Thursday, October 23, 2014

Milkfish fry fishery

According to the Food and Agriculture Organization of the United Nations (FAO) Milkfish (Chanos chanos) is one of the most important food fish species in the world. In Indonesia, Taiwan and the Philippines, more than a quarter of a million tonnes of milkfish are harvested annually in brackish ponds, which represents about 60% of the total fish production from aquaculture in Southeast Asia. This huge amount sourced from a single fish commodity is projected to further increase in the coming years to meet the dietary protein needs of the ever-growing population in Southeast Asia. 

Milkfish farming in Southeast Asia started about six centuries ago. Culture methods in a variety of enclosures are constantly being improved upon. The traditional milkfish industry depended totally on an annual restocking of farm ponds with juvenile fish reared from wild-caught fry. Seasonal and annual variations in fry availability made the industry vulnerable. During the past decade, research focused on the mass production of fry in hatcheries to become independent from wild-caught fry. However, it seems this hasn't been taken up completely. Large quantities of fry are still taken from the Ocean and that causes another problem:

Milkfish fry fishery, an important industry in the Philippines, uses non-selective fishing gears and push nets in coastal areas which lead to the capture of other non-targeted juvenile aquatic species. Unfortunately, information on the amount and the identity of by-catch species is lacking thus the extent of impact of the fry fishery is not known.

A new study from the Philippines shows that by-catch fish species of the milkfish fry industry included various marketable food fish, culture species and aquarium trade species. The researchers used DNA Barcoding to  identify postlarval and juvenile fish samples that were collected from the catch of local fishers using traditional fishing gears and push nets, with milkfish fry as target species.

By-catch in fisheries is a well known global problem. In 2003 it was estimated that approximately 20 million metric tonnes, representing about a quarter of the total world catch are actually by-catch. This represents a serious threat to biodiversity and coastal ecosystem integrity. The present study shows the utility of DNA Barcoding in identifying the juvenile fish species threatened as by-catch in fry fishery. It proves to be very valuable in aiding management efforts for the sustainability of these natural resources.

Wednesday, October 22, 2014

Biological Control of Hemlock Woolly Adelgid

hemlock woolly adelgid
The hemlock woolly adelgid (Adelges tsugae), a native of Asia, is a <1 mm long reddish purple insect that lives within its own protective coating. White, woolly masses that shelter these sap-feeding insects can be found at the bases of hemlock needles along infested branches. The presence of these white sacs, which resemble tiny cotton balls, indicate that a tree is infested. The hemlock woolly adelgid is a threat to North American hemlock forests. As of 2007, 50% of the geographic range of eastern hemlock (Tsuga canadensis) had been impacted. The feeding activities of these hemipterans reduces new shoot growth, premature needle drop, thinned crowns, branch tip dieback, and eventual tree death. 

Laricobius osakensis
Aside from recommending the use of insecticides researchers focused on biological control measures for this pest. In 2006 the derodontid Laricobius osakensis was imported from Japan to the United States for study in quarantine facilities as a potential biological control agent. Four years later it was granted release from quarantine by the U.S. Department of Agriculture. However, it seems that this was premature. A new study published in the Southeastern Naturalist describes what happened not much later:

However, after sequencing DNA barcodes for members of the L. osakensis colony in the fall of 2011, it was discovered that the colony was contaminated by another Japanese species, Laricobius naganoensis. 

The problem is that regulations clearly state that insects shipped from abroad must not contain unauthorized species; therefore the presence of L. naganoensis within the L. osakensis colony resulted in the placement of the L. osakensis colony back into quarantine before beetles were released in the field.

Laricobius naganoensis is a species that lives in sympatry with Laricobius osakensis. Both species are morphologically very similar which makes it difficult to differentiate them. Females cannot be reliably differentiated using morphology and males only by their genitalia but this identification requires dissection of dead specimens which is something one would like to avoid if the goal is to release the beetles as biological control agent.

