Monday, March 31, 2014

From Puffins to Plankton

One of the most valuable and accessible ecological information is often what a predator eats. Based on this information we can derive predator-prey relationships and use those to describe food chains, which provide the framework to understand how energy flows through an ecosystem. Comprehensive food web are used to interpret ecosystem functioning which is essential to develop effective management  and conservation strategies.

Atlantic puffins (Fratercula arctica)  and their main prey, Atlantic herring (Clupea harengus) represent a simple food web model system that has been studied extensively using conventional methods. Puffin chick diet is for example known from hundreds of hours of observing adults provisioning their chicks as part of long-term seabird research programs. As adult puffins forage at sea it is impossible to obtain any sufficient amount of guano containing identifiable components of their prey. Therefore, chick diet has been used as a best estimate for adult diet for birds, an assumption supported by similar levels of nitrogen isotopes in chick and adult blood. These results contradict common theories on optimal foraging which predict that adult puffins should feed their chicks a less diverse diet of high quality food while they feed on a more varied assortment of potentially lower quality prey. 

DNA-based dietary analysis of fecal samples provides an opportunity to test the similarity between adult and chick diet. A new study uses multi-locus (16S and COI DNA Barcodes) next-generation sequencing of feces samples of Atlantic puffin chicks and adults, and the stomach contents of their main prey, Atlantic herring to investigate this simple food web. By investigating the diet of the major prey of puffins, the researchers tried to gain insight in the potential effect of secondary consumption. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis.

This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain. Both puffin and herring diet were described with more diversity at a higher taxonomic resolution with our molecular approach compared to conventional methods, enhancing our knowledge of the biology of and interactions between these animals. The sensitivity of these techniques to detect the prey of prey is an important consideration for molecular scatology, particularly when de novo diet assembly with universal primers is concerned. We suggest that results of DNA-based diet studies be viewed from the perspective of a food chain, rather than simply diet, due to the effect of secondary consumption. Further, because of the considerable discrepancies in the types, coverage, and frequency of occurrence of prey taxa between markers, we recommend the use of multiple barcoding markers for taxon identification.

Another interesting find of the study was that both herring and puffins, previously considered to be part of a planktonic food web only, proved to be part also of inshore or intertidal food webs, as a number of benthic organisms showed up in the herring samples. Secondary consumers such as the puffin in this case can no longer be assumed to derive their energy and nutrients from planktonic production alone. No doubt this is a very important message for any management and conservation effort that is intended to preserve puffin habitat.

Friday, March 28, 2014

Management of scientific collections

About a week ago the US government announced a new policy on management of scientific collections. It aims to improve the quality, organization, access, and long-term preservation of such collections for the benefit of the scientific enterprise and society. The full memorandum is rather detailed but I went through and took the liberty to pick some points listed under the management objectives for scientific collections which I find intriguing and it would be great if other governments could adopt similar strategies and policies:

a) Develop and clearly describe procedures for making scientific collections more  accessible to educators and researchers, including non-Federal scientists, to maximize public benefit. 

b) Work with the Smithsonian Institution to ensure that information on the contents of and how to access the agency’s scientific collections is available on the Internet in a central Federal clearinghouse and to maintain participation in the Federal clearinghouse once it is established. 

c) Use machine-readable and open formats, data standards, and common-core and extensible metadata for all new information creation and collection to facilitate search and discoverability and provide clear public guidance for accessing collections materials, consistent with the Executive Order on Making Open and Machine Readable the new Default for Government Information. 
d) When available and where not limited by law, make freely and easily accessible to the public all digital files in the highest available fidelity and resolution, including, but not limited to, photographs, videos, and digital 3D models, and associated records and documentation, describing or characterizing objects in government-managed scientific collections. 

e) Associate digital files describing or characterizing scientific collections with the agency’s collections catalog and the central Federal clearinghouse referenced in Section 3(b) of this memorandum. By default, this information should be in machine-readable and open formats. 

I believe this is the first time that a government has issued such clear policies to improve accessibility of scientific collections that are managed by them. 

h/t Scott Miller

Locust in Pakistan

Locusts are the swarming phase of certain species of short-horned grasshoppers in the family Acrididae. These are species that can breed rapidly under suitable conditions and subsequently become gregarious and migratory when their populations become dense enough. Such swarms can be highly destructive and migrate in a more or less coordinated way and capable of causing massive damage to crops. 

