Friday, June 28, 2013

From the inbox

Found this invite today:

‘1st International Conference on the Biodiversity of the Congo Basin’
first half of June 2014, Kisangani, DR Congo
We are pleased to announce the ‘1st International Conference on the biodiversity of the Congo Basin’ at Kisangani, D.R. Congo.
This conference is an initiative of the Consortium Congo 2010 (the University of Kisangani, the Royal Museum for Central Africa, the Royal Belgian Institute of Natural Sciences and the National Botanic Garden of Belgium) and the ‘Centre de Surveillance de la Biodiversité’ in Kisangani to facilitate interactions and collaborations among Congolese, Belgian and international teams and experts involved in various fields of biodiversity-related research in the Congo Basin.
The conference will take place during four consecutive days in the first half of June 2014 at the ‘Centre de Surveillance de la Biodiversité’ at Kisangani. Financial support is provided by the Belgian Federal Public Planning Service Science Policy (Belgian Science Policy).

We anticipate the participation of more than 120 experts, 60-70 % of which from the DR Congo and countries within the Congo Basin. We count on the presence of scientists as well as representatives of organizations involved in this topic.
To help us plan this event, we kindly request you to indicate your interest and willingness to participate at this conference by sending an e-mail with your contact details to

More on the Congo Biodiversity Initiative here.

Thursday, June 27, 2013

Freshly squeezed Barcodes

Almost a year ago I posted about a technology that could provide fast, robust and reliable identifications of a handful of species that are not easy to distinguish based on morphology. A Scottish researcher used High Resolution Melt (HRM - see box below for details) to help with the identification of a handful of closely related fish species. The result was a HRM protocol that represented a quick and cost effective method of genetic screening and an alternative to DNA sequencing between the four genetically very similar species.

Today I came across a new publication from Portugal that described a proof of concept study utilizing HRM for fruit juices authentication. Fruit juices labeled as 100% fruit are a growing market world wide. In the European Union alone their sales represent approximately two-thirds or 7 billion liters of total EU juice sales in 2011. The increased consumer demand for premium juices has also led to a dramatic rise in the  requirement for freshly squeezed juices. Those are usually higher priced and therefore favorite targets for adulteration. Adulteration of fruit-based products is mostly performed by blending original products with cheaper and more available fruits.

The researchers from the University of Porto picked a marker that had been proposed and discussed for plant DNA Barcoding: the trnL intron. This choice was mainly an opportunistic one as at the time of the study GenBank contained sequences for most of the fruit species in question. The tests were conducted using fresh fruits from the species Citrus sinensis (orange); Mangifera indica (mango); Prunus persica (peach); Pyrus communis (pear); and Ananas comosus (pineapple) purchased at local markets and immediately processed to juices in a home fruit processor. Pulp was removed and 3 different extraction methods applied to determine the most efficient one. In order to test the effect of blended fruit juices on the melt profile assignment different mixtures of juices in different ratios were tested. Not only could all species be correctly identified but also the individual quantities. 

These are very promising results and consider this:
The method consisted of a single step closed tube procedure, took approximately 3 h to complete and costed approximately €2.00 per sample (including DNA extraction and HRM reagents). Now that sounds affordable to me even when it comes to larger quantities. I guess industry and inspection agencies are left with not many excuses when it comes to more rigorous testing for consumer protection.

Tuesday, June 25, 2013

Look behind the scenes of a malaise trap

We have a new gadget that is intended to help us with education and outreach projects - the GoPro Hero3.
Today I did a first test of its time lapse function. I placed camera inside a Malaise Trap pointing at the 'exit' that leads into an ethanol filled bottle. Here is the result - 1h in 30s:

I only corrected the brightness at bit and added the music (Bert Jansch - Angie). The latter was done in Windows Movie Maker which is not an optimal but sufficient solution for this first quick and easy edit.

D for Dominican Republic

The Dominican Republic is known for lush, tropical beaches, its food and its rich culture. It is also considered one of the most biologically diverse countries in the Caribbean. The country is part of the Caribbean Challenge. The goal of the Challenge — currently endorsed by five Caribbean nations — is to not only permanently establish a network of 20 million acres of marine parks across the territorial waters of at least 10 countries, but also to ensure that once established, the protected areas also receive sufficient and sustainable funding. Last year, by Presidential Decree the Dominican Republic added 31 new protected areas into its national protected areas system. The new protected areas encompass a total of  3.2 million acres — of terrestrial and marine habitat.

