Friday, January 30, 2015

Insects are picky eaters

...uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here, we use a global dataset to investigate host range for over 7,500 insect herbivore species covering a wide taxonomic breadth and interacting with more than 2,000 species of plants in 165 families. We ask whether relatively specialized and generalized herbivores represent a dichotomy rather than a continuum from few to many host families and species attacked and whether diet breadth changes with increasing plant species richness toward the tropics.

After decades of field work from dozens of sites around the world, and after two years of combing through and analyzing data, researchers have reported on global patterns in the diets of insect herbivores. They report that most insect herbivores, such as caterpillars, find and feast on just one kind of plant in any one location, rather than eating everything in sight.

This result is something that many scientists have known intuitively for a long time, but it has not before been quantified on such a large scale. Actually a lot of prior studies had disagreed on whether or not insect herbivores in the tropics have more narrow diets than their temperate relatives. The study shows that insects in  the tropics are indeed more specialized, and this was evident across hemispheres and across unrelated taxonomic groups.

No doubt this study is important for ecosystem management. Variation in insect diet has implications for numerous ecological and evolutionary processes, including effects of environmental disturbance, the stability of networks of interacting species and the top-down effects of predators being controlled by the level of herbivore diet specialization. 

We need to know what insects eat when doing ecosystem restoration, and we shouldn't assume that species with generalist feeding habits will necessarily fill the same ecological roles as more specialized species.

While I was reading this new publication I was reminded of another one, today almost 11 years old and one of the most frequently cited DNA Barcoding paper:

A. fulgerator is a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness.

Maybe it is time to revisit our species number estimates once again. Not only did we learn that in the tropics herbivore insect species are largely specialists but also we've come to accept that they are hard to find due to a lack of morphological variation between species. 

Thursday, January 29, 2015

DIY Barcoding identifies fungus on lemon

An unknown mold on a Citrus limon tree was isolated and identified using standard microbiology protocols: streaking, microscopy, and DNA barcoding. This was done to identify invasive mold that was hindering the growth of C. limon fruit and to catalog its relationship with other similar fungal species. The method details an efficient and cost-effective way to isolate and identify a wild-type organism.

This is the abstract to a paper I came across earlier this week. It sounds very standard and provides yet another great example for the utility of the DNA Barcoding method. However, there is something very unusual about this publication that makes it very special: It has been published in the newest issue of BioCoder and this journal is a newsletter of the Biology DIY movement. 

The research presented in this paper is the result of the DIY efforts of a web developer and a network security expert both of them with a strong interest in biology. These two hobby researchers provide us with a neat little study on the identification of mold species that negatively impact fruit tree growth. Not only an ingenious idea but also an extremely well executed and professionally presented study:

Louis Huang and Alan Rockefeller
Cataloging Strains: Isolation and Identification of Invasive Fungi on Citrus limon

What makes such reports even more valuable from a research point of view is the intrinsic attention to detail when it comes to methods. DIY research enthusiasts actually are very eager to share the methods they've used to arrive at their results. Researchers of course do the same to allow the community to reproduce the results and build on them. However, the DIY movement thrives on this aspect as there is a lot more emphasis on finding simple and cost effective ways to reach the same level of professionalism and quality of results. Amateurs that engage in research are taking their work very seriously and are not always met with the full appreciation of the scientific community but papers such as this one show that we should look very closely at what they are doing. We as professionals can actually learn a great deal from them especially when it comes to simplicity, accessibility, and meticulousness.

Wednesday, January 28, 2015

ERC Starting Grants - What about biodiversity research?

The European Research Council (ERC) has selected 287 scientists in its sixth Starting Grant competition, which is the last one under the EU's Seventh Research Framework Programme (FP7). They are awarded nearly €400 Million, with grants being worth up to €2 million each. This call attracted 3,373 applications, about a third of those (1037) in the category life sciences. Of the latter 124 were awarded a grant. Not bad also given that this (12%) is above the general success rate of ~10%. The other two categories are social sciences and physical sciences/engineering.

The categories are subdivided following the ERC panel structure and here are the nine panels for the life sciences:
  • Molecular & Structural Biology & Biochemistry
  • Genetics, Genomics, Bioinformatics & Systems Biology
  • Cellular and Developmental Biology
  • Physiology, Pathophysiology & Endocrinology
  • Neurosciences & Neural Disorders
  • Immunity & Infection
  • Diagnostic Tools, Therapies & Public Health
  • Evolutionary, Population & Environmental Biology
  • Applied Life Sciences & Non-Medical Biotechnology
It doesn't take an expert to see that the system is skewed towards medical research and biotechnology. Consequently one will not find any grant awarded to a project with a focus on biodiversity not even among the 11 projects of the only panel (LS8) one might be able to find this kind of research. 

What does that tell us? Well, one could argue that no such project was actually among the submissions. Wrong. I know that some of my young European colleagues have submitted proposals and I was a reviewer on another one that clearly fit the bill and from my point of view was actually brilliant. I shouldn't be surprised as I am sitting in North America where the trend leading away from basic research started. The majority of governmental funding now goes into research that can be directly applied in industry or health care. DNA Barcoding luckily falls into some of those categories and we were fortunate enough that a few years ago some governmental funding partners (federal and provincial) were willing to take a risk. However, for others things are often quite different. Just ask some of my Canadian colleagues how comparatively easy it is to get research council funding once you have a partner in industry. There are specific programs that have no limiting deadlines and decisions are made swiftly within 4-6 weeks. Now that is different from my experience with e.g. the German Science Foundation were it could took a year or longer for a decision. I believe it takes about 9 months for the ERC starting grant decision.

