Tuesday, September 30, 2014

New bulletin

Our new issue of the Barcode Bulletin is out. Get your copy here (just click on the image):

Discoveries of the week

Species diversity of Brazilian cave fauna has been seriously underestimated. A karst area located in Felipe Guerra, northeastern Brazil, which is a hotspot of subterranean diversity in Brazil, has revealed more than 20 troglobitic species, most of them still undescribed. Based on recent samplings in this karst area, we document the occurrence of the suborder Cavernicola (Platyhelminthes) in South American hypogean environments for the first time and describe a new genus and species for this suborder. Hausera Leal-Zanchet & Souza, gen. n. has features concordant with those defined for the family Dimarcusidae. The new genus is characterized by two unique features, viz. an intestine extending dorsally to the brain and ovovitelline ducts located dorsally to the nerve cords, which is complemented by a combination of other characters. The type-specimens of Hausera hauseri Leal-Zanchet & Souza, sp. n. are typical stygobionts, unpigmented and eyeless, and they may constitute an oceanic relict as is the case of other stygobiotic invertebrates found in this karst area in northeastern Brazil.

This is a typical cave-dwelling organism, unpigmented and eyeless. It was discovered in a karst area located in northeastern Brazil. The animal constitutes a new genus and species of freshwater flatworm and may even be an oceanic relict. The species, named after the late Prof Dr Josef Hauser SJ as acknowledgement of his great enthusiasm for the study of freshwater flatworms, represents the first obligate cave-dwelling flatworm in South America.
no DNA barcode

Dendrobatid frogs are among the best known anurans in the world, mainly due to their toxicity and associated bright colors. A recently described dendrobatid genus, Andinobates, comprises frogs distributed among the Colombian Andes and Panama. During field work in the Distrito de Donoso, Colón province, Panama, we found a poison frog that we here describe as a new species. The new species belongs to the A. minutus species group and is described herein as Andinobates geminisae sp. nov. This new species differs from all other members of the group by having uniformly orange smooth skin over the entire body and a distinctive male advertisement call. The new species is smaller than other colorful dendrobatids present in the area, such as Oophaga pumilio and O. vicentei. We also provide molecular phylogenetic analyses of mitochondrial DNA sequences of dendrobatids and summarize genetic distances among Andinobates species. Andinobates geminisae occurs in Caribbean versant rainforest on the westernmost edge of the known distribution of A. minutus, and represents the fourth species within this genus in Panama. This is vulnerable to habitat loss and excessive harvesting and requires immediate conservation plans to preserve this species with a restricted geographic range.

This bright orange poison dart frog with a unique call has been discovered in Donoso, Panama. Because this new frog species appears to be found in only a very small area, habitat loss and collecting for the pet trade are major threats to its existence. 
DNA Barcodes available (although not public on BOLD)

Two new species of Fissocantharis Pic are described, F. bifoveatus sp. n. (CHINA: Yunnan) and F. acuticollis sp. n. (CHINA: Zhejiang, Fujian, Guangdong, Hunan). F. pieli (Pic, 1937) is redescribed and F. kontumensis Wittmer, 1989 is provided with a supplementary description. F. shanensis (Wittmer, 1997) is synonymized with F. kontumensis. For the above four species, illustrations of male genitalia are provided, for the latter three also photos of female genitalia and abdominal sternites VIII, and for the new species photos of male habitus and antennae are presented. Additionally, the specific name of F. wittmeri (Y. Yang et X. Yang, 2009), preoccupied by F. wittmeri (Kazantsev, 2007), is replaced by F. walteri Y. Yang et X. Yang, nom. n. And F. wittmeri (Kazantsev, 2007) is found to be a junior objective synonym of F. denominata (Wittmer, 1997).

The specific name bifoveatus is derived from the Latin bi (two) and fovea (pit), referring to a structure on some of the beetles antennas. The name of the second new species is also derived from Latin, this time referring to the shape of the pronotum angles.
no DNA barcodes

Hisonotus acuen
A new species of Hisonotus is described from the headwaters of the rio Xingu. The new species is distinguished from its congeners by having a functional V-shaped spinelet, odontodes not forming longitudinal aligned rows on the head and trunk, lower counts of the lateral and median series of abdominal figs, presence of a single rostral fig at the tip of the snout, absence of the unpaired figlets at typical adipose fin position, yellowish-tipped teeth, absence of conspicuous dark saddles and stripe on the body and higher number of teeth on the premaxillary and dentary. The new species, Hisonotus acuen, is restricted to headwaters of the rio Xingu basin, and is the first species of the genus Hisonotus described from the rio Xingu basin. Hisonotus acuen is highly variable in aspects of external body proportions, including body depth, snout length, and abdomen length. This variation is partly distributed within and among populations, and is not strongly correlated with body size. PCA of 83 adult specimens from six allopatric populations indicates the presence of continuous variation. Therefore, the available morphological data suggest that the individuals inhabiting the six localities of rio Xingu represent different populations of a single species. Low intraspecific variation in mitochondrial Cytochrome oxidase subunit I (COI) provides corroborative evidence.

And another new Loricariid. I had presented one about two weeks ago. It is great to see that one by one they are described and get proper names, and they come with DNA Barcodes. The species is named for the Xavante indigenous peoples, who are also known as “acuen”. They are living in the margins of the rivers Culuene, Mortes, Araguaia, and Xingu. The type specimens were found in the latter.
DNA Barcodes available (but not yet released on Genbank)

Syzygium sahyadricum

A new species of the tree genus Syzygium (Myrtaceae), S. sahyadricum is described and illustrated from the Montane Shola forests of Anamalai and Palni Phytogeographical region of Western Ghats. Although phenotypically closely similar to S. spathulatum and S. malabaricum, the new species is easily recognizable by the pale yellow coloured tender leaves with horizontal secondary nerves and white flowers in reduced metabotryoid, pedunculate inflorescence, which are flattened towards the apex. Scanning the Syzygium collections in various herbaria revealed that similar specimens from various localities of this phyto-region are available and most of them with erroneous ascriptions. The report of S. spathulatum Thwaites, a Sri Lankan endemic species in India, was due to misinterpretation of Beddome’s collection. In this paper taxonomic peculiarities of the new species and allied taxa are discussed for better understanding.

A new species of myrtle found by scientists from the Kerala Forest Research Institute in the Western Ghats. It grows on hills above at an altitude of 1800 m. The species blooms in December and bears edible fruits from March to May.
no DNA barcodes

Verbascum duzgunbabadagensis
Verbascum duzgunbabadagensis (Scrophulariaceae) is described and illustrated as a new species endemic to eastern Anatolia, Turkey. In this study, diagnostic morphological characters of this and closely related species (V. luciliae and V. rupicola) are discussed. Pollen and seed morphology of the new species and of similar taxa are documented. The seeds of this group are brown in color and oblong in V. luciliae and V. rupicola, whereas they are dark brown in color and ovate in shape in V. duzgunbabadagensis. Furthermore, distribution maps for the three taxa are provided.

