Friday, October 31, 2014

Happy Halloween

...and then there were two

The tephritid fruit fly genus Bactrocera is very large and contains about 500 described species. One of those, the oriental fruit fly, Bactrocera dorsalis, is considered a very destructive pest of fruit in all areas it occurs. It is established in numerous regions in Asia, and is often intercepted in the United States, sometimes reestablishing infestations that were previously eradicated. 

The species belongs to a species complex that contains almost 100 morphologically very similar taxa. Most species in this complex are of no economic concern; however, the oriental fruit fly and four of its closely related species, namely the Asian Papaya fruit fly, Bactrocera papayae , the Philippine fruit fly, Bactrocera philippinensis , the Carambola fruit fly, Bactrocera carambolae, and the Invasive fruit fly, Bactrocera invadens, belong to the world's most important horticultural pests.

The high morphological and even genetic similarity between all these species makes identification notoriously difficult and species boundaries were hotly debated. Reason enough to start a multidisciplinary approach to solidify taxonomic reassignments. Such an integrative taxonomic study has now been published by a large group of researchers. They provide multiple lines of evidence across a range of disciplines (morphology, molecular genetics, cytogenetics, sexual compatibility, chemoecology) undertaken by independent research groups spanning a period of 20 years. Based on their evidence  they actually propose the synonymy of Bactrocera papayaeBactrocera invadens, and Bactrocera philippinensis under the senior name Bactrocera dorsalis. Bactrocera carambolae on the other hand is still considered a valid species.

That leaves us with the question on the actually impact of these results. The authors have a lot to say about that as they think the impact of the name changes are significant:

Currently, the distributions of B. dorsalis complex species dealt with in this paper are almost entirely disjunct, with most countries having only one of the species (Thailand is unique in having three – B. dorsalis, B. papayae and B. carambolae). Under the rules of the International Plant Protection Convention, a country with one of the species but not another has a sovereign right to impose risk reduction treatments on commodity imports from a country with another pest member of the B. dorsalis complex species; this reality severally restricts trade for many nations. Recognition that B. dorsalis, B. invadens, B. papayae and B. philippinensis are one species will ease restrictions to fresh commodity trade between countries where these are native or nonregulated invasive taxa.

A key element of quarantine is risk assessment. As demonstrated by Hill & Terblanche (2014), basic quarantine issues such as enhanced predictive power to determine the likely spread, and ultimate distribution, of invasive members of the B. dorsalis complex are greatly improved by accurately recognizing species boundaries.

Pest management
Many pest management tools will be improved by resolving the species limits, of which application of the SIT [Sterile Insect Technique] is one. The SIT requires mass release of sterilized male flies to mate with, and so make infertile, wild conspecific females. A great body of SIT knowledge exists for B. dorsalis, but much less so for the other members of the complex. The recognition of conspecificity among key pest taxa within the complex will allow B. dorsalis SIT to be applied in new countires and regions.

Thursday, October 30, 2014

Metabarcoding soil and leaf-litter

Today I came across a new very interesting paper published in Ecological Indicators. An international group of researchers used established metabarcoding protocols to compare soil and leaf-litter samples with malaise trap samples in southern China and to compare leaf-litter samples with canopy-fogging and morphologically identified spider samples in central Vietnam.

For those that are not so familiar with the term metabarcoding here a text fragment from my most successful blog post ever (sic!): Metabarcoding is a rapid method of biodiversity assessment that combines two technologies: DNA based identification and high-throughput DNA sequencing. It uses universal PCR primers to mass-amplify DNA Barcodes from mass collections of organisms or from environmental DNA. The PCR product is sent to a next generation sequencer and the result is a wealth of DNA sequences. Such sequence collections are auditable, because sites can be sampled by independent parties, or samples can be split, and analysed by certified entities following a standardized protocol. They can also be verified by fieldwork to confirm the presence or absence of particular species. These metabarcode data sets are taxonomically more comprehensive, many times quicker to produce, and less reliant on taxonomic expertise.

