Thursday, November 27, 2014

Honey bee conservation

In order to compensate the dramatic losses of honeybee colonies that we see globally for many years now, beekeepers try to restore their apiaries by importing colonies or queens in the hopes that those survive better than their previous bees. Such imports increase the level of introgression with local honeybee populations in which genetic variability is geographically highly structured. 

In response to this a number of European countries started to preserve honeybee endemic diversity through conservation programs. They've realized that healthy natural populations can act as a reservoir against losses due to occasional diseases. Dedicated conservation programs will eventually provide various honeybee strains and traits that are suitable for sustainable beekeeping.

In a newly published study, researchers analysed the relationships between individuals of the honey bee subspecies Apis mellifera mellifera in a conservation centre, a drone congregation area, and the surrounding populations. 

Honeybees have a very complex mating system in which drones and virgin queens meet mid-air to mate in areas that have been named drone congregation areas. Drones assembled in such a drone congregation area come from several surrounding colonies and thereby represent the diversity of the entire local population. These congregation areas are considered panmictic structures of honeybee reproduction and ensure a sufficient level of recombination. 

The aim of this study was to analyse the effects of setting up a honeybee conservation centre regarding 1) the putative influence of the surrounding populations, 2) the drone congregation area variability over the years and its potential impact on the conserved honeybee populations and 3) the temporal composition of the drone congregation area located within the conservation centre, to estimate the risks of future introgressions on the conservation centre by external drones.

By using mtDNA COI-COII intergenic region and a restriction enzyme approach the French-American team was able to show that the colonies of the conservation centre and the drones of the congregation area show similar stable profiles when compared to the surrounding populations. This means that the centre studied represents an efficient conservation approach although it is located in an area with a high risk of geneflow from the surrounding populations.

In conclusion, this study introduced a new tool for setting up and monitoring honeybee conservation centres. This approach is based on the mtDNA marker to sort the colonies and to follow the evolution of the haplotype frequencies either in the conservation centre or in the DCA. This approach is particularly important to estimate the efficiency of the conservation process in the long term, so that quick measures can be taken when facing a risk of introgression.

Wednesday, November 26, 2014

Weevil diet

The weevil  species Centricnemus leucogrammus lives predominantly in European dry-hot (xerothermic) habitats and steppes. The species was probably more widespread during the Pleistocene glaciations, while its current distribution is limited to what some call 'warm-stage refugia.' Their habitats in central and eastern
Europe sustain very high biodiversity of plants and insects. Unfortunately, these analogs of the Eurasian steppes are seriously threatened as a result of their already patchy distribution combined with human induced transformation and degradation.

Our little friend, the weevil, is a polyphagous insect that over the past years has been used as a model species understand the phylogeography and conservation genetics of xerothermic beetle species. Earlier research showed that weevil populations cluster into geographically separated clades. A Polish colleague was interested if such genetically and geographically distinct units are also ecologically separated. Not much is known about the composition of the beetle's diet and data collection by direct observation is severely limited. The colleague decided to used DNA Barcoding to overcomes these limitations:

The objective was to compare standard ABI Sanger sequencing with new high throughput sequencing (Illumina MiSeq) technique and the two selected plant barcodes (rbcL gene and trnL intron) in terms of the identification of host plant composition for the selected beetle species.

Not surprisingly the next generation sequencing (in this case Illumina) provided more exhaustive results than the Sanger method. The latter identified about 30% less genera present in the diet of Centricnemus leucogrammus. Moreover, the study shows that the two-locus approach (rbcL and trnL) provided good results useful for host plant identification, at least at the genus level. I am a little hesitant to call this a barcoding approach (as the author does) because only one marker is actually an agreed upon standard locus. It would be interesting to find out how matK does, or even ITS which has been proposed as third plant barcode by a number of researchers.

Direct observations either in the field or in laboratory trials identified 9 genera the beetles feed on. This study identified 30 plant taxa as host plants for our weevil, 25 of which have xerothermic representatives in central and eastern Europe. Other plants are either frequent on xerothermic turfs or similar habitats, ruderal or simply widespread. A comparison of host plant composition among distant populations also revealed that the species did not feed uniformly across its range which indicates some ecological adaptation within these distinct populations.

These findings, beside broadening basic knowledge on the use of barcoding and sequencing techniques for host plant identifications in insect populations, can have implications for conservation studies and strategies for rare and endangered species. Precise identification of feeding preferences and behavior could be very important for planning conservation and management of populations and habitats. Without detailed data about host plants, it would be impossible to efficiently protect some herbivorous species and whole insect assemblages. This should be especially important for habitats sustaining very rich flora and fauna, such as the xerothermic habitats of central and eastern Europe.