This new species is called after Düzgün Baba Mountain, the unique area where this species has

been recorded. It was found during a field exploration in Turkey in 2012. Also a higher altitude species as it was found in rock crevices at 1800−2050 m.
no DNA barcodes

Monday, September 29, 2014


Sclerotia are hard, compact masses of fungal mycelium that usually form in soil or plant tissue. They are thought to serve as resting structures that can survive and remain quiescent in adverse environmental conditions until circumstances become favorable for fungal growth. Some sclerotia have been used as food and medicine for a long time in human history.

The fungus Cenococcum geophilum forms sclerotia in forest soils. It is one of the most common ectomycorrhizal fungi encountered in forest ecosystems. Its geographic distribution is cosmopolitan and it is found in ecosystems with a wide range of environmental conditions, very often in high numbers. Because of its wide distribution and abundance in forest soils, it is probably one of the most well-studied fungal species. 

A new study suggests that Cenococcum sclerotia act as a substrate for many other fungi. A team of American and Japanese researchers used DNA Barcoding  to document the fungal communities growing inside sclerotia that were collected from forest soils. They were able to detect at least 85 other fungal species in sclerotia across many sites which suggests that these fungi may be active parasites of Cenococcum sclerotia or at least use sclerotia as a nutrient source. 

Understanding the effects of sclerotia-associated fungi on the viability of Cenococcum sclerotia will be important in order to fully understand the biology and lifecycle of Cenococcum in nature. In the future, in vitro studies that combine microscopy, inoculations of specific sclerotia-associated fungi, and the use of both fresh and old sclerotia for experiments may help to elucidate the ecological interactions between Cenococcum sclerotia and other soil fungi.

Friday, September 26, 2014

Long distance kelp rafting

Bull kelp (credit www.seaweedsofalaska.com)
Today's post is about a new paper by a good friend of mine, Gary Saunders from the University of New Brunswick in Fredericton, Canada. Gary is happily barcoding seaweeds pretty much since the first days of DNA Barcoding and he assembled some 12 000 specimens barcodes to date. Every time we have a chance to meet at conferences, symposia, or even in the field, sure enough he will have a very interesting story to tell and most of the time they have to do with findings that stem from his barcoding work on algae. 

Last year at the international DNA Barcoding conference in Kunming he gave a talk about something that had puzzled him for a while and we had a few discussions over beer in the evenings. I think it is best to quote Gary at this point and let him describe the observations:

Routine DNA barcoding of the Haida Gwaii seaweed flora revealed ‘endemic species’ attributed initially to this region's past as a glacial refugium. However, subsequent barcode records from central California rapidly eroded this list leaving species characterized by disjunct distributions between California and Haida Gwaii. This observation prompted a more detailed look at species for California and British Columbia and revealed that 33 of 180 DNA-barcoded genetic groups in common between these regions (~18%) predominantly displayed disjunct distributions between California and northern British Columbia.

Such a distribution pattern points to long distance dispersal and in marine environments there are several mechanisms that could have been at work. Passive dispersal through currents or rafting on debris or other organisms are possible explanations. A few years earlier a red abalone shell found in Haida Gwaii (far north of its range) had a float-bearing kelp (Nereocystis luetkeana) holdfast attached to it, which shows one possible reason for the pattern Gary observed. The kelp simply hitch-hiked on a mussel that was carried northward through a current.

Consequently, Gary now postulates the The kelp conveyor hypothesis which describes the migration of Californian species growing on substrata that are carried along with kelp rafts to Northern British Columbia on the winter Davidson Current which is a coastal countercurrent of the Pacific Ocean running north along the western coast of the United States from Baja California, Mexico all the way up to Alaska.

A lot of this would have never been discovered without extensive DNA Barcoding work and several recent seaweed invasions demonstrated how important it is for us to understand distribution mechanisms of algae. It seems that these new findings brought us a little forward:

The work here and that cited by colleagues all point to seaweed dispersal by buoyant seaweed as a significant contributor to global macroalgal biogeography. This conclusion is not overly surprising as in this author’s experience there are few floras that lack at least some buoyant seaweed species.

Thursday, September 25, 2014

Fungal communities and forest degradation

The change of land-use, e.g. deforestation, is one of the greatest threats to biodiversity worldwide, particularly within tropical ecosystems. There are quite a few projections out there that aim to predict extinction rates  in relation to climate change. However, such estimated extinction risks might be higher than projected if future potential locations of suitable climate do not coincide with other essential resources such as soil type or food resources. 

One aspect that is still poorly understood is the response of soil fungal communities to land-use change. Fungal communities are known to be affected by nutrient availability and plant species composition which suggests that any alteration to these factors by a change in land-use could result in a shift of soil fungal communities which in turn might have strong effects on the affected ecosystem.

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites.

An international team used a combination of next generation sequencing of the fungal barcode region ITS1 and the chloroplast trnL intron region for plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation in the Brazilian Amazon rainforest.

They found that changes in fungal community composition were more correlated to plant community composition than to changes in nutrient availability or geographic distance. This means that knowledge of an ecosystems's plant community composition is a better predictor of microbial community composition than e.g. soil chemistry. 

Modern DNA Barcoding technologies allowed the authors to do community analysis on a scale that was previously not possible and they a quick to point out:

A clearer understanding of interactions between plant and fungal communities could prove useful to conservation and restoration biology, as it could identify management strategies that better promote both reforestation and the recovery of microbially mediated ecosystem functions in degraded areas.

Wednesday, September 24, 2014

The smallest European beetle

Photo: Natural History Museum of Denmark
Baranowskiella ehnstromi, a member of the family Ptiliidae (featherwing beetles), is the smallest known beetle species in Europe. It was discovered and described in 1997 by Mikael Sörensson in his home country Sweden. Meanwhile, scientists found the only 0.5mm long animal in Norway, Denmark, Switzerland, Austria and Germany. 

This little creature is as thin as a human hair and on top of that very elusive as it lives only in pores of the parasitic bracket fungus Phellinus conchatus, which grows on goat willow (Salix caprea). It took a while until beetle experts figured out the best way to collect specimens. They collect bracket fungi from willows and let those dry over a dish in the laboratory. The beetles (and all other inhabitants) will move out of the drying fungus and end up in the dish.

Yesterday, researchers from the Zoological State Collection in Munich announced that they retrieved some DNA Barcodes for Baranowskiella ehnstromi. They hope that with the rather simple collection method described above they will be able to collect more individuals to show that the species is actually as widely distributed across Middle Europe as its fungal host. The fact that they now have reference DNA Barcodes will make future species determination much easier as it won't require a Ptiliidae specialist.

