Friday, May 24, 2013

DNA Barcoding for Undergrads

a guest post by Ralph Imondi


A statewide alliance of California colleges will enlist the participation of undergraduate students in building the global DNA barcode library

Ventura-based Coastal Marine Biolabs (CMB) recently partnered with California State University Channel Islands (CSUCI; Camarillo, CA) and the North Valley Biotechnology Center of American River College (NVBC; Sacramento, CA) to assemble a consortium of 10 California colleges that will adopt DNA barcoding as an embedded research component of undergraduate biology courses. 

This new effort represents an undergraduate extension of the NSF-funded Barcoding Life’sMatrix program – a research education project that engages a national network of high schools in building the DNA Barcode reference library.  Although the project was originally established by CMB as a discovery science-based model to enhance teaching and learning in high school settings, it has attracted widespread interest from college faculty who seek new opportunities to bridge research and undergraduate science education through student participation in iBOL. The assembly and submission of validated reference barcode records by undergraduates will be aided by BOLD-SDP, the customized student interface to the Barcode of Life Data Systems that was formally launched in spring 2013

Beginning in fall 2013, faculty from Mira Costa College (San Diego), Orange Coast College (Costa Mesa), Mt. San Jacinto College (Menifee), Fullerton College (Fullerton), Los Angeles Valley College (Valley Glen), Southwest College of Los Angeles (Los Angeles), Oxnard College (Oxnard), Ventura College (Ventura), Santa Barbara CityCollege (Santa Barbara), and Ohlone College (Fremont) will integrate the barcoding project into various upper- and lower-level biology courses.  


This pilot effort is supported by the U.S. Department of Education, and by a CA state grant. 


grant details: [Achieving a Collaborative College Education through STEM Opportunities (Project ACCESO), Title V, Hispanic-Serving Institutions STEM Grant] to CSUCI, and [California Community Colleges Economic and Workforce Development: Applied Biotechnologies (12-317-038)] to NVBC. 
 


Thursday, May 23, 2013

Top 10 New Species 2012

A global committee of taxonomists announced its list of top 10 species from 2012 today. Each year, the International Institute for Species Exploration (IISE) at Arizona State University international committee of taxon experts evaluates the hundreds of new species that have been nominated by the public, IISE staff, scientists, scientific journal editors and by the committee members themselves. 

And here we go - the top 10 with short descriptions by the IISE:

Lilliputian Violet
Viola lilliputana
Country: Peru
Tiny violet: Not only is the Lilliputian violet among the smallest violets in the world, it is also one of the most diminutive terrestrial dicots. Known only from a single locality in an Intermontane Plateau of the high Andes of Peru, Viola lilliputana lives in the dry puna grassland eco-region. Specimens were first collected in the 1960s, but the species was not described as a new until 2012. The entire above ground portion of the plant is barely 1 centimeter tall. Named, obviously, for the race of little people on the island of Lilliput in Jonathan Swift’s Gulliver’s Travels.

Lyre Sponge
Chondrocladia lyra
Country: NE Pacific Ocean; USA: California
Carnivorous sponge: A spectacular, large, harp- or lyre-shaped carnivorous sponge discovered in deep water (averaging 3,399 meters) from the northeast Pacific Ocean off the coast of California. The harp-shaped structures or vanes number from two to six and each has more than 20 parallel vertical branches, often capped by an expanded, balloon-like, terminal ball. This unusual form maximizes the surface area of the sponge for contact and capture of planktonic prey.

Lesula Monkey
Cercopithecus lomamiensis
Country: Democratic Republic of the Congo
Old World monkey: Discovered in the Lomami Basin of the Democratic Republic of the Congo, the lesula is an Old World monkey well known to locals but newly known to science. This is only the second species of monkey discovered in Africa in the past 28 years. Scientists first saw the monkey as a captive juvenile in 2007. Researchers describe the shy lesula as having human-like eyes. More easily heard than seen, the monkeys perform a booming dawn chorus. Adult males have a large, bare patch of skin on the buttocks, testicles and perineum that is colored a brilliant blue. Although the forests where the monkeys live are remote, the species is hunted for bush meat and its status is vulnerable.