The researchers were looking for  a quick and inexpensive assay to identify both species and evaluated non-lethal DNA extraction methods. They designed a restriction fragment length polymorphism (RFLP) assay based on two enzymes (AluI and MboII ) using DNA Barcodes. In addition they found out that a single antenna from a specimen is sufficient to retrieve a DNA Barcode sequence. Further research will have to show if the removal of an antenna will have an impact on beetle survival and reproduction but this is a very promising result:

Without the proper permits, L. naganoensis cannot be released legally in the US. Therefore, distinguishing between L. osakensis and L. naganoensis is currently necessary for universities and state or federal agencies that will be importing L. osakensis from Japan for biological control of Hemlock Woolly Adelgid. The RFLP assay developed here is less expensive and less time consuming than DNA sequencing, and the equipment needed for this assay is available in most basic molecular labs. The enzymes AluI and MboII were each sufficient for distinguishing the species. However, since there is likely to be more natural diversity than we have sampled to date, possibly resulting in additional banding patterns, we recommend using both enzymes independently and sequencing any individuals for which the assay results do not match or which produce new gel patterns not reported here.

Tuesday, October 21, 2014

Discoveries of the week

It is Tuesday again, time for some new species accounts.

We propose the name Bumba as a new name for Maraca, preoccupied by Maraca Hebard, 1926 (Orthoptera). We describe and illustrate Bumba lennoni, a new theraphosid species from Caxiuanã, Pará, Brazil. This species differs from the other species of the genus in the extremely reduced keel on male palpal organ and in the higher number of labial and maxillary cuspules. Females additionally differ in the spermathecal morphology. As a consequence of the name replacement, three new combinations are established.

The name of the new species came across when the authors of the study found out that they are all great fans of Beatles music. The new tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon. The genus name, Bumba, which is a proposed replacement of the former name Maraca, already taken and used within the order Orthoptera, is taken from the Brazilian theatrical folk tradition of the popular festival called Boi-bumbá (hit my bull), which takes place annually in North and Northeastern Brazil.
no DNA Barcodes

Angulobaloghia rutra
Three new species of the family Rotundabaloghiidae are discovered and described from Sabah, Malaysia. The unusual Angulobaloghia rutra sp. n. differs from the other known Angulobaloghia Hirschmann, 1979 species in the long anterior process of the female’s genital shield. Rotundabaloghia (Circobaloghia) tobiasi sp. n. has very long and apically pilose dorsal setae and two pairs of bulbiform setae, which are unique in the subgenus Rotundabaloghia (Circobaloghia) Hirschmann, 1975. The long, serrate and curved setae in the big ventral cavity of Depressorotunda (Depressorotunda) serrata sp. n. is a so far unknown character in the subgenus Depressorotunda (Depressorotunda) Kontschán, 2010.

These are all tiny mites that live in soil, leaf litter and moss.The maximum of their diversity is found in tropical rain forests and these new species from Sabah, Malaysia are the first reported from this region.
no DNA Barcodes

Pseudapanteles is a moderately diverse genus of Microgastrinae parasitoid wasps (Hymenoptera: Braconidae), endemic to the New World and with the vast majority of its species (including many undescribed) in the Neotropical region. We describe here 25 new species from Area de Conservación Guanacaste (ACG), northwestern Costa Rica, based on 400 studied specimens. A key to all 36 known species of Pseudapanteles is provided (except for P. brunneus, only known from a single male), and species are placed in three newly created species-groups. Host records are known for only 25% of the species; most are solitary parasitoids of the caterpillars of several families of small Lepidoptera (Crambidae, Elachistidae, Gelechiidae, Incurvariidae, Sesiidae, Tineidae). DNA barcodes (part of the CO1 gene) were obtained for 30 species (83%), and provide a start for future study of the genus beyond ACG. Brief descriptions (generated by Lucid 3.5 software) and extensive illustrations are provided for all species. The following new taxonomic and nomenclatural acts are proposed: Pseudapanteles moerens (Nixon, 1965), comb. n., Pseudapanteles brunneus Ashmead, 1900, comb. rev., a lectotype is designated for Pseudapanteles ruficollis (Cameron, 1911), and the following 25 species nova of Pseudapanteles (all authored by Fernández-Triana and Whitfield): alfiopivai, alvaroumanai, analorenaguevarae, carlosespinachi, carlosrodriguezi, christianafigueresae, hernanbravoi, jorgerodriguezi, josefigueresi, laurachinchillae, luisguillermosolisi, margaritapenonae, mariobozai, mariocarvajali, maureenballesteroae, munifigueresae, oscarariasi, ottonsolisi, pedroleoni, raulsolorzanoi, renecastroi, rodrigogamezi, rosemarykarpinskiae, soniapicadoae, teofilodelatorrei.

