Cool project

Pretty cool project for students of a Diploma of Laboratory Technology program run at Holmesglen Institute of TAFE in Melbourne, Australia:

Culex in Turkey

Arboviruses are a group of viruses that are transmitted by arthropod vectors. The word arbovirus is actually an acronym (arthropod-borne virus) for a rather long list comprising four families of viruses one nastier than the other. The most prominent representatives are Dengue, West Nile, Yellow fever, and Tick-borne encephalitis.

Among the arthropod vectors that are often involved in the transmission of arboviral and parasitic diseases worldwide are mosquitoes of the genus Culex . This genus is huge, with well over 1200 described species which is about one third of all known mosquito species. Culex adults are usually drab, unicolorous mosquitoes which means attempts to identify them on a larger scale involving non-experts are more or less futile. However, a prerequisite to successful control of these diseases is the accurate identification of the mosquito vector species involved. BOLD currently lists about 170 species that have at least one COI Barcode sequence but only 90 of them are publicly available. Now, that I don't understand. I know that colleagues have a long list of reasons for keeping data private although I find most of their justifications not very convincing. In this particular case it simply makes me angry as it is slowing down progress and community interaction both badly need to fight arborviral diseases.

There is no doubt that DNA Barcoding can help not only to identify known mosquitoes on a regular basis as part of preventive measures but also to confirm the identity of invasive or previously undocumented species that local experts are unfamiliar with and are most likely to misidentify.

A good example was just published in Acta Tropica. The study brought together researchers from Turkey and the USA to produce a baseline faunal survey of Culex species in Turkey. Specimens were collected in 11 provinces across Turkey between 2005–2011. Morphologically identified representatives of 10 species (185 specimens) were subjected to an integrated systematics approach using both morphology and DNA barcoding. DNA Barcoding recovered 13 distinct species increasing the Culex of Turkey count to 15 recognised species:

Herein we show that including DNA barcoding in baseline faunal surveys reveals more species than by morphology alone. Our limited study on the Culex of Turkey, clarified the identities of Cx. pipiens and Cx. territans, adding four species to the Turkish faunal list. This included the previously undetected presence of Cx. quinquefasciatus, a highly efficient arboviral vector. Given that we now have quality reference barcode sequences, retrospective vector incrimination by DNA will be much more accurate, even in the absence of voucher specimens. We advocate the use of integrated faunal baseline surveys as precursors to establishing successful mosquito and arbovirus surveillance programmes in future.

Where have all the taxonomists gone?

"Erosion of taxonomic experts"

For a good number of years colleagues kept pointing out that taxonomy as science is in decline because of the ever shrinking number of active taxonomists - professionals and amateurs alike. However, all the numbers that were thrown out were mostly not backed up by actual extrapolations resulting from dedicated studies. Well, that has now changed. A study looked at the development of the taxonomic workforce in the past years and also provides projections into the future. The scope of the study was Bavaria, Germany but I am fairly confident that the numbers will look very similar if one would do similar work in other countries e.g. in Europe or North America. Unfortunately, these important findings documented in a 100-page publication are only available in German. I strongly believe the publication should be translated into English and widely distributed as the authors didn't stop at painting a very bleak picture but also provided potential ways to counteract the issues they've detected. Here my humble attempt to provide a summary.

The study surveyed 70 experts of various groups such as environmental assessment companies, land administration offices, universities, NGOs and conservation authorities. The results are alarming as they show a loss of 21% of taxonomic experts over the last 20 years. However, the full scope of the problem is currently concealed by the fact that most of them are older than 60 years and still actively involved. Only 7.6% of the current taxonomists are younger than 30. Within the next 10-20 years the study projects a drastic decline in expertise given that the average age of taxonomists in Bavaria currently is ~50 years.

There are a variety of reasons for the decline of interest in taxonomy, such as a plethora of extracurricular activities for children and youth, a decline of taxonomic knowledge in teachers, dramatic reductions of learning opportunities in schools and universities (entire systematic and taxonomy programs disappeared), and a huge image problem of conservation activities. Naturalists and conservation activists are often disrespectfully called ‘tree huggers’ and perceived as quixotic, anti-economy, and naïve.

