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.

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.

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.

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.

Italian Consortium for DNA Barcoding

Researchers oft the University of Modena and Reggio Emilia and the University of Milano-Bicocca have created the 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.

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 buggguide.net)

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.