Friday, February 27, 2015

Feather mite barcoding

Feather mites are members of several very diverse groups of mites present in almost all groups of birds. They feed mainly on secretions of the uropygial gland of birds. This gland, probably better known as the preen gland or the oil gland, produces preen oil which is believed to help maintain the integrity of the feather structure, provide waterproofing, and - ironically - is supposed to have an anti-parasitic effect. 

The nature of the biological relationship between feather mites and birds is still poorly understood, and empirical studies show a puzzling scenario: some studies have shown that feather mite abundance correlates positively with bird's body condition, while others have found no significant correlation or even negative correlations. In other words it is unclear if feather mites represent true parasites or commensals. Generally, they are thought of as ectoparasites and in some cases they really cause problems for the affected bird (e.g. feather damage).

One of the reasons for the lack of knowledge on their life history might be the fact that feather mite species identification is a really difficult task. Females and immature stages of many taxa are often indistinguishable, and even for males that usually carry the characteristic species traits, accurate identification requires advanced taxonomic skills and a lot of time and patience. 

Here, we tested DNA Barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded.

The colleagues determined that a 200-bp minibarcode region showed the same accuracy as the full-length DNA Barcode and in addition that it is flanked by regions sufficiently conserved to make them potentially useful for group-specific primers. 

Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the P. pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species.

Thursday, February 26, 2015

Tracing Leaf Miners

A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant – leaf miner – parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies.

Leaf miners are plant feeding insects, mainly consisting of flies, moths, and beetles. Many of them are agricultural pests and are therefore considered economically important organisms. They feed on a wide range of plants, which unfortunately also includes cultivated plants and crops. Females lay their eggs either on the leaf surface or in a hole they punctured into the leaf. The hatched larvae will start feeding on leaf tissue making a tunnel which is called 'mine'. 

The problem is that despite their potential impact on a range of commercially important crops, we know only little about leaf miners and their interactions with other species. They are poorly studied organisms, partly due to their cryptic life-cycle which can create major challenges when attempting to incorporate leaf mining insects into complex ecological networks.

A new study is now presenting a novel way to construct precise plant - leaf miner - parasitoid interactions. Morphological identification is very difficult in all the groups and usually requires rearing of collected larvae. However, laboratory rearing is very difficult because collecting infested leaves and rearing adults from larvae within the mines often results in premature death, or one finds the mines empty as the larvae already hatched or moved on to form a new one. In order to overcome these problems the authors of the new study developed a new molecular approach based on DNA Barcoding of remnant DNA within the mines, and it worked quite nicely:

... we show how a molecular approach can be used to determine difficult and cryptic species interactions, even when an adult insect has left its leaf mine. Our molecular approach found more species and interactions than traditional approaches based on insect rearing methods, altering network structure as well as identifying previously unknown species interactions. Thus networks constructed using these molecular methods are better resolved and more useful for network ecologists.

It is very difficult to effectively control for leaf miners. Infected leaves are usually removed and discarded and pruning is often required in the event of a heavy infestation. Many species of leaf miners overwinter in fallen leaves and soil beneath the host plant. Doing a fall clean up can be beneficial in reducing these overwintering sites. In general leaf miner control relies on the use of a combination of cultural practices, including the collection and disposal of infected leaves, as well as the removal of weeds that can act as alternate hosts. That in turn requires extensive knowledge about the species-species interactions. Far more than we know at this point. This new study might help to speed up this process and gain knowledge that eventually will turn into some useful strategies.

Wednesday, February 25, 2015

The fossil calibration database

Fossils are not only fascinating finds that allow a glimpse into past biodiversity, they also provide the age data needed to unlock the timing of major evolutionary events. Very often fossil data are used to calibrate molecular clocks which can reveal the ages of groups that lack good fossil records. An example is shown in the image on the left. I did this analysis about 10 years ago and some values in the tree are marked with an asterisk. These represent calibration points based on fossil records. I also remember quite well but not fondly that finding these dates required a substantial amount of literature research hindered by the fact that a good number of the publications wasn't easily accessible.

Gladly things have changed. This week a new resource for researchers went live, and it is designed to help answer just those kinds of questions. The Fossil Calibration Database is a free, open-access resource that stores vetted fossil data. More than twenty paleontologists, molecular biologists, and computer programmers from five different countries contributed to the design and implementation of this new database.

The launch of the database was accompanied by five peer-reviewed papers and an editorial on the topic published in Palaeontologia Electronica:

  1. Constraints on the timescale of animal evolutionary history
  2. Fossil calibration of Magnoliidae, an ancient lineage of angiosperms
  3. Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves
  4. Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)
  5. Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations

This exciting field of study, known as 'divergence dating,' is important for understanding the origin and evolution of biodiversity, but has been hindered by the improper use of data from the fossil record. The Fossil Calibration Database addresses this issue by providing molecular biologists with paleontologist-approved data for organisms across the Tree of Life. 

The authors also promote best practices for justifying fossil calibrations and citing calibrations properly. These best practices have been published a couple of years ago and I would encourage anyone who plans to do some molecular clock work to read that paper before jumping into any analysis.

Tuesday, February 24, 2015

Discoveries of the week #27

The exploration of Earth's biodiversity is an exciting and ongoing endeavour. Here, we report a new species of seadragon from Western Australia with substantial morphological and genetic differences to the only two other known species. We describe it as Phyllopteryx dewysea n. sp. Although the leafy seadragon (Phycodurus eques) and the common seadragon (Phyllopteryx taeniolatus) occur along Australia's southern coast, generally among relatively shallow macroalgal reefs, the new species was found more offshore in slightly deeper waters. The holotype was trawled east of the remote Recherche Archipelago in 51 m; additional specimens extend the distribution west to Perth in 72 m. Molecular sequence data show clear divergence from the other seadragons (7.4–13.1% uncorrected divergence in mitochondrial DNA) and support a placement as the sister-species to the common seadragon. Radiographs and micro-computed tomography were used on the holotype of the new species and revealed unique features, in addition to its unusual red coloration. The discovery provides a spectacular example of the surprises still hidden in our oceans, even in relatively shallow waters.