It is a paradox situation. In recent years everything related to biodiversity gained more attention in media and politics resulting in efforts to protect and preserve our environment. At the same time we are losing the ability to identify, count, and assess what we aim to protect. Even DNA Barcodes can help only to a limited extend by providing legitimate shortcuts to identification.

The authors determined factors that are beneficial for the development of knowledge about species. Motivation at home is a crucial one especially when supported by hands-on experience in natural environments. They identified two stages in a human’s life that are very important for the development of taxonomic expertise, an earlier phase around 13.5 years and a later one at about 22.5 years. A lot of the suggested solutions take these findings into account when it comes to potential target groups.

The list of suggestions is rather long but shows that we are anything but short of ideas to meet the challenges:

- Implementation of strong biodiversity and nature conservation programs at universities

- National coordination centers for taxonomic groups 

- Targeted support of junior staff and students

- Mentor systems for children, youth and seniors in conjunction with conservation authorities

- Options to obtain nature conservancy certifications

- More broader environmental teaching and learning 

- Programs for children and youth to experience nature (not just learn about it)

The authors of the study emphasize that the problem can only be tackled by an interdisciplinary approach. Most institutions don’t have the money to finance new programs which means only a concerted effort will help but they also call for targeted federal funding programs to stop the downward trend.

I really like this study as it puts some numbers to the trend we all witnessed and to all the concerns we voiced over the last years. Time to do something about it.

Microarray barcoding

With the rise of various next generation sequencing technologies, RT-PCR based probes, HRM and other methods, one was led to believe that microarray technology for the purpose of species identification is outdated. That's not true. There is still a small research community that looks into the development of microarray chips, as those, once developed, can be simple, mass produced, and can target a specific group of species of interest in a single assay. Past work showed that various mitochondrial sequence markers perform differently and at the time COI was not suitable for the design of oligonucleotide probes despite the wealth of available data, but it seems that might not be the case anymore.

Meanwhile, the microarray technology became a well-established and efficient molecular biological tool and new developments refined the approach. The application of mid-infrared chemical imaging (IRCI) is one of those. This technology uses microarrays in which hybridized spots had been selectively augmented with nanogold–silver to facilitate detection. This layer of silver, selectively bounds to hybridized spots in a microarray, thereby forming reflective substrate that can be detected. 

In a study that was just published in Applied Spectroscopy researchers of the US Food and Drug Administration tested the utility of this technology for species identification of fishes, in particular Non-Ictalurid catfish species that are marketed as catfish in the USA. 

The researchers designed species-specific DNA probes targeting three different regions per species of the DNA Barcoding gene and were able to identify all species correctly.

The infrared imaging read-out method for DNA microarray platforms was successfully applied for identifying seven catfish species, including several commercially important species in the families Ictaluridae and Pangasidae. To the best of our knowledge, this is the first time IRCI has been used as a read-out for a DNA microarray targeting fish species. The results of this study demonstrated that this approach enables discrimination among species within the economically relevant families Ictaluridae and Pangasidae using a single general primer set and multiple species-specific oligoprobes.

I like this part of their discussion in particular:

...we feel CO1 can be successfully used with the three probe format adopted in the present study. This is facilitated by the fact that there are so many CO1 sequences for fish species available for use as a result of its popularity as the barcoding gene.

Maybe this is the next step towards an automated and easy-to-handle method to identify fish, and fish products. 

Snake bites

Bites from venomous snakes are common in many parts of the world and an especially serious unresolved health problem to millions of people living in South and Southeast Asia, as well as Africa and Latin America. Although there are no reliable numbers at the global scale, it has been estimated that at least 421,000 cases of venom snakebites with up to 94,000 deaths occur worldwide each year. However, experts warn that these figures may underestimate the real problem, which is believed to affect several million people bitten by venomous snakes annually and hundreds of thousands who die or survive disabled, suffering from amputation or deformed limbs as a result of unavailable or delayed treatment.

People bitten by snakes often do not seek treatment at a medical facility, and if they do, the vast majority don't take the snake with them although it is often killed. Of course they also can't identify the species that actually bit them. However, knowing the species of snake is critical to determining the best course of treatment. And even if the victims do everything right, the clinical personal does not necessarily has the expertise to identify the snake species.

At the current annual meeting of the American Society of Tropical Medicine and Hygiene in New Orleans a team of scientists from Nepal, Germany and Switzerland present a clinical study on the DNA-based species identification of snakes responsible for venomous bites in rural Nepal (Abstract #692, page 209).

