknown to science have been discovered on the seafloor near Antarctica, clustered in the hot, dark environment surrounding hydrothermal vents. The discoveries include new species of yeti crab, starfish, barnacles, sea anemones, and potentially an octopus.

Molecular mechanism links temperature with sex determination in some fish species

Researchers have found the epigenetic mechanism that links temperature and gonadal sex in fish. High temperature increases DNA methylation of the gonadal aromatase promoter in females.

Sunlight and bunker oil a fatal combination for Pacific herring

The 2007 Cosco Busan disaster, which spilled 54,000 gallons of oil into the San Francisco Bay, had an unexpectedly lethal impact on embryonic fish, devastating a commercially and ecologically important species for nearly two years, reports a new study.

Sea cucumbers: Dissolving coral reefs?

Coral reefs are extremely diverse ecosystems that support enormous biodiversity. But they are at risk. Carbon dioxide emissions are acidifying the ocean, threatening reefs and other marine organisms. New research analyzed the role of sea cucumbers in portions of the Great Barrier Reef and determined that their dietary process of dissolving calcium carbonate (CaCO3) from the surrounding reef accounts for about half of at the total nighttime dissolution for the reef.

Ocean acidification: Some organisms already experiencing ocean acidification levels not predicted to be reached until 2100

Ocean acidification research is a relatively new study topic as scientists have only appreciated the potential extent of acidification within the last decade. As greenhouse gas emissions have accelerated in the past century, the oceans have taken up about a third of the carbon dioxide produced by human activities. That excess beyond natural levels increases amounts of carbonic acid in seawater. New research shows that some organisms are already experiencing ocean acidification levels not predicted to be reached until 2100.

Belize protected area boosting predatory fish populations

A 14-year study in an atoll reef lagoon in Glover's Reef, Belize has found that fishing closures there produce encouraging increases in populations of predatory fish species. However, such closures have resulted in only minimal increases in herbivorous fish, which feed on the algae that smother corals and inhibit reef recovery.