Tuesday, November 25, 2014

Discoveries of the week

The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.

This publication confirms the discovery of a new bird species more than 15 years after the elusive animal was first seen on the Indonesian island of Sulawesi. The Latin name the team gave the bird pays homage to the late ecologist and ornithologist Navjot Sodhi, who was one of the authors' former mentor and a professor at the National University of Singapore. Several animal species have been named after Sodhi, including a snail, a fish and a new genus and species of crab.
DNA Barcodes available (once released, but I started to share my finds with GenBank on a regular basis)

A new species of paracalanid calanoid copepod Parvocalanus leei sp. n., is described from specimens collected in shallow waters of Western Korea. The new species is closely similar to Parvocalanus arabiensis (Kesarkar & Anil, 2010), P. crassirostris (F. Dahl, 1894), P. latus Andronov, 1972, and P. scotti (Früchtl, 1923) in having two short terminal spines on the distal segment of the fifth leg and a similar rostrum in the female, but can be readily distinguished from its congeners by the body size, relative length of antennules, segmentation of endopod of leg 1, and pattern of ornamentation of spinules on legs 1 to 4 in the female. The taxonomic position of Parvocalanus arabiensis and the validity of the genus Parvocalanus Andronov, 1970 are also discussed.

A new copepod species from Western Korea named after Mrs. Jungah Lee, wife of the senior author, as a token of appreciation for her encouragement and support to him.
no DNA Barcodes

A new fern-feeding aphid species, Micromyzus platycerii, collected in Sakaerat Research Station in Thailand, is described.

Science knows about 66 species of fern-feeding aphids worldwide. Most of them are specialized on ferns and occur in tropical and subtropical regions and their geographical ranges overlap considerably. This new species is named for the host plant from which it was collected: Platycerium coronarium.
no DNA Barcodes

Three new species of the pygostenine genus Doryloxenus Wasmann, viz., D. aenictophilus sp. n. (from Zhejiang), D. tangliangi sp. n. (from Zhejiang), and D. songzhigaoi sp. n. (from Yunnan), are described, illustrated and distinguished from the Asian congeners. An identification key to the Chinese species is given.

Members of this beetle genus are commonly found in a symbiotic relationship with army ants. The name of the first new species is a combination of the generic name of the ant host, and the Greek stem ‘philos’, meaning ‘to be fond of’. The name of the second species is dedicated to Dr. Liang Tang, who found the colony of the associated host ants. Species number three is named after Mr. Zhi-Gao Song, the senior author’s father.
no DNA Barcodes

Hypsugo was regarded as a subgenus of Pipistrellus by many authors, but its generic distinctiveness is now widely accepted. According to recent taxonomic arrangements, nine species are known to occur in Southeast Asia. During the investigation of material recently collected from Lao PDR and Vietnam we identified an additional species and hence describe it here as Hypsugo dolichodon n. sp. It resembles H. pulveratus, but is larger with conspicuously long canines and differs considerably in the DNA barcode gene sequence.

From the Greek words “dolichos” for enlarged and “oodontos” which means tooth the species epithet refers to the long upper canine of the new species which separates it from its South East Asian congeners. The proposed English name for the new species is Long-toothed Pipistrelle.

A new troglobitic species of the amphipod family Artesiidae Holsinger, 1980 is described from a cave in the municipality of Santa Maria da Vitória, in the Brazilian state of Bahia, northeastern Brazil. Spelaeogammarus titan sp. nov. differs from the others in the genus by its body length, rising up to 18.3 mm, the antenna 1 with accessory flagellum 6-articulate, propodus of the first gnathopod 1.8 X longer than basis, the largest in the genus, coxa 5 with posterior lobe slightly concave, inner ramus of pleopods with 10 to 13 setae, outer ramus of uropod 3 with 22 simple setae, and telson with 1 apical plus 3 subapical stout setae in each lobe. With this study, the knowledge of Spelaeogammarus is improved to 5 species, all of them exclusive to caves in the northeastern Brazilian state of Bahia. A comparative table with the diagnostic characters of the species of Spelaeogammarus is provided.

A new species of cave-dwelling amphipods. The species name refers to the  rather large size of this species compared to its congeners.
no DNA Barcodes

Monday, November 24, 2014

Learning from Fisheries

Sometimes we tend to forget that all our efforts to build an all-encompassing library of DNA Barcodes generate very valuable byproducts. Probably one equally important legacy is the huge number of DNA extracts and in many cases the associated tissue samples that stored in various places and hopefully available to future generations.

