Tuesday, December 23, 2014

Barcoding Christmas delicacies

During Christmas you may wonder if your Christmas ham really contains pork, the herring in the tomato sauce really is herring, if the sausages you just bought contain beef, or if the Christmas anchovies have anchovies in them. No need to fret over this, DNA Barcoding can rescue the family Christmas dinner.

The NTNU University Museum in Trondheim analysed the DNA from ten randomly selected traditional Norwegian Christmas dishes found in grocery stores. When compared with the BOLD reference library the results showed that, overall, the ingredients corresponded to the descriptions on the packaging.

The colleagues from Norway sampled and sequenced products such as traditional Christmas sausage, Christmas ham, pressed ham, patties, sodd (a traditional Norwegian dish with mutton and meatballs), Christmas anchovies, pickled herring and pickled herring in tomato sauce. The results were mostly positive, products were labelled correctly with one minor exception: The Christmas anchovies contained sprat (Sprattus spp.), not anchovies (family Engraulidae with Engraulis encrasicolus being the main European commercial anchovy).  

In Norway products that are labeled as anchovy often traditionally contain sprat. The reason is most likely simple marketing because a label such as ‘Christmas sprat’ probably wouldn't sell as well. While researching in the web I also found out that in Scandinavia the name anchovy is more related to a traditional seasoning and not so much to a particular fish species. Even herring can be sold as 'anchovy-seasoned'. 

Overall good news for Norwegian Christmas dinners. It looks like the customers actually get what they pay for.

Friday, December 19, 2014

CBD Training for trainers

The Secretariat of the Convention on Biological Diversity will be launching a capacity-building “training for trainers” course in DNA Barcoding that will be made available to interested Parties to the Convention, thanks to financial support from the Government of Japan. This activity will be facilitated by the Biodiversity Institute of Ontario in Canada and will focus on building technological capacity to help Parties achieve Aichi Biodiversity Target 9, specifically, detection and monitoring of invasive alien species (IAS).

This course will include a distance education module (our Introduction to DNA Barcoding course), followed by hands-on training at the Canadian Centre for DNA Barcoding for selected national experts. It will cover standard operational workflows used in barcoding of IAS and will provide participants with specialized skills that can be used to apply this technology and approaches in their home countries. Training modules are geared toward professionals involved in national regulatory and monitoring organizations overseeing quarantine and management of IAS. The course is open to additional self-funded experts from countries that are not eligible for SCBD financial support.

On-site training for up to five participants will overlap with the International Barcode of Life Conference, allowing them to participate in it.

The call for applications will be announced in January 2015 on the CBD website. For inquiries on eligibility, selection criteria, and application procedure, please contact the CBD Secretariat.

Thursday, December 18, 2014

New Issue of the Barcode Bulletin

We've just published our newest issue of the Barcode Bulletin. Once again packed with interesting news and findings. Everything DNA Barcoding - the perfect read for any seasonal holiday :-)

Just click on the cover photo and you will be redirected to the pdf file.

6th International Barcode Conference

I know many of you have been waiting for more details on the 6th International Barcode of Life Conference that will happen here in Guelph next August. The waiting has an end as the conference website just went life and it contains all the relevant information you might have been looking for. I think it looks just great. 

Just click on the image and you will be redirected.
I hope to be able to meet a lot of my readers at the conference.

Wednesday, December 17, 2014

After more than 100 years

Without abundant material it were ridiculous to attempt a wide revision of these insects; and ... a mass of this material causes one's courage to sink at the sight of so uniform and apparently characterless a group.
Claude Morley, 1912

Back in 1912, three species of the parasitic wasp genus Ophion were described by two different entomologists, one of them was Claude Morley. This increased the number of known species in North America to eleven. Since then no new species was described although it has long been known that the actual diversity must be much higher. Everyone simply assumed that Ophion are just too difficult to tell apart and therefore didn't bother to face the challenge of sorting them out. 

However, with the advent of new taxonomic tools, it is no longer necessary to rely solely on the challenging morphology of the group. In a newly published study two Canadian colleagues used a combination of molecular and morphometric methods to define a new species group within Ophion, and to delimit and describe six new species within this group. The molecular work involved the analysis of three different genetic markers (ITS2, COI, and 28S D2-D3), while the morphometric analyses included both an analysis of wing venation and a more traditional approach of measuring various body parts.

All the different methods used provided remarkably congruent results, which gave the authors a lot of confidence in the new species they described. This also reemphasizes the point that all these new methods are essentially a new toolkit for studying species in morphogically-challenging groups. Not a very surprising new message for the hard-core DNA Barcoding researcher but good news nevertheless. 

... we have shown that by using an iterative analysis of morphology, molecular analysis and morphometrics, we can delimit and describe species within a genus that is so morphologically challenging that no new species have been described in North America for more than a hundred years. Furthermore, molecular and morphological recognition of this species group will now allow more targeted specimen collection and museum research, supporting a global revision of the species group in its entirety.

We are only at the beginning of understanding the real diversity of parasitic wasps and there are already researchers who think that we might need to change our perception of the beetles and butterflies being the most diverse insect groups. Actually, the order hymenoptera might be much larger than both of them. One indication of that is the recent flood of new species described as the result of studies utilizing new tools such as DNA Barcoding to delineate them. 