However, the leading question in this publication is focusing on the sampling technology rather than the actual analysis in laboratory: Is it possible to substitute ground-level (soil or leaf litter) samples for aboveground samples when conducting biodiversity surveys? The colleagues argue that a soil or leaf-litter sample can be collected in minutes, whereas an aboveground sample, such as from Malaise traps or canopy fogging, can require days to set up and run, during which time they are subject to theft, damage, and deliberate contamination.

It is no secret that we run a lot of malaise traps of the course of Canada's summer seasons and we had only very few instances of damage due to other animals (damage caused by a bear) or vandalism (one case during our school project). However, as reported in the paper there are examples were traps have been damaged by larger animals or uniformed people. New to me was the deliberate adulteration of environmental surveys mentioned. Another disillusioning fact to think about and frankly it makes me angry to think that brilliant minds have to waste their time designing experiments and monitoring tools to counteract potential fraud and vandalism. 

On the other hand it is great to learn that the world we didn't really dare to enter (soil and leaf litter samples) in our efforts to catalog the life on our planet one barcode at a time, can be explored just as effectively as the one literally just centimeters above, which we target with our hundreds of malaise traps:

Here we show that while the taxonomic compositions of soil and leaf-litter samples are very different from aboveground samples, both types of samples provide similar ecological information, in terms of ranking sites by species richness and differentiating sites by beta diversity. In fact, leaf-litter samples appear to be as or more powerful than Malaise-trap and canopy-fogging samples at detecting habitat differences. We propose that metabarcoded leaf-litter and soil samples be widely tested as a candidate method for rapid environmental monitoring in terrestrial ecosystems.

The authors are still cautious with respect to the prospects of metabarcoding but the technology has made substantial progress in the last few years. Some of the issues described already sound like mere technicalities that can be overcome with some creativity and smart testing. 

I think it is necessary to mention that they used different marker systems for the different samples. For the ground-level samples they took 18S and for anything above ground they used COI which could introduce a bias in the analysis but the researchers took this (at least partially) into account:

We caution that the higher prevalence of nematodes and annelids in the ground-level samples could reasonably be attributed to the different genetic markers used; the 18S primers were designed to amplify across the Metazoa, whereas our COI primers are only known to amplify successfully across the Arthropoda (Our COI primers cannot be used to amplify from soil and leaf-litter samples because >99% of returned OTUs are bacterial). Regardless, the taxonomic compositions of the metabarcode datasets are consistent with the microhabitats from which the samples were collected. Soil and leaf-litter microhabitats are indeed highly species-rich in spiders, mites, centipedes, millipedes, roundworms, and ringed worms, whereas canopy-fogging and Malaise-trap samples do capture mostly insects.

I have to admit that I disagree with the authors a little as it is my hope that efforts will be made to develop functional COI primers to amplify DNA Barcodes for all metazoan groups (only very few groups will remain to be a problem) which would allow us to match undetermined metabarcoding samples to reference specimens.

Wednesday, October 29, 2014

Landscape genetics

Landscape genetics is a discipline that combines the fields of population genetics and landscape ecology to facilitate understanding of how geographical and environmental features structure genetic variation. Its analysis involves detection of genetic discontinuities and the correlation of these discontinuities with landscape features. The idea was developed about 11 years ago, so around the same time DNA Barcoding entered the stage. In a recently published review the leading author of the initial publication states that the main objective of modern landscape genetics is to improve our understanding of the effect of global change on genetic patterns to address these two key questions:
  • how has recent global change (i.e., land use and land cover as well as climate change) affected patterns of neutral and adaptive genetic variation; 
  • are species likely to adapt to ongoing global change on an ecological time scale?
The Asian tiger mosquito (Aedes albopictus), which is native to Southeast Asia, was spotted in Houston in 1985. By 1986 it had already reached states like Missouri or Florida, both not bordering Texas. Today it can be found in all of the southern states and as far north as Maine. The mosquito arrived in the U.S. in a shipment of used tires from Japan. Aedes albopictus lays eggs that can survive even if any water evaporates, so they're very easy to transport.

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. It is an aggressive daytime biter with an affinity for humans. 