Nevertheless the country's biological wealth needs to be inventoried and the Hispaniola Barcode of Life Initiative is a first step. It aims to inventory and generate DNA Barcodes of the animal species that inhabit a small wildlife refuge in the city of San Pedro de Macorís (see map). 

The project is funded by a small grant from the Ministry of Higher Education, Science and Technology of the Dominican Republic and led by two enthusiastic researchers: Dionel López and David Hernandez from the Universidad Central del Este.

Friday, June 21, 2013

C for Cambodia

It's a while ago that I started a virtual tour around the world. Time to get back on track.
Here a video about DNA Barcoding in Cambodia:

The first time I heard about this project was at the last International DNA Barcoding conference in Adelaide 2011 and if I remember correctly it was Vittoria Elliott who was telling me about it. A real important and wonderful educational program. Also probably not very well known -it's time to change that.

Wednesday, June 19, 2013

Digitization through DNA Barcoding and Informatics

This landed in the inbox today:

The Consortium for the Barcode of Life (CBOL) at the Smithsonian Institution and CSIRO in Canberra, Australia, are the co-organizers of a full-day symposium/workshop on "Connecting Biodiversity Collections in the Pacific: Digitization through DNA Barcoding and Informatics".  The event will take place during the 12th Pacific Science Association Inter-Congress, Suva, Fiji 8-12 July 2013

To make the event as accessible as possible, it will be webcast as a GoToWebinar.  Registrants will see and hear all presentations and discussions and will be able to pose questions to the presenters.  The sessions are:

Collection digitization, chaired by Beth Mantle, CSIRO: Wednesday afternoon from 14:20 to 17:30 (Fiji time, GMT +12 hours)
DNA barcoding, chaired by David Schindel, CBOL, Smithsonian Institution: Thursday morning from 11:00-12:20 (Fiji time)

Information on the symposium/workshop and the webinar registration form can be found here.

Thursday, June 13, 2013

It's all about foot colour

Cerithiopsidae is a family of marine gastropods, probably including hundreds of species, living mostly from the intertidal zone down to about 200 m. All of them are associated with, and feeding on sponges. The genus that gave the family its name, Cerithiopsis, comprises a group of small species usually less than 10 mm long. 

Traditionally, shell characters are primarily used to identify and delineate gastropods, yet the identification of Cerithiopsis species by shell morphology alone can be very difficult or impossible because of their small size, frequent encrustations and damage, the extreme variability within some species (phenotypic plasticity) or extreme similarity of shell features between different species (morphological stasis)

In many instances genital morphology is the best resource for species identification. But have you ever dissected a 10 mm long snail in order to find some diagnostic characters associated with its reproductive organs? I have and it is indeed as difficult as it sounds. It also requires a considerable level of experience to make the right judgement which in some cases leaves us only with a handful of people capable to do species identification for particular gastropod families. In other cases the knowledge is already lost as experts literally went extinct.

Sounds like a case for DNA Barcoding and it seems that the community of mollusk researchers is moving ahead albeit in some instances at a snail's pace. The more I am happy to find examples where DNA helps to overcome obstacles of morphological identification or simply helps to find the right morphological character. A group of Italian researchers used DNA Barcoding to confirm that Mediterranean gastropods usually identified as Cerithiopsis tubercularis in fact represent a complex of cryptic species, which can also be reliably diagnosed by the colour pattern of their head-foot. The only issue with this method is the fact that the animal needs to be alive. Dead specimens loose the characteristic patterns very quickly. Well, there is always a DNA Barcode that can help with that.

Tuesday, June 11, 2013

Italian Consortium for DNA Barcoding

I found a few Italian news articles today containing the announcement and with the help of Google translate and some of my rudimentary knowledge of Italian I was able to find out that...

...up to now Italian laboratories had been working independently  The national group was formed to create a network of research laboratories that use DNA Barcoding. The objectives of the Consortium are: to grow a network of laboratories that use or plan the use of DNA Barcoding; to identify hubs for educational activities aimed principally at young upcoming researchers in the field, to identify the main topics of active research in Italy also with a focus on planning common projects; to connect with international groups to share issues, research and results; to connect research institutions and commercial entities both dealing with identification of living organisms.

One of the first activities of the Consortium was to organize an introductory course on DNA Barcoding that runs today and tomorrow at the University of Modena and Reggio Emilia.