Several organisations around the world aim to monitor locust populations. They generate forecasts detailing regions likely to suffer from locust plagues in the foreseeable future. They generally use morphological identification but those have a number of limitations such as the fact that morphological keys are often limited to particular life stages, limiting the effectiveness of any identification. Furthermore, a high level of proficiency is required to use such keys and not all persons involved in control efforts are taxonomic experts.

Progress on grashopper DNA Barcoding has been slow until recently. Initially it was rather difficult to find good working primers but studies such as this one show that this issue has been resolved. Some researchers were also very cautious due to the frequent encounter of pseudogenes in grasshoppers and crickets. Pseudogenes, also known as nuclear mitochondrial DNA (NUMTs), are non-functional copies of mitochondrial sequences  that have become incorporated into the nuclear genome. When these sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were the real sequences. However, as such copies of existing genes tend to mutate at a much higher rate than the original they often develop certain features that make them rather easy to spot. The most obvious alteration is the occurrence of a stop codon which should catch a researchers eye immediately when dealing with a protein coding gene such as COI. No doubt, NUMTs of COI occur frequently but I doubt that they pose any threat to any diligently conducted DNA Barcoding study.

A new study from Pakistan targeted some particular difficult to identify species occurring in Azad Kashmir:
To remove identification conflicts among 26 morphological species of the family Acrididae from Poonch, and to add species sequences to the international barcode reference library, studies were performed to identify the grasshoppers morphologically and by DNA barcoding.

It is a neat little study focusing rather on the local fauna but species were picked to help with a local problem and in order to improve control strategies. Agriculture is the major part of Azad Kashmir's economy. Low-lying areas with larger populations grow crops like barley, mangoes, millet, corn, and wheat, and also breed cattle. In the higher altitude areas that are less populated and more scattered, forestry, corn, and livestock are the main sources of income. It is easy to see the economic importance of grasshoppers and their potential impact on crops in region which triggered the need for correct identification of this group. The researchers were able to add 21 species to the DNA Barcode library and this will strengthen future control measures.

Wednesday, March 26, 2014

Nocturnal moths shine light on dark taxa

Aside from probing the efficacy of DNA Barcodes as a tool for species identification, the present study has examined the correspondence between sequence clusters recognized by the BIN system and known species. The results of this analysis indicate the strong capacity of the BIN system to estimate species diversity (1 515 BINs versus 1 541 species), supporting the conclusion of an earlier investigation. These results suggest that DNA barcoding is poised to resolve a long-standing question – how many animal species are there on the planet? Moreover, the BIN system has the capacity to do more than just to deliver a species count when it is coupled with a well-parameterized barcode reference library. In this situation, in most cases, each BIN can be automatically assigned to a higher-level taxon. Automated phylum-level assignments are now secure and class and ordinal placements are correct in more than 90% of cases for terrestrial animals (pers. obs.). Further parameterization of the barcode library will undoubtedly lead to robust familial assignments. Although Ekrem et al. correctly pointed out that DNA Barcodes can only deliver a species-level assignment when a fully parameterized reference library is in place, the BIN system will provide a species count for each major compartment of biodiversity long before all species gain description.

I decided to start today's post with the end of a publication. The first part of the above paragraph summarizes the results of a new study published yesterday on PLoS ONE. Part two discusses BINs and their potential. It took the liberty to highlight two parts in the text that I find very promising especially in the light of this new paper as it makes a strong case for them.

The study is based on a very strong dataset - Some 30 000 DNA Barcodes of Canadian owlet moths (noctuoids) representing 99.1% of all known species. That alone is impressive enough: 1 555 noctuoid species occur in Canada and 1 541 of them have a DNA Barcode. However, this publication goes much further and uses the dataset to test the concordance between BIN assignment and species boundaries in Canadian noctuoids in order to evaluate utility and constraints of the BIN system for species delineation.

The study provides two different numbers on this. The first reflects the actual concordance between taxonomic names and sequence clusters delineated. 1 082 species (70%) were assigned to a unique BIN, while the total number of BINs estimated for the dataset is 1 515. The latter is very close to the actual number of morphospecies used for the study but it should not be considered an estimate for congruence. There are a variety of reasons for discordance - 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16.

The exciting result is how close the BIN estimate is to the species numbers determined by conventional methods. I am sure that colleagues working on DNA Barcoding will start using similar approaches to test if this holds true for other groups, regions or settings but something tells me they will end up with similar results. Actually I would like to encourage everyone to do put this to the test also with respect to completeness of libraries and in case you don't find this publication worthy I'd be more than happy to offer a guest post in this blog (sorry, no impact factor, but much less work and word gets out to the community).