Looking at a map of the current range of Aedes albopictus in the U.S., it is impossible to know how the mosquito spread from its point of introduction, although it could hardly have been by wing power alone, since an adult mosquito flies less than a kilometer in its lifetime. In order to find out how the tiger mosquito spread from the point of introduction, a group of US researchers used landscape genetics as it provides a way to rigorously test competing hypotheses for dispersal.

As a first step they had to establish the genetic structure of the U.S. population. As a so called container mosquito, Aedes albopictus lays its eggs just above the waterline in old tires, flower pot saucers, water bowls, bird baths, and most importantly for this study in cemetery flower vases. To sample the mosquito population the colleagues collected larvae from abandoned flower vases in cemeteries both on the edge and within the core of the mosquitoes' U.S. range in both rural and urban areas.

The immature mosquitoes were raised to adults in the laboratory so the species could be accurately identified (well, DNA Barcoding might have helped to speed this up). Subsequently, DNA was extracted from clipped legs and genotyped at nine different microsatellite locations. The genetic structure retrieved by the microsatellite analysis was then compared to those predicted by 52 different models of mosquito dispersal that variously took into consideration habitat and highways.

It turned out that gene flow over long distances was correlated with highways and bodies of water. People had carried mosquitoes from the core of their range to its edge along highways, likely by semi-trailers or in cars. Wetlands and lakes were important, not because they are breeding sites, but because they tend to occur in areas where frequent rainfall refills artificial containers and supports mosquito growth.

The scientists also looked more closely at what was happening at the range edge. Because Aedes albopictus lays eggs in treeholes and is often found resting at forest edges, they expected forests at the northern edge of the mosquitoes' range to act as natural corridors for dispersal. However, it turned out forests were barriers rather than corridors, perhaps because Aedes albopictus had not been able to displace the native treehole mosquito, Aedes triseriatus.

Our results revealed a combined role of natural and human-aided dispersal throughout the range of Aedes albopictus only two decades after its initial introduction into the USA. Naturalized populations have become sufficiently dense that dispersal and recolonization are now naturally sustained, but long-distance dispersal, particularly between range-core and range-edge sites, is ongoing. A similar trend may be expected for introductions of other exotic species, particularly those that spread rapidly via human-aided transport and then establish dense, naturally connected sites. Our results affirm the importance of denying entry of exotic species as well as rapid responses to eradicate soon after introduction. In addition, multiple introductions can increase genetic diversity and adaptive potential for some established invasive species; potential ports of introduction should remain vigilant to continued importation of Aedes albopictus in used tires and other shipments with the potential to contain eggs and/or larvae from other continents where Aedes albopictus is now established. Finally, the spread of disease is often linked to human-aided transport, land-use change and climate-change ; recent advances in genetic and geographic techniques may improve the utility of landscape genetics as a viable assessment tool for mitigating disease risk, including disease vectors such as Aedes albopictus, at a global scale.

Tuesday, October 28, 2014

Discoveries of the week

A new species of marine interstitial wormshrimp, Ingolfiella maldivensis, is described from coral sand on the inner and outer reef off Magoodhoo island, Faafu atoll, Maldives. Six females were found and compared to other species from the Maldives and those bordering the Indian Ocean and beyond. Morphological resemblance ties it to a species from the Caribbean island of Curaçao. Both species are found in shallow sublittoral interstitial spaces.

Obviously this new species was named after the group of islands where it was found, in the Republic of the Maldives. Wormshrimps are actually amphipods that live exclusively subterranean in most forms of aquatic habitats.
no DNA Barcodes

Tomopaguropsis ahkinpechensis

A new hermit crab species of the family Paguridae, Tomopaguropsis ahkinpechensis sp. n., is described from deep waters (780–827 m) of the Gulf of Mexico. This is the second species of Tomopaguropsis known from the western Atlantic, and the fifth worldwide. The new species is morphologically most similar to a species from Indonesia, T. crinita McLaughlin, 1997, the two having ocular peduncles that diminish in width distally, reduced corneas, dense cheliped setation, and males lacking paired pleopods 1. The calcified figs on the branchiostegite and anterodorsally on the posterior carapace, and the calcified first pleonal somite that is not fused to the last thoracic somite, are unusual paguroid characters. A discussion of the affinities and characters that define this new species is included, along with a key to all five species of Tomopaguropsis.