Tuesday, September 23, 2014

Discoveries of the week

New species as every Tuesday. Let's start with some fishes:

The genus Paracobitis from Iran and Iraq is reviewed, and diagnoses for all nine recognized species are presented. Accordingly, P. longicauda, P. malapterura, P. rhadinaea, P. smithi and P. vignai are considered valid; P. iranica is treated as a synonym of P. malapterura; and four new species are described. Paracobitis basharensis, new species, from the Karoun (Karun) drainage in the Iranian Tigris catchment, is distinguished by having the dorsal-fin origin behind the vertical of the pelvic-fin origin, and a colour pattern comprising of many small irregularly shaped brown blotches. Paracobitis molavii, new species, from the Sirvan and Little Zab drainages in the Iranian and Iraqi Tigris catchment, is distinguished by having a truncate caudal fin, a stout body and the dorsal-fin origin situated in front of the vertical of the pelvic-fin origin. Paracobitis persa, new species, from the Kor drainage in Iran, is distinguished by having a prominent, irregularly shaped midlateral stripe, a shallow adipose crest, and the tube of the anterior nostril not fully overlapping the posterior nostril when folded back. Paracobitis zabgawraensis, new species, from the Great Zab drainage in the Iraqi Tigris catchment, is distinguished by a very elongate body, a reticulate, often indistinct colour pattern, and the dorsal-fin origin situated below or slightly behind of the vertical of the pelvic-fin origin. All species, except unstudied P. basharensis, P. longicauda, P. rhadinaea, P. smithi and P. vignai are also characterized by fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region.

Some of these species have been named for the rivers (P. basharensis, P. zabgawraensis) or regions (P. persa) they've been collected . P. molavii was named for Jalal ad-Din Muhammad Balkhi, also known as Mowlavi, Molavi, a Persian poet, jurist, theologian, and Sufi mystic.

Physocyclus peribanensis
A new species of spider from Michoacán, Physocyclus peribanensis sp. nov. is described. This description is based on a male holotype and one female paratype. Also, the first description of the female of Physocyclus paredesi Valdez-Mondragón from Oaxaca, Mexico is provided, as well as the redescription of the male. This paper provides a cladistic reanalysis of the spider genus Physocyclus Simon, corroborating the monophyly of the genus with morphological data. The phylogenetic reanalysis was done with 54 morphological characters (44 binary and 10 multistate) using equal and implied weighting approach. The equal weighting analysis found two most parsimonious trees, whereas the analysis with implied weighting found just one most parsimonious trees with the concavity values (K= 5–10). The genus Physocyclus is composed by two clades or species groups: the globosus and the dugesi groups. Physocyclus peribanensis sp. nov. belongs to the dugesi group composed of 21 species, and P. paredesi to the globosus group composed of 11 species. With the new species described here, the number of known species of the genus Physocyclus increases to 32 species. The globosus group has a biogeographical distribution pattern in the Mesoamerican and Mexican Mountain biotic components, whereas the dugesi group has a biogeographical distribution in the Mesoamerican and Continental Nearctic biotic components.

These spiders were collected in a dry tropical deciduous forest in Mexico. Their specific name refers to the municipality of the type locality: Peribán, Michoacán.
no DNA Barcodes

Riama yumborum
A new species of Riama lizard from the western slopes of the Andes in northern Ecuador is described herein. Morphologically, Riama yumborum sp. nov. can be distinguished from all other congenerics by having an incomplete nasoloreal suture and a cylindrical hemipenial body with diagonally orientated flounces on its lateral aspect. Phylogenetic analyses of mitochondrial and nuclear DNA support the monophyly of the new species and its sister taxon relationship with R. labionis, which occurs allopatrically.

The name for these beautiful lizards honors the Yumbo culture (800–1660 A.D.), a pre-Incan civilization that inhabited the same area where the new species was found.
no DNA Barcodes (lots of sequencing happened but not the right region)

Pratylenchus quasitereoides
Pratylenchus quasitereoides n. sp. is described from Western Australia. It is characterized by 2 external incisures in the head cuticle, 4 lateral incisures at mid body, stylet length 17 μm to 19 μm, V greater than 75%, PUS less than 2 body diameters long and crenate tail terminus. Molecular data confirm the separation of the new species from morphologically similar and sympatric congeners. The host range also differs from P. teres as well as the sympatric P. neglectus, P. thornei and P. penetrans. Reproduction rates on oat and lupin differed between the new species and P. neglectus. The species was originally described as P. teres, but the species concept of P. teres now encompasses a considerable range of different attributes spread over two described subspecies and three variant populations. The new species differs from all these subspecies and populations in at least two characters. It differs from all populations of P. teres teres most notably in having four rather than 6 lateral lines and a more posterior vulva. It differs from P. teres vandebergae in having a longer stylet and longer overlap of the intestine by the oesophageal glands. Characters which can be used under low magnification to separate the new species from the closest sympatric congeners (P. thornei and P. crenatus) are discussed.

The specimens in this study were collected already in 1998/99. Similar to other nematode studies 28S was used for phylogenetic analysis.  The name indicates this species similarity with another of the same genus (P. teres).
no DNA Barcodes

Schizopelex genalica
Schizopelex festiva, a close relative of the new species

The West Palearctic genus Schizopelex McLachlan 1876 is represented by eleven recognized species. The center of its  distribution area is in Turkey, where seven species have been reported (Malicky 2004; Sipahiler 2005, 2012; Oláh 2010; Sipahiler & Pauls 2012). These 7 species are S. anatolica Schmid 1964, S. rhamnes Malicky 1976, S. sinopica Sipahiler 2012, S. yenicensis Sipahiler & Pauls 2012, S. boluensis Sipahiler 2012 (in Sipahiler & Pauls 2012), S. cacheticaMartynov 1913a, S. pontica Martynov 1913b. Schizopelex cachetica and S. pontica have also been reported from the Caucasus and the Transcaucasia, respectively (Martynov 1913a, 1913b; Ivanov 2011). In addition, two species (S. huettingeri Malicky 1974 and S. persica Schmid 1964) are known from the Balkans and Iran, respectively. The two remaining species are distributed in the southwestern West Palearctic region (southwestern Europe): Schizopelex  furcifera McLachlan 1880 has been reported from the northeastern Iberian Peninsula and the Pyrenees (González et al.  1992; Martínez-Menéndez & González 2010); Schizopelex festiva (Rambur 1842) is distributed throughout most of the  Iberian Peninsula and the Maghreb (González et al. 1992; González & Martínez 2011). In this paper is described and illustrated for the first time a new species of Schizopelex from the southern Iberian Peninsula.