No to the Mine! Snake
Sibon noalamina
Country: Panama
Snail-eating snake: A beautiful new species of snail-eating snake has been discovered in the highland rainforests of western Panama. The snake is nocturnal and hunts soft-bodied prey including earthworms and amphibian eggs, in addition to snails and slugs. This harmless snake defends itself by mimicking the alternating dark and light rings of venomous coral snakes. The species is found in the SerranĂ­a de TabasarĂ¡ mountain range where ore mining is degrading and diminishing its habitat. The species name is derived from the Spanish phrase “No a la mina” or “No to the mine.”

A Smudge on Paleolithic Art
Ochroconis anomala
Country: France
Fungus: In 2001, black stains began to appear on the walls of Lascaux Cave in France. By 2007, the stains were so prevalent they became a major concern for the conservation of precious rock art at the site that dates back to the Upper Paleolithic. An outbreak of a white fungus, Fusarium solani, had been successfully treated when just a few months later, black staining fungi appeared. The genus primarily includes fungi that occur in the soil and are associated with the decomposition of plant matter. As far as scientists know, this fungus, one of two new species of the genus from Lascaux, is harmless. However, at least one species of the group, O. gallopava, causes disease in humans who have compromised immune systems.

World’s Smallest Vertebrate
Paedophryne amanuensis
Country: New Guinea
Tiny frog: Living vertebrates — animals that have a backbone or spinal column — range in size from this tiny new species of frog, as small as 7 millimeters, to the blue whale, measuring 25.8 meters. The new frog was discovered near Amau village in Papua, New Guinea. It captures the title of ‘smallest living vertebrate’ from a tiny Southeast Asian cyprinid fish that claimed the record in 2006. The adult frog size, determined by averaging the lengths of both males and females, is only 7.7 millimeters. With few exceptions, this and other ultra-small frogs are associated with moist leaf litter in tropical wet forests — suggesting a unique ecological guild that could not exist under drier circumstances.

Endangered Forest
Eugenia petrikensis
Country: Madagascar
Endangered shrub: Eugenia is a large, worldwide genus of woody evergreen trees and shrubs of the myrtle family that is particularly diverse in South America, New Caledonia and Madagascar. The new species E. petrikensis is a shrub growing to two meters with emerald green, slightly glossy foliage and beautiful, dense clusters of small magenta flowers. It is one of seven new species described from the littoral forest of eastern Madagascar and is considered to be an endangered species. It is the latest evidence of the unique and numerous species found in this specialized, humid forest that grows on sandy substrate within kilometers of the shoreline. Once forming a continuous band 1,600 kilometers long, the littoral forest has been reduced to isolated, vestigial fragments under pressure from human populations.

Lightning Roaches?
Lucihormetica luckae
Country: Ecuador
Glow-in-the-dark cockroach: Luminescence among terrestrial animals is rather rare and best known among several groups of beetles — fireflies and certain click beetles in particular — as well as cave-inhabiting fungus gnats. Since the first discovery of a luminescent cockroach in 1999, more than a dozen species have (pardon the pun) “come to light.” All are rare, and interestingly, so far found only in remote areas far from light pollution. The latest addition to this growing list is L. luckae that may be endangered or possibly already extinct. This cockroach is known from a single specimen collected 70 years ago from an area heavily impacted by the eruption of the Tungurahua volcano. The species may be most remarkable because the size and placement of its lamps suggest that it is using light to mimic toxic luminescent click beetles.

No Social Butterfly
Semachrysa jade
Country: Malaysia
Social media lacewing: In a trend-setting collision of science and social media, Hock Ping Guek photographed a beautiful green lacewing with dark markings at the base of its wings in a park near Kuala Lumpur and shared his photo on Flickr. Shaun Winterton, an entomologist with the California Department of Food and Agriculture, serendipitously saw the image and recognized the insect as unusual. When Guek was able to collect a specimen, it was sent to Stephen Brooks at London’s Natural History Museum who confirmed its new species status. The three joined forces and prepared a description using Google Docs. In this triumph for citizen science, talents from around the globe collaborated by using new media in making the discovery. The lacewing is not named for its color — rather for Winterton’s daughter, Jade.

Hanging Around in the Jurassic
Juracimbrophlebia ginkgofolia
Country: China
Hangingfly fossil: Living species of hangingflies can be found, as the name suggests, hanging beneath foliage where they capture other insects as food. They are a lineage of scorpionflies characterized by their skinny bodies, two pairs of narrow wings, and long threadlike legs. A new fossil species, Juracimbrophlebia ginkgofolia, has been found along with preserved leaves of a gingko-like tree, Yimaia capituliformis, in Middle Jurassic deposits in the Jiulongshan Formation in China’s Inner Mongolia. The two look so similar that they are easily confused in the field and represent a rare example of an insect mimicking a gymnosperm 165 million years ago, before an explosive radiation of flowering plants.