The EU Commissioner for Research, Innovation and Science Carlos Moedas said: To create tomorrow’s innovation and growth, cutting-edge research is a must. With its Starting Grants, the European Research Council nurtures the next generation of excellent scientists allowing them to follow their scientific curiosity and take risks. To be at the forefront, Europe needs this gutsy mindset, and to invest in young talent.

Obviously only a carefully selected subset of researchers is allowed to follow their curiosity as long as the results are immediately and directly applicable to industry or health care. Where is the risk in that? Talking about an opportunity to take risks in the context of this ERC program is actually a slap in the face of colleagues that do basic research as they are largely left out. What concerns me most is the fact this this particular program is intended to support young researchers at the beginning of their career. Europe is clearly setting the course in the wrong direction. 

I used to be very proud of my European heritage and the fact that countries such as my home Germany were traditionally strong in basic research and everything related to natural history and biodiversity. Nine years ago when I left Europe I already saw signs that things were taking a turn for the worst and here we are - the place where biodiversity science originated is steering its brightest young minds away from it. Well done, EU!

Tuesday, January 27, 2015

Discoveries of the week #24

Garra jordanica, new species, is described from the northern Dead Sea basin in Jordan and Syria. It is related to G. ghorensis from the southern Dead Sea basin from which it is distinguished by having 8 1 /2 branched dorsal-fin rays; 33-35+2 lateral line scales; 5-7 scales between the pelvic-fin base and the anus; a large round, black blotch on the flank at the middle of the posterior extremity of the caudal peduncle; the pelvic fin not overlapping the anus in individuals larger than 70 mm SL; shorter barbels; and details in the arrangement of tubercles on the head. Garra jordanica also differs from G. ghorensis by a nearest neighbor distance of 4.1 % K2P in its COI barcode region. It had previously been postulated that G. ghorensis from southern Jordan has a close relationship to G. tibanica or to G. rufa. Of the two contradicting hypotheses our results support a closer relationship of G. ghorensis to G. rufa.

This genus belongs to the family Cyprinidae. These sucker-mouthed barbs are often kept in aquaria to keep down algae.  The infamous doctor fish of Kangal (Garra rufa) also belongs in this genus. This species has been integrated as spa treatment, where the fish feed on the skin of patients with psoriasis. However, this treatment is still debated on the grounds of efficacy and validity. The new species is named after the Hashemite Kingdom of Jordan and for the Jordan River.

Three new species of Tarsonemidae, Daidalotarsonemus oliveirai Rezende, Lofego & Ochoa, sp. n., Excelsotarsonemus caravelis Rezende, Lofego & Ochoa, sp. n. and Excelsotarsonemus tupi Rezende, Lofego & Ochoa, sp. n. are described and illustrated. Measurements for these species are provided, as well as drawings, phase contrast (PC), differential interference contrast (DIC) and low temperature scanning electron microscopy (LT-SEM) micrographs. Some characters, which have not been used or clearly understood, are described herein. Biological, ecological and agricultural aspects about the role of these species in the rainforest and its surrounding environment are briefly discussed.
Daidalotarsonemus oliveira

Three new species of a group called thread-footed mites or white mites. One species was named after Dr. Anibal Ramadan Oliveira a mite researcher. The second species was found at the place where the first Portuguese explorers arrived in Brazil, at the end of 15th century. On their trip, they used caravels, which had characteristic big sails. The name caravelis was used in reference to several dorsal setae of this mite species which are held in the upright position resembling those sails. The third species was named in honor of a Tupi people, one of the most important native indigenous tribes in Brazil which used to live the coastal region where this mite species was found.
no DNA Barcodes

The Neotropical genus Cephaloleia Chevrolat (Coleoptera: Chrysomelidae: Cassidinae) includes 214 species distributed from the south of Mexico to Argentina. Cephaloleia beetles feed mostly on plants from the order Zingiberales. The interactions between Cephaloleia beetles and their Zingiberales host plants is proposed as one of the oldest and most conservative associations. Here we describe a new species of Cephaloleia (C. kuprewiczae sp. n.) that feeds on two species of bromeliads (Pitcairnia arcuata and P. brittoniana, Bromeliaceae: Pitcairnioideae). Cephaloleia kuprewiczae was previously described as Cephaloleia histrionica. This study includes evidence from DNA barcodes (COI), larval and adult morphology and insect diets that separates C. kuprewiczae from C. histrionica as a new species.

A new species of beetle that likes to fee on bromelia. It was found in a montane forest in Costa Rica. The new find was named after Erin K. Kuprewicz, who discovered it and its interaction with Pitcairnia (Bromeliaceae) host plants. 

As a result of an expedition to Ecuador in 2014, a new species of mite harvestman was discovered. This new species belonging to the genus Metagovea Rosas Costa, 1950 – Metagovea ligiae sp. n. – is described, based on male and female specimens from Napo Province, Ecuador. This is the fourth species described for the genus and the second from Ecuador. A simple terminology is proposed for the microtrichiae of the spermatopositor and genital characters in the family are discussed. The genus Brasiliogovea Martens, 1969 is consistently misspelled in the literature as Brasilogovea. The description of Metagovea ligiae offered opportunity to discuss some aspects of systematics of the family.

A new species of mite harvestmen which are considerable smaller (adults ranging from 1 to 6mm) than the more familiar "daddy long-legs" harvestmen. The new species was named after a friend and fellow arachnologist of the authors. They want to honor  Ligia Benavides for her work on Neotropical Neogoveidae.
no DNA Barcodes

Metaeuchromius glacialis Li, sp. n. is described from the Tibetan glacier area of China. The new species is similar to M. circe Bleszynski by the distal projection of costa exceeding the apex of valva, and the phallus with strong spine-like cornuti in the male genitalia. Images of male adult, tympanal and scent organs as well as genitalia of the new species are provided.