The species name of this new caddisfly refers to the Genal River (Málaga, South Spain) where it was collected.
no DNA Barcodes

Aa lozanoi, Aa figueroi

Two new species of the Andean genus Aa (Orchidaceae, Spiranthoideae) are described: Aa lozanoi Szlach. and S. Nowak, and Aa figueroi Szlach. and S. Nowak. They are restricted in distribution mainly to Cordillera Oriental in the department of Cundinamarca, however, A. lozanoi was also collected in Cordillera Central and A. figueroi in Sierra Nevada de Santa Marta, in northern part of Colombia. Each species is described and illustrated, detailed habitat and distribution data are provided. A distribution map of the new species is presented. A dichotomous key for determination of the Colombian species of Aa is provided. Brief discussion about the most important threats for plants in Andes is presented.

A strange genus name indeed. It is said that the name apparently was rendered by the author to always appear first in alphabetical listings. So much for certain egos. Both new species were collected in Andean Colombia and named after G. Lozano (co-collector of a type specimen) and Y. Figueroa ( also collector of type material).
no DNA Barcodes

Monday, September 22, 2014

Living in the dark

Their world is always dark. They don't have eyes not even antennae. They live in soil, mosses, or in leaf litter. Minimalistic, small creatures called protura, sometimes nicknamed coneheads. These animals are tiny (0.5-2mm length) wingless insects that lack pigmentation which means they are usually white or pale brown. These little critters were overlooked for a long time and only discovered 1907 in a botanical garden at the University of Genoa.

Not much is known about this group and the natural history of its species. They seem to have a preference for forest soil with population densities of several 10 000 per square meter. Perhaps they feed on mycorrhizal fungi . Because the first leg pairs are held pointing forwards scientists use to believe that proturans were predators of small mites. Today it is thought that this most peculiar character is most likely a functional compensate of the lack of antenna and its sensory features. 

About 800 species of protura are known but identification is notoriously difficult. Diagnostic characters are very inconspicuous and difficult to recognize. Taxonomic work requires patience, special skills and a lot of experience. A pilot study just published in PLoSONE describes efforts to determine if DNA Barcoding might be a useful additional approach to delimiting and determining proturan species.

About 100 specimens were subjected to a non-destructive DNA extraction method. Due to the minuteness of proturans, species can only be determined unambiguously after a clearing treatment in which all tissues are removed and subsequent slide mounting of the specimen. The authors used two molecular markers, the standard DNA Barcoding for animals (COI) and a fragment of the nuclear 28S rDNA. 

Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0–21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%).

This study is part of a larger research project which is dedicated to explore the role of the protura in the evolution of insects. Past findings indicated a relationship to the group of the diplura. The last common ancestor of both groups dates back more than 440 million years (Ordovician Period) which is around the time when land plants appeared.

Friday, September 19, 2014

A social media experiment

Boxes waiting to be picked up
The School Malaise Trap Program is up and running again!

Last week boxes filled with Malaise traps and supplies went out to 60 schools across Canada. Starting next week classrooms will collect insects on their school yards and we will be helping them by barcoding some of their finds. 

It is the 4th run of this very successful educational program and this time we were seriously oversubscribed. For the 60 slots we have available over 150 schools applied and our only marketing was a single email during the summer break announcing it to principals and teachers in Canada. For the first time we offered it outside of Ontario and as you can see from the map we have quite a few schools from other provinces.

We've also started an experiment with social media by inviting all participating classrooms to blog about their experiences. The blog on the programs website is also intended to stimulate dialog between the different schools which in some cases are more than 5000 km away from each other.

The main reason to limit the number of participating schools is limited amounts of funding available to us. For the same reason we are not offering it outside of Canada so far although it would be fairly straightforward to do so. I have been overseeing this project for 2 years now and every time I was amazed how much it meant to the kids to be able to participate at such a program. Part of my job is to pass on some of that excitement to people that are looking for new, meaningful ways to invest their money. Fingers crossed for the coming years.

Thursday, September 18, 2014

DNA Barcoding and killing agents

source INBio Costa Rica
[..] sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). 

This is part of an abstract to a brand-new paper that just appeared in Molecular Ecology Resources. Ever since we started using molecular methods it has been one of the most discussed issues and many researchers started with the question what killing and preservation method should be used to ensure sufficient DNA quality while keeping the potential voucher specimen intact? Chemicals such as ethyl acetate and formaldehyde have been discussed as substances that have the potential to degrade DNA and as such may not be appropriate for the collection of samples for any DNA-based research. Especially formaldehyde represents an issue as killing agent but even more so as preservation liquid. It still is probably the most widely used preservation option we have. It is cheap and provides stable long term storage conditions that keep a specimen intact for future morphological analysis. However, especially over a longer period it will inevitable destroy DNA in an irreversible manner. Colleagues have looked into this issue in a lot of detail simply because most museum fluid collections are using formaldehyde and therefore seem to be lost for any molecular work. 

As for killing methods entomologists are mostly using either ethyl acetate, cyanide or freezing. A molecular biologist would probably always advise to use freezing. No chemical involved would mean no risk for DNA damage and assuming the temperature is low enough it would also help to keep the specimen intact (including coloration). However, in the field very often this is not suitable as you either have to transport the animals alive to the next available freezer or even take a cryogenic shipper with you. Ethanol or other liquids (DMSO-solution, RNAlater) would be an alternative as well and are certainly not DNA-damaging. However, the killing and storage of insect specimens in solutions may not be appropriate for groups where fragile morphological features such as scales on external parts of the body such as the wings may be damaged by wet killing and storage. Furthermore, most insect collections contain pinned specimens and those are in much better shape if they haven't been in any liquid before. 

In this study the colleagues from the University of KwaZulu-Natal in South Africa examined the recoverability of DNA Barcodes from lepidoptera specimens collected using the three common methods described above. Their results are intriguing although currently limited to one insect order. 

All Lepidoptera collected produced DNA barcodes of good quality and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis. 

I am fairly confident that future studies with other arthropod groups will show similar results although I can imagine that issues rather correlate with specimen size or duration of treatment.

Wednesday, September 17, 2014

Blastocystis in dogs and cats

Companion animals (specifically, domestic dogs and cats) are prone to several protozoan gastrointestinal infections, with Giardia duodenalis [syn. G. lamblia, G. intestinalis] and Cryptosporidium parvum both being of significant concern in animals with gastrointestinal disease, and as potential zoonotic infections. Recently, increasing interest has been given to the stramenopile organism Blastocystis spp. as a potential cause of gastrointestinal disease in human beings.