While researching the two known species of seadragons as part of an effort to understand and protect the exotic and delicate fish, scientists at Scripps Institution of Oceanography made a startling discovery: A third species of seadragon which was named for Mary ‘Dewy’ Lowe, for her love of the sea and her support of seadragon conservation and research, without which this new species would not have been discovered.
no DNA Barcodes (seven genetic markers but no COI, sigh)

Two new species of the genus Zospeum Bourguignat, 1856 are described from caves in the Sierra de Aitzgorri (Gipuzkoa) and the Sierra Salvada (Burgos) in Northern Spain. The taxa Z. vasconicum sp. n. and Z. zaldivarae sp. n. have recently, without a formal name, been included in a molecular study of worldwide members of the Carychiidae. In the present paper, the shell morphology and variation of these species is described and illustrated.

Two new species in the subterranean genus Zospeum. These blind gastropods barely reach 1 mm in shell size and inhabit caves at depths as deep as 950 m. One species is named after the pre-Roman Era Vascones Tribe which is considered albeit disputed the ancestor of the Basque People. The second species is named after Mª Pilar Zaldívar, a biologist and speleologist from the Niphargus Speleological Team, who discovered the species in the 1980’s.

The first species of the small Afrotropical family Ammodesmidae discovered in central Africa (Democratic Republic of the Congo) belongs to the genus Ammodesmus Cook, 1896, which was hitherto known only from two species in western Africa. A key is given to incorporate A. congoensis sp. n., a species also showing an evident sex dimorphism: ♂ densely hirsute, ♀ with much longer and sparser tergal setae.

This new species belongs to a millipede family with members that had only been known  from western Africa (Guinea, Liberia and Ivory Coast), and eastern Africa (Kenya, Tanzania and Malawi). This huge geographical gap has been a mystery for a while. The species was named after the county of origin.
no DNA Barcodes

Paracreptotrema rosenthali sp. n. was discovered in the intestine of Xiphophorus malinche and Pseudoxiphophorus jonesii, collected from the headwaters of Río Malila, tributary of Río Conzintla, in the Río Pánuco basin, Hidalgo, México, during 2008–2009. The new species differs from the five known species of Paracreptotrema Choudhury, Pérez-Ponce de León, Brooks & Daverdin, 2006 by having vitelline follicles that extend from a level anterior to the pharynx to mid-testes, the seminal vesicle which is more extensively folded, and a wider cirrus sac. The new species resembles P. heterandriae in the length of its ceca, which surpasses the posterior margin of the ovary but do not reach the testes. A key to the species of Paracreptotrema is provided.

A newly discovered helminth parasite that infects swordtail fishes.The species is named in honor of Gil G. Rosenthal, co-founder of the CICHAZ field station in Mexico.
no DNA Barcodes

Pseudancistrus kayabi, Pseudancistrus asurini
Two new species of Pseudancistrus, a genus diagnosed by non-evertible cheek plates and hypertrophied odontodes along the snout margin, are described from two drainages of the Brazilian Shield: P. kayabi from the rio Teles Pires (rio Tapajós basin) and P. asurini from the rio Xingu. The new species are distinguished from congeners (P. barbatus, P. corantijniensis, P. depressus, P. nigrescens, P. reus, and P. zawadzkii) by the coloration pattern. Pseudancistrus kayabi has dark bars on the dorsal and caudal fins which are similar to that of P. reus from the Caroní River, Venezuela. Pseudancistrus asurini is unique among Pseudancistrus in having whitish tips of the dorsal and caudal fins in juveniles to medium-sized adults.

And another week with new members of the Loricarid family, perhaps better known as suckermouth catfish. One species is named after the Kayabi indigenous people that inhabited the region of the rivers Arinos, dos Peixes and Teles Pires, in Mato Grosso State, Brazil and the second name refers to the Asurini indigenous peoples who inhabit the right margin and middle portions of Rio Xingu,  in Pará State, Brazil.
no DNA Barcodes

Thismia hongkongensis
A new species, Thismia hongkongensis S.S.Mar & R.M.K.Saunders, is described from Hong Kong. It is most closely related to Thismia brunonis Griff. from Myanmar, but differs in the number of flowers per inflorescence, the colour of the perianth tube, the length of the filaments, and the shape of the stigma lobes. We also provide inferences on the pollination ecology and seed dispersal of the new species, based on field observations and interpretations of morphology. The flowers are visited by fungus gnats (Myctophilidae or Sciaridae) and scuttle flies (Phoridae), which are likely to enter the perianth tube via the annulus below the filiform tepal appendages, and exit via small apertures between the filaments of the pendent stamens. The flowers are inferred to be protandrous, and flies visiting late-anthetic (pistillate-phase) flowers are possibly trapped within the flower, increasing chances of pollen deposition on the receptive stigma. The seeds are likely to be dispersed by rain splash.

A new species in the genus Thismia which comprise of small herbaceous plants with extremely reduced vegetative structures resulting in a lack of chlorophyll. The plants rely solely on fungal symbionts. The species name reflects the geographical origin of the species in Hong Kong.
no DNA Barcodes

Monday, February 23, 2015

Happy Scallops

Yes, this blog is still alive. I was knocked out by disease for a week but I am back and ready to catch up on all things missed. Let's start the new week on a more positive note with some encouraging news.

Fisheries for king and queen scallops is a growing business worldwide and e.g. in the UK it has become a very important one, generating more than 90 million dollar first sale every year. As a result fisheries for scallops have grown dramatically over the past decade, but there are concerns over the damage to the seabed caused by the dredges and trawls normally used to catch them. 

Both the English and Scottish governments have recently declared networks of marine protected areas (MPAs) around their coasts and are currently deciding on how to manage them. However, there are concerns that the preferred option of both governments is to do little to actually restrict fishing within these MPAs despite good experience documented by countries such as the US. New research also confirms that this would be a wasted opportunity.