The species name is derived from the Mayan “Ah-Kin-Pech” (meaning “place of snakes and ticks”), a name given to a settlement where nowadays the Mexican city Campeche,, can be found. The new species was found near Campeche Bank.
no DNA Barcodes

Cynegetis chinensis
The first species of the genus Cynegetis Chevrolat is recorded from China. Cynegetis chinensis Wang & Ren, sp. n. is described from the Ningxia Province in North China. A key to the known species of Cynegetis is given. Diagnostic similarities and differences between Cynegetis and Subcoccinella Agassiz & Erichson are discussed and illustrated.

Cynegetis is a small genus, containing only two species occuring in the Palaearctic region. The group was not known to occur in China until some comprehensive investigations of Chinese ladybird collections revealed this new species, hence the name 'chinensis'.
no DNA Barcodes

Dorstenia luamensis
A new species of Dorstenia L. (Moraceae), D. luamensis M.E.Leal, is described from the Luama Wildlife Reserve, west of Lake Tanganyika and north of the town of Kalemie in the eastern part of the Democratic Republic of Congo (DRC). This species is endemic to the region and differs from any of the other species by its fernlike lithophytic habit and lack of latex. A description and illustration of this species is presented here. Dorstenia luamensis M.E.Leal inhabits moist and shady vertical rock faces close to small waterfalls in the forest; the species is distributed in small populations within the type locality, and merits the conservation status of endangered (EN).

A new member to the large fig family. The genus Dorstenia is the second largest in the family with 105 species. It is unique among all Moraceae due to extremely diverse growth habits and life forms. The species name of the 106th member of the genus refers the Luama Wildlife Reserve where the new species was collected.
no DNA Barcodes

Pilea matthewii, Pilea miguelii, Pilea nicholasii, Pilea nidiae
Pilea matthewii

Four new species of Pilea (Urticaceae) from the Andes of Venezuela are described and illustrated: Pilea matthewii sp. nov., P. miguelii sp. nov., P. nicholasii sp. nov., and P. nidiae sp. nov. The affinities of these species and their positions within the informal classifications of Pilea proposed by Weddell and Killip are discussed. Notes on other species of Pilea found in Venezuela also are presented.

The genus Pilea is another large genus with over 700 species. It belongs to the nettle family. Member species are found worldwide in tropical, subtropical, and temperate areas although the group is absent from Australia, New Zealand, and Europe.
All four species are named in honor of researchers that participated at various field expeditions in which the new species were collected.
no DNA Barcodes

Tynanthus densiflorus, Tynanthus espiritosantensis
Tynanthus densiflorus
Tynanthus is a genus of lianas that is broadly distributed through the Neotropics. Two new species of Tynanthus from Brazil are here described and illustrated: T. densiflorus, from Amazonas, and T. espiritosantensis, from Espírito Santo. T. densiflorus is recognized by the conspicuous interpetiolar glandular fields, a feature rarely found in Tynanthus, and the dense thyrses. Tynanthus espiritosantensis, on the other hand, is recognized by the bromeliad-like prophylls of the axillary buds and the lax thyrses. Information on the distribution, conservation status and morphologically similar species are provided.

Two new species of lianas. The term liana does not represent a taxonomic grouping, but is rather a description of the way the plant grows, much like the terms tree or shrub. Lianas may be found in many different plant families, here the family Bignoniaceae. The names refer to the density of flowers and the type locality respectively.
no DNA Barcodes

Monday, October 27, 2014

Barcoding Diatoms

Diatoms are microscopic algae living in both fresh and salt water.  They are unicellular organisms with silica impregnated cell walls. Living diatoms are among the most abundant forms of plankton and represent an essential part of the food chain in the ocean. Diatoms are responsible for at least 25% of global carbon dioxide fixation. Once dead, their shells accumulate on the seabed and eventually form siliceous sediment deposits.