This study is really good news especially when you think of all the data records on BOLD and other data repositories that have no species designation (and lacking perhaps even more). A BIN assignment will make those data more useful for a lot of biodiversity and ecology related questions. Rod Page once called those records without species ID 'dark taxa'. Perhaps they are not so dark anymore.

Tuesday, March 25, 2014

A small village of indomitable Lemmings

Last year I had posted about the Norwegian lemming, (Lemmus lemmus) an iconic small mammal that is unique to the Fennoscandian mountain tundra. Known for its dramatic fluctuations in population size, it is a keystone species in the mountain tundra ecosystem. As lemmings function as the main trophic link between vegetation and predators in most tundra ecosystems, their high amplitude population density cycles often have a major impact on tundra food webs.

However the origin of the Norwegian lemming has until now remained somewhat of a mystery but a new ancient DNA study shows that it has quite a unique history

Twenty thousand years ago, Fennoscandia was covered by a thick ice sheet. Animals and plants in the region are therefore thought to originate from populations that lived to the south or east of the ice sheet, and colonized the region as the ice retreated. With this in mind, and international team of scientists, led by researchers at the Swedish Museum of Natural History, set out to investigate from where the Norwegian lemming originated at the end of the last Ice Age. To do this, the researchers analysed ancient DNA from lemming populations that surrounded the ice sheet during the last Ice Age. The study used DNA from 54 Late Pleistocene Lemming jaw bones 12 000 to 48 000 years old and collected from 11 paleontological sites across the genus' glacial range in mid-latitude Europe. The researchers used a combined data set of fragments of the mitochondrial control region and cytochrome b.

While populations surrounding the ice sheet were closely related to modern day lemmings, none of them were similar enough to be the direct ancestor of the Norwegian lemming. After eliminating these populations as potential sources, the colleagues concluded that the only remaining explanation was that the Norwegian lemming originates from a population that  may have survived the last Ice Age in the far north, sealed off from the rest of the world by gigantic ice sheets. The exact location where the Norwegian lemming could have survived  is not clear, but likely places include coastal areas or mountain plateaus sticking out from the ice sheet. 

A fascinating new story about this adorable and quite resilient creatures.

Monday, March 24, 2014

New Bulletin is out!

It's time again for the new iBOL Barcoding Bulletin. The March 2014 issue consists of 18 pages jam packed with information and news related to DNA Barcoding. By the way if you are interested in the publications that are associated with some of the articles we have added hyperlinks to the text that will direct you to the original source.

Just click on the image to open the pdf. 

The iBOL Barcoding Bulletin is an online newsletter, so there are no print issues. Those are too expensive and frankly at this day and age it would be strange to publish on paper. However, we are actually looking into the option of issuing a tablet version but it is not as easy as it might sound. Perhaps in one of the upcoming issues of the year.

Friday, March 21, 2014

GBOL Altitude record

Plutella geniatella
I just browsed through this weeks press releases and articles and found some interesting news from Germany. Since it is only available in German I thought I translate a brief part and share it with a wider audience.

Last summer Jörg Spelda, Stefan Friedrich und Roland Melzer, researchers of the Bavarian State Collection of Zoology in Munich went on a field trip to Germany's highest mountain, the Zugspitze (2,962m) with the goal to comprehensively catalog the peak fauna. They caught a moth very close to the peak, barcoded it and it is now considered the record holder in the category highest altitude DNA Barcode in Germany.

This little moth belongs to a rather rare species (Plutella geniatella) which  in Germany was observed the last time in 1989. It is only known from mountain tops in the Alps and the Carpathian Mountains. It is a relative of the diamondback moth that I blogged about a while back.

The German common name is not only a tongue-twister but to me represents a fascinating attempt to be creative, descriptive, and comprehensive at the same time: 

Felsenblümchen-Schleierfalter which means by my literal translation  Rockfloret-Veilmoth.

Wednesday, March 19, 2014

Taxonomist Appreciation Day

In case you didn't know - today is Taxonomist Appreciation day!

Some people have accused us DNA Barcoders that we are working hardly on accelerating the global extinction of taxonomists. On the contrary, we have the greatest admiration for their work and efforts and it is our hope that we have been able to build a tool to help them out with some really big tasks. 
After all a good reference barcode is only as good as its taxonomy!

The Taxonomist Appreciation day was an idea of Terry McGlynn of Small Pond Science. It is the first official one I believe and many people are spreading the word. Just check out Twitter with the hashtag #loveyourtaxonomist.