The first and only fully protected marine reserve in Scotland is Lamlash Bay marine reserve created 2008 off the Isle of Arran, following a decade-long campaign by the local Community of Arran Seabed Trust (COAST) and it is this backing from the local community that has been crucial to its success. COAST assisted with the research and encouraged the community to keep a watchful eye on activities in the area. In other marine reserves illegal fishing has been a problem, but in this case any suspicious activity has been reported to the authorities and in several cases fishing boats have been encouraged to move on by COAST members.

A new study reports on monitoring surveys conducted inside and outside the marine reserve by researchers in the Environment Department at the University of York from 2010 to 2013. Over the course of this new study, the abundance of commercially important juvenile scallops was consistently higher within the reserve than outside. These scallops were strongly associated with seaweeds and other marine life thriving on the seabed within the protected area. The colleagues found strong evidence that protecting Lamlash Bay from fishing has allowed seaweeds, hydroids and other organisms on the seafloor to recover. These animals act as a magnet for settling juvenile scallops which seek out these habitats for shelter, and to mature to adulthood.  Adult scallops showed benefits too. Their size and reproductive capacity was much higher inside the reserve by the end of the study. The resultant high level of breeding within the reserve is likely to be seeding the surrounding fishing grounds.

The authors conclude that protecting some areas from fishing activity can benefit both conservation and fisheries:

Overall, this study is consistent with the hypothesis that marine reserves can encourage the recovery of seafloor habitats, which, in turn, can benefit populations of commercially exploited species, emphasising the importance of marine reserves in the ecosystem-based management of fisheries.

Scallop fisheries are ideally suited to management using protected areas. This approach can protect sensitive habitats, which also act as nursery grounds for scallops and other species, while boosting the overall productivity of the fisheries. We urge the UK governments to create more highly protected areas which can provide this win-win scenario for the management of our oceans.

Friday, February 13, 2015

National Cockroach Project

In 2009, high school students found novel DNA barcode types in American cockroaches (Periplaneta americana) in New York City. These first preliminary results also indicated that cockroaches in certain city neighborhoods of New York share the same genetic makeup but differ from roaches in their neighboring hoods. This led to a new national project for high school students spearheaded by Mark Stoeckle, Rockefeller University, New York. The goal of the project was to learn more about this feared and despised yet ineradicable urban denizen.

The National Cockroach Project was announced in late 2012 called on high school students and other citizen scientists across the US to sample cockroaches and send them in for barcode sequencing. The main questions of the project were:

Do American cockroaches differ genetically between cities?
Do US genetic types match those in other parts of the world?
Are there genetic types that represent undiscovered look-alike species?

Now a little over 2 years later the project came to a close and the results were just published in Scientific Reports:

Our sampling effort generated 284 cockroach specimens, most from New York City, plus 15 additional U.S. states and six other countries, enabling the first large-scale survey of P. americana barcode variation. Periplaneta americana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate from other Periplaneta species. We found three distinct P. americana haplogroups with relatively small differences within (≤0.6%) and larger differences among groups (2.4%–4.7%). This could be interpreted as indicative of multiple cryptic species. However, nuclear DNA sequences (n = 77 specimens) revealed extensive gene flow among mitochondrial haplogroups, confirming a single species.

According to the authors, the most likely explanation for the detected genetic pattern is multiple human-mediated introductions from allopatric source populations followed by global dispersal among commercial centers. In fact, the different haplogroups must have diverged long before human-aided dispersal, even if the highest mutation rate estimates of insect mtDNA are applied.

This project is a great example for a citizen science project that did important research which has been recognized by being published in a peer review journal. Remarkably one of the study authors is a high school student and another one is a college undergrad. 

Thursday, February 12, 2015

Deep sea mining

Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules.

Recently the CCZ has seen a lot of prospectors and scientists exploring the extend of manganese nodule rock formations that lay amid the sea floor’s sediment. These were discovered as far back as the 1870s during the British Challenger Expedition and but only at the beginning of the 1960s researchers began scientific exploration. 

They nodules look like many black rocks, but they are deposits formed millions of years ago. Rich in metals, including nickel, copper, cobalt and rare earth elements. These minerals became crucial materials necessary for the production of cell phones, computers, and construction materials. It is expected that the mining operations will begin in the next 10-20 years and as per usual nothing is known about its impact on the local fauna. After all nodules are not just simply removed but large amounts of sediment will be displaced and the mechanical extraction represents a considerable impact on these usually very small patches of fauna. 

Mining will affect large areas of the seafloor owing to direct mining disturbance (estimated scales of 300–600 km2 per year) and re-deposition from sediment plumes (over scales of 10–100 km from the mining site), which calls for a systematic conservation planning process and associated establishment of a marine protected area network and adjacent buffer zones across the CCZ.

What's urgently needed is a baseline to get a better understanding of the biodiversity of the affected regions. This is not an easy task as we are looking at water depths of up to 5000 m. Our understanding of the deep sea fauna is patchy at best. Expeditions are costly and the catches are usually very limited in abundance. This does not necessarily mean that live down there is sparse, it is just much harder to find it.

A group of German researchers and one French scientist just published a study in which they assessed macrofaunal distribution patterns in these polymetallic nodule fields. They used DNA Barcoding to examine variations in genetic diversity and connectivity of isopods and polychaetes across the region. 

Specimens were collected from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes.  The expeditions brought back 1900 specimens that could be subjected to genetic analysis. With 44% for the polychaetes and 31% for the isopods the success rates were rather low but it seems that the authors only attempted COI amplification with standard Folmer primers which do not work well for both taxonomic groups. Despite this relatively low sequencing success, this study is very comprehensive compared to others investigating species distribution in such regions, and the results are remarkable:

Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. 