Wednesday, May 22, 2013

International Day for Biological Diversity

In 1993 the United Nations proclaimed May 22 the International Day for Biological Diversity (IDB) to increase understanding and awareness of biodiversity issues. The aim of the day is to promote the need for  preservation of our planet, and in this context to make sure that the biodiversity that populates it remains just that, diverse.

The loss of too many species potentially destroys the fragile system that keeps our planet healthy and functional. That's why the Convention on Biological Diversity was created as an internationally legally binding treaty. The three main goals of the Convention are: 
  • conservation of biological diversity, 
  • sustainable use of its components and , 
  • fair and equitable sharing of benefits arising from genetic resources.


This years theme for the IDB is Water and Biodiversity which was chosen to coincide with the United Nations designation of 2013 as the International Year of Water Cooperation:

Water sustains all life on Earth. It is vital for all people and ultimately determines our way of life. Providing and sustaining water for the needs of people around the world is already well recognized as a major challenge for sustainable development in most areas in both developed and developing countries. The ecosystems of our world, but particularly forests and wetlands, ensure that clean water is available to human communities. Water in turn underpins all ecosystem services. 

Wetlands can help reduce risks from flooding. Restoring soils can reduce erosion and pollution and can increase water available for crops. Protected areas can assist in providing water to cities. These are but a few examples of how ecosystem management can help us solve water-related problems.

Education and public awareness represent a substantial part of the Convention and events such as Biodiversity Day, awareness of global issues and concerns can be raised. It is a good opportunity to educate the general public on things that can be done to rectify or reduce these issues. If you want to know what is going on in your country on this day have a look at this page.



Tuesday, May 21, 2013

The away-field advantage



Few species reside solely in the location where they originated. In fact, the migration of species is a predominant feature of life on Earth. Species expand, contract and shift their geographical distributions constantly. It is our perception of these ecosystems and the boundaries in time and space that we draw around them that makes us discriminate between native and non-native species - a fully arbitrary process. Nevertheless, we have become very concerned about recent species invasions mainly because of the tremendous damage some non-native species can cause to ecological systems, our health, and our economy.

Although many species have been introduced outside of their home ranges, relatively few introduced species become abundant and widespread in the new ranges. Identifying the mechanisms driving profound invasions when they do occur is the focus of a large body of research in invasion biology. It has long been assumed the worst invasive species have an "away-field advantage." meaning they succeed because they do better in their new territories than they do at home. They escape their natural enemies, use novel weapons and defense mechanisms on unsuspecting  natives and generally outcompete local flora and fauna by disrupting the balance of the existing ecosystem.

Now a new study led by the Smithsonian Environmental Research Center reveals that this fundamental assumption is not nearly as common as we might think. To determine whether individuals of invasive introduced species are generally larger, more fecund, or more abundant in their novel ranges, the researchers quantitatively evaluated population data from both the native and introduced range for 53 introduced species that are considered to be invasive, including 36 species categorized as among the “World's Worst Invasive Alien Species” a list assembled within the Global Invasive Species Database

Although their data generally support the idea that invasive species exhibit increased performance in their introduced range, roughly half of the species investigated performed similarly between the home and away ranges. One implication of this finding is that novel ecological and evolutionary conditions in the introduced range may only partly explain success in a new range. Indeed, there has been much recent progress in determining the traits that make some species invasive across a range of environmental conditions, with growing evidence that many successful introduced species share similar traits with successful native species. The authors conclude that species' traits, and particularly the interaction between traits and environmental context, may be a better predictor of invasion success than novel conditions alone.

Friday, May 17, 2013

How three became one

The genus Anopheles comprises about 460 species. Over 100 can transmit human malaria, but only 30–40 commonly transmit parasites of the genus Plasmodium, which cause malaria in humans. The major vector of malaria in India, Anopheles fluviatilis has been described as a complex of three closely related species, named as S, T and U, based on variations in chromosomal inversions. Over-sized chromosomes, so called polytene chromosomes, have developed from standard chromosomes and are commonly found in the salivary glands of flies (and their close relatives, the mosquitoes). These polytene chromosomes are also used to identify species e.g. of Chironomid larvae that are notoriously difficult to identify. This method is not free of error and researchers have been trying to find reliable DNA markers that confirm the species S, T, U in the case of Anopheles fluviatilis. Two DNA regions (ITS2 and the D3 region of 28S) had been used by some researchers whereas others showed that both show insufficient variation and in one case even a 100% similarity to another congener Anopheles minimus.