Tuesday, December 16, 2014

Discoveries of the week

Salmo kottelati sp. n., is described from Alakır Stream (Mediterranean basin) in Turkey. It is distinguished from other Anatolian Salmo species by a combination of the following characters (none unique to the species): general body colour greenish to silvery in life; 7–9 parr marks along lateral line; four dark bands on flank absent in both sexes; black ocellated spots few, present only on upper part of flank in individuals smaller than 160 mm SL but in larger both males and females black spots numerous and located on back and middle and upper part of flank; red spots few to numerous, scattered on median, and half of lower and upper part of flank; head long (length 29–33% SL in males, 26–32 in females); mouth large (length of mouth gape 13–19% SL in males, 12–15 in females); maxilla long (length 10–13% SL in males, 8–12 in females); 105–113 lateral line scales; 24–29 scale rows between lateral line and dorsal-fin origin, 17–19 scale rows between lateral line and anal-fin origin; 13–15 scales between lateral line and adipose-fin insertion.

The genus Salmo is widely distributed in rivers and streams of basins of the Marmara, Black, Aegean and Mediterranean seas. The genus is represented by 12 species in Turkey alone. This description adds another one to this list. The new species is named for Maurice Kottelat, who contributed to the knowledge of the fish fauna of Europe and Asia.
no DNA Barcodes available

We discuss 45 Costa Rican species of Ethmia Hübner, 1819, including 23 previously described: E. delliella (Fernald), E. bittenella (Busck), E. festiva Busck, E. scythropa Walsingham, E. perpulchra Walsingham, E. terpnota Walsingham, E. elutella Busck, E. janzeni Powell, E. ungulatella Busck, E. exornata (Zeller), E. phylacis Walsingham, E. mnesicosma Meyrick, E. chemsaki Powell, E. baliostola Walsingham, E. duckworthi Powell, E. sandra Powell, E. nigritaenia Powell, E. catapeltica Meyrick, E. lichyi Powell, E. transversella Busck, E. similatella Busck, E. hammella Busck, E. linda Busck, and 22 new species: E. blaineorum, E. millerorum, E. dianemillerae, E. adrianforsythi, E. stephenrumseyi, E. berndkerni, E. dimauraorum, E. billalleni, E. ehakernae, E. helenmillerae, E. johnpringlei, E. laphamorum, E. petersterlingi, E. lesliesaulae, E. turnerorum, E. normgershenzi, E. nicholsonorum, E. hendersonorum, E. randyjonesi, E. randycurtisi, E. miriamschulmanae and E. tilneyorum. We illustrate all species and their male and female genitalia, along with distribution maps of Costa Rican localities. Immature stages are illustrated for 11 species, and food plants are listed when known. Gesneriaceae is added as a new food plant family record for Ethmia. CO1 nucleotide sequences (“DNA barcodes”) were obtained for 41 of the species.

Another glimpse into the diversity of the Área de Conservación Guanacaste (ACG) in northwestern Costa Rica. Of the 45 species of Ethmia found in Costa Rica, 22 are new and described in this paper. For this paper 41 of the Costa Rica species were actually barcoded and sequences can be found both on BOLD and GenBank. Only the taxonomy needs to be cleaned up in both databases. That would also allow the journal publisher to use the full potential of ZooKeys which includes the ability to link from paper to a large number of online databases.

Bivalve mollusk shells were collected in 2350 m depth in the Beaufort Sea, Arctic Ocean off northern Alaska. Initial identification suggested the specimens were a member of the bivalve family Thyasiridae, but no known eastern Pacific or Arctic living or fossil thyasirid resembled these deep-water specimens. Comparisons were made with the type of the genera Maorithyas Fleming, 1950, Spinaxinus Oliver & Holmes, 2006, Axinus Sowerby, 1821, and Parathyasira Iredale, 1930. We determined the Beaufort Sea species represents a new genus, herein described as Wallerconcha. These specimens also represent a new species, herein named Wallerconcha sarae. These new taxa are compared with known modern and fossil genera and species of thyasirds.

A new genus and species. The genus is named in honor of Thomas R. Wallerfor his contributions to the understanding of the evolution, biogeography and systematics of fossil and modern marine bivalves. The specie epithet  was chosen for Sara Powell, daughter of one the authors.
no DNA Barcodes available

A new tiger beetle species, Cicindelidia melissa Duran & Roman, sp. n., of the tribe Cicindelini, is described from high elevation montane forests of southeastern Arizona and Mexico. It appears to be most closely related to C. nebuligera (Bates) but is distinguished on the basis of multiple morphological characters and geographic range. The new species is also superficially similar to the widespread C. sedecimpunctata (Klug), but distinguished on the basis of multiple morphological characters and habitat. Habitus, male and female reproductive structures, and known distribution map are presented.

A new species of these fast running predators. The fastest Tiger beetle species can run at a speed of 9 km/h, which is the equivalent of a human running at 770 km/h. With about 2600 species a pretty big group that just got another new member named after the first author’s wife. 
no DNA Barcodes available

Bellevalia pseudolongipes (Asparagaceae) is described and illustrated as a new species from Siirt province in South Eastern Anatolia, Turkey. Diagnostic morphological characters, a full description and detailed illustrations are provided. It is morphologically similar to B. longipes but easily differs in both several morphological characters and chromosome number. The somatic chromosome number was determined as 2n = 12 in B. pseudolongipes.

A new species from Southeastern Turkey. It is closely related to Bellevalia longipes and sometimes can be found growing together with the former. No proper image for the species as the description is behind a paywall for me. Instead an image of its somatic chromosomes, one of the differences between the new species and its sister species.
no DNA Barcodes available

Rotala dhaneshiana, a new species of Lythraceae collected from a semi-marshy area of Wayanad Wildlife Sanctuary in Kerala, India is described and illustrated. It is closely allied to R. malampuzhensis usually in having trimerous flowers, but differs in having 4-angled, narrowly winged stems, long epicalyx lobes alternating with sepals, obovate-apiculate petals, and absence of nectar scales. It resembles R. juniperina, an African species in having trimerous flowers but differs in having sessile, decurrent-based leaves and sessile pistil.