This new mineral rush - if not properly controlled - would have a devastating effect on these often unique ecosystems we don't even fully understand. As usual it is easier and cheaper to just go ahead and extract more resources from planet Earth rather than investing more into research that looks at renewable and recyclable solutions to an ever increasing demand. The good news is that the International Seabed Authority requires every contractor to report on environmental status, current biodiversity of the area as well as population structure and standing stocks. The problem is that we know so little and that seriously hampers any such assessment. This study is certainly a step forward in the right direction but once again one done by researchers.

This study represents only a first step towards understanding diversity of two macrobenthic groups in the CCZ and there are furthermore few comparable data to measure our findings against. However, the high genetic diversity, especially the high proportion of cryptic species even in good dispersers and at very small spatial scales, leads to the assumption that the central Pacific might indeed be listed amongst the World’s most diverse deep-sea ecosystems

Wednesday, February 11, 2015

Subway mircobes

These news came out sometime last week and I am somewhat late posting about it. Nevertheless, a very interesting study.

New York City's subway system is used by an average of 5.5 million people per day which makes it an ideal place for some serious microbial ecosystem studies. Therefore, a group of researchers from different institutions of the city decided to undertake a large-scale metagenomic study.

Over a period of 17 months a team of students used nylon swabs to collect DNA from turnstiles, wooden and metal benches, stairway hand railings, trashcans, and kiosks in all open subway stations in 24 subway lines in five boroughs of New York City. They also collected samples from the inside of trains, including seats, doors, poles and handrails. 

All these samples were sequenced as the colleagues sought to characterize the NYC metagenome by surveying the genetic material of the microorganisms and other DNA present in, around, and below NYC, with a focus on the highly trafficked subways and public areas.

The results were quite interesting. What struck me most was the fact that about half of the sequences of DNA collected could not be identified. They did not match any organism in GenBank or other databases, e,g. at the CDC. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet quite literally right under our fingertips.

The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs - even a few DNA fragments associated with anthrax and Bubonic plague. The publication contains a citywide microbiome map which the colleagues call  "PathoMap". They see their work as a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York.

What I particularly like about this publication is the wealth of data that came with it. The supplementary data part of the paper is huge (about 100MB zipped) and the paper is open access because the authors choose to pay for this option. A great example of reproducible science.

Tuesday, February 10, 2015

Discoveries of the week #26

A distinctive new monotypic genus from Gabon is described in the tropical plant family Annonaceae: Sirdavidia, in honor to Sir David Attenborough. Molecular phylogenetic analyses confirm that Sirdavidia, which is very distinct from a morphological standpoint, is not nested in any existing genus of Annonaceae and belongs to tribe Piptostigmateae (subfamily Malmeoideae), which now contains a total of six genera. The genus is characterized by long acuminate leaves, fully reflexed red petals, 16–19 bright yellow, loosely arranged stamens forming a cone, and a single carpel topped by a conspicuous stigma. With just three known collections, a preliminary IUCN conservation status assessment is provided as “endangered” as well as a distribution map. The discovery of Sirdavidia is remarkable at several levels. First, it was collected near the road in one of the botanically best-known regions of Gabon: Monts de Cristal National Park. Second, its sister group is the genus Mwasumbia, also monotypic, endemic to a small area in a forest in Tanzania, some 3000 km away. Finally, the floral morphology is highly suggestive of a buzz pollination syndrome. If confirmed, this would be the first documentation of such a pollination syndrome in Magnoliidae and early-diverging angiosperms in general.

It is about time to honor this man - Sir David Attenborough, In case you don't know him is a British broadcaster and naturalist, best know for his extraordinary natural history programs. His passion for nature has influenced and inspired a generation of biologists and naturalists, including the authors of the paper and the author of this blog. The species name highlights the resemblance with flowers of some species of Solanum, which is rather unusual and new for a flower of this family.

The present study deals with the description of a new species of Rhinolekos. It can be distinguished from its congeners by having 31 vertebrae, the anterior portion of the compound supraneural-first dorsal-fin proximal radial contacting the neural spine of the 9th vertebra, the absence of transverse dark bands in the pectoral, pelvic and anal-fin rays, 24–28 plates in the dorsal series, the lack of odontodes on the ventral tip of the snout, the absence of accessory teeth, a greater prenasal length, a smaller head length, and by a greater snout length. Rhinolekos capetinga is restricted to the headwaters of the rio Tocantins and it is the first species of this genus in the Amazon basin. Additionally, we present a brief discussion of a biogeographic scenario that may explain the dispersal of the new species from the rio Paranaíba to the rio Tocantins basin. We suggest that the ancestral lineage of R. capetinga reached the rio Tocantins from portions of the rio Paranaíba at the end of the Miocene, about 6.3 Mya (4.1–13.9 Mya 95% HPD), probably as a result of headwater capture processes among adjacent drainages.

And another species of the Loricariid family. I mentioned three others last week in this column. This new species was give the name 'capetinga' from the Tupi-guarani dialect which  is in reference to the old and unused name of the São João D´Aliança municipality. The name 'capetinga' means white, or clear water.

The freshwater genus Hyalella Smith, 1874 has a distribution restricted to the Western Hemisphere with most species being found in South America. In this report we describe a new species of Hyalella from the Atlantic Forest of the Misiones province, Argentina.

The amphipod genus Hyalella includes about 70 valid species with a distribution limited to the Americas. So far nine of those have been recorded for Argentina and here comes number ten found in the province of Misiones, hence the species name.
No DNA Barcodes

Bythinella anatolica sp. n., Bythinella istanbulensis sp. n., Bythinella magdalenae sp. n., and Bythinella wilkei sp. n. from western Turkey are described herein. Illustrations of the shell and genitalia of the newly described taxa, together with comparisons with previously known Bythinella taxa and a key to the species from western Turkey, are also provided.