In his post to the occasion Terry showed a video which I find great. It has been created by some undergrads that went on an expedition sampling ants throughout remote areas of Mesoamerica. A nice animation that shows a lot of what fieldwork in biodiversity science is all about:

With that I like to send out greetings and my best wishes to all the taxonomists I had the pleasure of working with in the past 12 years. Among those are experts for fishes, marine invertebrates and terrestrial arthropods. Too many to list them all here but in case they read this post they'll know they are meant. 

A sincere Thank You to all of them!

DNA Barcoding in High Schools

Still not convinced that DNA Barcoding is perfect for school education?
Here are some recent examples demonstrating the opposite:

At the Connecticut Science & Engineering Fair last week at Quinnipiac University in Hamden, students from several Greenwich schools garnered dozens of awards after presenting their research. The event showcased the scientific and engineering work of about 700 students from approximately 130 schools. Here are three projects that were honored:

Kylinn Askew and Emma Novick, both 11th grade. Project: Truly Vegetarian? Using DNA barcoding to detect possible contamination of vegetarian products.

Sabrina Carrozzi, Alexa Granser and Grace McKenney, all 11th grade. Project: Nice to Meat You: Using DNA barcoding to detect mislabeling in the meat industry.

Emily Sabia and Claren Hesburgh, both 11th grade. Project: Using DNA barcoding to detect the potential contamination of herbal products.

Or take this news bit from Hawaii:
Students of a biotechnology class at Hawaii Preparatory Academy are tasked with extraction, amplification, sequencing and identification of DNA Barcodes of the barred sand bass (Paralabrax nebulifer).

Students at High Point Regional High School participated in the Barcoding Life’s Matrix program (so did the students from Hawaii) that is run by our friends at the Coastal Marine Biolabs in Ventura, California. Have a look at the video:

Recently I have been starting to work with grade 11 co-op students that are interested in coding. They are well versed in Java and are currently developing tools that support the analysis and manipulation of data retrieved from BOLD. We are focusing on BIN information first with the goal to create small publicly available routines that help to extract information important for alpha- and beta-diversity studies. I believe we are the first in using a bioinformatics approach to DNA Barcoding in school education. 

So far educators have been generating DNA Barcodes as workflows are simple enough that students can gain exposure to all aspects of the analytical chain from specimen collection to data interpretation. This goes one step further and involves them in data manipulation and analysis. There is an increasing need for coding capabilities and a couple of initiatives try to push this into schools as it is seldom taught as part of a curriculum. Here a video from the most prominent initiative

I will keep you posted on our progress as the students are very eager to show what they've accomplished and following open source policy everything will be available for everyone (including Java code). 

Monday, March 17, 2014

Taxonomic workflow

A first critical issue in DNA barcoding is accuracy which depends especially on the extent of, and separation between, intraspecific variation and interspecific divergence in the selected marker. How well does that gene sequence perform in delineating and identifying species? The more overlap there is between genetic variation within species and divergence separating sister species, the less effective DNA Barcoding becomes. Initial efforts to test barcoding suggested that we need a significant “barcode gap” between intra- and interspecific variation.

The second key point is that there are indeed two different applications for DNA Barcoding that shouldn't be confused. The primary motivation to do DNA Barcoding is the prospect of being able to identify an unknown organism based on a short sequence. This process of querying a DNA Barcode reference library with sequences of an unidentified specimen should bear the name species identification.

However, more and more is species identification confused with species discovery. Building a DNA Barcoding reference library often exposes new species. Despite the semantic difference it should be noted that both species identification and species discovery need different methodologies.

Over the last years a variety of algorithms and programs have been generated that are intended to help with both and more and more publications show up that compare different analytical methods. A new one has seen the light of day last week and I think it is a very good one:

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths.

The authors use DNA Barcodes as a taxonomic exploration tool, grouping specimens into OTUs intended to be the first step towards a framework for subsequent phylogenetic and taxonomic work. The novelty lies in examining the congruence of OTUs resulting from three delimitation methods (GMYC, ABGD, BIN) and the subsequent evaluation of cases of discordance in OTU boundaries employing monophyly, diagnostic characters and sympatry as criteria for clarifying their status. This scheme has the advantage of keeping the initial step of OTU designation separate from the detailed analysis required for full-blown taxonomic characterization. Because the varying steps in species delineation require different sampling strategies and types of data, the primary delineation of OTUs with single-locus data has the advantage of employing one extensive data set with clearly defined criteria to produce a stable outcome.