Given that diatoms are photosynthetic algae, they are restricted to the sunlight zone, i.e. the depth of the water in a lake or ocean that is exposed to sufficient quantities of sunlight to allow for survival.  They are highly sensitive to any environmental changes such as light availability, temperature, salinity etc.  In general, diatoms prefer cold, nutrient rich waters. This is what makes them so valuable as indicators for water quality. The specific composition of diatom communities is a very sensitive instrument to measure changes in aquatic environments.

Diatoms have been regularly used as bioindicators to assess water quality of surface waters, especially in developed countries. Many of the widely used diatom indices have been developed from studies of European rivers and they are integrated in policies such as the European Water Framework Directive.

However, Diatom-based indices require unambiguous taxa identification to species level and that is challenging. Morphological approaches require expert taxonomic knowledge and often expensive infrastructure as many of the characters can only be detected by scanning electron microscopy or similar high-resolution technologies. 

It comes to no surprise that researchers working with diatoms are looking into the application of DNA Barcoding to overcome the difficulties of identification. The community is still discussing which marker to use but to me it seems they slowly gravitate towards a fragment of the 18S rDNA (V4 region) and thereby following the suggestions of the protist working group. A good example for this is a new study by a group of German researchers:

We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. 

Samples from seven different sites along the River Lusatian Neisse and the River Odra were taken and split into three subsamples. One of those was used for next generation sequencing of the 18S V4 region, the second for morphological analysis, and the third for the establishment of clone cultures from individual cells. The colleagues found that next generation sequencing almost always led to a higher number of identified taxa, which was subsequently verified by morphology. Taxa retrieval varies considerably but not necessarily because of natural variation but more as the result of varying taxonomic coverage in available reference databases. The authors conclude:

Next-generation sequencing based eDNA barcoding is not a swiss army knife, but provides a more comprehensive insight into diatom diversity or other protist communities and therefore could be the basis for the ecological projection of global diversity. If thoroughly conducted, the here presented approach not only bears the potential to supplement and improve the old identification system, but beyond that opens up many new opportunities and challenges: diversity data from NGS eDNA barcoding of environmental samples can easily be compared and combined on different spatial (α-, β-, γ-diversity), temporal and taxonomical levels. Therefore, it is applicable for large scale biomonitoring and the quality management of water bodies, for example under governmental frameworks. 

Friday, October 24, 2014

The Sugarcane Borer

The sugarcane borer moth, Diatraea saccharalis, is widespread throughout the Western Hemisphere, and is considered an introduced species in the southern United States. Although this moth has a wide distribution and is a pest of many crop plants including sugarcane, corn, sorghum and rice, it is considered one species.

The larvae bore into the sugarcane stalks. In mature plants the tops tend to weaken or die, sometimes breaking off. In young plants the inner whorl of leaves is killed, resulting in a condition known as "dead heart." The amount and purity of juice that can be extracted from cane is reduced when borers are present, and sucrose yield may be decreased 10 to 20%. Lastly, when seed cane is attacked, the tunneling by borers makes the seed piece susceptible to fungal infection. Sugarcane borer attacks plants in the family Poaceae (true grasses). Though principally a pest of sugarcane, this insect also will feed on other crops such as corn, rice, sorghum, and sudangrass. However, the damage to those is usually fairly modest.

Despite the damage caused by this pest species only few studies have investigated the existence of cryptic species or the population structure of this moth. Especially for species with a widespread distribution it should be determined whether they are truly one species, or rather a complex of sibling species. In addition, it is unknown if this insect may have been introduced into the southern United States once or on several occasions which would be reflected in genetically distinct populations which can vary in their susceptibility to natural enemies and control measures. 