A new grass moth species from rather high altitudes. Fittingly the species was named glacialis in reference to the environment it was found in.
no DNA Barcodes

Rhododendron bailiense

Rhododendron Linnaeus (1753: 392) is one of the largest genera in the family of Ericaceae, which is subject to much ongoing taxonomic debate. About 1,025 species are recognized; these are distributed from the northern temperatezone, throughout tropical Southeast Asia, to northeastern Australia (Chamberlain et al. 1996). In China, there are 571 species classified in 6 subgenera, of which 405 species are endemic (Fang et al. 2005). Apart from Xinjiang and Ningxia, Rhododendrons have been documented in all other provinces (Ma et al. 2014; Wu et al. 2005). The Baili Rhododendron Nature Reserve is located in a highland region in NW Guizhou that extends over an area of approx. 130 km2, and is characterized by the dominance of Rhododendrons. Previous field investigations regarding Rhododendrons had reported about 35 species belonging to six subgenera, six sections and seven subsections, respectively (Chen et al., 2010). However, this conclusion remains unclear, as some of newly described species were actually hybrids between sympatrically dominant species there (e.g. Rhododendron delevayi, R. irroratum and R. decorum). In 2013, a joint project was launched via the staff from the Baili Rhododendron Nature Reserve, involving plant taxonomists from the Royal Botanic Garden Edinburgh and Kunming Institute of Botany from Chinese Academy of Sciences, to clarify the Rhododendrons in that area. During field work on Baili Rhododendron Nature Reserve, a Rhododendron species with distinct leaves was brought to our attention and collected for further study. After careful examination of specimens and relevant literature, its status as a distinct new species was confirmed. This species shows strong affinities with R. auriculatum and R. chihsinianum, two species that have been traditionally placed in Subsection Auriculata in Subgenus Hymenanthes. This subsection is now considered to be synonymous with Subsection Fortunea.

The name of the new species refers to the site (Baili Rhododendron Nature Reserve) where it was first discovered and collected.
no DNA Barcodes

h/t Matthias Geiger

Monday, January 26, 2015

A way to save the mammals of Borneo?

Borneo native Eonycteris major, credit: Matthew Struebig
Responses of biodiversity to changes in both land cover and climate are recognized but still poorly understood. This poses significant challenges for spatial planning as species could shift, contract, expand, or maintain their range inside or outside protected areas. We examine this problem in Borneo, a global biodiversity hotspot, using spatial prioritization analyses that maximize species conservation under multiple environmental-change forecasts.

Borneo is the third-largest island in the world and the largest island in Asia. It is a world renowned hotspot of biodiversity, and there is no question that the island's many rare species are in big trouble. 

Now researchers of the Borneo Mammal Distribution Consortium claim that with targeted conservation measures there is hope for the mammalian species on the island.

Based on climate projections alone, up to one in every three Bornean mammal species is expected to lose 30% or more of their habitat by the year 2080. With additional losses as rainforests are cut, nearly half of Borneo's mammals could see suitable habitats shrink by a third or more in the coming decades. The colleagues show that deforestation and climate change are both expected to hit lowland forests of Borneo the hardest. While lowland forests and especially peatlands will remain important for endangered species such as the otter civet (Cynogale bennettii) and flat-headed cat (Prionailurus planiceps), higher-elevation reserves deserve special attention as they might help to mitigate the threat of climate change.

With the evidence base now in place, the researchers say they hope the findings will make an important difference to conservation efforts on the ground. The team, which includes conservation organizations and government institutions, is now presenting their portfolio to government representatives in Indonesia, Malaysia, and Brunei through the Borneo Futures initiative

As much as I welcome any good news related to biodiversity conservation, I am a bit concerned that this study focused only on mammals. All conclusions that are now presented to authorities are based on this limited view of biodiversity. All remaining vertebrates (and there are lot in Borneo) and invertebrates as the most diverse group of all are not considered. Can higher-elevation reserves also help mitigating the threat to those groups? The study seems to be a good start and a great proof of concept. However, the proposed methods should also be used by colleagues that work with the actual majority of life on Borneo.

Friday, January 23, 2015

Counting fishes

Underwater video cameras (UVC) provide a non-lethal technique to sample fish in dense submersed aquatic vegetation. Fish often inhabit densely vegetated areas, but deficiencies of most sampling gears bias relative abundance estimates that inform fisheries management. 

Cameras have been used to document fish behavior -- including eating and breeding but never to count fish in e.g. underwater plant habitats. Australian researchers studying fish ecology have used cameras to count fish in the relatively clear waters at the Great Barrier Reef, but no research has peered through a lens to detect fish in thick vegetation.

However, it would be great if one could accurately count freshwater fish, even in the thickest of underwater vegetation. This is very important as it is commonly assumed that dense and invasive plants, e.g. hydrilla (Hydrilla verticillata), can drastically change fish habitat quality, primarily through changes in dissolved oxygen levels, water chemistry and habitat structure. Whether these changes are good or bad for fish has previously remained uncertain due to sampling problems in dense plant habitats. 

This is a big problem, especially with hydrilla, a plant that has invaded lakes throughout Florida, much of the U.S., Central America, South Africa and Australia. Florida likely spent up to $14 million per year throughout the 2000s to manage hydrilla, while the U.S. spent about $100 million per year in the 2000s for aquatic plant management. Another invasive aquatic plant with similar effects is Eurasian Watermilfoil (Myriophyllum spicatum).

Researchers from the University of Florida Institute of Food and Agricultural Sciences used underwater cameras to show that fish can be properly counted with this technology. Furthermore, they were able to show that fish actually do us habitats that were previously thought to be too stressful for fish habitat.

They lowered a camera into the water from a boat in three experimental ponds in Gainesville. The colleagues were able to count fish captured on video even those hidden in the nooks and crannies of hydrilla and other vegetation. Fish were counted during 13 weeks in the summers of 2011 and 2012, and then the ponds were drained to obtain actual fish densities.