Tissue samples today are either preserved in formalin, at temperatures between - 80 and - 90 C, or in liquid nitrogen, at about 193 C. The formalin method works well for preserving the carcass of a specimen, but certainly not for any material that is intended for further molecular work. No doubt, freezing at very low temperatures is the number one choice but the energy costs are often prohibitive and for years researchers are trying to find alternatives. There are some industry products out there that bind DNA and allow for storage at room temperature but quite a few of them are either not suitable for long term storage (as in museum tissue collection) or they haven't been tested accordingly. The latter is no surprise at it is admittedly difficult to simulate storage over decades.

Some Norwegian researchers have been looking at the salt cod industry for a potential tissue sample drying technology that could save money without sacrificing tissue quality. In their new paper they describe how took samples from the lungs, heart, liver and kidneys from lab animals and froze these rapidly in liquid nitrogen. The frozen material was dried at + 5 and - 10 C in a heat pump drier at atmospheric pressure, which is a variation of the method used in the fisheries industry to dry salt cod. Drying things at low temperatures allows water to sublimate.

The type of heat pump used was originally developed in the 1970s, during the oil crisis. It was initially developed as a fuel-efficient way to dry fish, but it has since become an industry standard. Naturally, the heat pumps have changed some since then, but the principle is the same.

The colleagues determined the quality of RNA, which is usually even more unstable than DNA. They measured the quality of the extracted RNA by using spectrophotometric analysis immediately after freezing, and again after five months. This was done by examining the fragmentation of the molecules. The different types of samples were also tested using optical and electron microscopes, to see how well tissue and cell structures were preserved.

Preliminary results show that drying at temperatures of about 0 degrees is best for preserving RNA, with about the same amount of decomposition of molecules in samples that were dried compared to samples that were stored conventionally. This was true for all five types of tissue that were tested. Cell structures were mostly preserved, although some fine details in the cells seemed to have been affected by this method.

Overall very promising:
...the technology seems promising for research biobanking, with its main advantages being low cost, high energy efficiency, and relative independence on an advanced technical infrastructure. Further study will be needed in order to clarify the possibilities and limits, and further refinement and optimization will be needed in order to unleash the full potential of the methodology.

The commercial prospect of a drying technique capable of producing high-quality material suitable for long-term storage seems bright in view of the rapidly growing market of research biobanking.

Friday, November 21, 2014

Selective logging

Selective logging is the logging practice of entering a forest and only removing some trees, usually those which are unhealthy or in dense areas. Sometimes the logging is performed on the ground, but to not harm surrounding forest, it is more often done by air using a helicopter. Selective logging has been well-documented to improve forest health and reduce the dangers of wildfire and has been endorsed by the National Forest Service as the better alternative to clear-cutting. It is also supported by the UN. Another advantage is that through selection of which trees to log, rare species can be saved from the logger's saw. (Conservapedia)

It is true, selective logging doesn't have a strong impact on the overall species richness and diversity of tropical forest, however, it has been shown that this can vary considerably depending on the intensity of logging. This could result in changes in the composition of species, as forest-interior specialists disappear and are replaced with edge-tolerant, gap specialists. What's even more important is what happens after logging. The conversion of logged forest to agricultural land uses has a far greater negative impact on biodiversity than logging alone. Conversion to agriculture results in a major reduction in biodiversity. It is affecting a wide range of organisms and because it changes soil pH, carbon and nutrient content, it can cause major shifts in soil microbial communities such as fungi. These play crucial roles in the ecosystem as decomposers, pathogens and plant symbionts. Despite this, little has has been done in the tropics to assess the effect of land use changes on soil fungal communities.

Palm oil cultivation has been heavily criticized for severe environmental impacts especially through increased deforestation. Aside from its use as a food ingredient  it is increasingly used to produce biodiesel. However, the deforestation caused by oil palm plantations is perhaps more damaging to the climate than the benefits gained by switching to biofuel and that doesn't even includes the effects on the local biodiversity.

A new soil fungal community study looked at the effects caused by different intensities of logging. Researchers tried to evaluate if conversion of forest to oil palm plantation has a stronger impact on soil fungi than logging, as is the case for many other taxa. They utilized next generation technology to obtain fungal DNA Barcodes (ITS1 region) from extracted soil DNA. The results were used to compare communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, as well as areas cleared for oil palm, in Sabah, Malaysia. 

Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure.

Even from a more economic point of view this is alarming because radical changes in fungal communities might impact the long-term sustainability of oil palm agriculture. The results also show that logging has more subtle long term effects on the relative abundance of ectomycorrhizal fungi, which might affect tree recruitment and nutrient cycling . They are the fungal partner of the symbiosis between fungi and the roots of various plant especially tree species. However, to my surprise, in general the logged forest retains most of the diversity and community composition of unlogged forest. 