Human infections are found at a rate of 5-10% in most developed countries with elevated rates for individuals that work with animals. In developing countries the rate can be as high as 50%. However, only 50% and 80% of individuals infected with Blastocystis will show any symptoms. Symptoms associated with the infection are diarrhea, nausea, abdominal cramps, bloating, and excessive gas. Most cases of the infection are diagnosed as irritable bowel syndrome, which is actually a symptom-based diagnosis with no known organic cause but characterized by the very same symptoms. 

Because of a growing interest in Blastocystis as a potential enteric pathogen, and the possible role of domestic and in-contact animals as reservoirs for human infection, researchers of the College of Veterinary Medicine at Oregon State University tried to estimate the prevalence of Blastocystis spp. in shelter-resident and client-owned companion animals in the US Pacific Northwest region.

They used the proposed DNA Barcode standard for protists, 18S (or SSU rRNA) to detect the presence of Blastocystis sp. Their findings indicate that shelter-resident animals were carrying a variety of Blastocystis subtype while they couldn't detect the protist in any fecal sample from client-owned animals. In addition no relationship was seen between Blastocystis carriage and the presence of gastrointestinal disease signs in either dogs or cats. These data suggest that, as previously reported for other enteric pathogens, shelter-resident companion animals are a higher risk for carriage of Blastocystis spp. The lack of relationship between Blastocystis carriage and intestinal disease in shelter-resident animals suggests that this organism is unlikely to be a major enteric pathogen in these species.

There is more good news especially for those that want to adopt shelter animals. The majority of identifiable specimens belonged to a subtype with no evidence of carriage in human beings. Therefore, it is unlikely that shelter resident animals in the Pacific Northwest of the USA represent a potential risk for zoonotic infection of animal handlers or owners.

Tuesday, September 16, 2014

Discoveries of the week

Spasskia brevicarinata
The genus Spasskia Belokobylskij, 1989 (Hymenoptera: Braconidae: Helconinae) is reported for the first time from China. Two species, namely Spasskia brevicarinata Yan et Chen sp. n. and Spasskia indica Singh, Belokobylskij et Chauhan, 2005 are described and illustrated. A key to the species of this genus is updated to include the new species.

The new species is rather small - adults are less than one centimeter long. It is similar to a previously described species called Spasskia indica, but the ridges on some of its body segments are different. In fact, the species epithet brevicarinata refers to a short ridge on its first tergite, as "brevi" is Latin for short and "carinata" is Latin for ridge.

no DNA barcode

A new species of Neoplecostomus is described from the rio Doce basin representing the first species of this genus in the basin. The new species is distinguished from its congeners by having enlarged, fleshy folds between dentaries, two or three series of developed papillae anterior to premaxillary teeth and a adipose-fin membrane present, and by lacking enlarged odontodes along snout lateral margins in mature males, a well-developed dorsal-fin spinelet wider than dorsal-fin spine base, lower number of lateral-line figs and developed membrane on the dorsal portion of the first, second and third pelvic-fin branched rays. Additionally, we present a brief discussion of biogeographic scenarios that may explain the distribution of the new species in the rio Doce basin. We suggested that the ancestral lineage of the new species reached the rio Doce from the upper portions of rio Paraná drainages about 3.5 Mya (95% HPD: 1.6–5.5) indicating a colonization route of the N. doceensis ancestral lineage from the south end of Serra do Espinhaço, probably as a result of headwater capture processes between the upper rio Paraná and rio Doce basins.

Neoplecostomus is one genus of armored catfishes which are native to South America. The Loricarids are extremely diverse and for a long while a good number of species only had a number with an 'L' as prefix. There are still many of those out there and a large number of specimens with provisional names. The name doceensis for this species is a Latin noun meaning being located or having connection with the Rio Doce basin. This hydrographic system is located in the southeastern region of Brazil.

The present study reports on three species of terrestrial isopods from western Iran. The genus Mongoloniscus Verhoeff, 1930 is recorded for the first time from Iran, with description of a new species: M. persicus sp. n. Protracheoniscus ehsani sp. n. is described and P. darevskii Borutzky, 1975 is redescribed based on Iranian specimens. The diagnostic characters of these species are figured and their geographical distribution is presented on a map.

Woodlice are terrestrial crustaceans with a rigid, segmented, long exoskeleton. This isopod group comprises over 5,000 known species and now two more have been added to the list. The first species is named after the old name for Iran, Persia. The second species was named after a friend of the author who tragically passed away during a field study.
no DNA barcodes

Three new species of the genus Senecio (Asteraceae, Senecioneae) belonging to Senecio ser. Suffruticosi subser. Caespitosi were discovered in the tributaries of the upper Tambo River, Moquegua Department, South Peru. Descriptions, diagnoses and discussions about their distribution, a table with the morphological similarities with other species of Senecio, a distribution map, conservation status assessments, and a key to the caespitose Peruvian species of Senecio subser. Caespitosi are provided. The new species are Senecio moqueguensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio pucapampaensis Beltrán, Senecio sykorae Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio gamolepis Cabrera, and Senecio tassaensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio moqueguensis Montesinos.

Senecio is one of the largest genera of flowering plants including ragworts and groundsels. Despite several revisions it still contains some 1500 species. 175 of those occur in Peru and a large number (94) of them are endemic. All three new species are endemics as well and unfortunately all of them have been already categorized as critically endangered.
The name of the first species refers to the region Moquegua, where the species was encountered. The next Senecio is named after Karlè Sýkora, a well-known Dutch vegetation scientist who was the authors mentor in phytosociology. The third species is named after the town of Tassa in the Moquegua Region where the species was found.
no DNA barcodes

The genus Kuzicus was established by Gorochov (1993), and was divided into two subgenera: Kuzicus and Neokuzicus. The type species is Teratura suzukii Matsumura & Shiraki, 1908. He transferred Xiphidiopsis denticulatus Karny, 1926  and Xiphidiopsis cervicercus Tinkham, 1943 to the subgenus Kuzicus (Kuzicus), and described one new species, Kuzicus  (Neokuzicus) uvarovi. Ingrisch & Shishodia (2000) erected another new subgenus Parakuzicus, and described two new  species: Kuzicus (Parakuzicus) cervicus and Kuzicus (Parakuzicus) excavatus, and transferred Xiphidiopsis forficatus Bolívar, 1900 to the subgenus Kuzicus (Parakuzicus). Mao et al. (2009) reviewed the genus Kuzicus from China, and  reported one new species, Kuzicus (Kuzicus) multifidous Mao & Shi, 2009. Up to now, the genus Kuzicus includes 3 subgenera and 13 species all over the world (Bolívar, 1900; Matsumura & Shiraki, 1908; Tinkham, 1943; Gorochov,  1993; Ingrisch & Shishodia, 1998; Ingrisch & Shishodia, 2000; Sänger & Helfert, 2004; Sänger & Helfert, 2006a, 2006b; Ingrisch, 2006; Mao et al., 2009). This paper describes one new species. The type specimen is preserved in the Museum of Hebei University. Morphological images were acquired using Leica DFC 450 digital imaging system. The following conventions were adopted for the specimen measurements: Body—the distance from apex of fastigium of vertex to the posterior margin of tenth abdominal tergite;  tegmen—the distance from the base of tegmen to the apex; hind femur—the distance from base of postfemur to the apex of genicular lobe.