New research, just published in PLoSONE, focused on the population structure of  sugarcane borers in the southern United States with the hopes to contribute to its management as well as to help identify future introductions and their likely region of origin. A group of US researchers investigated this question by collecting D. saccharalis in Texas, Louisiana and Florida and by examining their population structure using amplified fragment length polymorphisms (AFLPs). In addition, a 658 base pair region of the mitochondrial DNA COI gene was sequenced from several individuals from each southern United States population. The mitochondrial COI sequences were compared to publicly available COI sequences for D. saccharalis, to investigate potential source populations for those established in the southern US, as well as to estimate the number of potential cryptic species which may exist within this species.

The DNA Barcode data of the study indicated the existence of at least three distinct lineages: A Florida lineage, a lineage including Texas, Louisiana and Mexico, and a third lineage from South America that includes Brazil, Argentina, and Bolivia. In the literature a fourth lineage from Colombia is also discussed. Both AFLP and COI analysis show that the Florida lineage represents a genetically distinct cluster. This degree of genetic divergence suggests that Florida D. saccharalis could represent a distinct species.

The authors make clear that it would be premature to speak of several new cryptic species:
To be robust, defining species limits should include multiple lines of evidence. Such an approach is referred to as integrative taxonomy and should include morphological, behavioral, molecular and geographic data. Thus, although our data strongly suggests the existence of a D. saccharalis cryptic species complex, further lines of evidence would provide additional support of this assertion.

However, even if we don't know if we are looking at several distinct species or not, the study represents a big step forward:  Genetically distinct lineages may differ in their damage potential and/or in their vulnerability to pest control strategies such as biological control. The ability to characterize and identify genotypes of D. saccharalis and related species or as of yet undiscovered species will improve pest management efforts against this pest and improve area-wide control efforts across its geographic distribution.

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.
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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. 
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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.
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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.

Tuesday, October 14, 2014

Discoveries of the week

Aegista subchinensis (Möllendorff, 1884) is a widely distributed land snail species with morphological variation and endemic to Taiwan. Three genetic markers (partial sequence of the mitochondrial cytochrome c oxidase subunit I [COI], the 16S rDNA and the nuclear internal transcribed spacer 2 [ITS2]) were analysed to infer phylogenetic relationships and genetic divergence of closely related species of the genus Aegista, A. vermis (Reeve, 1852) and A. oculus (Pfeiffer, 1850). A new species from A. subchinensis has been recognized on the basis of phylogenetic and morphological evidences. The nominal new species, A. diversifamilia sp. n. is distinguished from A. subchinensis (Möllendorff, 1884) by its larger shell size, aperture and apex angle; wider umbilicus and flatter shell shape. The northernmost distribution of A. diversifamilia sp. n. is limited by the Lanyang River, which is presumed to mark the geographic barrier between A. diversifamilia sp. n. and A. subchinensis.

With more than 300 land snail species, Taiwan holds a remarkable diversity of these creatures and still continues to surprise. During a recent study scientists discovered a new endemic snail species of the genus Aegista from eastern Taiwan and named it to support recent efforts for same-sex marriage rights in Taiwan and around the world. 

One new species of the delphacid genus Kakuna Matsumura, K. taibaiensis Ren & Qin, sp. n. is described from Mt. Taibai in Shaanxi Province, China. Dicranotropis montana (Horvath, 1897) is reported for the first time from China. Habitus photos and illustrations of male genitalia of the two species are given.

The genus Kakuna belongs to the large group of leaf hoppers. To date, only five Kakuna species are known exclusively from China and Japan.  This new species is named after its type locality, Mount Taibai in Shaanxi, China.
no DNA Barcode available

A new quadrannulate species of Orobdella, Orobdella masaakikuroiwai sp. n., from the mountainous region of central Honshu, Japan is described. This is only the second small species known within this genus, with a body length of less than 4 cm for mature individuals. Phylogenetic analyses using nuclear 18S rDNA and histone H3 as well as mitochondrial COI, tRNACys, tRNAMet, 12S, tRNAVal, 16S, and ND1 markers showed that O. masaakikuroiwai sp. n. is the sister species of the quadrannulate O. whitmani Oka, 1895. Phylogenetic relationships within O. masaakikuroiwai sp. n. conducted using mitochondrial markers reveled a distinction between eastern and western phylogroups.