A genus of small (1-3 mm) freshwater snails occuring mostly in cold water springs (10 °C). The genus is rather large with 132 species and (sigh) subspecies. Here are four new members named either after location (Bythinella anatolica, Bythinella istanbulensis) or malacologists (Bythinella magdalenae, Bythinella wilkei). The latter was named after Thomas Wilke, who used to work in the ecology and evolution group at the Goethe University Frankfurt around the same time I did my final undergrad and diploma work there. Congrats to him.
No DNA Barcodes

A comparative analysis of gemmular architecture adaptive morpho-traits at family level is reported for Metaniidae together with the discovery and description of a new species from the River Mangoky (High Plateau), Madagascar. The new Malagasy species, ascribed to Metania for diagnostic traits of the skeleton and the gemmular architecture, differs from all the other known species of the genus in its unique combination of diagnostic traits. Metania madagascariensis sp. nov. is characterised by encrusting growth form, conulose surface, specialized ectosomal skeleton, alveolate-reticulate choanosomal skeleton, two types of megascleres as smooth oxeas (α) and acanthoxeas (β) ornamented with spines and/or tubercles, one type of microsclere as acanthoxeas with dense spines/tubercles bearing rosettes of microspines at tips; gemmules with or without cage of megascleres and frequently surrounded by microscleres; gemmular theca trilayered with pneumatic layer of fibrous spongin, boletiform (trumpet-like) gemmuloscleres with proximal true rotule large, smooth and with irregular blunt margins, and distal knob-like pseudorotule notably smaller, with a few hooks at the margins. M. madagascariensis belongs to the Afrotropical species group of Metania. Identification keys and an annotated checklist at global level are also provided together with a species-level discussion of Metania focusing on morphology, taxonomy, nomenclature
and biogeography.

A new species of freshwater sponges found on Madagascar. The species name is derived from the name of Madagascar as this is so far the only species of the genus Metania reported from the island.
No DNA Barcodes

Four species of palicoid crabs, Neopalicus jukesii (White, 1847) and Rectopalicus ampullatus Castro, 2000 of the family Palicidae, and Crossotonotus spinipes (De Man, 1888) and a new species of Pleurophricus A. Milne-Edwards, 1873 of the family Crossotonotidae, are recorded from the Ogasawara Islands, Japan. Diagnostics for the new species are the protruded bilobed front, six subacute lobate teeth at each lateral margin of the carapace, six rounded lobes at the posterior margin of the carapace, a crested armature of the cheliped carpus, and the strongly depressed ambulatory legs, which readily distinguish it from its two congeners, P. cristatipes A. Milne-Edwards, 1873 known by two males from Australia and the Kai Islands in Indonesia, and P. longirostris (Moosa & Serène, 1981) known by a female from the Sunda Strait, Indonesia.

A new crab species fund close to the Ogasawara Islands. Named from the Latin stella for “star” in reference to its general appearance, 
No DNA Barcodes

Monday, February 9, 2015

From hickory to walnut

Back in 2010 researchers of the Italian National Research Council found an unknown leafmining moth in southern Italian walnut orchards. It soon appeared to belong to the North American genus Coptodisca, very small but beautiful moths of about 2.5 mm length. However, establishing the identity of the species was less easy. It looked similar to Coptodisca juglandella, the only genus member known to attack walnuts (Juglans spp.), but an unambiguous identification couldn't be made because of the insufficient characterization of this group of leafminers.

Around the same time a researcher from the Naturalis Biodiversity Center in Leiden, Netherlands had collected North American larvae of another leafminer that was invading North Italian vineyards (Antispila oinophylla). Surprisingly, when both research groups compared their results, DNA Barcodes of North American Coptodisca larvae collected on hickories appeared to be very similar to those of the Italian walnut feeding moths. Hickories (Carya spp.) belong to the same family as the walnut tree - Juglandaceae. All these similarities and the fact the entire group was essentially understudies triggered the curiosity of the researchers and they began to study moths from several North American collections and finally decided on the basis of both morphological and genetic studies that the mysterious species is Coptodisca lucifluella, described in the 19th century from hickory. 

The leafminer Coptodisca sp. (Lepidoptera: Heliozelidae), recently recorded for the first time in Europe on Italian black and common walnut trees, is shown to be the North-American Coptodisca lucifluella (Clemens) based on morphological (forewing pattern) and molecular (cytochrome oxidase c subunit I sequence) evidence. 

These moths have a beautiful color pattern consisting of silver, black and yellow spots, and measure only 4 mm in wingspan. The larvae make short galleries in leaves and at the end cut out a small shield, leaving a characteristic hole at the end of the leafmine. The larva attaches the shield to the leaves or other surfaces and pupates inside. 

Coptodisca lucifluella naturally occurs in eastern North America. Its larvae feed on several species of wild hickory and commonly on pecan in orchards, It has never been considered more than a minor pest and in North America the moth has never been found on walnut. However, in Italy the species is widespread and happily feeding on Walnut.

The phylogenetic relatedness of three species feeding on Juglandaceae suggests that C. lucifluella has likely shifted, within the same host plant family, from its original North-American hosts Carya spp. to Juglans spp.

It is likely that the insects hitchhiked as larvae or pupae as those protected by their shield attach easily to leaves or stems. Global trade provides excellent transportation. It is interesting that the moth shifted to a new host plant once arrived in Europe, a phenomenon that has been observed with other invading insects. 

Considering its widespread presence and rapid reproduction, C. lucifluella might quickly increase its abundance and distribution in Italy and other European countries. Nevertheless, as also observed for other Heliozelidae and excluding the outbreaks, the level of damage does not seem to be worrisome. The possibility remains, however, that damage by C. lucifluella, if continued for a number of years, might lead to a progressive reduction in carbohydrate reserves and a gradual decline in tree health and performance. Based on the high mortality recorded and on the large number of parasitoids being collected, it would be preferable to encourage biological control rather than performing chemical treatments. 

Friday, February 6, 2015

LEGO® in the lab

We present a pinned insect manipulator (IMp) constructed of LEGO® building bricks with two axes of movement and two axes of rotation. In addition we present three variants of the IMp to emphasise the modular design, which facilitates resizing to meet the full range of pinned insect specimens, is fully customizable, collapsible, affordable and does not require specialist tools or knowledge to assemble.

