Thursday, October 8, 2015

Insect diversity in our gardens

If you think about it, you're driving around the suburban environment, and every time a new development goes in, you have a lot of decision making happening as to what plant species are going to be planted around those properties. If we do all that landscaping with non-native plants, are we limiting the wildlife and conservation support system that could be available within that given plot of land? What the gardens we constructed for the study are trying to replicate are landscaping decisions that people might make if they wanted to support native insect communities that in turn support much of the diversity around us.

Researchers of the University of Delaware tried to understand how the composition of the plants that homeowners plant in their yards affects herbivore communities. To conduct the study, they planted imitation yards with different common gardens of both native and non-native tree species and collected data over a three-year period, determining the herbivore communities and species found on those plants. They compared native trees to non-native trees that had no close native relative and to non-natives that are closely related to the native community.

Within the distantly related group, they found that herbivores were less diverse when they looked at individual non-native tree species, and as they moved from one non-native tree species to another, they found similar species of herbivores using those trees. Non-native plants reduced the diversity of insect populations in gardens, even when these non-native plants are closely related to the native plants.

You get this compounding effect where you have a lower diversity of herbivores per tree but then you also are getting more similar species as you move between trees species and among sites, so you end up with even less diverse communities than you would expect. There is this group of species of non-natives that do not have any close native relatives at all. These non-natives support more generalized and redundant herbivore communities than the native plants that they're potentially replacing on landscapes.

Wednesday, October 7, 2015

Caterpillar chemistry

Vismia baccifera
The tropical plant Vismia baccifera protects itself by producing a number of repellent chemicals, including three compounds that are toxic to living cells. Few plant-eating insects can stomach such a cocktail, but for those that can, the advantages are clear - less competition for a meal, and a chemical toolkit they can use in their own defense.

One of them is the skipper butterfly Pyrrhopyge thericles. Their caterpillars only eat plants of the genus Vismia. In contrast the caterpillars of the large saturniid, Periphoba arcaei, have a much broader diet, including Vismia plants and many others. The caterpillars of both species are brightly coloured, one with conspicuous stripes, and the other blue-green with bristles. For potential predators such flashy looks are associated with toxicity. Now it would seem that the skipper butterfly that exclusively consumed plants containing toxic chemicals would more easily incorporate toxins into its body than the one with a broad diet. 

A new study by the Smithsonian Tropical Research Institute (STRI) in Panama found the opposite. They compared the diets of the caterpillars of the two species at several life stages and tested for the presence and concentration of plant toxins called vismiones. While two vismione compounds are found at a ratio of 1:6 in the plants, in the specialist butterfly caterpillars the compounds were barely detectable, and at roughly equal ratios. Meanwhile, the generalist moth caterpillars contained significant quantities of the rarer of the two compounds, suggesting that they were able to actively store this plant chemical in their own bodies. Both caterpillars' fecal matter revealed a 1:2 ratio of the plant compounds, indicating that their bodies might uptake compounds selectively or convert molecules of one type over the other.

We know very little about just how each plant-eating insect handles these chemicals--how they store them or eliminate them. Some insects might isolate the compounds so they do not cause them harm, while others might convert the molecules into forms that are harder to detect. Insects that process harmful toxins without damaging their own cells have a survival advantage. For a generalist species, the ability to sequester toxic compounds might be an early evolutionary breakthrough, the first step along the pathway to becoming a toxic plant specialist.

Tuesday, October 6, 2015

eTrade in invasive plants

Passiflora edulis (highly invasive in the tropics)
Every day, hundreds of different plant species -- many of them listed as invasive -- are traded online worldwide on auction platforms. This exacerbates the problem of uncontrollable biological invasions as they are often introduced as ornamental plants. Those in turn spread into the wild, where they now threaten the native flora. The vast majority of invasive species can be easily obtained with just a click of the mouse.

To get an estimate of how much of the global trade in invasive plants is actually done online, a group of researchers at the ETH Zurich monitored online trade on eBay and nine other online trading platforms.

For 50 days, the researchers tracked which plant species were offered for sale in various countries, and how often. They used a software specifically developed for the study taking advantage of the fact that all online platforms make sale listings accessible to external software build to systematically search for and analyse online content. All findings were crosschecked against common lists of invasive plants, established by various institutions such as the International Union for the Conservation of Nature (IUCN).

Over the course of the study the colleagues found 2,625 different plant species offered for sale on eBay. Of those, 510 are known to be invasive in at least one region of the world. And out of that group, 35 are on the IUCN's list of the 100 worst invasive species.

These are astonishing numbers and sellers found in the study were located in 65 countries. Offers to sell invasive species came from 55 of these countries, including Australia. Dealers there offer invasive plants - that are known to be harmful in other parts of the world - on a grand scale. That was unexpected, since the Australians don't allow you to bring any invasive plants across their borders. But surprisingly, there are apparently no controls in place to make sure potentially harmful plants don't leave the continent.

Rules governing the trade in these plants are halfheartedly enforced, if at all. And it's virtually impossible for the dealers to keep track of all the laws and regulations concerning import and export of potential invasive species in different countries. A new threat is also emerging: regions that previously had no access to trade flows can now participate thanks to the internet. South Africa is now showing up on our map. We have no idea whether the plants that are being put on the global market from this corner of world will prove to be invasive species. It may well be that several of them could become invasive in other regions.