The specific epithet is in honour of Mr. P. Dhanesh Kumar, Divisional Forest Officer, South Wayanad Forest Division, Kerala who received the ‘Sanctuary Wildlife Award - 2012’, instituted by the Sanctuary Asia Magazine for his valuable and tireless efforts in protecting the forest of the State. 
no DNA Barcodes available

Monday, December 15, 2014

Asian Carp detection

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. 

Since 2010, detection of Asian Carp environmental DNA testing warns scientists, policymakers, and the public that these invaders are knocking on the Great Lakes' door. However, new research published by scientists of the University of Notre Dame shows that the tools currently used for Asian Carp eDNA monitoring often fail to detect the fish. By comparison, new eDNA methods described in this study capture and detect Asian Carp eDNA more effectively.

Using an experimental pond containing Asian Carp the researchers found that currently used methods detect speciess-specific eDNA less than 5% of the time. In contrast, their new methods detected Asian Carp eDNA 95% of the time. The new, more sensitive toolkit includes an updated DNA capture method and a new genetic test to both detect and quantify DNA. Due to the high mitochondrial DNA similarity between the two species Hypophthalmichthys nobilis and Hypophthalmichthys molitrix and their extensive hybridization in the some regions the researchers designed a genus-specific qPCR assay to exclusively measure the concentration of bigheaded carp eDNA in environmental samples. 

This quantification allowed them to demonstrate that the new method captured five times more Asian Carp eDNA than the current method. Since the new method is also 40 times cheaper, they recommend the new toolkit to replace old methods in ongoing efforts for early detection of Asian Carp in the Great Lakes region and beyond.

Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Friday, December 12, 2014

500 posts

I almost missed this milestone. Today I wrote my 500th post for the DNA Barcoding blog. My posts have on average a length of 400 words which means I have written about 200 000 words about DNA Barcoding and Biodiversity Research. According to Amazon's Text Stats feature, the median length for all books is about 64,000 words - go figure.

A big thank you to all my readers for making this possible. Believe or not, this blog's audience is still growing continuously.

Fin-Eating Fish

Some freshwater fish in sub-Saharan Africa have a rather nasty habit where they bite off and eat the fins of other fish. This behaviour called pterygophagy is rare and the fish have actually evolved highly specialized jaws for fin-eating. As juveniles, some of them eat smaller fish as a whole, but by the time they become adults, they switch to biting of fin pieces.

This behaviour reminds me of the scale-eating cichlid fishes in Lake Tanganyika who became text-book examples for frequency-dependent natural selection. This species (Perissodus microlepis) occurs in two distinct morphological forms. One of them has mouth parts twisted to the left, enabling the fish to eat scales off its victim’s right flank. In contrast, the other morph, whose mouth is twisted to the right, eats scales off its victim’s left flank. The relative abundance of the two forms is regulated by frequency-dependent selection.

A new study on pterygophagous fish reveals some insights into prey selection:
To further investigate pterygophagy in distichodontids and shed some light on evolutionary and ecological aspects of this highly unusual trophic strategy, DNA barcoding was used to identify prey species from fin fragments found in the stomachs of Phago, Eugnathichthys, and Ichthyborus specimens. Information on prey identity was then used to determine whether pterygophagous distichodontids are opportunistic generalists or strict specialists with regard to prey selection, and to test Roberts’s (1990) hypothesis that aggressive mimicry is used as a strategy for successful pterygophagy in distichodontid fishes.

Previous work has suggested these fish target specific prey while employing aggressive mimicry to blend in with their victims. But this study shows these fish (at least the three genera studied) will target just about any species — including their own.

This study demonstrates how DNA barcoding can be used to shed light on evolutionary and ecological aspects of highly specialized ectoparasitic fin-eating behaviors by enabling the identification of prey species from small pieces of fins found in fish stomachs.

I couldn't agree more and I wonder if someone has some gut content of Perissodus microlepis for a similar look at the scale eaters. As far as I can remember colleagues didsome morphological work on their stomach content but there was no DNA Barcoding used so far. I also wonder if there is any connection between the two unusual feeding habits or at least similarities in the way both evolved.

Thursday, December 11, 2014

Gingko or not Gingko

For many centuries, leaves from the Ginkgo biloba tree have been a common treatment in Chinese medicine. Over the last few decades an increasing number of people started to take ginkgo supplements in the belief that they will improve memory and sharpen thinking. Sales of Ginkgo biloba herbal supplements, in the United States of America, totaled more than US$25.8 million during 2012  - making G. biloba the fifth best-selling herbal supplement.

Ginkgo improves blood flow to the brain and acts as an antioxidant. These effects may translate into some benefits for certain medical problems. Some studies have shown that it can help with memory problems caused by dementia or Alzheimer’s disease and sometimes it was found to modestly boost memory and cognitive speed in healthy people. It seems to help prevent the progression of dementia symptoms, especially if the dementia is thought to be the result of atherosclerotic vascular disease. However, it does not seem to prevent dementia or Alzheimer’s in general.

There also is solid evidence that ginkgo might ease leg pain caused by clogged arteries. It might also help with some other circulation problems. Ginkgo has been studied for many other conditions, including ADHD, depression and other psychological conditions, multiple sclerosis, tinnitus from a vascular origin and prevention of high altitude sickness. However, there are currently no conclusive results that show any related benefits.

We know from earlier studies that herbal supplements on the market are often subject to mislabeling, and therefore consumers may not be getting the products and benefits they are paying for. This is a rather serious problem as there are some potential dangers of mislabeled supplements. Some adulterants are either toxic alone or in combination with other substances that are part of the supplement product. Another problem is the fact that consumers may not receive the health benefit they seek from the supplements, which might worsen their health.