In practical terms, researchers and conservation managers could use this technolgy to better understand how fish use invasive aquatic plants in general. Such approaches can be quite valuable in advising conservation plans and can help resolve stakeholder issues associated with these invasive plants.

This ability to use video cameras to estimate fish abundance is a tremendous asset to fisheries management, allowing us to evaluate fish habitat use in areas where previously no sampling method was effective,

Thursday, January 22, 2015

Alpine bat diet

Credit: © A Alberdi
The alpine long-eared bat, Plecotus macrobullaris was discovered 2002. It is considered the only bat to feed above the tree line, but it uses its foraging ability at lower altitude too. Not long after its discovery it was found far away around the Mediterranean coasts, where the climate is pretty different from any at high alpine altitude.

So how alpine is this bat? In summer, they can be found between 1,500 and 2,500 m. The bats take advantage of meadows in flower that provide insects with shelter and food. This enables the bats to exploit a different food source compared with their cousins hunting at lower altitudes. Earlier survey showed that this species specializes on moths while other long-ear bats (genus Plecotus) feed on greater varieties of insects. The limited diet of Plecotus macrobullaris is probably the result of the limited high-mountain environment.

A study that was published a while back used DNA Barcodes to pin-point prey species of the alpine long-eared bat. I came across this paper during my research on high-altitude specialists for yesterday's post. The researchers were able to identify a number of moth species found in feces from bats trapped using mist nets. 

One of the advantages of the study was the fact that the order Lepidoptera is one of those taxa with an extensive amount of available DNA Barcodes (more than 80,000 species, almost 100,000 BINs). Such comprehensive reference libraries allow for very specific analyses.

Consequently the colleagues were able to identify 44 moth species in the bat's diet. Most of them were owlet moths (Noctuidae) but they also found individuals of the small elephant hawk moth (Deilephila porcellus). 

Rather than indicating any selective behaviour, these results likely reflect the actual prey availability at high elevation, because noctuids and geometrids are almost the only lepidopteran taxa present in alpine environments, the former eight times more abundant than the latter. 

Prey species also occurred at many different altitudes, indicating a broad range of hunting grounds. Most of the moths occur in subalpine meadows and the habitats bordering those, all of them are rather open. 

In our study, results show that the Mountain Long-eared Bat P. macrobullaris is a moth specialist that forages in high mountain meadows and rocky areas during summer. However, our data are restricted to summer and we should not dismiss the possibility that P. macrobullaris forages at lower elevations and in different habitats during other seasons, especially spring, when alpine habitats are moth-impoverished.

Wednesday, January 21, 2015

Ants on mountains

Many Neotropical species whose range is restricted to tropical montane cloud forests (TMCF) are in danger of local or total extinction due to warming and drying as air warmed by climate change ascends these mountains. While the species richness of many arthropod higher taxa declines at high elevations, those species that do reside in TMCF are often highly specialised and endemic, rendering their natural history especially interesting. However, we know little about these TMCF arthropods.

The species of the ant genus Adelomyrmex are good examples for such arthropods and indeed little in known about them. They are small ants mostly found in leaf-litter samples. The genus is believed to have a distribution across the tropics. However, central American cloud forests seem to be the centers of diversity and abundance. One challenge researchers faced was the fact that for most species only workers were found in samples but males or even queens have not been encountered at all. The same is true for actual nests of many species.

A new study shines a little light on these mysterious creatures and this quite literally as the colleagues present the very first video recording of an Adelomyrmex colony in the wild. In addition through using DNA Barcoding they were able to link male samples to known worker finds which is another big step forward in understanding this group. Queens remain yet to be found.

Here is the video with the 'historical' footage:

What I find fascinating is that the video that shows activity at the colony entrance was shot with a small USB Digital Microscope. Dino-Lite microscopes are affordable and versatile microscopes. Certainly not high-end when it comes to optical resolution but enough to produce some very nice footage on a low budget. The prizes range from $99 to $1000 depending on features, magnification and resolution. Pretty cool idea and the perfect present for kids as it provides high tech to explore the living world around them.

A neat little study that shows how new technology can facilitate discovery in biology. These new tools are also enabling everyone - not only the well-funded, high-tech field scientist - to investigate and encounter an hitherto little known natural world:

Ongoing field collections, using multiple collection methodologies, facilitated by technologies only recently widely and affordably available (digital field microscopy and DNA barcoding) enabled us to eliminate some of the mysteries surrounding the reproductive biology of one species of Costa Rican mountain-top Adelomyrmex. We expect that each of these technologies will become increasingly more affordable and thus expect that other inventories of tropical arthropods will standardise the incorporation of such technologies when appropriate or useful. For example, we note that external magnification lenses for cell phone cameras can already be purchased for $50–70 CAD. Democratising access to such tools will help to resolve many other mysteries of reproductive biology and natural history.

Tuesday, January 20, 2015

Discoveries of the week #23

Aphanius marassantensis, new species, is described from the Kızılırmak River drainage in northern Anatolia based on colouration, meristic and morphometric characters, and the mtDNA COI barcode region. It is distinguished from other Anatolian Aphanius by one or several of the following characters: a stout body shape (BD/SL 28.2–39.6%), complete scale cover, and 25–28 scales along the lateral line. Males have 8–13 dark-brown lateral bars, of which the antepenultimate bar anterior to the caudal-fin base is 0.9–1.8 times wider than the anterior white interspace, 2–3 vertical rows of spots on the caudal fin, a black dorsal fin, sometimes with a narrow whitish-grey base, a white anal fin with 1–3 rows of black spots, in some individuals with a black margin, and hyaline pelvic fins. Females do not have vertical rows of dark-brown spots on caudal or anal fins, but numerous dark-brown spots on the flanks, arranged in 1–3 lateral rows behind a vertical from the dorsal-fin base. Their dorsal fin is hyaline with tiny dark-brown spots on rays and membranes; pectoral fins, caudal and anal fins are hyaline, and one prominent large dark-brown blotch is situated in mid-lateral position on the hypural plate. The new species is also distinguished by 11 fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region. The description of this new species, which brings the number of Anatolian Aphanius species to 12, underlines the character of Anatolia as a region of extraordinarily high biodiversity.

