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