So, logged forest might not be an irretrievably damaged and violently altered system. Actually, protecting it from conversion to oil palm plantation may have considerable conservation benefits.

Thursday, November 20, 2014

Type material on GenBank

I consider it very good news - GenBank now includes annotation of type material:

Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database  now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. 

In a recently published paper Scott Federhen from GenBank provides all the necessary details to this new feature. GenBank has indexed the Nucleotide domain of their Entrez database with ‘sequence from type [filter]’ which allows the user to retrieve sequence entries that are derived from type material. At the time of publication of the paper they listed 72 750 type sequences from different genes, representing 18 847 different species. These are available in the taxonomy dump files on our FTP site, and are searchable in Taxonomy Entrez and in the taxonomy browser.

From my research for my weekly column on new species descriptions I know how few of them actually make use of genetic data let alone DNA Barcodes. I am sure there is a plethora of reasons for this. It certainly would be too easy and almost an excuse to always blame it on the lack of funds. Very often it might also be the lack of any incentive. If I can publish a regular fully valid species description solely using morphology why would I want to add e.g. DNA Barcoding to it? It costs more, it is extra work, and even worse, some of my colleagues would actually criticize me for doing it. So, why are there taxonomists doing it anyway? The answer is rather simple - once they used it they started seeing the value in it. First and foremost it makes their work easier and allows them to focus on discovery. Increasingly often, molecular genetics leads to discovery of hitherto unrecognized species. A secondary effect is what it means for the scientific community at large. 

One key element of the Barcode standard that has been adopted by GenBank back in 2005 is an unambiguous link to the voucher specimen from which the Barcode was derived. If this voucher happens to be a type specimen the associated DNA Barcode is tightly linked to the original species description. Provided that all other requirements of the standard are met this becomes an ideal DNA Barcode. I did a very quick search on GenBank using the new annotation filter for types and the reserved keyword BARCODE and found 158 sequences for 90 species. Not a lot but a good start also given that this is a new feature. Not all sequences have been assigned the type designation. I just looked at one extreme example, the Butcher et al. paper from 2012 in which 179 new species of parasitic wasps were described largely using DNA Barcodes. The sequences are on GenBank and they have the magic BARCODE keyword but the connection to the types hasn't been made yet. 

It is probably time to look at all our GenBank submissions and check if they need an update. They could be from a type and deserve the extra recognition. Lots of work to do, but certainly worth the effort as Scott also states in his conclusions:

Sequence from type is a high-value subset of GenBank for which we can maintain a very high level of confidence in the taxonomic identification. Nomenclatural acts involving type material are carefully documented in the taxonomic literature, so we can reasonably hope to keep these identifications current...Diligent curation of sequences from type material in GenBank as outlined above can make this set even more reliable. Species with problematic taxonomy are still problematic, but egregious misidentifications can be found and corrected. This does not solve the more general problem of misidentified entries in GenBank, but does provide a reliable backbone of correctly identified entries that could help support a more general solution.

Wednesday, November 19, 2014

Discoveries of the week

Megaselia shadeae
A new Megaselia species, M. shadeae, with a large, central, pigmented and bubble-like wing spot and a greatly enlarged radial wing vein fork, is described from Zurquí de Moravia, Costa Rica. As part of the Zurquí All Diptera Biodiversity Inventory (ZADBI) project, it represents the first of an incredible number of new phorid species to be described from this one Costa Rican cloud forest site. A new, streamlined method of description for species of this enormous genus of phorid flies is presented.

The genus Megaselia is extremely rich in species (>2000) and has been characterized as an "open-ended taxon" due to its diversity and the complexity in describing new species. This single genus contains about half of the species of the Phoridae family, a majority of which are hitherto undescribed. This study not only provides a species description but also proposes an innovative method for streamlining Megaselia species descriptions to save hours of literature reviews and comparisons. The new species was named for the first author's niece.
no DNA Barcodes available