A new member of the pupfish, a group of small killifish belonging to several genera of the family Cyprinodontidae. The species name was derived from Marassanta, the Hittite name for the Kızılırmak River.

Europe has one of the best-known Lepidopteran faunas in the world, yet many species are still being discovered, especially in groups of small moths. Here we describe a new gracillariid species from the south-eastern Alps, Callisto basistrigella Huemer, Deutsch & Triberti, sp. n. It shows differences from its sister species C. coffeella in morphology, the barcode region of the cytochrome c oxidase I gene and the nuclear gene histone H3. Both C. basistrigella and C. coffeella can co-occur in sympatry without evidence of admixture. Two C. basistrigella specimens show evidence of introgression. We highlight the importance of an integrative approach to delimit species, combining morphological and ecological data with mitochondrial and nuclear sequence data. Furthermore, in connection with this study, Ornix blandella Müller-Rutz, 1920, syn. n. is synonymized with C. coffeella (Zetterstedt, 1839).

A new moth species from the Eastern Austrian Alps. It's  name refers to some characteristic wing markings.

A number of stylasterid corals are known to act as host species and create refuges for a variety of mobile and sessile organisms, which enhances their habitat complexity. These include annelids, anthozoans, cirripeds, copepods, cyanobacteria, echinoderms, gastropods, hydroids and sponges. Here we report the first evidence of a diverse association between stylasterids and scalpellid pedunculate barnacles and describe a new stylasterid species, Errina labrosa, from the Tristan da Cunha Archipelago. Overall, five stylasterid species are found to host eight scalpellid barnacles from several biogeographic regions in the southern hemisphere (Southern Ocean, temperate South America and the southern Indo-Pacific realms). There is an apparent lack of specificity in this kind of association and different grades of reaction to the symbiosis have been observed in the coral. These records suggest that the association between pedunculate barnacles and hard stylasterid corals has a wide distribution among different biogeographic realms and that it is relatively rare and confined largely to deep water.

A new coral species for a change. This species belongs to the stylasterid corals which are considered habitat-forming species because they contribute to the structuring of deep and shallow water coral banks. the species name was taken from the Latin word labrum (lip) for a characteristic lip of at its gastropores.
no DNA Barcodes available

The results of the study of many specimens preserved in different European museums are reported. The tribe Terpnistrini Brunner von Wattenwyl, 1878 is resurrected. The distribution of the following species is enhanced: Pardalota asymmetrica Karsch, 1896, Diogena denticulata Chopard, 1954, Diogena fausta (Burmeister, 1838), Plangiopsis adeps Karsch, 1896, Poreuomena sanghensis Massa, 2013 and Tylopsis continua (Walker, 1869). Further, for their peculiar characteristics, two African representatives of the American genus Symmetropleura Brunner von Wattenwyl, 1878 are included in two new genera: Symmetrokarschia africana (Brunner von Wattenwyl, 1878), comb. n. and Symmetroraggea dirempta (Karsch, 1889), comb. n. A new genus and species from the Democratic Republic of Congo, Angustithorax spiniger gen. n., sp. n., and a new genus and species from Tanzania, Arostratum oblitum gen. n., sp. n. are described. Finally Melidia claudiae sp. n. and Atlasacris brevipennis sp. n. are described and compared with related species.

One of these four new bush crickets, Arostratum oblitum, has in fact been waiting for over 100 years in European Natural History museums to be discovered and described. This curious fact also inspired the name of the new species to be 'oblitum', which means 'forgotten' translated from Latin.
no DNA Barcodes available

A new species of Chapelieria was discovered during a recent field trip to the Masoala National Park in eastern Madagascar, and is described here as Chapelieria magna Kainul., sp. nov. This species is readily distinguishable from previously described species of the genus by its quadrangular shoots, triangular-calyptrate stipules, sessile leaves, pubescent styles, and ridged fruits. It also differs in the larger number of ovules and the much larger size of leaves and fruits.

Madagascar is not only home to an incredible diverse and largely endemic fauna. There are also a lot of plants waiting to be discovered. Here is one recent example from the family Rubiaceae, sometimes called the coffee family which is a bit misleading as there are about 13000 members in this group and most are not coffee. 
no DNA Barcodes available

Two new species of Psoralea L. are described: Psoralea diturnerae A. Bello, C.H. Stirt. & Muasya, sp. nov. and P. vanberkelae C.H. Stirt., A. Bello & Muasya, sp. nov. Psoralea diturnerae is endemic to the Outeniqua mountains (Camferskloof) and is characterised by a mass of numerous basal shoots out of which emerge 2–3 woody stems up to 2 m tall, 3-foliolate needle-like leaflets at the base of the seasonally growing shoot reducing to one towards the apex and bearing numerous 1–3-flowered axillary inflorescences along its length; each mauve to purple and white flower subtended by a trifid cupulum. Psoralea vanberkelae is characterised by its spreading mounding habit, short tightly packed fleshy leaves, with large impressed papillae, densely glandular short broadly triangular stipules, pale to intense mauve to deep blue flowers, standard with a dark purple central blotch above a M-shaped white patch situated above claw, and khaki seeds with purple flecks.