A new study that just appeared in Genome presents a novel mini-DNA Barcode assay for the authentication of Ginkgo biloba in herbal dietary supplements and the author used it to estimate the frequency of mislabeled ginkgo supplements on the market in the United States. A 166-bp matK mini-barcode was designed and it unambiguously differentiates Ginkgo biloba from all other gymnosperms by the presence of a C at nucleotide position 107. All other gymnosperms have a T at this position. This new mini-Barcode seems to work quite fine and here the short form of the results:

In total, 31 of 37 (83.8%) assayable herbal dietary supplements contained identifiable G. biloba DNA and six supplements (16.2%) contained fillers without any detectable G. biloba DNA.

For the supplements in which the author found no evidence of ginkgo, it cannot be ruled out that this is because the DNA was destroyed throughout processing for example by drying at very high temperatures. However, if I understood correctly these samples did contain DNA and filler species could be identified as well. Chances are high that the samples simply did not contain any ginkgo.

It is hoped that the matK mini-barcode assay described here will be used by supplement manufacturers to ensure that their supplements not only contain the classes of compounds used for standardization but also contain Ginkgo biloba.

For the sake of any customer I would indeed hope so.

New DNA Barcoding video

A new video on DNA Barcoding. It was produced by Agriculture and Agri-Food Canada, a department of Canada's federal government. Pretty neat, both the video but also the fact that a governmental institution is using its resources to produce a video to educate the public about the methods they are using and how everything works.

Wednesday, December 10, 2014

German beetles

No doubt, beetles are the most diverse group of animals. The order coleoptera currently comprises of about 400 000 species which represents ~40% of all insects. The idea of barcoding all of them seems very challenging and a quick look at BOLD 'only' shows some 26 000 public BINs for this group. However, if we take the second largest insect order, lepidoptera, as an example for how things can be done, it starts to look a little more promising. At this point BOLD holds some 100 000 public BINs for moths and butterflies. About 180 000 species are currently known for this order. The impressive number of DNA Barcodes in this group is the result of a decade of dedicated efforts. I don't see any reason why this shouldn't work with beetles and as a newly published study shows I am not alone in my thinking

The colleagues in Germany provide a DNA barcode reference library for Coleoptera for 15,948 individuals belonging to 3,514 species (53% of the German fauna) with representatives from 97 of 103 families (94%). This release is a direct result of the Barcoding Fauna Bavarica project which is led by the Bavarian State Collection of Zoology. Bavaria is the largest German state and contains almost all major habitat types in Germany which the exception of the coastal regions. As a result the state harbors 90% of the terrestrial and freshwater species known from the entire country. 

Within five years some 540 000 beetle specimens were collected of which more than 25 000 specimens were submitted for sequence analysis. Almost 16 000 of them yielded full length DNA Barcodes and although the beetle fauna in central Europe was thought to be well known the dataset held some surprises: 

The relatively high number of 1089 specimens, representing 176 potentially overlooked species was surprising, especially because many of these cases did not involve the specious and taxonomically difficult Staphylinidae, Curculionidae and Elateridae but the well-studied Carabidae, Cerambycidae, Haliplidae and Hydrophilidae.

The study not only presents advances in building a reference library for the German coleoptera but also a good starting point for future taxonomic work. The authors conclude:

Despite the fact that taxonomic research on German Coleoptera has been underway for more than 200 years, our study revealed 209 cases where the results from DNA barcoding and traditional taxonomy are discordant...We encourage the coleopteran scientific community to join the DNA barcoding projects on BOLD, to aid clarification of the status of species and to assist in the description of possibly overlooked species. Discussion and commenting on specific specimens on BOLD is possible for all registered users.

Tuesday, December 9, 2014

Leaf litter organisms

This is a very nicely done video introducing the little known fauna of leaf litter most notably springtails:

Discoveries of the week - #19

Thirty new spider species of the family Linyphiidae
Nasoonaria circinata

Eight new genera and 30 new species are described: Cirrosus gen. n. (type species Cirrosus atrocaudatus sp. n. (♂♀)), Conglin gen. n. (type species Conglin personatus sp. n. (♀)), Curtimeticus gen. n. (type species Curtimeticus nebulosus sp. n. (♂)), Gladiata gen. n. (type species Gladiata fengli sp. n. (♂)), Glebala gen. n. (type species Glebala aspera sp. n. (♂)), Glomerosus gen. n. (type species Glomerosus lateralis sp. n. (♂)), Smerasia gen. n. (type species Smerasia obscurus sp. n. (♂♀)), Vittatus gen. n. (type species Vittatus fencha sp. n. (♂♀)); Batueta cuspidata sp. n. (♂♀), Capsulia laciniosa sp. n. (♂), Dactylopisthes separatus sp. n. (♀), Gongylidiellum bracteatum sp. n. (♀), Houshenzinus xiaolongha sp. n. (♂♀), Laogone bai sp. n. (♂), L. lunata sp. n. (♂♀), Maro bulbosus sp. n. (♀), Nasoonaria circinata sp. n. (♂♀), Neriene circifolia sp. n. (♂♀), Oedothorax biantu sp. n. (♀), Oilinyphia hengji sp. n. (♂♀), Paikiniana furcata sp. n. (♂♀), Parameioneta bishou sp. n. (♂♀), P. multifida sp. n. (♂♀), P. tricolorata sp. n. (♂♀), Tapinopa undata sp. n. (♂), Theoa bidentata sp. n. (♂♀), Theoa vesica sp. n. (♂♀), Vittatus bian sp. n. (♂♀), V. latus sp. n. (♂♀), V. pan sp. n. (♂♀). The male of Kaestneria bicultrata Chen & Yin, 2000 and the females of Asiagone perforata Tanasevitch, 2014 and Batueta similis Wunderlich & Song, 1995 are described for the first time; photos of Bathyphantes paracymbialis Tanasevitch, 2014 are provided.