Seven new species of the genus Dongodytes
Credit: Mingyi Tian; CC-BY 4.0

Recent cave biodiversity surveys carried out in Du’an County and its adjacent areas of northwestern Guangxi, China, have revealed some exciting scientific findings. In a very limited area seven new species of the cavernicolous trechine genus Dongodytes Deuve, 1993 were found and are described: Dongodytes (s. str.) elongatus sp. n., D. (s. str.) troglodytes sp. n., D. (s. str.) lani sp. n., D. (Dongodytodes) brevipenis sp. n., D. (Dongodytodes) jinzhuensis sp. n., D. (Dongodytodes) inexpectatus sp. n. and D. (Dongodytodes) yaophilus sp. n. Diagnoses and notes on the genus, subgenera, and two known species in Du’an Karst, Dongodytes (s. str.) baxian Tian, 2011 and D. (Dongodytodes) deharvengi Tian, 2011, are also given. A key to subgenera and all species of Dongodytes is provided. To date, Dongodytes becomes one of the richest in species genera of subterranean carabid trechines in China with 12 species which are arranged into two subgenera. Dongodytes (s. str.) Deuve is composed of seven species, four of which from Du’an County, each of other three from Bama, Fengshan and Tian’e Counties, respectively. All species of the subgenus Dongodytodes Tian, 2011 are recorded from Du’an Karst. By having 10 species (nine Dongodytes and one Libotrechus Uéno, 1998), Du’an Karst holds the richest specific diversity of cavernicolous Trechinae in China. Dongodytes species are distributed in a very limited area of the river Hongshui He drainages in northwestern Guangxi, and the river acts as a natural barrier of Dongodytes dispersal at only a specific level. However, all members of Dongodytodes are recorded from the eastern or northern bank of Hongshui He.

Like most cave dwelling species, Dongodytes cave beetles show specific adaptations, such as the lack of eyes and colour, traits common among cave living organisms. The new species belong to the genus Dongodytes whose members are easily recognizable by their extraordinary slender and very elongated body. Members of this genus are usually very rare in caves, with only five species reported from China.
no DNA Barcodes available

Hemibrycon sanjuanensis

Hemibrycon sanjuanensis, new species, is described from the upper San Juan River drainage, Pacific versant, Colombia. It is distinguished from H. boquiae, H. brevispini, H. cairoense, H. colombianus, H. mikrostiktos, H. metae, H. palomae, H. rafaelense and H. tridens by the presence of a circular or oblong humeral spot that is located two scales posterior to the opercle (vs. 3–4 scales in H. palomae, H. rafaelense, H. brevispini and H. cairoense, and 0–1 scales, in H. metae and H. boquiae). It further differs from H. colombianus in having a round or oblong humeral spot (vs. rectangular). It differs from H. beni, H. dariensis, H. divisorensis, H. helleri, H. huambonicus, H. inambari, H. jabonero, H. jelskii, H. mikrostiktos, H. polyodon, H. quindos, H. raqueliae, H. santamartae, H. surinamensis, H. taeniurus, H. tridens, and H. yacopiae in having melanophores on the posterior margins of the scales along the sides of body (vs. lacking melanophores on margins of scales along entire length of the sides of body). The new species differs from all congeners mentioned above in having, among other features, six teeth in the outer premaxillary row arranged in a straight line (vs. five or fewer teeth not arranged in straight line except H. cairoense with two to six teeth in the outer premaxillary row).

The genus Hemibrycon has its greatest diversity in Andean streams and high mountain habitats with a few exception such as the new species. This new representative is named for the San Juan River Basin, a Pacific drainage, where the type series was collected.
no DNA Barcodes available

Ochetostethomorpha secunda

Ochetostethomorpha secunda sp. nov. from Namibia, the second species of the South African endemic genus is described, illustrated, and compared with O. nollothensis Schumacher, 1913. The new species is the third of the subfamily Sehirinae known from Namibia. Moreover, a DNA barcode sequence was generated for this new species (827 bp of cytochrome oxidase I) and was deposited in GenBank.

It is always nice to find a new description that is associated with a DNA Barcode. Unfortunately, both GenBank numbers provided lead nowhere. They are simply not released yet. Don't get me wrong. That's not a GenBank's fault. They need to be informed by the authors that the paper is available and therefore the sequences need to be released as well. I know that GenBank staff is screening papers as well and will make data available if they find published work associated with their accession numbers, however, that is tedious work and frankly, it shouldn't be them doing that. We need to make this a habit. Once our manuscripts are accepted we should inform GenBank about the release (and release BOLD data) or even better: we release once sequences are uploaded. I personally don't see any reasons to hold back sequence data. In this case I have notified GenBank of the publication. They are pretty quick in sequence release - but again, it is neither their nor my job to find out about releases. Maybe journals could help with that, either by following up on this or changing their rules accordingly.
This little hemipteran was named secunda to indicate that it is the second species of the genus.
DNA Barcode data theoretically available.

Corynoneura ecphora

A new species of Corynoneura Winnertz (1846) from Oriental China, C. ecphora sp. n. is described and illustrated as male. A distribution map of adult males in Oriental China is given. A key to known males of Oriental China is provided.