This is not a joke but the abstract of a new paper just published in Zookeys which describes a very creative solution to a problem researchers at the Natural History Museum in London (NHM) were facing. They are working on the mass digitization of museum specimens and for years they have been using standard size commercial manipulators which are not flexible enough to work with a number of insect groups.

In such cases researchers usually resort to affordable DIY solutions but often those are made from materials and tools that are not readily available to everyone. Furthermore most of these setups are again not very flexible as they usually were designed for a particular group of insects and may not be of an appropriate size for other insect groups.

So what do you do? Well, you start using the perhaps most versatile toy ever invented - LEGO®. At least that's what the colleagues at the NHM did. To answer the challenges of mass digitization in their day-to-day digitization tasks they invented a pinned insect manipulator made entirely of LEGO® pieces. Their invention holds several advantages among which are universal applicability, availability, affordability and the ability to customize for each case at all times. Most importantly they ensure minimum handling of fragile specimens to reduce the risk of damaging very valuable vouchers.

This is fantastic. Not only does it seem to be an optimal solution to the problem at hand but it also gives adults a welcome excuse to play with LEGO® at work.

Thursday, February 5, 2015

Handheld sensor for fish identification

Grouper are one of the most economically important seafood products in the state of Florida and their popularity as a high-end restaurant dish is increasing across the U.S. There is an increased incidence rate of the purposeful, fraudulent mislabeling of less costly and more readily available fish species as grouper in the U.S., particularly in Florida.

So far that's likely no news to readers of this blog and the problem is unfortunately not limited to grouper species. Two years ago a group based at the University of South Florida developed a generic grouper assay that was capable to detect the majority of the grouper species listed on the US FDA Seafood List and it did so in 90 minutes.

The alternate technology was termed nucleic acid sequence-based amplification (NASBA). It is similar to PCR in that both involve the amplification of specific nucleic acid sequences via enzymatic reactions. However, NASBA targets RNA rather than DNA, and it is carried out at a constant temperature of 41 °C whereas PCR requires thermal cycling within large temperature ranges up to 95°C which also requires specific thermostable enzymes. As target the authors choose 16S rRNA as this form of RNA tends to be more resistant to degradation than messenger RNA (mRNA), which is the form of DNA Barcode RNA in tissue cells. It also seemed to be better suited for the grouper species the authors were targeting. However, they also made clear that COI might work better for other species and for fish identification on a larger scale.

Now, just two years later the same group presents their next invention: A handheld sensor assay for grouper identification based on the NASBA protocol. The QuadPyre RT-NASBA, assays the fish samples using a real-time version of the earlier procedure (RT-NASBA). The handheld instrument that purifies and identifies the sample's rRNA is a portable version of the lab-based benchtop model previously developed.

Using the hand-held device, a complete field assay, potentially carried out at the point of purchase, requires fewer than 45 minutes for completion and can be performed entirely outside of the lab.

The technology is already being commercialized by a spin off company called PureMolecular, LLC under the name GrouperChek (trademark pending). Is there a market for this. I do think so. It's estimated that up to 30% of the seafood on the U.S. market is fraudulently mislabeled, bilking fishermen, the seafood industry, and consumers for an estimated $20-25 billion annually. 

We believe there is heightened interest for a portable, uncomplicated technology such as the QuadPyre RT-NASBA assay that allows for rapid on-site screening of genetic material from seafood similar to point-of-care testing devices used for rapid diagnosis in clinical settings (Ahmad & Hashsham, 2012). What is more, the format of the handheld heated fluorometer allows for potential implementation of alternate RT-NASBA assays utilizing oligonucleotide sets to target other commercially important finfish groups such as snappers and tunas, which had the highest mislabeling rates according to the aforementioned Oceana investigation (Warner et al., 2013). Presenting personnel in seafood purchasing and regulation of such commerce with rapid and portable forensic technologies such as the one presented here will help close inspection gaps to better combat seafood mislabeling fraud.

Wednesday, February 4, 2015

Herbal supplements under suspicion

Some of you might have already read or heard that DNA Barcoding is in the news again (e.g. here and here). The New York State attorney general’s office accused four major retailers of selling fraudulent and potentially dangerous herbal supplements and demanded through an official cease and desist notification that they remove the products from their shelves. This new investigation was prompted by research at our institute. which back in 2013 found that about a third of herbal supplements tested did not contain the plants listed on their labels but cheap fillers instead.

It comes to no surprise that the industry reacted quickly to this new development and heavily criticized the attorney general. One of the many outlets that represent their views provided a list of 10 critical questions, and I thought it might be a good idea to respond to some of them as someone with considerable experience in DNA Barcoding. I usually don't put an emphasis on my credentials but since this is one angle of the criticism I thought I should state that upfront. And now without further ado the questions as found here (all questions are highlighted in italics to indicate that they are not mine - some were left out as they are outside my area of expertise):

1. DNA Barcoding is not an established method for extracts. Why did the AG and the researcher choose this method?
It is true that isolating DNA from herbal products such as the supplements in question is not an easy task. The fabrication process is often damaging DNA which usually means that it is broken down in smaller chunks (degradation). However, this does not necessarily mean that there isn't sufficient DNA information left to provide a species identification. Laboratory procedures need to be adjusted and tests need to be repetitive, a single attempt won't suffice. Still, there is a chance that no usable DNA is left but that hardly warrants this kind of criticism. The cases where the supposed ingredient was not found showed other species such as fillers like powdered rice, asparagus and houseplants. That tells me that there was indeed sufficient DNA left but unfortunately not from the right organism. Nevertheless, I think it is important to make one thing clear: The fact that a species was not detected can mean two things:
- it is indeed not present in the sample, or
- there wasn't enough specific DNA left to provide a sequence
The latter is what is in the center of the criticism. There is indeed a chance of a false negative result. However, if so it also means that the concentration is likely very low and - very important for any customer - it does not explain why there are contaminants present. Careful interpretation on both sides is needed here.