The only way to contain invasions is by limiting and monitoring the trade. The study shows that it is theoretically possible to continuously monitor this trade in order to spot newly traded species, which could signal future invasions. Many countries already have sets of rules and regulations in place with the goal of curbing the spread of invasive species. 

As online trade blossoms, it makes it even more urgent for the authorities to take action or for responsible large commercial nurseries to adjust their product ranges.

Monday, October 5, 2015

DNA Barcodes from types

Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain.

Earlier studies have shown that standard molecular methods can also be applied to type material of soft-bodied insects but success is rather mixed. Dried, mounted specimens can yield viable DNA even over 100 years after collection from as little as a single leg. Past studies usually included a number of PCR reactions to generate a set of short amplicons which could be assembled into a barcode contig. The problem is that templates can be depleted before the full sequence is recovered especially when many amplification reactions are required. This is extremely problematic if only one type specimen for a species is available.

In a new study coming out of BIO my colleagues used multiplex PCR to generate short amplicons covering the barcode region and then Next Generation Sequencing (NGS) for their characterization. They started with conventional Sanger sequencing of 1820 type specimens of the moth family Geometridae from the Natural History Museum,London as part of a project to develop a strongly validated taxonomic system to support species inventories and studies of host plant use in Papua New Guinea. For their comparative NGS run the colleagues picked single representatives from 30 different genera of the family, all between 102 and 123 years old.

They were able to recover sequence information from all specimens with average read lengths ranging from 458bp to 610bp which is impressive. But the inevitable question is if such an approach is not cost-prohibitive at this point. This is what the study authors have to say and I find that very encouraging:

By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.  

Friday, October 2, 2015

Spiders are the stars at the Scripps Coastal Reserve

I am a big fan of crowd sourced funding and in the past few years a couple of really good research programs could be started using such a large community based resource. For that reason and because I know both researcher and proposed research location I am happy to support a UC San Diego project by spreading the word through this blog.

Yesterday, Heather Henter from the Natural Reserve System group at the UCSD wrote to me (and I believe to many, many others):  My students and I are working on an effort to document biodiversity at the Scripps Coastal Reserve, a UC nature reserve adjacent to campus. The students are a group of spider enthusiasts that are using DNA barcoding to identify and inventory all of the spider species at the reserve.  This is really important because the diversity of little animals like insects and spiders is so poorly known and because San Diego is such a hotspot of endangered biodiversity.  There are a lot of species that only occur here, and a lot of habitat that is disappearing.  We think that the first step to conserving biodiversity is just knowing what is there! We hope you can help us, or pass along our video to others that might be interested.

No problem, consider it done:

Are you interested in supporting Heather and her students to build a DNA Barcode reference library? Here is how

Thursday, October 1, 2015

A taxonomic backbone for Europe

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.

The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. The three key objectives of PESI include standardisation in taxonomic reference systems, enhancement of the quality and completeness of taxonomic data sets and creation of integrated access to taxonomic information. The five pillars of biological community networks, Zoology, Botany, Marine Biota, Mycology and Phycology, have been integrated in five infrastructural components: knowledge, consensus, standards, data and dissemination.

PESI provides standardised and authoritative taxonomic information by integrating and securing Europe's taxonomically authoritative species name registers and nomenclators (name databases) and associated expert(ise) networks and focal points that underpin the management of biodiversity in Europe. As a result, PESI comprises of a total of nearly 450,000 scientific names that are available online

Scientific names are key carriers of biodiversity information. Therefore, for the efficient exploring and integration of biodiversity data, the development of a functional taxonomic resolution system, including the establishment of a shared taxonomic standard (as a core component), is essential for all sorts of biodiversity assessments. PESI provides such an infrastructure for Europe, integrating the relevant technical (informatics) and social (knowledge & users) networks into a common work program, serving a wide community of biodiversity workers

Wednesday, September 30, 2015

Wonderful arthropods

After my rant yesterday, today on a much lighter note. The omnipresence of the internet might have its good and bad sides but one really good one is the fact that everybody has access to a myriad of wonderful images of live on our planet. The world is full of talented photographers that are able to capture the beauty of living things and nature itself. Not long ago I introduced you to Alexander Semonov and his beautiful images of marine life. Today I will add a few more names to the list.

The first is a colleague working as collections technician at our institute, Valérie Lévesque-Beaudin. Valérie is an entomologist with a passion for macro photography and of course most of her images show her favorite organisms - arthropods. I selected one photo (above) I particular like but have a look at her Flickr presence for a much larger selection.

Number two is Thomas Shahan, who was nicely introduced in an article by the Smithsonian magazine and on TV. Just look at the moth I grabbed from his Flickr site.

Number three used to work for BIO as well. His name is Jay Cossey and I had the pleasure to take him to an expedition to the Great Barrier Reef a number of years ago. His insect photo's are stunning and his work was recognized before, e.g. he did all 24 images for the first ever National Geographic Butterfly Calendar. I choose an image showing him in front of one of his photos. I believe this photo was taking for a university publication way back then.

The last of my 'photo heroes' today is Sam Harris who is a Graduate Student (Ph. D. in Biology) and Teaching/Research Assistant at the University of Tulsa. At least that's what his Flickr profile said where I found some awesome spider portraits.

There are of course many more talents out there and I promise to post more in the future. In case you know of any please let me know or add a link or a name in the comments.