A new grasshopper species with a name derived from the depressed tips of the male cerci.
no DNA barcode

Pseudopaludicola atragula

A new species of Pseudopaludicola is described from human-altered areas originally covered by Semideciduous Forest in northwestern state of São Paulo, southeastern Brazil. Morphologically, the new species differs from four species belonging to the P. pusilla group by the absence of either T-shaped terminal phalanges or toe tips expanded, and from all other congeners except P. canga and P. facureae by possessing an areolate vocal sac, with dark reticulation. The higher duration (300–700 ms) of each single, pulsed note (9–36 nonconcatenated pulses) that compose the call in the new species distinguishes it from all other 14 species of Pseudopaludicola with calls already described (10–290 ms). Absence of harmonics also differ the advertisement call of the new species from the call of its sister species P. facureae, even though these two species presented unexpected low genetic distances. Although we could not identify any single morphological
character distinguishing the new species from P. facureae, a PCA and DFA performed using 12 morphometric variables evidenced significant size differences between these two species.

The species name is derived from the Latin words “atra”, meaning dark, black, and “gula”, meaning throat . The males of this species show a dark throat region which is unusual within the genus Pseudopaludicola.
no DNA barcode (they sequenced 16S and wrongly call it DNA Barcode referring to a paper from 2005 in which COI was deemed not suitable. That should be off the table by now).

Monday, September 15, 2014

Applied evolutionary biology

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

A team of scientists from Denmark and the USA reviewed current progress in addressing a broad set of challenges in agriculture, medicine and environmental management using evolutionary approaches, approaches that consider species' evolutionary histories and the likelihood of rapid evolutionary adaptation to human activities. Above's quote is from the abstract their paper published in Science. They argue that our ability to solve societal challenges in food security, emerging diseases and biodiversity loss will require evolutionary thinking in order to be effective in the long run. Inattention to this will only lead to greater challenges such as short-lived medicines and agricultural treatments, problems that may ultimately hinder sustainable development.

The study finds an urgent need for better implementation of these approaches, for example in managing the use of antibiotics and pesticides in order to reduce the escalating problem of resistance evolution. Furthermore, current efforts are found insufficient to reduce the accumulating costs from chronic disease and biodiversity loss, two challenges ultimately caused by exposure to food and environments to which people and threatened wildlife are poorly adapted.

Applying evolutionary biology has tremendous potential, because it takes into account how unwanted pests or pathogens may adapt rapidly to our interventions and how highly valued species including humans on the other hand are often very slow to adapt to changing environments through evolution. Not considering such aspects may result in outcomes opposite of those desired, making the pests more resistant to our actions, humans more exposed to diseases and vulnerable species less able to cope with new conditions.

There is no shortage of examples for innovative solutions based on applying knowledge gained from evolutionary biology research. Just one example - farmers in the United States and Australia have used planting of pest-friendly refuges to delay evolution of insect resistance to genetically engineered corn and cotton. These genetically modified crops kill certain pests, but without refuges the pests quickly adapt. Providing refuges of conventional plants has been especially effective for suppressing resistance in the pink bollworm (Pectinophora gossypiella), an invasive pest of cotton. Now, one might have some reservations about genetic engineering but the general concept applies to all situations in which the development of resistance threatens our efforts.

Overall a very interesting read. I couldn't agree more with their final conclusion:

Successful governance of living systems requires understanding evolutionary history as well as contemporary and future evolutionary dynamics. Our current scientific capacity for evolutionarily-informed management does not match the need, but it can be increased through new and more widespread training and collaboration, monitored experimentation, and context-sensitive implementation. Like engineering, which is a multifaceted applied science with common core principles, shared vocabulary and coordinated methods, applied evolutionary biology has the potential to serve society as a predictive and integrative framework for addressing practical concerns in applied biology which share at their core the basic evolutionary principles governing life.

Friday, September 12, 2014

DNA origami

DNA origami are self-assembling biochemical structures that are made up of two types of DNA. To make DNA origami, researchers begin with a biologically derived strand of DNA called the scaffold strand. Then they design customized synthetic strands of DNA, called staple strands. Each staple strand is made up of a specific sequence designed to pair with specific subsequences on the scaffold strand.

Staple strands are introduced into a solution containing the scaffold strand, and the solution is then heated and cooled. During this process, each staple strand attaches to specific sections of the scaffold strand, pulling those sections together and folding the scaffold strand into a specific shape organised by the intrinsic chemical properties of the DNA sequences.

These structures are not just interesting and funny ways for scientists to kill time although the ones shown in the image on the right look indeed funny. Potential applications range from biomedical research to nanoelectronics. Examples include enzyme immobilization, drug carry capsules, and nanotechnological self-assembly of materials. They have also been discussed as active structures for nanorobotic applications such as molecular walkers (artificial molecular motor) on origami and switches for algorithmic computing.

So far DNA origami has been limited to a scaffold strand that is made up some 7,200 bases, creating structures that measure about 70 nm by 90 nm, though the shapes may vary. Researchers from North Carolina State University, Duke University and the University of Copenhagen have now created the world's largest DNA origami. They developed a custom scaffold strand that contained 51 kilobases which resulted in a structure measuring approximately 200 nm by 300 nm.

They also implemented a method to decrease the cost of origami production by improving the chip synthesis platform. The researchers did this by using what is essentially a converted inkjet printer to synthesize DNA directly onto a plastic chip.

Pretty cool stuff.

Thursday, September 11, 2014

What crab is it?

Originally from Asia, the brush-clawed shore crab appeared in Europe in 1993, likely transported through hull fouling or ballast water. The first specimens were found on a ship’s hull of a car-carrier in the harbor of Bremerhaven, Germany. However, no established reproductive population could be found at that time. A year later they started a real invasion at the Atlantic coast near La Rochelle quickly expanding their range north and south along French and Spanish Atlantic coasts. By the early 2000's the crab was encountered in the North Sea, e.g. in the intertidal alien Crassostrea-reefs in the Wadden Sea. Pacific oysters (Crassostrea gigas) have been invading the central Wadden Sea since 1998, predominantly settling on intertidal blue mussel (Mytilus edulis) beds which are increasingly transformed into Crassostrea-reefs. This habitat change is already considered to be a threat for waterbirds losing important feeding sites in the intertidal of the Wadden Sea and now it seems that this new habitat provides an ideal home for another invader.