DNA Barcoding is currently the best method to do species identification especially for processed, fragmentary remains of organisms. The reference library is steadily growing and accessible to anyone. These might have been the reasons why it was chosen.

2. Why is the Attorney General withholding the data?
There isn't much I can say but the name of the researcher and his lab are known. I would love to see the data myself but I can't tell if it is common practice to withhold them for the time being. The blog author also complains that the data hasn't been published in a peer-review journal. Now that would be very unusual. If all legal case related data need to go through peer review that would defy the purpose of the system and keep every researcher busy reviewing paper that do not constitute basic research. There is simply no need for a scientific publication in such as case and it would make the scientific community part of the legal system. I wouldn't want to review a manuscript that harbors the risk of being drawn into a legal battle.

4. How qualified is Dr. Schulte to be testing botanical products?
Well, Dr. Schulte is very experienced in molecular biology and working with DNA and that is usually well enough to start with DNA Barcoding. After all we use it in schools and have kids participating in the work. The first cases of market product testing were actually done by grade 11 students, e.g. Sushigate, green tea. Given the challenges of DNA isolation as described above it would be advisable to have at least a university molecular lab working on such a study but there is no need to be an expert botanist if you focus solely on DNA Barcoding as it was the case. That changes once you include other means of identification such as morphology but that does not work with supplements. It all comes down to experience with the technology, knowing about its challenges, and how to interpret the results.

5. What were the quantities of the contaminations detected?
DNA Barcoding won't be able to provide this answer. It is used to find contaminants but not to check if label requirements are necessary. I see the point here and understand the interest in such data but it bothers me to know that presence of an unwanted species is not perceived as the problem but the quantity. That would mean that meeting regulatory requirements is more important than customer satisfaction.

7. This paper was widely criticized - were these criticisms known to the AG and the researcher?
This question refers to the paper by Newmaster et al. 2013 which I mentioned above. Problem is that the "wide" criticism came only from one source which is the American Botanical Council (ABC). I am not going to comment a lot on this organisation. Have a look at their website and especially at their sponsors list

8. Why did the researcher not use the accepted methods (with monographs)?
What are the accepted methods? I can only guess that this refers to chromatography and microscopy but the latter e.g. doesn't work at all with extracts. The blog author claims that there is little to no cellular material left in an extract for a DNA analysis. Well, how are we supposed to do morphological identification? Of all the things that could be left after processing supplements it is fragments of DNA and proteins. Other accepted methods have failed to detect contaminations. That's why a new method (now 12 years old) was applied.

10. Will the industry response be heard?
I would think so. A lot of the press articles include the criticism voiced by industry. There is nothing one can do about the negative coverage. I agree the echo is one-sided but that is the result of a general mistrust in industry in general caused by such incidents. The problem might still be very isolated but the customer doesn't know that. We don't know who sells quality and who not.  Naturally we react with suspicion. 

I'd like to make clear that I am far from demonizing the entire industry. I have enough experience with similar incidents to know that there are also some very reliable retailers and manufactures. However, there are no independent control mechanisms in place that would provide a clearer picture than what we see through these spot checks. The fact that unwanted material shows up in supposedly clean products is very concerning and needs to be addressed. I believe it would be advisable for industry to embrace DNA-based identification methods instead of condemning them each time when they provide inconvenient truths. If it doesn't work perfect then by all means lets sit down and work on improving it together. An industry that works proactively to single out the black sheep among them is what we need. If species identification of herbal extracts is an issue we need to work on that. Probably it is advisable to test before the product is processed beyond recognition. I am well aware that such changes and additional testing come with extra costs but there are perhaps ways to cover those. 

It all comes down to trust. Does a customer trust a company enough to buy their product? Nobody will gain this trust by referring to regulations that are met. We know that regulations in this market segment are insufficient which is why these studies find contamination in the first place. People will buy products if they can be reasonably certain that those aren't contaminated and contain a pure substance, not a mixture that sometimes might not even contain the ingredient they were looking for.

Tuesday, February 3, 2015

Discoveries of the week #25

Cobitis avicennae
Cobitis avicennae, new species, from the Karkheh and Karun sub-drainages in the Tigris catchment is distinguished from other Cobitis species in the Persian Gulf, Kor and the southern Caspian Sea basins by having a single lamina circularis in males, a small comma-shaped black spot on the upper caudal-fin base, 5½ branched anal-fin rays, 5–6 rows of dark spots on the dorsal and caudal fins, scales below the dorsal-fin base with a small focal zone and pigmentation zone Z4 with 12–17 large, partly fused blotches. It is also distinguished from other Cobitis species in the comparison group by six fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region

A nice new little spined loach from Iran. The genus Cobitis currently comprises of 65 species and now there is one more from the Tigris drainage.  The species is named after the Persian polymath Abū Alī al-Ḥusayn ibn ʿAbd Allāh ibn Sīnā, commonly known as Ibn Sīnā or by his Latinized name Avicenna.

Peckoltia ephippiata
Three new species of saddled hypostomine loricariids are described. According to a recent phylogenetic analysis, these species are members of the genus Peckoltia. The species differ from all described Peckoltia except P. furcata and P. sabaji by having the dentaries meet at an angle greater than 90°. The species also have similarities to Hemiancistrus, and can be separated from all described species by having dorsal saddles. We discuss the taxonomy of Peckoltia, Hemiancistrus, and allied genera and recognize Ancistomus as valid for P. feldbergae, H. micrommatos, Ancistrus snethlageae, H. spilomma, and H. spinosissimus. We recommend descriptions of genera for several clades of Hemiancistrus and restriction of Hemiancistrus to the type species of the genus, H. medians. Chaetostomus macrops is transferred to Pseudancistrus and recognized as a junior synonym of P. megacephalus. The Hemiancistrus annectens group of species (H. annectens, H. argus, H. aspidolepis, H. fugleri, H. holostictus, H. maracaiboensis, H. panamensis, H. wilsoni) are recognized in Hypostomus. Multivariate analysis reveals that the newly described species differ from one another in shape space, but overlap broadly with other Peckoltia (P. lujani), narrowly with other Peckoltia (P. greedoi), or broadly with Etsaputu (P. ephippiata).