Congratulazioni. I am looking forward hearing more about the activities in your wonderful country.

Friday, June 7, 2013

School Malaise findings 5 - Midges and a dancing fly

Non-biting Midges (Chironomidae)
Chironomus plumosus
Chironomidae is a large family of flies whose members look much like mosquitoes. However, they do not possess the needle-like mouthparts of mosquitoes, so these midges do not bite! The males are easily recognized by their feathery antennae and are often seen in large swarms over a landmark such as a rock or bush. Their larvae are very common in many aquatic environments, where they usually feed on algae or decomposing plant material. The flying adults have a short lifespan in which males often assemble into huge swarms. Females join these swarms to mate, and shortly after the males die. The adults rarely eat as their lifespan is so short - they must focus on reproduction. The family Chironomidae is very diverse with over 8000 named species so far. As a result they are common in aquatic habitats around the world. They are notoriously difficult to identify to species level. Up to the point DNA methods became more accessible, the cytotaxonomical analysis of polytene chromosome banding patterns had been considered to be the only reliable method of Chironomid species identification. However, the method is time-consuming and requires considerable expertise, in particular for the interpretation of those banding patterns.

This family of midges also proved to be dominant in the School Malaise Trap Program as they were the most abundant and most diverse family of insects in the collections. Some 7000 sequences representing likely 250 species. Only about 1/5 matched records on BOLD that had a species name. The rest has not been identified so far or represents a new addition to the DNA Barcode library. 

Waltzing Fly (Prochyliza xanthostoma)
Prochyliza xanthostoma (credit
The Waltzing Fly  is a carrion fly commonly found in North America.  The larvae of this fly species often develop inside the bones of freshly killed animals (e.g. deer, moose) and in their final stages, they fall into the surrounding soil to pupate and soon after, emerge as adult flies. In Ontario's Algonquin Park, waltzing flies typically breed in early spring on the carcasses of moose that did not survive the Winter. In March and early April, they are one of the most plentiful insect species in the Algonquin forest. Males and females look quite different, with the male having larger antennae, head and forelegs compared to the female. These differences are due to the male’s unique courtship and combat behaviours. Males battle to defend their territory (see video) and dance to attract mates hence the name Waltzing Fly.

Thursday, June 6, 2013

The German Mosquito Atlas

Over the last couple of decades only a handful of enthusiasts and specialized researchers were interested in Germany's mosquitoes. This is largely due to the fact that since the 1950's Germany is considered Malaria-free. People lost interest in them as none of the 50 species living in the country seemed more than just a nuisance. That situation changed in 2006 when the bluetongue disease surprised German livestock owners as the disease is transferred via mosquito species (e.g. genus Culicoides). The disease does not affect humans but it became clear that climate change and globalization will inevitably lead to the introduction of new species that likely also carry viruses.

A good reason to start a national survey and to create a map that documents not only all current species but also their ranges. In April 2012 researchers from the Leibniz Centre for Agricultural Landscape Research started their work on the Mosquito Atlas for Germany. 120 traps were deployed nation-wide in the past months. However, the majority of sampling is actually done by citizen scientists. The institute issued several calls for help and last year they received more than 2000 envelopes with mosquito samples from amateur collectors. Although it will take several more years to complete the work initial results have already proven how valuable this work is.

Hulecoeteomyia japonica
The researchers were able to locate unknown colonies of Hulecoeteomyia japonica in a 2000 area in Western Germany. This species is invasive and has established itself notably at cemeteries where it starts to replace native species. The fact that it is one potential carrier of the West-Nile virus raises some concerns.

Stegomyia albopicta
Even more concerning are encounters of individuals of the Tiger mosquito (Stegomyia albopicta). This little beast is a very potent vector as it is known be able to carry more than 50 different viruses among those Dengue or Chikungunya. This species has been found in 20 European countries already and it seems only a matter of time that it establishes itself in Germany. The animals arrive through passive transport largely from Italy that is home to some stable populations and finds at Autobahn service stations in Germany give a hint on the mode of transportation. 

My hope is that this wonderful collection will be DNA barcoded to allow for fast and reliable identification of any mosquito species not only in Germany. The value for any medical prevention strategies seems clear.

School malaise findings 4 - the tiny ones

These little highly interesting animals are often undeserving overlooked. Not this time!