The names of the species have been chosen to honor volunteers of the Custodians of Rare and Endangered Wild flowers (C.R.E.W., South Africa) that brought these plants to the attention of the researchers. Ms. Di Turner, and Ms. Nicky van Berkel play a valuable role in establishing the conservation status of plants in their area. 
no DNA Barcodes available

h/t Matthias Geiger, Peter Huemer

Monday, January 19, 2015

Are we moving wildlife in the right direction?

Despite rapid growth in the field of reintroduction biology, results from scientific research are often not applied to translocations initiated when human land-use change conflicts with the continued persistence of a species’ population at a particular site. Such mitigation-driven translocations outnumber and receive more funding than science-based conservation translocations, yet the conservation benefit of the former is unclear. 

Over the past decades we saw an exponential rise in the use of translocations as a wildlife management tool. Living organisms are moved intentionally from one area to another but many of those wildlife translocations have evaded academic scrutiny and did not use a common set of accepted standards. 

A new study published in Frontiers in Ecology and the Environment estimates that millions of dollars are spent annually on moving animals out of the way of human interference, and may not be meeting the goal of preserving the populations as intended by legislation. Authors of a collaborative study* argue that because mitigation releases are economically motivated, outcomes may be less successful than those of releases designed to serve the biological needs of species. 

We contend that mitigation-driven translocations, while well-financed, are often inappropriately executed, poorly documented, and unquestioningly used without regard to larger, more strategic conservation goals.

The result - many of those mitigation-driven translocations fail, although the application of scientific principles and best practices would probably improve the success rate. The field of reintroduction biology is moving steadily forward but the scientific community has also failed to raise concerns. Mitigation-driven translocations are largely ignored by the scientific community. Even in a textbook on reintroduction biology, there is little mention of them despite detailed descriptions of several types of wildlife translocations including conservation-driven approaches.

So, what do the authors consider best practice? They provide a detailed conclusion at the end of their paper:

Mitigation-driven translocations, funded by developers rather than taxpayers, should conform to best-practice standards for conservation science. It should be the responsibility of the developers, their consultants, and the regulatory agencies to demonstrate the effectiveness of translocation as a tool to achieve conservation outcomes that are consistent with the regulatory intent. This process should be transparent, with clear goals for each translocation and data made freely available for public scrutiny. If current regulations and practices do not uphold these standards, they should be revised. When translocation as a tool is ill-suited to offsetting the impacts of a planned development on a protected species, then the regulatory framework should be flexible enough to allow other, more strategic approaches, regardless of whether they entail the loss of some individuals. Under these circumstances, better use of development mitigation dollars can be realized if applied to achieve range-wide strategic conservation priorities for the affected species.

Friday, January 16, 2015

Emerald ash borer eats more than ash

As many of my readers might know the Emerald Ash Borer (Agrilus planipennis) is an introduced insect pest from Asia that feeds on and kills ash trees. The borers attack trees by laying eggs on the bark. The serpentine feeding galleries of the larvae inside the bark disrupt the flow of nutrients and water and starve the tree. All species and sizes of ash trees (genus Fraxinus) are susceptible, except for the so called mountain ash which is actually not a true ash but belongs to the genus Sorbus.  If a tree has become infested, mortality will result usually within 2-3 years. 

In North America, the beetle was initially discovered in Michigan and southwest Ontario in 2002. Since then this insect pest from Asia that has killed millions of trees throughout the United States and Canada and has caused billions of dollars of damage. Fortunately, its damage has been limited to ash trees - or so we thought.

There is a new publication that provides evidence that the Emerald Ash Borer can also attack different species:

I report here evidence that emerald ash borer can attack and complete development in white fringetree, Chionanthus virginicus L., a species native to the southeastern United States that is also planted ornamentally. Four of 20 mature ornamental white fringetrees examined in the Dayton, Ohio area showed external symptoms of emerald ash borer attack, including the presence of adult exit holes, canopy dieback, and bark splitting and other deformities. Removal of bark from one of these trees yielded evidence of at least three generations of usage by emerald ash borer larvae, several actively feeding live larvae, and a dead adult confirmed as emerald ash borer.

White fringetree, a relative of ash, is a deciduous shrub or small tree that can grow up to 10 m tall. It has white flowers and a purple, olive-like fruit, and is growing in popularity as an ornamental. It is known for its relative lack of pest and disease problems, and until now has never been reported as a host to wood borers. 

Now this is indeed bad news which of course needs to be confirmed further and DNA Barcoding should play a big role in more widespread survey and monitoring programs. It is paramount to be able to identify all life stages of the animal to confirm that we are looking at a true infestation. This new observation might not raise big concerns today as the vast majority of infested trees are still ash trees. However, what will happen once the Emerald Ash Borer is done with those?

Thursday, January 15, 2015

Barcoding bees

Andrena bicolor
I have posted several times about the advantages DNA Barcoding has for bee research. The examples range from the conservation of honey bees, over pollen analysis to determining honey ingredients. Much of the global food crop production depends on pollination by insects and bees play a particularly important role in this ecosystem function. The more it concerns me that when people think of bees they only think of honey bees although there are thousands of bee species living on our planet. 

I had a quick look at BOLD and found out that about 6700 species of the Apoidea have been barcoded already. This is very impressive and shows that researchers have recognized the importance of a reliable identification system for these animals.

A new study from Germany presents an important national accomplishment as they are now very close to completion of an inventory of all bee species:

This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more.

This is a very impressive accomplishment especially given that many of the collected species are solitary bees that are rather elusive. It takes a lot of effort to assemble a collection such as the one at the Zoologische Staatssammlung in Munich and it needs to be emphasized that studies like this one are the result of hard work of both professional and amateur entomologists. Actually, in Europe, insect taxonomy was traditionally led by amateurs who have described most known species. 