This genus consists of solitary parasitoids of caterpillars of several families of small Lepidoptera. The publication is solely focusing on one area in Costa Rica (albeit the best studied one available) and already it provides 25 new members of a single genus. Experts for parasitoid wasps claim that there are likely thousands of species especially in the families Braconidae and Ichneumonidae awaiting discovery and descriptions.

A new species of the genus Isoperla (Plecoptera, Perlodidae), belonging to the oxylepis species-group is described, and the male mating call is characterized. Its range falls within a small region of the Southern Limestone Alps which is well known to be one endemism-centre of aquatic insects.

This new stone fly was collected was collected from the Karawanken Alps in southern Austria and the nearby Kamnik Alps in northern Slovenia. The species is named in honour of the second author’s wife Claudia. 
no DNA Barcodes

To assess the taxonomic relationship between G. nipponensis and G. sobaegensis, morphological features and molecular phylogenetic relationships using the nuclear 28S rRNA and the mitochondrial COI genes were examined. Detailed morphological observations revealed that G. nipponensis and G. sobaegensis were clearly distinguishable. In addition to the morphological differences, these two species were genetically diverged. In the course of this study, an undescribed species was found from Tsushima and Iki Islands and described here as G. mukudai. In the molecular phylogenetic analyses, monophyletic relationships of G. nipponensis, G. sobaegensis, and G. mukudai were shown but relationships among three species were unclear due to low statistical supports. Phylogeography of G. nipponensis, G. sobaegensis, and G. mukudai were discussed.

The genus Gammarus contains about 200 species mostly recorded from fresh, estuarine, and marine waters of the northern hemisphere. This new species is named in honour of Dr. Takao Mukuda of Hiroshima University who supported the work of one of the authors.

Exacum zygomorpha
Exacum affine
The paper provides a key for identification and a checklist of mycoheterotrophic species of the genus Exacum, representing a well-defined group of achlorophyllous members of Gentianaceae regarded sometimes in the limits of a separate genus Cotylanthera. One novel species, E. zygomorpha, discovered in northern Vietnam, is described and illustrated as new for science. Among other features the discovered species strikingly differs from its congeners in having distinctly zygomorphic flowers.

According to the authors all members of the genus are very rare unattractive plants easily overlooked in botanical surveys and poorly represented in the world's herbarium collections. Probably the best known species is Exacum affine, known as Persian violet. No image of the new species as the paper is hiding behind a pay-wall. So I chose its famous relative.
no DNA Barcodes

Monday, October 20, 2014

Stored product beetles

For farmer storing harvested food grains these names strike fear into them: Rusty grain beetle, flour mill beetle, flat grain beetle. These beetles can be found feeding on grain and cereal products, but also other dried material of plant origin, as well as packaged and processed goods. They have been recorded in wheat, corn, rice, barley, flour, oilseeds, cassava root, dried fruits and even chilies. Their larvae feed preferentially on the germ of the whole kernels, but sometimes they hollow out the entire kernel. Growth of mold in the kernel renders it more suitable as larval food. 

All these species belong to the genus Cryptolestes and apparently they unable to feed on sound grain, but instead need kernels with very slight imperfections or injuries. There are at least 15 species of the genus which are regarded as storage pests of economic importance and cause losses in temperate and tropical regions around the world.  Five of these species, namely Cryptolestes ferrugineus (rusty grain beetle), Cryptolestes pusillus (flat grain beetle), Cryptolestes turcicus (flour mill beetle), Cryptolestes pusilloides and Cryptolestes capensis, represent the most common Cryptolestes beetles found in stored products.

Identification of Cryptolestes species is traditionally based on morphological characters of adults. The species are small (c. 2 mm), similar in appearance, and difficult to identify on the basis of external morphological characters alone. The characters are variable and differences among species are not obvious . It is generally agreed that identification requires examination of male or female genitalia . Only experts can identify species of the genus Cryptolestes accurately. 