A new member of the family chironomidae. This taxon is extremely large and some people suggest that it might contain 10000 or more species. Having seen a large number of unnamed BINs over the last years of School Malaise Trap Program I don't doubt that at all. Non-biting midges are notoriously difficult to identify but at the same time very important indicator species for water quality.
The species name is derived from the Latin word ecphora, a projection in buildings, referring to sternapodeme (ingrowths from the exoskeleton of most arthropods that support the internal organs).
no DNA Barcodes available

Lophophysema eversa
We describe Lophophysema eversa sp. nov. (Porifera, Hexactinellida, Hyalonematidae) based on a single specimen collected from the South China Sea at a depth of 3683 m. The new species can be distinguished from the three known congeners by its unusual body shape with basalia on the side of the body, the lack of macramphidiscs, the combination of the pinular pentactins having spiny tangential rays and the pinular ray of atrialia longer than dermalia and canalaria. This is the first record of the genus Lophophysema from the South China Sea. We also use a partial sequence of the 16S rRNA gene to confirm the family assignment of the new specimen.

The species name for this sponge is derived from the Latin word "eversus", meaning everted, referring to the notably everted surface of the central cavity. Molecular data (16S) are available but no DNA Barcodes.
no DNA Barcodes available

Friday, November 14, 2014

Predators that save Millions

The enemy: Hypothenemus hampeii
Biodiversity loss will likely have surprising and dramatic consequences for human wellbeing. Identifying species that benefit society represents a critical first step towards predicting the consequences of biodiversity loss. Though natural predators prevent billions of dollars in agricultural pest damage annually, characterizing which predators consume pests has proven challenging. Emerging molecular techniques may illuminate these interactions. 

No doubt, invasive species, pests, and disease vectors are a danger to humanity and cost us a lot of money. In that context it would be great if we could identify those species and populations that actually provide benefits to society by simply consuming harmful organisms. Identifying those service providers, however, is anything but straightforward. It is not like we are witnessing these particular predation events. For example, pest control is a critical service and insect predators likely saved farmers billions of dollars annually in avoided pest damage. But how can we identify predators that are so valuable to us. Visual identification of prey gut content used to be the number one methodological choice but it seldom delivers the necessary taxonomic resolution. In addition the necessary inspection labor is considerable and sampling techniques often result in high mortality rates among caught predators.

The use of molecular methods, such as DNA Barcoding, seems to be advisable. Firstly, molecular identification  would allow researchers to shift to feces or regurgitates from carnivores, insectivores, and herbivores of diverse taxa to infer their diet, making much less intrusive and less dangerous for the test subjects. We also know that molecular methods provide a much better resolution and higher accuracy than the morphological inspection of partially digested remains.

Researchers from Stanford University used molecular fecal analysis to identify bird predators of coffee’s most damaging insect pest— the coffee berry borer beetle (Hypothenemus hampeii). This pest has invaded almost every coffee-producing country in recent years. Earlier experiments have shown that birds consume the borer, but further insights have proven difficult because of the borer’s small size (~2 mm) which makes witnessing predation impossible.

The researchers collected samples at coffee plantations in southern Costa Rica and conducted feeding trials to determine the sensitivity of the method. They used borer-specific primers to target an 185 bp segment of the DNA Barcode region and came up with promising and interesting results:

While feeding trials confirmed the efficacy of our approach, detection rates were low. Low detection rates suggest that there are other species that consume the borer that we did not identify. Nevertheless, we identified six species that consume the borer. The species we did identify shared traits that may be characteristic of these other predators. These species had narrow diet breadths, thin bills, and short wings; traits shared with borer predators in other systems. Borer predators were not threatened; therefore, safeguarding pest control necessitates managing species beyond those at risk of regional extinction by maintaining populations in farmland habitats. Generally, our results demonstrate potential for pairing molecular methods with ecological analyses to yield novel insights into species interactions.

Thursday, November 13, 2014

Ants of Manhattan

Credit: Shelby Anderson
Global urbanization is rapidly expanding and we know that most of the world's humans now live in cities. Most ecological studies have, however, focused on protected areas, such as national parks, as cities are often perceived as not having any ecology.

A group of colleagues decided to test if the theories developed to predict biodiversity in protected areas could also predict species diversity in urban environments. To explore this issue, the researchers decided to focus on ants, partly because ants are ecologically important, but also because the ant species composition in a given area can tell you a lot about its environment.

They collected ant samples at approximately 50 sites in Manhattan, including street medians, urban forests and recreational areas in city parks. They examined each site thoroughly, turning over rocks and sifting through leaf litter and  found not only a wide range of species, but also significant differences in the levels of biodiversity in different urban areas. In fact, they showed that the city has much more diversity than initially expected. In total they've encountered 42 different species across all sites and they exclusively used morphological species determination. I wonder if the results would have been different if they had added DNA Barcoding.