Until 2005, researchers assumed that they were looking at one particular species, the brush-clawed shore crab Hemigrapsus penicillatus. Then two researchers from Japan described a new sibling species as Hemigrapsus takanoi. That left especially European scientists with a question as both species occur sympatrically in Japan and may thus also coexist in European waters because of their similar ecology or the invader is only one species, but which one?

The distinction of both species using morphological traits is extremely difficult and unreliable. That's were a new study from Germany comes in:

To clarify the identity of the alien species, two mitochondrial (partial COI, partial 16S rDNA) and two nuclear genes (partial sodium-potassium ATPase α-subunit, complete 18S rDNA) of several German and Japanese specimens were analysed. In addition to molecular analyses, key morphological characteristics were assessed. As such this is the first integrative approach providing a specimen-specific analysis and a comparative description of both native and invasive specimens.

The colleagues identified their samples from the Central Wadden Sea as Hemigrapsus takanoi. As it turns out most of the specimens from Japan and a set of GenBank sequences of brush-clawed crabs from Japan, Korea and China which were traditionally classified as Hemigrapsus penicillatus in Asia turned out to be Hemigrapsus takanoi. I leave the conclusion of this study to the authors:

The study underlines the difficulty in distinguishing H. takanoi from H. penicillatus on the basis of morphological characteristics alone. We therefore recommend additional molecular identification of the alien species along the coasts of the Northeast Atlantic because several independent introductions may have resulted in regionally displaced invasions of H. takanoi and/or H. penicillatus. Besides natural dispersal, range expansion of the crabs via Pacific oyster transportations between aquaculture facilities is assumed to have facilitated the spread of the species in Europe. Enhanced alertness in identifying the invader is thus required in regions where intensive aquaculture or mussel transfer is practiced. Special attention should also be paid in areas where port operations are expected to increase in the future.

Wednesday, September 10, 2014

Roasted Barley tea

Barley (Hordeum vulgare) is rich in dietary fiber and nutrients such as starch, protein, fat, vitamins B1 & B2, calcium, phosphorus, iron, and phenolic compounds. Roasted barley tea is very popular in Japan and Korea where it is believed to contribute to the digestion of greasy food and to be beneficial for the stomach after long term alcoholism. Roasted barley tea, known in Japanese as mugicha or in Korean as boricha, is available as loose grains, in tea bags or as prepared tea drinks and is traditionally used for detoxification, to improve digestion and for urinary tract infections, among other applications although no such effect has been proven by research yet. However, a few studies found that it inhibits bacterial colonization and adhesion, specifically with the major cause of tooth decay, Streptococcus mutans, which also has been implicated to play a big role in cardiovascular diseases. It also has been shown to lower blood viscosity.

A group of Chinese researchers recently used DNA Barcoding to help with a trade dispute that involved roasted barley products that were returned by an unnamed country because it was suspected of being adulterated with other plant components apart from barley. Because the tea product consisted of ultra-fine powder, morphological identification was impossible. The colleagues used the two standard plant markers (rbcL, matK) and two other ones (trnH-psbA, ITS2) that have been discussed as supplementing barcodes. 

Of the 13 batches they analysed, one turned out to be exclusively made of Mulberry (Morus sp.). The remaining twelve contained Hordeum vulgare but only two of them were pure. Ten samples were contaminated with other plant material such as Mulberry (again), oats (Avena spp.), wheat (Triticum spp.), and fig-leaved goosefoot (Chenopodium ficifolium). There is a good chance that most of the other crops were introduced by sloppy sorting and unclean handling. Even the goosefoot could have entered the production at this stage as it is known as an agricultural weed. That clearly shouldn't happen but could be explained by accidental incidents. The mulberry that occurred quite frequently and in one case exclusively cannot not be explained so easily. Its ripe fruit is edible and is widely used in pies, tarts, wines, cordials and tea. Its leaves, particularly those of the white mulberry, are ecologically important as the sole food source of the silkworm (Bombyx mori) which hints to possible sources of the contamination given the extend of the silk industry in China.

I guess the country sending this batch back was right especially because the product was labelled as ‘pure’ or ‘100%’ barley powder. 

Tuesday, September 9, 2014

Discoveries of the week

And yet another round of new species.

A new collembolan species is described, Spinonychiurus sinensis sp. n., which has seven chaetae in the distal row of the tibiotarsi. It is placed in the genus Spinonychiurus due to two important characters: the two subsegments on Abd. III sternum and the absence of d0 on the head. This is the first report of the genus Spinonychiurus in China. The diagnosis of Spinonychiurus is broadened and the key to the world species is provided.

Found in the coniferous forests of the Changbai Mountain Range in China.
no DNA barcode

Very little information is available regarding marine free-living flatworms not only from Iran, but throughout the countries surrounding the Persian Gulf and the Gulf of Oman. The present study first introduces a new euryleptid species, and then reports four pseudocerotid polyclads which inhabit Iranian shallow rocky shores of the Persian Gulf and the Gulf of Oman. Maritigrella makranica sp. nov. is characterized dorsally by a medial cream or white reticulated appearance containing pale orange spots in a honeycomb pattern, a distinct orange submarginal band around the entire body margin and between the marginal tentacles, black spots scattered around mid-dorsal surface, becoming more sparse on raised median region and towards body margin, surrounded by a dark-grey halo around the body midline and orange-black halo towards margin. Three of the four pseudocerotids species belonging to the genera Pseudobiceros Faubel, 1984; Pseudoceros Lang, 1884; and Thysanozoon Grube, 1840, are new records for the studied areas, while the other has been reported in the Persian Gulf previously. Comments on Iranian species are provided and associations of flatworms with ascidians and sponges were observed.

The species name refers to the Makran area in the Gulf of Oman where the specimens were collected. These beautiful little flatworms feed on ascidians, crustaceans, gorgonians and hard corals.
no DNA barcode

Mesitiinae include 203 species classified in 22 genera and four tribes. In this work we proposed a new genus. Moczariella centenaria Barbosa & Azevedo gen. et sp. nov. are described from United Arab Emirates. The main diagnostic characteristics is body wholly unfoveolate, clypeus without lateral lobes, post-occipital depression present, propodeum with discal carinae incomplete, and without posterior one, propodeal spiracle placed laterally, claws single, and genital basal ring with dorsal half distinctly longer than ventral one.