Scientists from the Institute of Zoology with the Chinese Academy of Sciences have devoted years of their careers to study the astounding diversity hidden in the depths of the Xishuangbanna tropical rain forests. Xishuangbanna is situated in the southern part of Yunnan with the Lancang (Mekong) River flowing through it. The region is well-known for its rich biodiversity and is one of the few places in China that still maintains large tracts of tropical rain forest, which won its reputation as the Kingdom of Tropical Fauna and Flora.

A new species, Mygdonia milivoji sp. nov. (Coreidae: Coreinae: Mictini) from south-west Madagascar is described, illustrated and compared with widely distributed M. elongata Distant, 1879. A key to Mygdonia species based on females is given and distribution of both Madagascan species is briefly discussed.

This new hemipteran species was named after the collector of the specimen, a friend of the senior author (Miloš Trýzna friends call him ‘Milivoj’).
no DNA Barcodes

A new species of dustywings, Helicoconis tatricus sp. n., is described from the foothills of the Tatra Mountains in Slovakia. The new species differs from other species of the subgenus Helicoconis by structure of male genitalia—unfurcated styli and wide and short apophyses. The key for determination of all Palaearctic species of the subgenus Helicoconis is added and the distribution of Palaearctic species is discussed.

This species is a new member of the dustywings, Coniopterygidae, that are a family with some 460 species which belongs to the order Neuroptera. The animals have translucent brownish wings usually covered with a whitish dust of waxy scales, hence the name. The name of the new species refers to the name of type locality, the Tatra Mountains in North Slovakia.
no DNA Barcodes

Dasybasis antillanca
The females of Dasybasis antillanca and Dasybasis collagua, new species, are described from specimens collected in Osorno and Iquique Provinces, south and north Chile, respectively. Their relationships to other Dasybasis species are discussed.

The names of both new tabanid fly species refer to their respective type localities. The specimens examined were collected in the Antillanca, about 1.000 km south of Santiago city; and in the Collagua, 1.900 km north of Santiago city. 
no DNA Barcodes

The paper describes two new species of feather mites collected on Psilopogon virens (Boddaert) (Piciformes: Megalaimidae) in India (Meghalaya): Megalaimobius massarae sp. nov. (Analgoidea: Pteronyssidae) and Picalgoides arbenzi sp. nov. (Psoroptoidea: Psoroptoididae). Males of M. massarae sp. nov. differ from the other three species of the genus by the shape of the transventral sclerite which is much deeper concave. The female of the new species has the external copulatory tub with an acute apex (this structure has a truncated apex in females of other species). Males of Picalgoides arbenzi sp. nov. differ from the closest species P. capitonis Černý, 1974 mainly by the shape of adanal apodemes which are fused into a large arch encircling the anal field. Females of the new species have the hysteronotal shield with acute posterior angles and setae d2 situated on the lateral margins of this shield (in females of P. capitonis the hysteronotal shield has the posterior angles rounded and setae d2 situated at a short distance from the lateral margins of this shield).

Feather mites are very diverse and common ectoparasites of birds. One of the species is named in honor of Dr. Massar, the Principal of the Lady Keane College from Shillong (Meghalaya, India), for her support of the research on ectoparasites of birds. Thesecond species is named in honor of speleologist Thomas Arbenz (Matzendorf, Switzerland), one of the main organizers of the study-related expeditions “Caving in the Abode of the Clouds - Meghalaya, India”.
no DNA Barcodes

Fauveliopsid polychaetes have been collected at dredge disposal sites off Honolulu from 397–507 m depth. We report and describe the first Pacific record of Laubieriopsis cf. cabiochi (Amoureux, 1982), originally described from the North Atlantic. A new species, Laubieriopsis petersenae, n. sp. is described as being the species in the genus with the lowest number of body segments (15). Other distinctive features are the presence of bidentate aciculars on thoracic chaetigers, and unpaired genital papilla present on the right side of chaetiger 6/7. The new species is most similar to the L. brevis complex from the Atlantic and L. hartmanae and L. brevis japonica from the Pacific Ocean, but differs on the combination of the characters cited above. We provide an emended diagnosis for this genus to include the ultrastructure of the acicular with rows of spines, and a key to all described species.

Fauveliopsids are small benthic polychaetes that are mostly found in deeper waters. This species is named after the late Dr. Mary Petersen for her contribution to the study of fauveliopsid polychaetes, including the recognition and description of the genus Laubieriopsis
no DNA Barcodes

Friday, December 5, 2014

From the Inbox: NGS data anaysis

Where : University of Leicester, UK
What: Next Generation Sequencing Data analysis.
When: 7th-9th January 2015

A few places are still remaining and are available for external applicants. Places will be allocated on a first-come-first-served basis.

Next Generation Sequencing methods are becoming ubiquitous in all areas of biology. This three day workshop aims to enable wet-lab biologists to understand and implement basic pipelines for analysis of NGS data. Topics covered will include:

*         An overview of NGS technology
*         A brief introduction to library preparation
*         Common file formats
*         Quality Control
*         Genome Assembly
*         Mapping
*         Variant Calling

The workshop will consist of a mixture of short talks and practical work. Participants are required to have some basic knowledge of Unix to enable them to follow the practical work.

Thursday, December 4, 2014

School Project Results

Hurra - our Fall results are ready and will be send to all participating classrooms as I write this short post. For the first time we offered the School Malaise Trap Program to schools in all of Canada and the response was overwhelming as we actually had to turn down more schools than could participate. One day we might find the right funding sources that will allow us to include many more students than some 2500 as this time. We had 59 Malaise Traps at schoolyards for two weeks this fall. Collectively the schools found more than 3400 species which is an impressive number. To put that into context, this represents about 5% of Canada's known and described insect species collected in just two weeks. Imagine what we could do with more participants and more runs per year.