Springtails (Collembola)
Springtails are six-legged arthropods (hexapoda) which are closely related to insects, but are not true insects. They are relatively small, generally less than 6 mm long, variously colored, and are either round (globular springtail) or elongate (slender springtail). Most springtails have a long, forked appendage which can ‘spring’ them forward, propelling the creature into the air when threatened. Springtails are usually found in soil, moss, and leaf litter and they occur worldwide, often in very high numbers. It has been estimated that one square metre of soil may possess up to 10,000 Collembola! They are detritivores meaning that they consume decomposing matter, and considered one of the main organisms responsible for the control and the dissemination of soil microorganisms. Because of their abundance, Malaise traps often capture a very large numbers of springtails, but their species diversity tends to be low. Despite this, the School Malaise Trap Program led to the collection of 37 species of them, including two species that were new to our DNA barcode library.

Springtails are admirable little creatures. Have a look at this 2 minute video taken from the BBC's great Life in the Undergrowth documentary series.

Phytoseiid Mites (Phytoseiidae)
Phytoseiidae is a large family of mites, with more than 2500 described species. Phytoseiid mites are tiny, usually light to dark brown, with slightly hardened shells. These mites have very rapid life cycles, moving from egg to mature adult in less than 10 days. Some phytoseiids feed on plant tissue, but most are predators of small invertebrates (such as other mites) and usually live on plants. Since phytoseiids are very good predators, they are commonly used to control pests that attack crops. New species may be able to help protect more crops and the School Malaise Trap Program caught seven phytoseiid species new to the DNA Barcode library. In fact, some these possibly represent new species to science.

Here a video of one mite eating another mite.

Wednesday, June 5, 2013

School Malaise findings 3 - arachnids

Today two bits on our little friends with eight legs. We found quite a few in all the Malaise traps. Some expected, some unexpected.

Erigone atra
Dwarf spiders (Erigoninae)
Dwarf spiders are members of the sheet weaver spiders the second largest spider family in the world. There are more than 2000 described species of these spiders found around the world, with 650 in North America. They are very small, usually less than 1 mm, and vary in colour. Their small size allows these spiders to use “ballooning” as a method of transportation (see video below). When ballooning, the spider shoots out strands of silk that form a sort of parachute which is caught by the wind, floating them to a new location. As with most spiders, the Erigoninae are predators and play an important role in food webs. 

We were able to find two species of this subfamily new to the BOLD DNA barcode library. One specimen of Ceratinops crenatus and two specimens of Walckenaeria tibialis were at two schools.

There is only little available information about the biology of these two species as they are very rare.

Pseudoscorpions (Pseudoscorpiones)
Pseudoscorpions arachnids named “Pseudo” scorpions because they have pincers that resemble scorpions, but do not have the tail and stinger. They can be found anywhere from a tree canopy, to somewhere in your home where they feed on the larva of some household pests.

They can also be found in leaf litter, where they feed on other tiny arthropods. Males use  pheromones, and dancing behaviour, to attract females to mate.

These arachnids construct a silken cocoon which they use to protect themselves during the winter. Pseudoscorpions occur globally, but are rarely collected in Malaise traps. In total, four specimens were caught in the School Malaise Trap Program (out of 95000 specimens!).

Here an interesting video of a pseudoscorpion hunting springtails:

Tuesday, June 4, 2013

The rediscovery of the Hula painted frog

Latonia (formerly Discoglossus) nigriventer (Credit: Sarig Gafny)
The Hula painted frog was considered a member of the Discoglossus genus when it was first discovered in the Hula Valley of Israel in the early 1940s. The frog was thought to have disappeared following a drying up of the Hula Lake at the end of the 1950s, and was declared extinct by the IUCN in 1996. The dry up was part of a plan to transform the area into agricultural land and to combat malaria by eliminating the habitat of the disease-bearing mosquitoes. The sad consequence - the Hula painted frog was the first ever amphibian to have been declared extinct. The opportunity to discover more about this species' history, biology and ecology was thought to have disappeared.

Hula valley
But in November 2011 a routine patrol discovered an animal that was identified as Hula painted frog. Since then 10 more individuals were discovered. This was revealed in a study that was published today. But there is more the researchers were able to find out.

Based on new genetic analyses of rediscovered individuals and the morphologic analyses of extant and fossil bones, the team of Israeli, German and French researchers discovered that the Hula frog differs strongly from its other living relatives, the painted frogs from northern and western Africa. Instead, the Hula frog is related to a genus of fossil frogs, Latonia, known only as fossils from Oligocene to Pleistocene in Europe and therefore considered extinct for about a million years.