While sorting more than 40,000 specimens of flat wasps Bethylidae from United Arab Emirates, we found a sample containing a single unusual specimen which attracted our attention. I guess that says everything about the tedious work involved to surface this new species which was put in a new genus. The genus name Moczariella is in honor to László Móczár, the main contributor to the taxonomy of the subfamily this new group belongs to, Mesitiinae. The species epithet centenaria refers to the fact that in this year László Móczár is celebrating his hundredth birthday.
no DNA barcode

Three new species of Anteros Hübner, [1819] from south and southeastern Brazil are described: A. aliceae Dias & Siewert, sp. nov., A. zikani Siewert, Dias & Dolibaina, sp. nov. and A. ethani Dias, Dolibaina & Mielke, sp. nov. Habitus and genitalia of male and female specimens of the new species are illustrated, along with illustrations of the habitus and male genitalia of the most similar species for proper distinction. The following taxonomic changes are proposed: A. micon Druce, 1875, stat. rest., A. roratus Godman & Salvin, 1886, stat. rest., and A. theleia Stichel, 1910, stat. nov. Anteros formosus stramentarius Stichel, 1909, syn. nov. is sunk as a junior subjective synonym of A. formosus. Additionally, Ourocnemis axiochus (Hewitson, 1867), stat. rest., is recognized as a species distinct from O. archytas (Stoll, 1787); illustrations of the male genitalia and of the differential characters of the wing pattern of both species are provided. A male of the rare Ourocnemis boulleti Le Cerf, 1911, is reported from southeastern Peru. Distributional data and a map are provided for all
species studied.

Anteros aliceae was named after the first daughter of one of the authors and born about the same time the species was recognized as undescribed. Anteros zikani was named to honor the entomologist José Francisco Zikán, who lived and collected in the area were the holotype was found. Anteros ethani is named after the  the first son of another author.
no DNA barcode (which is a pity as I've noticed some specimens on BOLD with preliminary names. It would be great to be able to compare them)

Onuphis farensis sp. nov. (Annelida, Polychaeta) is described, based on a population inhabiting intertidal sandbanks in the mesotidal coastal lagoon of Ria Formosa (Southern Portugal). It can be distinguished from all other known species within the genus by having bi– and tridentate pseudocompound hooks on the first 4 chaetigers, single filament branchiae from chaetiger 5, and subacicular hooks from chaetiger 9. The species was previously collected in the Bay of Cádiz and Isla Cristina (SW Spain), in a similar habitat to Ria Formosa, but referred to O. geophiliformis Moore, 1903. The taxonomic status of other Onuphis species recorded in the European waters is also discussed. On the whole, O. pancerii Claparède, 1868, described from the Gulf of Naples, has been treated as a junior synonym of O. eremita Audouin & Milne-Edwards, 1833, but taking the more restrictive definition of this species accepted today, should be considered as a valid Mediterranean species. Finally, O. opalina (Verrill, 1873) and O. rullieriana (Amoureux, 1977) may be synonymous, as both species are similar morphologically, occur at similar depths, and have partially overlapping geographical distributions. The different diagnostic characters utilised for the new species are analysed, with the number of chaetigers with postchaetal lobes determined to be a poor taxonomic character for the genus Onuphis, proving to be size-related. A synoptic table with all worldwide species of the genus Onuphis is provided, together with a dichotomic key for the species hitherto recorded in the European and nearby waters.

The species name refers to the type locality of the species, being near the town of Faro, in Portugal. 
no DNA barcode

Solanum cordicitum
A new species of Solanum from Texas is described here. Solanum cordicitum S. Stern is a member of Solanum section Androceras. It is similar to S. citrullifolium and S. davisense but differs from both in having white corollas, and differs from the latter in having inflorescences with a significantly longer axis and larger flowers. In addition to the new species, three new combinations are proposed for species in Solanum section Androceras, Solanum setigeroides (Whalen) S. Stern, Solanum novomexicanum (Bartlett) S. Stern, and Solanum knoblochii (Whalen) S. Stern.

The species name is taken from the Latin “cordicitus“ for “from the heart” referring to the type locality of Valentine, Texas. The species is not only new but possibly endangered.
no DNA barcode

Monday, September 8, 2014

Species distribution modelling

Credit: Michele Menegon
Species distribution modelling (SDM) is commonly used to predict spatial patterns of biodiversity across sets of taxa with sufficient distributional records, while omitting narrow-ranging species due to statistical constraints. We investigate the implications of this dichotomy for conservation priority setting in Africa, now and in the future.

There are various ways to determine the spatial distribution pattern of species. Most attempt to predict species’ geographic ranges from occurrence records and environmental data from the same sites. Two types of output are very common: binary classifications of given sites as being within or outside the distribution, and probabilistic results often used to develop maps of predicted future distributions. 

Most species distribution models work with with basic ecological assumptions. Some of these assumptions relate to ecological processes that determine species’ distributions and abundances, whereas others are methodological and concern the way data are treated in species distribution modelling. In recent years, e.g. modeled impact of climate change on species distributions has become an additional consideration for conservation priority setting. 

A considerable body of literature exists on species distribution modelling and a couple of pitfalls have been identified. There are some known methodological issues and researchers try to address those by adapting either the algorithms used or the sampling regime:

Incomplete sampling of niche space
  Distributional data are often collected unevenly across a species’ range with respect to space, time, and environment. The collection of biological data is time-consuming and expensive. As a result many studies have to rely on limited amounts of data and researchers need to make the best out of those. This is one of the reasons for global initiatives such as GBIF or OBIS to aggregate as much data from all possible sources to fill the gaps.

Cause and correlation
  That is a dangerous one. Strong correlation does not automatically imply causation. For example climate data can be associated with many ecological phenomena for reasons other than causality. Strong correlations may allow climate data to predict species occurrences, even if climate has little to do with it. This is also true for the opposite scenario. Climate change might be the main cause for changes is species distributions but no significant correlations are obtained. 

Scale mismatch
  Some available data are more tightly parameterized than others (e.g., precipitation patterns), and their accuracy and resolution can have important ramifications any predictions.  The scale mismatch issue brings us back to the opening paragraph. Many species require specific small-scale habitat attributes that are likely to be overlooked by common species distribution models. 

A new study demonstrates that the majority of threatened species are 'invisible' when using species distribution modelling to predict species distributions under climate change. Using African amphibians as a case study, the researchers found that more than 90 per cent of the species listed as threatened on the IUCN Red List of Threatened Species are omitted by most popular modelling tools. The researchers examined data on 733 African amphibians in Sub-Saharan Africa. They found that 400 have too few records to be used in species distribution modelling at continental scales, including 92% of those listed as Vulnerable, Endangered or Critically Endangered.

These results show that unless we use appropriate analysis for the impacts of climate change on species such as amphibians, we risk leaving many rare species under-represented in conservation plans, with the potential to misguide conservation efforts on the ground.

Effective biodiversity conservation, both now and in the future, relies on our ability to assess patterns of threat across all species, but particularly those close to extinction. There are ways around the problem, such as combining simple measures of exposure to climate change with knowledge of species' ability to disperse or adapt -- methods less reliant on sophisticated modelling tools, which are impractical for many of the rarest species.