Interestingly the type of urban habitat seems to be more important in determining ant diversity than the proximity between habitats. Sites in urban forests that were far apart had more similar species than an urban forest site and a recreational area site that were right next to each other. 

Overall existing diversity theories from protected areas were fairly accurate at predicting the levels of diversity in urban spaces:

Many predictions derived from less modified ecosystems were supported by our findings: despite being the most intensively sampled habitat, high stress urban medians had less variability in ant composition –both within and among sites – than either urban parks or urban forests, the lowest stress habitat – urban forests-had significantly more accumulated species and a higher number of unique species than higher stress habitats, and urban parks, which have intermediate levels of chronic environmental stress, also had intermediate levels of variation in among-site species composition, accumulated species richness, and the incidence of unique species. The most common species also differed across Manhattan's urban habitat mosaic.

Only one prediction did not turn out as expected. The researchers thought there would be more exotic species in high-stress environments, e.g. street medians. As it turns out exotic species were equally common across all habitats.

This tells us that urban ecosystems are complex and deserve future study -- which could not only inform our understanding of urban ecology, but also our understanding of ecology as a whole. The good news is that it also tells us that existing biodiversity theories can help to guide that future work.

Wednesday, November 12, 2014

Weed adaptation

Oxford ragwort
Invasive species undergo behavioural, phenological and morphological changes when confronted with novel conditions. However, we know remarkably little about the trajectories invasive species follow through time. This limits our understanding of the process of invasion, our power to predict the establishment and ecological effects of invasive species, and our understanding of how species respond to environmental changes. The main aim of this paper is to fill this knowledge gap, by quantifying phenotypic change in three plant species through their first 200 years since introduction.

I stole this abstract from a new study which is likely the first to have tracked the phenotypic change of introduced plant species from the beginning of their invasion to the present day. This was only made possible by the centuries-old  tradition of storing plant specimens in herbaria and the collecting obsessions of many individuals - not only professionals.

The international research team looked at three common weeds: Oxford ragwort (Senecio squalidus), winter speedwell (Veronica persica) and a willow herb (Epilobium ciliatum) all of which were introduced to the UK between 120 and 220 years ago. Oxford ragwort was introduced into the UK from Sicily and was first recorded in the wild in 1794. This yellow daisy has spread widely along the railway lines of Britain. 
Winter speedwell is native to Eurasia and was first recorded in the UK in 1826. The willow herb Epilobium ciliatum is native to the Americas but was first recorded in in the UK in 1891.

The researchers found the weeds are getting increasingly better adapted to life in their new environment, so they will perhaps become even more problematic invaders as time goes on. The team measured changes throughout the centuries in leaf shape, leaf area and plant height, features which reflect how plants adapt to new water, nutrient and light conditions.

The Oxford ragwort underwent about a 20 per cent increase in both leaf area and plant height since its introduction. The leaves of the winter speedwell became rounder and 17% smaller, while plant height increased by 14 %. And the willow herb showed a 50 % decrease in leaf area. All three invasive species showed evidence of change at least in one trait during the last 50 years. Changes in the species' traits seemed to happen in spurts: changes are not in a consistent progression, but rather fluctuate through time.

The colleagues are well aware of the fact that the changes and patterns they observed could be due to phenotypic plasticity with little impact on the genotypic variation of the three species. Other plants such as dandelions are textbook examples for the ability of an organism to change  only its phenotype in response to changes in the environment. The only way to prove that the observed changes have a genetic basis is to use common garden experiments, and this approach does not allow researchers to follow the trajectory of change through time.

The authors conclude: Our results suggest that some invasive species are yet to demonstrate their full potential as invaders. Overall, our study shows that species are labile in the face of environmental change. Identifying the long term trajectories of invasive species’ phenotypic change during invasion provides important clues for their appropriate management.

Tuesday, November 11, 2014

Discoveries of the week

Mugilogobius hitam
A new species of Mugilogobius is described from Lake Towuti, central Sulawesi, diagnosed by its possession of a distinct transverse sensory papilla pattern on the cheek, overall blackish colour on head, body and fins and relatively large adult size for the genus. Although it may superficially resemble the black goby Mugilogobius amadi from Lake Poso, M. hitam, new species, lacks the numerous predorsal scales (22–36 in M. amadi versus 17–19), high second dorsal fin ray count (I,9, usually I,10, versus I,7–8) and narrow head and protruding chin of M. amadi. Cytochrome c oxidase subunit 1 (COI) data provide clear support for the species status of M. hitam, new species, indicate that all the Malili Lakes Mugilogobius may well represent a species flock and place M. sarasinorum from Lake Poso as its most likely sister taxon. In addition to the tectonic lake species, we report the occurrence of M. latifrons in streams of the Malili Lakes drainage.