These results imply that Latonia nigriventer is not merely another rare species of frog, but rather the sole representative of an ancient clade of frogs
There are plans in place to reflood parts of the Hula Valley and thereby restore the original swamp habitat, which may help to build a secure future for the rediscovered species. Actually partial reflooding already begun 1994. Maybe one reason why the remarkably resilient species showed up again. Either way good news for a change.

New Carnival of Evolution (#60)

Check out NeuroDojo for the latest edition of the carnival:

Party like it’s 1953 

School Malaise findings 2 - beetles

Welcome to part two of the most interesting creatures found during the School Malaise Trap program. Today a look at two examples of beetles.

Handsome Fungus Beetle (Phymaphora species)
In North America, there are only two described species of Handsome Fungus Beetles (family Endomychidae). One beetle sampled in the School Malaise Trap Program is mrophologically similar to one of them - Phymaphora pulchella, but its DNA barcode indicates it is likely a distinct species. This means that it is possibly a species that is new to science or at least new to North America. Phymaphora pulchella  is a tiny insect (3-4mm long) with a dark spot above its head, and another dark band across its back. It has yellow legs and antennae, and the particularly ‘handsome’ males have antennae with swollen tips. These beetles feed on fungi that grow under the bark of trees. Phymaphora pulchella is most commonly collected at fresh wounds in trees, although the reason is still a mystery to entomologists.
Mycetina perpulchra

Phymaphora pulchella

The new one - Phymaphora sp.

Flat bark beetles (Cucujidae)
Those beetles are a distinctly flat family of the order Coleoptera. They are relatively small with a flat, long body ranging from 6 to 25 mm in length. They are predominantly brown in colour, with some species that are black, bright red or yellow. Both the larval and adult forms of Cucujiidae can be found under the bark of dead tree, where they are believed to feed on other arthropods. Their range extends across all continents except Africa, and are most diverse in northern regions like Canada and Alaska. One of the species found in the program was the red flat bark beetle (Cucujus clavipes) which is widely distributed in Canada and possesses an interesting trait, its body produces antifreeze proteins. This allows the animal to survive extreme cold temperatures. Now that's a real Canadian life style.
Cucujus clavipes

Monday, June 3, 2013

School Malaise findings 1 - pests

As announced on Friday I will use some posts this week to showcase the results from the School Malaise Trap Program. We have provided the schools with a list of the top 10 most interesting discoveries which I will share with the blog readers. Today we will start with the ones that represent potential threats to agriculture and forest.

Onion fly (Delia antiqua)
The Onion Fly was the most abundant species collected in the School Malaise Trap Program (6%) in fact, it was found in 79 of the 81 traps! Furthermore, it was found earlier in spring than previously recorded. This fly is found in the temperate regions of North America, Europe, and Asia.

Onion flies are grey and look much like house flies, except their legs are longer and their abdomen is narrower. Adults lay their eggs in the soil near onion bulbs of any member of the genus Allium which contains Onions, Garlic, Leek, Chives. The larvae are 8-10 mm long, white, and feed almost exclusively upon those plants. Damage due to the larvae feeding on young seedlings often results in plant death. Onion flies have three generations per year in Ontario so there is great potential for widespread damage to Allium crops. So far it was assumed that the first generation peeks early to mid June. According to the results at all the schools we are looking rather at early May. Given the fact that the flies need just a little over a week to hatch, mate and lay eggs any week earlier than expected might make a big difference for commercial farming.

Pear thrips (Taeniothrips inconsequens)
Pear thrips are an invasive species from Europe. They arrived in California the early 1900’s and are now be found throughout most of the USA and increasingly often in Canada. They are tiny, measuring only 1.2 to 1.7 mm long, with brown - black colouration, two pairs of wings, and rasping mouthparts. They use these mouthparts to cut open leaves and buds of hardwood trees so they can feed on plant fluids. The collection of pear thrips by the School Malaise Trap Program marks the first time they have been DNA barcoded from a Canadian location. They were found in 53 out 81 traps.

This is a very interesting discovery, and could signal a threat to Canadian forests especially because these animals are not restricted to pear trees as the name might suggest. Actually they are known to feed on a variety of maple species as well. In the late 1980’s pear thrips were responsible for damage to 1.3 million acres of Pennsylvanian forest. In North America, only female pear thrips have been found; they reproduce by parthenogenesis, producing eggs that do not require fertilization by a male.