The results are live on the programs website and if you want to have a look at the final report all our schools get just click on the image below.

Computational tools for environmental samples

Microbes of interest to science rarely exist in isolation. Organisms that are e.g. essential to breaking down pollutants or causing illness live in complex communities, and separating one microbe from hundreds of companion species can be challenging. Environmental samples can be equally complex containing hundreds or even thousands of different species (not necessarily microbes).

The ability to identify and enumerate the organisms in complex communities using culture-independent, genomic technologies and associated bioinformatics algorithms is becoming more important as scientists study organisms that can't be grown in the lab or deal with samples that are so rich that any presorting effort is simply too much effort. The majority of the world's organisms resist traditional lab culture, meaning they have to be studied in the field and identified through genetic information. Of course the DNA Barcoder in me immediately thinks of metabarcoding and very similar challenges. 

While we have a number of extremely potent sequencing platforms available to us there is a shortage of computational tools designed to help identify and characterize the genetic diversity of the residents of these environmental samples.

A new National Science Foundation-supported project run by the Georgia Institute of Technology and Michigan State University, aims equip researchers with the tools needed to compare the genomic information of organisms they encounter against the growing volumes of data provided by the world's scientific community. The tools will be hosted on a web server designed to be used by researchers who may not have training in the latest bioinformatics techniques. A prototype system containing a limited number of computational tools is already available and is attracting more than 500 users each month. The system will initially operate on servers at Georgia Tech and Michigan State University, but if demand and data grow, additional resources may be sought, such as the National Science Foundation's XSEDE supercomputer.

The tools developed in the project will not be developed specific to any one discipline as some of the research questions and issues are universal. The main task is to develop computational solutions for the problems of keeping up with all the new data that become available. The solutions are supposed to provide high throughput in order to deal with data volumes that are increasing geometrically.

Although all tools are developed with the intend to deal with microbial communities they allow for much more and that is what makes me hope we can utilize a good number of them for metabarcoding challenges. Current techniques e.g. identify individual microbes by examining their small subunit ribosomal RNA (SSU rRNA) genes, but the new tools will allow us to analyze entire genomes and meta-genomes and provide the necessary flexibility to deal with a plethora of problems.

I will certainly keep an eye on this project and I believe every metabarcoder should do too. 

Wednesday, December 3, 2014

Four-stranded DNA

Time for some different DNA science - lets leave 'barcoding' out for a post and focus on DNA structure. While browsing through recent science news and publication announcements I stumbled over a paper on G-quadruplex motifs in the Maize genome. I admit I had to look this term up myself as I probably heard about it only once a while back and never followed any new research in that field despite the fact that it is really fascinating. 

The year 1953 marks the big breakthrough in our understanding of DNA as two connected strands known as the double helix. It is the year in which the famous Watson & Crick paper appeared in Nature. As a result just these two names are usually mentioned although there should be four (and they appear in papers within the same issue). There was also Maurice Wilkins who together with Watson and Crick received the Nobel Prize in physiology or medicine for the determination of the structure of DNA, but proper credit was never given to a very important contributor, Rosalind Franklin, respected authority in X-ray crystallography (which made the entire theory possible) and the only of the four researchers that had any degrees in chemistry. She was not properly credited for here contribution for a long time. Unfortunately, this is not the only example of women in science being marginalized, despite the importance of their work.

But back to the DNA structure. We know that the strands that make the double helix regularly separate so they e.g. can replicate. We also know for a while that the DNA comes in different conformations (e.g. A-DNA, B-DNA, and Z-DNA forms). Since the 1990s researchers have been looking at alternative shapes DNA can also twist into. One of those is the G-quadruplex, which is DNA rich in guanine and capable of forming a four-stranded structure. Four guanine bases can associate through hydrogen bonding to form a square planar structure, and two or more of those tetrads can stack on top of each other to form a G-quadruplex (G4 motif, see image). The quadruplex structure is further stabilized by the presence of a cation, especially potassium, which sits in a central channel between each pair of tetrads.

G-quadruplexes have been described as structures in search of a function, as for many years there was minimal evidence pointing towards a biological role for these structures. However, more recently they 

G-quadruplexes are present in genes that regulate cancer and cell division in humans, making it an important focus in scientific research. But not much is known about them. Only more recently they have been connected to immunoglobulin heavy chain switching and telomerase activity. The latter has implications for cancer regulation and made G-quadruplexes an important focus in scientific research. 

The authors of the aforementioned new paper wanted to know if certain the four-strand G-quadruplex DNA might exist throughout the genome of maize. They found 150,000 sequence motifs that could theoretically adopt the G-quadruplex structure, and those were distributed all over the chromosomes. Further examination showed that they were present in very specific places, as opposed to a random distribution. Given this strategic placement, the structure is likely to perform some sort of function:

Taken together, these data support a new hypothesis for functional significance of G4 motifs in maize and potentially elsewhere. Analysis of G4 motif distribution revealed their widespread association with genes for adjustment of cellular energy status, especially under extreme conditions. On the basis of these observations, we propose that G4 motifs reflect a previously unrecognized but widely conserved set of DNA sequences that could function in regulating genes central to the energy state of the cell.

The researchers believe that G-quadruplexes are part of a machinery that allows an organism to turn hundreds of genes off or on for example in response to stress. Very exciting new research and yet another good example for the fact that we don't know nearly as much about genomes as we would like to.