Starting with a simple DNA swab taken from fang marks on people bitten by snakes, an international research team correctly identified the species of the biting snake 100 percent of the time in a first-of-its-kind clinical study.

This study used a combination of  morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the relative contribution of  venomous and non-venomous species to the snakebite burden in southern Nepal. 

A 100% recovery rate is very impressive and shows the power of modern DNA-based ID systems. Based on these early results the research team is currently developing a rapid diagnostic "dip-stick" test that could be used to rule out certain common venomous snakes and help physicians more quickly to decide on the best course of treatment. Conversely, if for example, krait (Bungarus sp.) venom is detected, doctors could quickly give anti-venom instead of waiting for clinical signs poisoning, as is current practice. They would also accelerate the transfer of patients to referral hospitals with intensive care units able to ensure adequate respiratory support. Such a test would be easy to administer in rural healthcare settings with limited resources.

Discoveries of the week

Rana kauffeldi

We describe a new cryptic species of leopard frog from the New York City metropolitan area and surrounding coastal regions. This species is morphologically similar to two largely parapatric eastern congeners, Rana sphenocephala and R. pipiens. We primarily use bioacoustic and molecular data to characterize the new species, but also examine other lines of evidence. This discovery is unexpected in one of the largest and most densely populated urban parts of the world. It also demonstrates that new vertebrate species can still be found periodically even in well-studied locales rarely associated with undocumented biodiversity. The new species typically occurs in expansive open-canopied wetlands interspersed with upland patches, but centuries of loss and impact to these habitats give some cause for conservation concern. Other concerns include regional extirpations, fragmented extant populations, and a restricted overall geographic distribution. We assign a type locality within New York City and report a narrow and largely coastal lowland distribution from central Connecticut to northern New Jersey (based on genetic data) and south to North Carolina (based on call data).

More than a half century after claims that a new frog species existed in New York and New Jersey were dismissed, a team of scientists has proven that the frog is living in wetlands from Connecticut to North Carolina and are naming it after Carl Kauffeld, the ecologist who first noticed it.

no DNA Barcodes (lots of other mtDNA markers - sigh)

Atheroides vallescaldera

We report and describe the first species of Atheroides Haliday presumed to be native to North America, collected at the Valles Caldera National Preserve, New Mexico, USA. We hypothesize its placement among the Siphini based on morphological, phylogenetic analysis and extend the distribution of the genus to the Holoarctic. We expand the key of the known Atheroides to include the new species and discuss the current hypotheses of the geographic distribution of the type species, Atheroides serrulatus Haliday.

The specific epithet, vallescaldera, is derived from the locality in which the specimens were collected, the Valles Caldera National Preserve. This super-volcano caldera lies in the Jemez Mountains in northern New Mexico, USA, and constitutes a “sky island” at the southern end of the Rocky Mountains of North America. 

DNA Barcodes available

Chiromyscus thomasi

Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus), C. langbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name C. thomasi sp. n.

The new white-bellied rat species is named in honor of Oldfield Thomas (1858–1929), the British zoologist who named and described the genus Chiromyscus and the species chiropus.

DNA Barcodes available

Sylphella puccoon, Cookidrilus pocosinus, Stylodrilus coreyi

Cookidrilus pocosinus

Three new species of Lumbriculidae were collected from floodplain seeps and small streams in southeastern North America. Some of these habitats are naturally acidic. Sylphella puccoon gen. n., sp. n. has prosoporous male ducts in X–XI, and spermathecae in XII–XIII. Muscular, spherical atrial ampullae and acuminate penial sheaths distinguish this monotypic new genus from other lumbriculid genera having similar arrangements of reproductive organs. Cookidrilus pocosinus sp. n. resembles its two subterranean, Palearctic congeners in the arrangement of reproductive organs, but is easily distinguished by the position of the spermathecal pores in front of the chaetae in X–XIII. Stylodrilus coreyi sp. n. differs from congeners having simple-pointed chaetae and elongate atria primarily by the structure of the male duct and the large clusters of prostate cells. Streams and wetlands of Southeastern USA have a remarkably high diversity of endemic lumbriculids, and these poorly-known invertebrates should be considered in conservation efforts.