Unfortunately, more frequently found in stored products are body fragments and larvae, both of which lack specific features for species identification. Reason enough to test if DNA Barcoding can help with this issue. An international team of researchers now tested the suitability of DNA Barcoding for the identification of the five most common species (listed above).

In the present study, the five pre-identified Cryptolestes species were successfully diagnosed to species level by use of DNA barcoding. Also the larvae were successfully identified. The abdomens removed from adults in order to avoid their negative influence on sequencing (gut content) could also be used as voucher material, because the genitalia inside abdomens are decisive diagnostic characteristics for Cryptolestes sp. (Bank, 1979).

For their proof of concept study they used cultures of the five species that were obtained in labs on three different continents (Asia, Europe, North America). The researchers obtained 93 specimens of adults and larvae which were expert identified and subsequently subjected to a standard DNA Barcoding routine. Not surprisingly the colleagues were very pleased with the results:

For researchers or practitioners, with access to DNA sequencing facilities, our data make it possible to rapidly identify the five species of Cryptolestes based on simple DNA sequence comparisons and will facilitate the identification in quarantine inspection and other pest control efforts. The present study also provides a large set of sequences to design species-specific PCR primers annealing to regions displaying variation among species but not among populations or individuals of the same species, which makes it possible to design rapid identification kits.

Friday, October 17, 2014

3-D printed insect traps

The 3-D printed  insect trap in action
(Image credit Joshua Reid Carswell, FDACS)
If we want to monitor or reduce populations of insects or other arthropods we need to get our hands on them first. Everyone, that ever worked with insects had to handle an insect trap such as our famous Malaise trap or as simple as a sweep net. Not surprisingly, insect traps vary widely in shape, size, and construction, often reflecting the behavior or the ecology of the target species, and almost equally often the tight budget of scientists. The problem begins when your target species is not collected by the standard methods, or specimens are too damaged to provide any meaningful result. Another problem to consider is the maintenance of the traps. How often do we have to come back to the trap and check it? If you need a large array of traps or if you work in a remote location you will consider finding ways to collect less often.

All that considered the ideal trap would be unique and specifically designed to any particular research need. There are lot of modifications to standard traps out there and an even higher number of DIY versions created by desperate entomologists or ecologists.

But what if we could use modern technology to help with that? Researchers at the Florida Department of Agriculture and Consumer Services (FDACS) started to employ 3-D printing technology to build sophisticated, specialized and far more complicated contraptions.

Florida is currently battling the invasion of the Asian citrus psyllid (Diaphorina citri), a vector for bacteria that cause citrus greening disease. The sap-sucking hemipteran is infesting the famous state’s orange groves, and costing Florida an estimated $4.5 billion in lost economic output and more than 8,000 jobs during just a five-year period.

State inspectors are trying to monitor insect introductions into the state and mostly they are using simple sticky traps made with a glue known as tanglefoot. The glue is usually applied to some heavy duty tape that is wrapped around tree trunks. Insects walk over and are trapped in the glue but unfortunately specimens are often too damaged to do any further work with them not even molecular analysis simply because they don't contain any preservative. On the other hand its paramount to keep the insect intact, such that it is possible to isolate DNA and detect the pathogens.

The FDACS researchers studied the pest’s behavior for a long time which enabled them to tailor a trap to the insect. The trap is designed and drawn on a computer, and then someone just hits print. The plastic is then placed layer-by-layer to make the pieces that will form the insect trap. The new designs include such features as fake branches to fool insects. As an insect climbs along the fake branches, it falls into one of the small holes on the trap and immediately enters a pool of preservatives. 

The new 3-D printed traps seem to work better for disease monitoring because the insects can be recovered from a reservoir of preservative in which DNA of the specimens is conserved. Through its design the trap is also more selective.The costs in this case were actually fairly moderate. The 3-D printer with software was about $2300 and the traps cost $5 to $10 apiece to make. I think that is money well spend.

Thursday, October 16, 2014

Spider diversity

Female Aganippe sp. Image: WA Museum
Mygalomorphae is an infraorder of spiders including several families comprising e.g. tarantulas as well as the famous Australian funnel-web spiders. Quite a few species of this group are short-range endemics which makes them exceptionally well-suited for monitoring conservation status of terrestrial ecosystems. Mygalomorph spiders have been proposed as bioindicators for monitoring ecological changes despite secretive habits and a challenging taxonomy as only males can be reliably identified to species. 

