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.