This genus Orobdella comprises terrestrial macrophagous leech species that live in East Asia. These leeches are not of the  jawed blood-feeding type but are related to a group that contains only predaceous leech taxa. The species name honours Masaaki Kuroiwa, who accompanied the field survey in the Nagano Prefecture during which this species was collected.

Sinocyclocheilus brevifinus sp. nov. is described from a subterranean river at Maohedong Village, Guangxi Zhuang Autonomous Region, Southern China. The new species can be distinguished from all congeners in having functional eyes, last simple dorsal fin ray soft and without serrations along posterior margin, eye diameter small (3.4−5.0 %SL), tip of depressed dorsal fin not reaching vertical at anal fin origin, tip of depressed pelvic fin far from anus, maxillary barbel not reaching anterior edge of operculum, rostral barbel not reaching posterior edge of operculum, scales of lateral line row significantly larger than those of scale rows immediately above and below lateral line, and flanks with distinct black spots and blotches.

This genus of cave-dwelling fish contains about 60 described species with several types of adaptations to the unique environment. These vary by species but include degradation of eyes, loss of pigmentation, well-developed barbels, and in some cases, an elaborate and well-developed cephalic and body lateralis system. The species name is in reference to the short fins of the species.
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We describe a new species of large Oedura from the Oscar Range on the southern edge of the Kimberley Craton in northwestern Australia. Oedura murrumanu sp. nov. can be distinguished from all congeners by the combination of large size (snout-vent length to 103 mm), moderately long and slightly swollen tail, tiny scales on the dorsum, fringe of laterally expanded lamellae on each digit, and 6–7 paired distal subdigital lamellae on the fourth toe. The new species is the first endemic vertebrate known from the limestone ranges of the southern Kimberley; however, this area remains poorly surveyed and further research (particularly wet season surveys and genetic analyses) is required to better characterise regional biodiversity values.

This rather large gecko occurs close to some of the most frequently visited parts of the Kimberley, a region in north-west Australia with some geologically interesting formations consisting of an array of ancient and highly weathered exposed rock.
The species name is based on the word for gecko in the language of the Bunuba people of the south-west Kimberley: Murru manu (‘u’ pronounced as ‘oo’). This new species is probably entirely restricted to the traditional lands of the Bunuba.
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Bidens meyeri (Asteraceae/Compositae) is described and illustrated from Rapa, Austral Islands, (French Polynesia). This new species is presumed to be most closely related to Bidens saint-johniana from nearby Marotiri Island. Bidens meyeri may be distinguished from B. saint-johniana based on the length of the peduncle (3 cm versus 10 cm), apex of the inner involucral bracts (glabrous vs. puberulent), smaller leaves (2.0–2.3 cm vs. 5–6 cm), and the general smaller size of the new species. Known from less than 50 individuals and restricted to one remote location, Bidens meyeri falls into the IUCN Critically Endangered (CR) category.

This species was collected on Rapa which belongs to the Austral Islands which situated in the Southern Pacific and are part of French Polynesia. The new species was named in honor of Dr. Jean-Yves Meyer, Délégation à la Recherche, Polynésie Française.
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Friday, October 10, 2014

Drinking coffee maybe good for your liver

The beverage on the right is good for your liver.
I am not so sure about the cookies though.
Important news for academia!

Researchers from the National Cancer Institute report that decaffeinated coffee drinking may benefit liver health. Results of a new study show that higher coffee consumption, regardless of caffeine content, was linked to lower levels of abnormal liver enzymes. This suggests that chemical compounds in coffee other than caffeine may help protect the liver. The compounds are yet to be identified though. 

For this study researchers used data that included some 28 000 participants, 20 years of age or older, reporting on coffee intake per 24-hour period. The team measured blood levels of several enzyme markers of liver function to determine liver health.

Participants who reported drinking three or more cups of coffee per day had lower levels of all tested enzymes compared to those not consuming any coffee. The scientists also found low levels of these liver enzymes in participants drinking only decaffeinated coffee.

And yet another good excuse for a morning coffee.