Another new species of the huge fish family Gobiidae. This new species is so far known only from a single site in Lake Towuti, Central Sulawesi. The species name, hitam, is the Bahasa Indonesia word for black.
DNA Barcodes available

Pseudobarbus verloreni
Pseudobarbus verloreni, a new species, is described from material collected in the Verlorenvlei River system on the west coast of South Africa. It differs from its congeners (except P. skeltoni, P. burchelli, and P. burgi) by the presence of two pairs of oral barbels. Pseudobarbus verloreni sp. n. can be distinguished from the three currently described double barbeled Pseudobarbus species by the following combination of characters: pigment pattern, generally deeper body relative to standard length, a longer intestine associated with the deeper body form, shorter snout relative to head length, and much shorter anterior barbels relative to head length. The new species is distinguished from P. burgi in the neighbouring Berg River system by its longer head and longer pre-dorsal length. It seems as if Pseudobarbus verloreni sp. n. has been extirpated from the Langvlei River system and face several threats to its survival in the Verlorenvlei River system.

And another new fish species. This one was discovered in the Verlorenvlei River system in South Africa after which the species was also named.
no DNA Barcodes available (it totally eludes me why cyt b was used)

Cyphomyia baoruco

A new species of Cyphomyia Wiedemann, C. baoruco sp. n., is described from the Dominican Republic. A key to the species of Cyphomyia known from the Caribbean islands is provided.

This paper should get a prize for the shortest abstract. The author doesn't waste any space and provides what is needed to understand what the paper is about. Great. This new fly species is named after a mountain range, Sierra de Baoruco in the Dominican Republic, where the holotype specimen was collected.
no DNA Barcodes available

Parapinnanema hawaiiensis
A new species from the family Chromadoridae is described from samples collected during Dr Mortensen’s Pacific Expedition 1914–16 to Honolulu, Hawaii. Parapinnanema hawaiiensis sp. nov. is characterized by a low c’ ratio and especially by a peculiar complex morphology of the median part of the gubernaculum. An updated and modified key to all the valid species of Parapinnanema is proposed.

This species was actually collected during a Pacific Expedition from 1914–1916 by Dr Theodor Mortensen  in an unspecified coastal area of Honolulu, Hawaii. About 100 years later researchers dug out this nematode specimen mounted for light microscopy and deposited at the Natural History Museum of Denmark. The species name refers to the geographical origin.
no DNA Barcodes available

Chironius diamantina

We describe a new species of Chironius Fitzinger, 1826 from the highlands of Chapada Diamantina, state of Bahia, Brazil. The new species is distinguished from all currently recognized congeners by a unique combination of states of characters on coloration, scale counts, scale ornamentation, and hemipenis. The new species closely resembles Chironius flavolineatus (Jan, 1863) in color pattern, but differs from the later taxon by the presence of two to four posterior temporal scales; cloacal shield entire; six to ten rows of keeled dorsal scales at midbody; ventral scales with posterior dark edges forming conspicuous transverse bars along almost the entire venter; conspicuous dark longitudinal stripes (in “zigzag”) in the midventral portion of subcaudals; region of medial constriction of hemipenis slightly covered with spinules separating calyces of apex from spines below region of constriction; and sulcus spermaticus situated on convex face of hemipenis in lateral view. The new species is apparently restricted to Chapada Diamantina, corroborating the biological importance of this region from a conservational perspective.

A new member of the largest family of snakes, the Colubridae. Most colubrids are nonvenomous or have venom that is not harmful to humans. This new species was found in the Chapada Diamantina, central region of the state of Bahia in Brazil, hence the species name.
no DNA Barcodes available

Aulacoseira veraluciae
Aulacoseira lirata
Examination of samples from different aquatic environments from Brazil revealed the presence of a new Aulacoseira species. Aulacoseira veraluciae Tremarin, Torgan & T. Ludwig is described and illustrated with light and scanning electron microscopy, and its morphology compared with that of similar species, such as A. muzzanensis (Meister) Krammer, A. granulata (Ehrenberg) Simonsen and A. agassizii (Ostenfeld) Simonsen. The new species is characterized mainly by the straight pervalvar rows of areolae, morphology of the linking spines, shape and position of the rimoportulae on the valve mantle, deepness and thickness of the ringleiste.

A new diatom species found in the Rio Grande do Sul, Patos lake, Brazil. No image of the original species but a relative as the original paper is hiding behind a paywall.
no DNA Barcodes available

Monday, November 10, 2014

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.

Friday, November 7, 2014

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.

Thursday, November 6, 2014

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. 

Wednesday, November 5, 2014

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.

Tuesday, November 4, 2014

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)

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. 

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.

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