The suckermouth armored catfishes family has about  800 known species and is a taxonomically very difficult group. So difficult that a numbering system was invented that helped registering putative new species waiting for a sufficient taxonomic treatment. The system is by no means based on any scientific system. As a result specific L-number classifications do not guarantee discrete species, multiple L numbers have been given to different populations of the same species. To add to the confusion, sometimes a single L-number may actually be used for multiple species. 
no DNA Barocodes

We describe a new species of Telmatobius from the Pacific slopes of the Andes in central Peru. Specimens were collected at 3900 m elevation near Huaytará, Huancavelica, in the upper drainage of the Pisco river. The new species has a snout–vent length of 52.5 ± 1.1 mm (49.3–55.7 mm, n = 6) in adult females, and 48.5 mm in the single adult male. The new species has bright yellow and orange coloration ventrally and is readily distinguished from all other central Peruvian Andean species of Telmatobius but T. intermedius by having vomerine teeth but lacking premaxillary and maxillary teeth, and by its slender body shape and long legs. The new species differs from T. intermedius by its larger size, flatter head, and the absence of cutaneous keratinized spicules (present even in immature females of T. intermedius), and in males by the presence of minute, densely packed nuptial spines on dorsal and medial surfaces of thumbs (large, sparsely packed nuptial spines in T. intermedius). The hyper-arid coastal valleys of Peru generally support low species richness, particularly for groups such as aquatic breeding amphibians. The discovery of a new species in this environment, and along a major highway crossing the Andes, shows that much remains to be done to document amphibian diversity in Peru.

Telmatobius is a genus of frogs native to the Andean highlands. This new species from Peru is named for the golden yellow and orange coloration on the ventral parts of its body and limbs. 
no DNA Barocodes

Four new species of shallow-water marine gastropods belonging to the family Rissoidae are described from the Archipelago of the Azores: Setia alexandrae sp. n., S. ermelindoi sp. n., S. netoae sp. n., and Manzonia martinsi sp. n. These novelties increase the regional rissoid fauna to 39 species, of which 29 live in shallow-water habitats. A list of the species of Rissoidae from the Azores is presented based on data from the literature and new material examined.

Four new species from the Azores. One (Setia alexandrae) named after the wife of one of the authors, the second after a regional a writer and historian, the third after an Azorean marine phycologist. and the last after a malacologist of the University of the Azores.
no DNA Barocodes

The paper integrates two independent studies of numeric morphology-based alpha-taxonomy of the cryptic ant species Temnothorax crassispinus (Karavajev, 1926) and T. crasecundus sp. n. conducted by different investigators, using different equipment, considering different character combinations and evaluating different samples. Samples investigated included 603 individual workers from 203 nests – thereof 104 nest samples measured by Seifert and 99 by Csösz. The material originated from Europe, Asia Minor and Caucasia. There was a very strong interspecific overlap in any of the 29 shape characters recorded and subjective expert determination failed in many cases. Primary classification hypotheses were formed by the exploratory data analysis Nest Centroid (NC) clustering and corrected to final species hypotheses by an iterative linear discriminant analysis algorithm. The evaluation of Seifert’s and Csösz’s data sets arrived at fully congruent conclusions. NC-Ward and NC-K-means clustering disagreed from the final species hypothesis in only 1.9 and 1.9% of the samples in Seifert’s data set and by 1.1 and 2.1% in Csösz’s data set which is a strong argument for heterospecificity. The type series of T. crassispinus and T. crasecundus sp. n. were allocated to different clusters with p = 0.9851 and p = 0.9912 respectively. The type series of the junior synonym T. slavonicus (Seifert, 1995) was allocated to the T. crassispinus cluster with p = 0.9927. T. crasecundus sp. n. and T. crassispinus are parapatric species with a long contact zone stretching from the Peloponnisos peninsula across Bulgaria northeast to the southern Ukraine. There is no indication for occurrence of interspecifically mixed nests or intraspecific polymorphism. However, a significant reduction of interspecific morphological distance at sites with syntopic occurrence of both species indicates local hybridization. The results are discussed within the context of the Pragmatic Species Concept of Seifert (2014). The taxonomic description and a differential diagnosis of T. crasecundus sp. n. are given.

I am not an ant expert and therefore I will refrain from commenting on the methods used to delineate this species although they seem to be very sound and reliable. My problem with this paper is with a certain passage: A curator of a museum collection should not allow destructive DNA sampling from a type specimen of a small insect and there is no doubt that next generation sequencing in our 600 dry mounts would be enormously costly and time-consuming. I beg to differ as there are non-destructive methods available that would allow for DNA extraction without harming the voucher specimen, Next-generation sequencing of 600 dry mounts might indeed cost a bit of money but time consuming? I doubt it would be more time spend than what has been described here. 
no DNA Barocodes

Gymnosporia swazica
Gymnosporia swazica, a new restricted-range southern African species, is described and illustrated here. Known from only a few localities in Swaziland and bordering parts of South Africa (Mpumalanga and northeastern KwaZulu-Natal), G. swazica grows as an understorey shrub or small tree in forest, often among granite boulders. Diagnostic characters for G. swazica include chartaceous leaves, usually shorter than 25 mm, 3-valved capsules usually 6–7 mm long, which are smooth, green
turning yellow, and a white aril partially covering the brownish seed. Its closest relative appears to be G. buxifolia (capsules rugose, mottled white-and-brown), one of the most widespread members of the genus in southern Africa, but it can also be confused with G. maranguensis (capsules red, 2-valved) and G. harveyana (capsules pink to red, 3-valved; aril orange, completely covering the seed).

A new species found on the Lebombo Mountains in Swaziland, hence the species name.
no DNA Barocodes

h/t Matthias Geiger