I particularly like the last paragraph of the paper:

As opposed to a threat, we see DNA barcoding as a great opportunity for both amateur and professional entomologists to contribute to the progress of science by adding records to the Web-accessible BOLD, arguably the most important tool that is globally available for taxonomic research. Based on our experience, insect taxonomy has been held in rather low esteem for decades, a major reason for systematics losing academic participation and resources. External perceptions of taxonomy and its capacity to deliver new scientific insights will be advanced through the large-scale adoption of new technologies, particularly genetic approaches, provoking the funding and academic interest which will reinvigorate taxonomy as a major field in entomology.

Wednesday, January 14, 2015

Canadian National Parks Malaise Program

The Canadian National Parks (CNP) Malaise Program, a collaboration between Parks Canada and the Biodiversity Institute of Ontario (BIO), represents a first step toward the acquisition of detailed temporal and spatial information on terrestrial arthropod communities across Canada. The program addresses the current lack of a systematic approach for tracking shifts in the species composition of terrestrial communities in response to environmental disturbance or global climate change.

It is no secret that here at BIO we work a lot with Malaise traps and one of the reasons is the fact that assessments of terrestrial environments are lacking a standard protocol to derive biotic indices. This is very different from e.g. water quality assessments which are routinely based on surveys of freshwater invertebrate species composition. Terrestrial assessments often rely on a handful of indicator taxa which are very often vertebrates and plants. The problem is that most species in terrestrial ecosystems and others for that matter are invertebrates.

The Canadian National Parks Malaise program started in 2012 and by the end of 2014 it covered pretty much all of Canada (see map above). Not long ago the team at BIO finished analyzing the year 2013 which in total means that 227 weekly samples with some 280 000 specimens were analyzed. About 240 000 of those provided a DNA Barcode with sufficient length to allow for a BIN assignment. Some 17 500 BINs were found for the year 2013 with 14 sites. Numbers that are pretty impressive and even more so when the previous year is added to the picture. Just have a look at the BIN/species accumulation curve on the right. The colleagues here have generated reports for each participating park and I highly recommend checking those out. Each reports starts with an overview and summary of the total results before looking into the details of the particular site.

The comparisons between the sites are pretty impressive, too. I particularly like one figure, a chord diagram of species overlap between all National Parks probed in the years 2012 and 2013. It looks beautiful and perhaps confusing at first but there is a lot of information in it. The width of each wedge is proportional to the number of BINs captured in a given park. The width of the internal humps reflect the number of unique BINs within each park. Arcs connecting the parks reflect the proportion of shared species between the parks. The parks have been arranged according to geography and neighborhood.

Species overlap can also be documented over time at a given location. The last figure shows overlap between weekly (A) and bi-weekly (B) samples over the collection period in 2013. The node size is proportional to the number of BINs per sample while the width of arcs reflects the number of species shared between each sample. 

The images might be a bit small when embedded in the text but you should be able to click on them to enlarge them to a reasonable size. If that doesn't work for some reason I'll recommend the original reports

My blog post can only be a teaser for these very data rich reports. Personally I find these comprehensive studies very fascinating and going back to the original intent of this project - this is definitely a way to provide standardized and systematic assessments of terrestrial environments. It is already far more detailed than any report one could get even from a comprehensive survey of a freshwater environment and it is done using a lot of human workforce and traditional sequencing. After all we are still assembling the DNA Barcode library for Canada's life. Just imagine what will happen when we are done and start to introduce metabarcoding...

Tuesday, January 13, 2015

Discoveries of the week #22

Brazilian cave diversity, especially of invertebrates, is poorly known. The Bodoquena Plateau, which is located in the Cerrado Biome in central Brazil, has approximately 200 recorded caves with a rich system of subterranean water resources and high troglobitic diversity. Herein we describe a new troglobitic species of Girardia that represents the first obligate cave-dwelling species of the suborder Continenticola in South America. Specimens of the new species, which occur in a limestone cave in the Bodoquena Plateau, in the Cerrado biome, are unpigmented and eyeless. Species recognition in the genus Girardia is difficult, due to their great morphological resemblance. However, the new species can be easily recognized by a unique feature in its copulatory apparatus, namely a large, branched bulbar cavity with multiple diverticula.

This is a new species of free-living freshwater flatworms. The species name refers to a number of excrescences in a cavity of the male genitalia.
no DNA Barcodes

A small bodied, free-living marine nematode, Rhynchonema dighaensis sp. nov., is described from the intertidal sand of the east coast of India. It is characterized by having a small buccal cavity, longer left spicule and symmetrical dorsal gubernaculum apophysis. Other species of the genus are discussed with their type locality. A modified key has been prepared for species of Rhynchonema with an illustrated guide. Species of Rhynchonema primarily differ from each other by the shape and size of the spicules, shape of the gubernaculum and dorsal apophysis, size of the buccal cavity and position of the amphid.

A new free-living nematod species named after the type locality Digha in West Bengal, India.
no DNA Barcodes

Platypalpus graecoides sp. n. (Italy), P. pyreneensis sp. n. (Andorra), and P. silvahumidus sp. n. (Czech Republic) are described. All three species are illustrated and keyed. Platypalpus hallensis Grootaert & Stark, 1997 is first reported from France and Spain.