A group of colleagues from India have now published a study that shows that two members of this 'species complex' rather represent genetically con-specific intermixing populations with negligible genetic differentiation. The third 'species' had previously been shown to be a phenotypic variant of Anopheles minimus. The authors used DNA Barcoding and contrasted the results with those from the other two markers and found very little variation in the barcode region and cross-reactivity in one of the other markers (ITS2). Some of the specimens couldn't be assigned to either subgroup as both 'species' variants were found in some individuals.

Very interesting study also in line with the fact that all supposed species were capable of carrying the parasite.

Wednesday, May 15, 2013

Inconspicuous life - lichens

Lichens are symbiotic organisms consisting of a fungus and a partner capable of photosynthesis either either a green alga or cyanobacterium. The body of most lichens is different from those of its partners growing separately. The fungus surrounds the algal cells, often enclosing them within complex fungal tissues unique to lichen associations. In many species the fungus even penetrates the algal cell wall. The lichen association is a close symbiosis and extends the ecological range of both partners. However, is not always obligatory for their growth and reproduction in natural environments. Especially the algae can live independently.

Lichens are commonly used to monitor ecosystem health and the impact of atmospheric pollution. In addition, some lichens are potentially valuable sources of pharmaceutical products, including antibiotics, and antioxidants. Despite their occurrence in all terrestrial ecosystems and their overall ecological importance, lichens are commonly overlooked. Furthermore, robust species delimitation and accurate identification remains challenging. There are more than 18, 000 currently accepted species of lichen-forming fungi and an estimated diversity of more than 28, 000 species. On the other hand the number of photosynthetic partners is very low (usually only two genera).

A new study now presents reference sequences using the fungal ITS marker as a DNA Barcode for identifying species within a species complex (Rhizoplaca melanophthalma). Overall, the study demonstrates the potential for accurately identifying lichen species by using DNA Barcoding to identify the lichen-forming fungi. The researchers also formally describe five new species within the group they studied.

Their conclusion:
As molecular sequence data become more readily available, they will allow us to better understand the diversity of lichenized fungi. Their use in identifying species will become increasingly important and routinely applied. Other disciplines such as ecology, conservation and physiology will benefit from a more objectively based species circumscription, enabling us to interpret distribution and ecological patterns better and more accurately monitor environmental disturbance and climate change.

Tuesday, May 14, 2013

The SpongeMaps Project

Contemporary collections of sponges in the Indo-west Pacific have escalated substantially due to pharmaceutical discovery, national bioregional planning, and compliance with international conventions on the seabed and its marine genetic resources beyond national jurisdictions. These partially processed operational taxonomic unit (OTU) collections now vastly outweigh the expertise available to make them better 'known' via complete taxonomy, yet for for many bioregions they represent the most significant body of current available knowledge. Increasing numbers of cryptic species, previously undetected morphologically, are now being discovered by molecular and chemical analyses. The uncoordinated and fragmented nature of many collections, however, means the knowledge and expertise gained from a particular project are often lost to future projects without a biodiversity informatics legacy.

This is the first part of the abstract of a paper that was recently published in Integrative and Comparative Biology. The SpongeMaps Project represents a legacy of the Marine Barcoding project (MarBOL) which I led over the four year of its existence. While the DNA Barcoding activities will carry on as part of iBOL other sub-projects have been finished. The SpongeMaps project was intended to provide an online collaborative platform to integrate morphometric data with DNA Barcodes and other DNA fragments that were generated as part of the Porifera Tree of Life (PorTol). Over time it evolved into a workspace focusing on specimen data that are aggregated into OTUs. It contains all infrastructure to compare images, descriptions, distribution, and chemical components. The approach has some similarities to the BOLD BIN pages (sponge example here) but is certainly more specialized and detailed when it comes to the peculiarities of sponges. By June 2013, 50 000 georeferenced specimens will be online together with 60 000 images (photos in situ, on deck, of preserved specimens, light micrographs, SEMs, line drawings, and sketches). All that will be connected to geographical and genetic data.

SpongeMaps can generate output data in a format that is useful for the Encyclopedia of Life (EOL) and the Atlas of living Australia (ALA) by producing individual ‘‘species-pages’’ that are published directly to both online portals.