A sexually-mature male mygalomorph will typically spend several weeks travelling above ground, looking for females. Not only does this make him vulnerable to predators such as birds or ghost bats, he also has a problem in case he is lucky enough to find a female as in some cases she will simply kill and eat him if he is unable to escape after mating.

A large portion of all specimens collected and stored in museums are juveniles or females, which have very limited morphological features that can be used for species-specific classification. The life of an adult mygalomorph spider male is usually short and they only mature into a male at certain times of year. That makes taxonomy within this group rather difficult as species have typically been classified by the adult male's unique sex organ. 

Sure enough, DNA Barcoding of spiders becomes increasingly popular and a new publication from Australia shows once more how little we really know in terms of biodiversity.

To assess mygalomorph diversity and the distribution of species in the Pilbara, we employed a molecular barcoding approach. Sequence data from the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene were obtained from 1134 specimens, and analysed using Bayesian methods. Only a fraction of the total mygalomorph fauna of the Pilbara has been documented, and using a species boundary cut-off of 9.5% sequence divergence, we report an increase in species richness of 191%.

191% increase with a very conservative cut-off value (9.5%) in a limited bioregion. This is a remarkable number largely owing to the fact that male spiders needed for morphological determination are so rarely available. A big step forward and the authors seem quite excited about the possibilities:

Barcoding provides a rapid, objective method to help quantify mygalomorph species identifications and their distributions, and these data, in turn, provide crucial information that regulatory authorities can use to assess the environmental impacts of large-scale developments.

Wednesday, October 15, 2014

Bee pollen

Pollen collection system (from the study)
The current pollen demand for human nutrition has drastically increased due to its therapeutic value, with potential for medical and nutritional applications. Pollen pellets collected by honeybees (Apis mellifera L.) contain proteins, all the basic amino acids, carbohydrates, lipids, such as Omega-3 and Omega-6 fatty acids, vitamins and minerals. Based on the presence of these compounds, pollen is eligible as human food, and national pollen standards exist in a number of countries. Consequently, many beekeepers have transitioned their interests to pollen collection, and currently, the global pollen production is approximately 1500 tons per year, with Spain the most important producer.

Honeybees tirelessly fly from flower to flower collecting thousands of pollen grains that adhere to the tiny hairs on the back of their hind legs while using a bit of nectar from their stomach to help pack the pollen into pellets. Carrying two pellets at a time they travel back to the hive with their bounty and feed it to their young.

Beekeepers sometimes attach a small box fitted with a screen in the doorway of a hive to allow the bee to enter but harmlessly remove the pollen granules from their legs. Beekeepers have to be careful to collect only a small amount from any given hive, so as not to deprive the bees of this important food source for their young. The collected pellets are then either sold fresh, or frozen or dehydrated.

Pollen composition and the diversity of its source directly influences the quality and safety of all honeybee products. Not long ago I published a post on a study that looked at antibacterial effects of honey and a similar study appeared a few days ago. The identification of plants visited by honeybees is of fundamental importance for beekeepers to assess the quality of their products, and guarantee the consumer of product safety. In addition, the geographical origin of pollen strongly affects its commercial value

As shown in the earlier studies, DNA Barcoding is perfectly suited to help with such analyses. Reason enough for a team of Italian researchers to put the pollen to the test. By the way, they also published one of the studies I mentioned above

The team collected pollen pellets using modified beehives placed in three zones at different altitude within the Grigna Settentrionale Regional Park in Italy. The park is a protected area in the Bergamo alps. In order to test the plant composition of collected pollen pellets the authors assembled a DNA barcoding reference libray including rbcL and trnH-psbA sequences of 693 plant species representing about 45% of the entire flora of the region.

Needless to say, they have been very successful and they were able to document substantial variability in pollen composition between higher and lower altitudes as well as between seasons. Overall, they were able to find 52 different plant species in the pollen collected and among those, nine were rare and in some cases endemic species. At one site, the pollen contained known alien species, such as Lonicera japonica and Pelargonium x hortorum. The colleagues conclude:

Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.