These are three new member of a huge genus (~500 species) in the family of dance flies. One species was named after its similarity with another species (Platypalpus graecus), another after the location the type was found (Pyrenees). The last species name depicts the typical biotope of this species (silva = forest, humidus = damp).
no DNA Barcodes

The taxonomic treatment of Begoniaceae for the state of Bahia, Brazil, led to the recognition of three new species of Begonia with narrow distributions, which are described and illustrated here: B. delicata Gregório & J.A.S. Costa, sp. nov. is a herb restricted to the region of the Recôncavo; B. elianeae Gregório & J.A.S. Costa, sp. nov. is a shrub endemic to the Atlantic forest of the southern part of the state; and B. paganuccii Gregório & J.A.S. Costa, sp. nov. is a subshrub known only from the type material, collected in the Piedmont of Paraguaçu. Notes on morphology, comparisons with morphologically similar species, etymology, geographic distribution, habitat and phenological data for each species are also presented. Furthermore, keys are provided as an aid to separating the new species from congeneric species that occur in their surroundings. Due to the sparse knowledge of the new species, there is as yet insufficient data to accurately assess their conservation status.

Three new members for one of the larger angiosperm genera. Begonia comprises currently about 1500 species and quite a few are known as ornamental plants. All three new species are from Brazil. One name refers to the fragility and delicacy of the plant. The second one was named  in honour of Dr. Eliane de Lima Jacques, a botanist who has contributed extensively to the knowledge of  Begonia in Brazil. The third species was named in honour of Dr. Luciano Paganucci de Queiroz, expert on the flora of Bahiaand collector of the type material.
no DNA Barcodes

Four new species of “non-spiny” Solanum from South America are described. Solanum longifilamentum Särkinen & P.Gonzáles, sp. nov. (Morelloid clade) is widespread from Ecuador to Bolivia and is most similar to S. macrotonum Dunal from Central and northern South America. Solanum antisuyo Särkinen & S.Knapp, sp. nov. (Morelloid clade) is found on the eastern Andean slopes in Ecuador, Peru and Bolivia and is most similar to the widespread lower elevation species S. polytrichostylum Bitter. Solanum arenicola Särkinen & P.Gonzáles, sp. nov. (Morelloid clade) is found in low elevation habitats on the eastern Andean slopes and in Amazonia of Peru and Bolivia and is most similar to the higher elevation species S. aloysiifolium Dunal of Bolivia and Argentina. Solanum mariae Särkinen & S.Knapp, sp. nov. (Potato clade) is endemic to Cajamarca Department in Peru, and is most similar to the widespread S. caripense Dunal. Complete descriptions, distributions and preliminary conservation assessments of all new species are given.

Another large genus in the plant world with the centre of diversity in South America. Therefore, it comes to no surprise that these four new species are from South America as well. The first species is named after is unusual long filaments. Number two's name refers to the Quechua word Antisuyo, for the eastern region of the Inca territory where the species is most abundant. The third is named for its habitat preference as as it prefers growing on sand (cola = “live on”, and arena = “sand”). The last species is named after biologist Maria Baden who collected the first specimen.
no DNA Barcodes

A new nemacheilid loach species, Triplophysa qilianensis, is described from Heihe River in Haibei Tibetan Autonomous Prefecture, Qinghai, China. It can be distinguished from all other species of Triplophysa by the following combination of characters: body long and compressed; skin smooth, scaleless; head short (20.1–23.1% of stand length); head convex from the position of posterior nostrils; posterior chamber of air bladder completely degenerated; intestine short, bending in zigzag patter posterior to stomach; unbranched rays of pelvic fin ii; caudal fin forked, upper lobe and lower lobe equal in length; and pointed fin tips. A key to the known species of Triplophysa from the Heihe River is provided.

Every week a new fish species it seems. Quite interesting to witness the rate of discovery in a vertebrate group other than frogs and toads. This new loach was named after the type locality, Pinyin Qilian in China.
no DNA Barcodes

Monday, January 12, 2015

IUCN Red List of Ecosystems

Since the 1950s, humans have changed ecosystems more than during any other similar span in history, causing staggering losses of biodiversity. Informed policy is urgently required to slow these losses, but is hampered by the lack of a consistent scientific framework for tracking the conservation status of Earth’s ecosystems, and of objective and transparent criteria for identifying those more likely to disappear. Recognizing this major scientific gap, the IV IUCN World Conservation Congress (Barcelona, Spain, 5-14 October, 2008) set in motion a process to develop risk assessment criteria that will eventually lead to a new tool for conservation policy: a global IUCN Red List of Ecosystems.

The new system and the already well established Red List of Threatened Species are designed to complement each other and provide better measures of biodiversity loss and recovery. Monitoring the status of both species and ecosystems provides a more complete picture of the state of biodiversity. Ecosystems may collapse, while species that lived in them continue to live elsewhere or within novel ecosystems. Likewise species may go extinct even though the ecosystems in which they occurred remain functional and unperturbed. 

The Red List of Ecosystems uses categories that are very similar to the ones in the species Red List. The endpoint of ecosystem decline is collapse which is for example the analogous concept of species extinction. The risk of collapse is evaluated using five criteria based on variables which may be specific to particular ecosystem types with appropriate standardization procedures:

(A) ongoing declines in distribution, indicating ongoing threatening processes that result in ecosystem loss
(B) restricted distribution, which predisposes the system to spatially explicit threats, along with manifested
decline, threat or fragmentation.
(C) degradation of the abiotic environment, reducing habitat quality or abiotic niche diversity for component biota (e.g. ocean acidification,soil fertility loss).
(D) disruption of biotic processes and interactions, which can result in the loss of mutualisms, biotic niche diversity or exclusion of component biota.
(E) quantitative estimates of the risk of collapse.

A paper that provides guidance to the application of the Red List of Ecosystems Categories and Criteria has been published in the Philosophical Transactions of the Royal Society as part of a discussion meeting issue. The paper makes a very interesting read especially if you are not familiar with this new system. I have to admit that I belong to the group of people that didn't know much about it before, maybe heard about it once or twice, but never learned about it in more detail. This paper represents a very good start and now I will have a closer look at all the other contribution to this special issue. The theme is 'Phylogeny, extinction and conservation’. Sounds promising.

h/t Alexander Weigand