Tuesday, December 2, 2014

Discoveries of the week

This paper represents the first of two contributions that cover the floristic diversity in north central New Mexico. The area encompasses the Tusas Mountains and the Jemez Mountains (including Sierra Nacimiento) of the Carson National Forest and Santa Fe National Forest. Also included is Bandelier National Monument, Valles Caldera National Preserve, Bureau of Land Management (Taos District), and other federal, state, and private lands west of the Rio Grande. The second paper will discuss the floristics of the portions of the two forests and periphery to the east of the Rio Grande, thus primarily the Sangre de Cristo Range. The goal of this two-part series is to enumerate results of the most intensive floristic inventory ever conducted in New Mexico. Here, we report on 19,929 numbered collections of vascular plants (the sum for the entire area covering more than 3.7 million acres is 35,857 new collections). A total of 1,384 unique taxa, including 93 infraspecics and 10 hybrids, are documented from 107 families. Of these, 154 are exotics (14 are designated as noxious in New Mexico), 22 are species of conservation concern, 28 represent first reports or their confirmation for New Mexico, and finally 17 are endemics to New Mexico. Based on verified material at four herbaria, 64 additional unique taxa are included in the Annotated Checklist; thus the grand total is 1,445.

No need to travel to a remote rainforest to discover a new species of plant. Researchers have uncovered a rare hedge-nettle just 50 miles from Charleston, and they named it Stachys caroliniana, after the only state where it has been found.
no DNA Barcodes

Lithobius (Monotarsobius) zhangi sp. n. (Lithobiomorpha: Lithobiidae), recently discovered from Nanshan Park, Yantai City, Shandong Province, and Wuyishan County, Nanping City, Fujian Province, from China, is described. Morphologically it resembles L. (M.) songi Pei, Ma, Shi, Wu, Zhou, 2011 from Province Hebei, China, but can be readily distinguished from the latter by antennae composed of 15+15–19+19 articles versus 19+19–21+21 articles, terminal claw of female gonopods inner tooth broader than the outer vs dorsal and ventral tooth about same in size, ventral plectrotaxy 01320, dorsal plectrotaxy 10210 in the 14th legs, 01210 and 10200 respectively in L. (M.) songi. A key to the Lithobius (Monotarsobius) species of China and Korea is presented.

A new centiped species found in China and named in honor of the myriapodologist Professor Chongzhou Zhang from the Chinese Academy of Sciences.
no DNA Barcodes

Plankton samples obtained from the lagoon system Laguna Navío Quebrado, in northern Colombia, yielded male and female specimens of an undescribed cyclopoid copepod of the genus Halicyclops. The new species belongs to the highly diverse and widely distributed thermophilus-complex. It closely resembles H. clarkei Herbst, 1982 from Louisiana and H. bowmani Rocha & Iliffe, 1993 from Bermuda. These species share the same armature of P1-P4EXP3, with a 3443 spine formula and the terminal antennary segment with 5 setae. However, H. gaviriai sp. n. can be separated from both H. clarkei and H. bowmani by the morphology of the anal pseudoperculum, the proportions of the fourth antennulary segment, the length of the inner basipodal spine of P1, the P1EXP/inner basipodal spine inner length ratio and the length/width ratio of the caudal rami. This is the third species of Halicyclops recorded from Colombia and the first one described from this country. With the addition of H. gaviriai sp. n., the number of species of Halicyclops known from the Neotropics increases to 19. The regional diversity of the genus is probably underestimated.

Found in plankton samples that were taken from the Laguna Navío Quebrado in Colombia. This new copepod was named after named after Dr. Santiago Gaviria to honor his work on Colombian copepods and for his leadership in the formation of new generations of plankton experts.
no DNA Barcodes

Coleophora nepetellae Baldizzone & Nel, sp. n. is described from the southern Alps (Italy and France). It belongs to the Coleophora lixella species group. Its host plants are Nepeta nepetella L. (Lamiaceae) and an unidentified Poaceae. The fifth instar larva, its case, the adult habitus, and genitalia are illustrated. The species is compared to C. nevadella Baldizzone, 1985, here newly confirmed from France and whose larvae feed on Nepeta latifolia DC. in the Eastern Pyrénées. DNA barcodes are shown to be distinct and congruent with morphological differences among species of the lixella group. Barcodes revealed that C. tricolor Walsingham, 1889, formerly known only from Great Britain, is also present in France and Greece.

This new species not only has DNA Barcode sequences but the description also contains a BIN assignment. However, the species name of the BIN on BOLD is different (C. samarensis). The authors might want to update that. The species epithet is derived from the species name of its larval host, the lesser cat-mint (Nepeta nepetella).

We describe a new species of Allobates from the south of eastern Amazonia, Brazil. This species inhabits fluvial springs and the banks of small streams in terra-firme forests along the Tapajós River basin. Average snout-to-vent length is 17.78 mm (range 16.09–19.59 mm) among males and 19.50 mm (range 17.97–20.84 mm) among females. Surface of dorsum is marked by a distinct dark color pattern, with three convex areas, triangle and diamond-shaped. The species has a diffuse pale dorsolateral line (absent in some specimens), while the oblique lateral bar is defined. Dark-brown transversal stripes are present on femoral and tibial dorsal surfaces, which align with each other in live specimens when at rest. Tadpoles have short papillae on anterior (8–10 papillae on each side) and posterior labium (>30 papillae). Posterior labium is projected to the front, hiding posterior tooth rows. Eggs are deposited in nests on rolled or cranked dead leaves on the forest floor. Egg membranes and jelly-nests are transparent. Advertisement calls are mainly characterized by the continuous emission of single notes that might shift sporadically to note-pairs, emitted during short periods. Notes are split by regular silent intervals, with peak frequency ranging between 4273–4867 Hz. 