The genus name Sylphella refers to Sylph, the Latin name of an elemental spirit of the air that suggests the Latin silva, for woodland, followed by the Latin diminutive -ella. The specific name puccoon is the Algonquian Indian word which means pokeberry (Phylolacca species). The species name of Cookidrilus pocosinus refers to pocosin, “swamp-on-a-hill” in the Algonquin Indian language. Most specimens were collected in two sites draining pocosin areas. The last species is named in honor of Jesse Edward (Ed) Corey III, an Inventory Biologist at the North Carolina Division of Parks and Recreation. 

no DNA Barcodes available

Musserakis sulawesiensis

Musserakis sulawesiensis gen. et sp. n. (Nematoda: Heterakidae) is described from the large-bodied shrew rat, Echiothrix centrosa, one of the old endemic rats of Sulawesi, Indonesia. Musserakis is readily distinguished from other heterakid genera by having non-recurrent and non-anastomosing cephalic cordons, by lacking papillae between papillae groups around precloacal sucker and cloacal aperture and by lacking teeth in the pharyngeal portion. The spicules are equal but with marked dimorphism among individuals. Heterakids collected from other old endemic murids examined, i.e., Crunomys celebensis, Tateomys macrocercus and Tateomys rhinogradoides, and the new endemic rats of Sulawesi, were Heterakis spumosa Schneider, 1866, a cosmopolitan nematode of various murids. It is suggested that M. sulawesiensis is specific to Echiothrix.

The new genus name  Musserakis is dedicated to Dr. G. G. Musser, a mammalogist, who has made contributions on the murid rodents of Sulawesi for many years. The species epithet is named after the type locality, the island of Sulawesi.
no DNA Barcodes available


Petrolisthes tuerkayi

A new species of porcellanid crab, Petrolisthes tuerkayi n. sp., is described from the Persian Gulf. The new species is closely related to P. rufescens Heller, 1861, but is easily distinguishable by having three or four large spines distally on the posterior margin of the carpus of chelipeds, whereas the posterior margin of the cheliped merus in P. rufescens is unarmed.

The species is named after Prof. Dr. Michael Türkay, curator of the crustacean department of the Senckenberg Museum in Frankfurt, who dedicated 45 years of his life to the taxonomy of decapod crustaceans, in particular in the northern Indian Ocean. Michael Türkay was supervisor of the Ph.D projects of the both authors. I remember him as well as I used to listen to some of his lectures and seminars as part of my zoology undergrad training. He is a fount of knowledge that never runs dry especially when it comes to his 'pet group', the crustaceans.
no DNA Barcodes available

Planting a tree in the city is not enough

No doubt, the creation of green spaces in cities has environmental benefits. They filter pollutants and dust from the air, they provide shade and lower temperatures in urban areas, and they even reduce erosion of soil into waterways. However, it has also been assumed that planting trees and creating green space in cities is good for attracting species but according to a study from the University of Iowa it may not be enough to ensure biodiversity in these artificially build environments.

The researchers surveyed two types of tree in an urban area in Iowa, and recorded the abundance of two insects that interact with them. They found that while there were plenty of the trees, black cherry and black walnut, they didn't find a corresponding abundance of the insects, in this case fruit flies that feed on the walnuts and black cherries and a parasitic wasp that feeds on the flies.

We found that herbivorous insect densities were decoupled from host tree densities in urban landcover types at several spatial scales. This effect was amplified for the third trophic level in one of the two insect systems: despite being abundant regionally, a parasitoid species was absent from all urban/suburban landcover even where its herbivore host was common. Our results indicate that human land use patterns limit distributions of specialist insects. Dispersal constraints associated with urban built development are specifically implicated as a limiting factor.

The colleagues believe that barriers found in urban landscapes, such as built structures and paved areas, may make it difficult, if not impossible, for the insects to reach other trees, mate with other populations and thus enrich the gene pool. In addition to this fragmented environment  insects have to deal with highly diverse plant resources that are configured in complex mosaics of disparate habitat types often characterized by frequent disturbance as well as altered biogeochemical, hydrological, and temperature regimes.

The senior researcher of the project concludes:

The responses of the diversity of organisms that could potentially share these developed areas with us can be really idiosyncratic. To promote the full diversity, we really have a lot to learn. That doesn't mean our efforts are wasted, but it definitely means that we need to continue trying to learn to do a better job and be thoughtful about it.