There was some sequencing done for this description of a new frog species but unfortunately 16S rRNA instead of a DNA Barcode. Not new in the world of amphibians but I thought that we clarified the issue. The species was named for Dr. William (Bill) E. Magnusson, a professor from Instituto Nacional de Pesquisas da Amazônia who has trained many students to understand and love the Amazon forest and its frogs. 
no DNA Barcodes

We describe a new species of the Scinax catharinae Group from Municipality of Porto Seguro, State of Bahia northeastern Brazil. The new species is mainly characterized by its small size, nuptial pad dark colored, and compound pectoral fold. Additionally, we describe the structure of its nuptial pad and compare it with that of S. agilis. We also briefly discuss its phylogenetic relationships within Scinax.

And another new frog species described this week.  The species name melanodactylus is derived from the Latin words melano for black and dactylus for finger. The name is an allusion to the black nuptial pad, a so far exclusive feature among all known species of the genus Scinax.
no DNA Barcodes

From the inbox

GBIF Ebbe Nielsen Challenge

Today the GBIF Secretariat launched the inaugural GBIF Ebbe Nielsen Challenge, hoping to inspire innovative applications of open-access biodiversity data by scientists, informaticians, data modelers, cartographers and other experts competing for a €20,000 first prize.

As most of you will know, for the past 12 years, GBIF has awarded the Ebbe Nielsen Prize to recognize outstanding contributions to biodiversity informatics while honouring the legacy of Ebbe Nielsen, one of the principal founders of GBIF, who tragically died just before it came into being.

The Science Committee, working with the Secretariat, has revamped the award for 2015 as the GBIF Ebbe Nielsen Challenge. This open incentive competition seeks to encourage innovative uses of the more than half a billion species occurrence records mobilized through GBIF’s international network. We expect that these creative applications of GBIF-mediated data will come in a wide variety of forms and formats—new analytical research, richer policy-relevant visualizations, web and mobile applications, improvements to processes around data digitization, quality and access, or perhaps something else entirely. A jury composed of experts from the biodiversity informatics community will judge the Round One entries on their innovation, functionality and applicability, before selecting three to six finalists to compete for a €20,000 First Prize later in 2015. 

The Challenge site is now live. We encourage anyone interested in the Challenge to create a profile and register on ChallengePost so that they receive timely alerts, updates, and other communications about the competition. It’s worth noting, too, that the ChallengePost platform provides access to a community for finding and communicating with developers, software creators and other creative partners about collaborating on submissions, which are due on Tuesday, 2 March 2015.

Help us spread the word

Monday, December 1, 2014

Are Lionfish picky?

Almost two years ago I wrote a blog post on a rapid marine invasion that is currently occurring in the western Atlantic. In the mid-1980s lionfish of the species Pterois volitans were released in Florida. The fish were likely dumped into the ocean by some aquarium fish owners that for some reason didn't want to keep their fish anymore. The native range of this species is around Indonesia but they are now established on coral reefs across the western Atlantic Ocean, Caribbean Sea and Gulf of Mexico, and the invasion continues to spread while reef biodiversity and biomass rapidly declines. The high rate of fish mortality also poses an additional threat to coral reefs themselves, which can become covered with algae if enough fish are not present to eat the algae and keep it under control.

At the time of my post two studies utilized DNA Barcoding of lionfish stomach content to identify prey species for a better estimate on the breadth of the diet of these invaders. It turned out that the lionfish, as it is often with invasives, are generalists. Prey fish were members of groups that fit within the gape size range of lionfish. I was part of one study and we concluded that only well-resolved diet information combined with prey availability data can help to identify the species most at risk from lionfish predation.

Consequently, some of my coauthors now started to identify general traits of prey that predict vulnerability to predation, and examine diet selection at different spatial scales. This new study confirmed that lionfish have a voracious appetite and will eat almost any fish smaller than they are, but it also shows that they do have their favorites.

They find it easier to stalk and attack solitary fish, rather than those in schools. They like to hunt at dusk, near the bottom, and for some reason tend to avoid fish that clean off parasites from other fish species that are common in a marine environment. Together, vulnerable traits heighten the risk of predation by a factor of nearly 200.

Having all the traits that make them vulnerable, for instance, raises a serious question about the ability of some species to survive the lionfish invasion, such as the Exuma Goby (Elacatinus atronasus), a small fish native to one area of the Bahamas. It not has its own Facebook page but more importantly many traits lionfish prefer and maybe therefore threatened by the invader.

Some of these findings may even be relevant to other invasive species problems, such as expansion of the Burmese python in the Florida Everglades and the spread of Asian tiger prawn into the Gulf of Mexico.

Finally, our study shows that a functional, or trait-based, approach has value for generating predictions about the effects of prey selection on the structure of ecological communities. Current thinking about predator–prey interactions can be broadly characterized into two prevailing paradigms: a species-based view, in which food webs are constructed by quantifying the interaction strength between pairs of predators and prey , and a size-based view, which classifies predator–prey interactions based on body size, largely ignoring species identity. Our study is the first to identify general traits of prey that predict vulnerability to predation and indicates that a trait-based view of predator–prey interactions, in which variation in morphology and behaviour determines prey selection, also has significant influence on species interactions within ecological communities. It is also, to our knowledge, the first to examine diet selection simultaneously at two spatial scales. Importantly, both our in situ observations of predation and broadscale analyses of stomach contents identified the same prey traits as important drivers of diet selection. 

DNA Barcoding course in 2015

Registration for the next offering of our DNA Barcoding course is open.

This course was developed together with our experts for distance education here at the UofG. It is an exclusively web-based course offered over an eight week period starting on March 2nd 2015. On average, six to eight hours of study time are required each week to study the course material consisting of reading, audio and video material. Participants will have weekly assignments/quizzes and have plenty of opportunities to participate at discussions that are happening in designated chatrooms. The number of participants is limited to ensure adequate mentoring by the instructor (me).

Course Dates: March 2 to April 24, 2015

If you are interested please have a look at www.dnabarcodingcourses.com. The site details course content, tuition fees, requirements, etc.