I couldn't summarize the advantage of their approach better than the authors themselves so I won't even try:

We emphasize that the delimitation of putative species based on DNA barcode data not only increases objectivity, but accelerates work on poorly studied groups and enables inexperienced taxonomists to make a valuable contribution. As many groups of arthropods lack expert taxonomists, the need to recruit new experts is obvious and barcode-based approaches provide an easy path for initial engagement. Even without detailed study, an accurate estimate of the species count is obtained through the simple algorithmic processing of barcode data. While decisions based on analysis of single-locus mtDNA data and on small sample sizes do pose interpretational risks, they are inconsequential if the outcome is viewed as a scaffold for taxonomy rather than as the sole criterion for species description.

Tuesday, March 11, 2014

Saffron barcoding

Saffron is the dried stigma from a small, purple crocus (Crocus sativus). It is the world’s most expensive spice. That’s because each flower provides only three stigmas, which are picked and dried by hand, and it takes tens of thousand of individual strands to produce one ounce of saffron.  The plant blooms only once a year and the harvest of stigmas, by manual picking, should be performed within very short time. Fortunately, a very little goes a long way. Just one or two threads can add flavour and colour to an entire pot of rice. Saffron imparts a pungent, aromatic flavour and an inten yellow colour to dishes. It is used around the world dating back to ancient Egypt, Greece and Rome where it was used as dye, perfume, spice and even as drug in the traditional treatment of numerous diseases.

Since the middle ages, the high economic value of saffron has caused its adulteration with natural or synthetic substances. As a consequence there are international standards (ISO/Technical Specification 3632 2003) in place to define saffron quality. These standards recommend the use of spectrophotometric and chromatographic analyses to ensure spice color, taste and aroma. However, they do not provide guidance on the issue of species identification.

Given all that it is about time to start using DNA Barcoding as a means to control the species identity of saffron spice products. Collaborative research between Universidad Politécnica de Madrid (UPM) and the University of de Tor Vergata has now confirmed that the DNA Barcode standards for plants work well with a variety of Crocus species. This proof of concept study also allowed some insight into the mystery of the origin of Crocus sativus, a sterile, triploid species. A number of morphological studies support the theory that it would have been originated through hybridization of other Crocus species, especially Crocus thomasii, Crocus hadriaticus and Crocus cartwrightianus. The study was only able to show that Crocus sativus could have evolved due to a series of independent factors relating to geography. The authors were able to find marked genetic differences between Spanish and the Italian saffron varieties but it seems too early for a final answer. However, the good news is that there is another case we can add to the countless other ones demonstrating the applicability of DNA Barcoding. Societal benefits? Just think of it the next time you eat a good Paella

Monday, March 10, 2014

A Barcode Based Marine Biotic Index

Marine ecosystem health is frequently monitored by using marine benthic macroinvertebrates as indicators. Complex biological information such as community composition is summarized in benthic indices and marine conservation initiatives often rely on such assessments of ecological integrity and health status. They allow managers to identify impacted sites and enable them to make decisions on habitat restoration measures.

A plethora of different benthic indices have been proposed over the years. One of the more successful indices is the AZTI's Marine Biotic Index (AMBI), which is officially used in many European countries and has been tested in America, Africa, Asia and Oceania. It is based on abundance-weighted pollution tolerances of species present in a sample. Tolerance is categorized into five groups (sensitive to pressure, indifferent, tolerant, second order opportunist, first order opportunist). The system currently contains about 6000 species with assigned tolerance but this index - as most others - requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample.

Reason enough for the researchers that developed AMBI to have a closer look into alternatives. They tested DNA barcoding and more specifically metabarcoding as these methods have the potential to increase speed, accuracy and resolution of species identification, while decreasing its cost in biodiversity monitoring. Quite often molecular methods are incorrectly perceived as costly although large scale morphology-based species identification requires a lot of expert time and thereby becomes more costly than any molecular alternative.

The goal of the study was to analyze the genetic resources available for the AMBI species, and determine the minimum reference library size and content required to calculate an accurate index. Additionally, we identify the best primers to retrieve the most complete representation of the AMBI taxonomic diversity and provide sequences for 22 species for which no genetic resources were available.

This publication represents a very nice proof of concept and I found the results very promising. What I like in particular is the approach to the problem of incompleteness. Instead of claiming that the DNA Barcode library is incomplete and leaving it at that (there are many studies doing just that) the colleagues try to find ways to deal with the current shortage by estimating the minimum of species necessary to calculate accurate indices:

Overall, our results place DNA barcoding as a viable alternative to visual species identification in the context of taxonomic assignment for gAMBI [gene-based AMBI] calculation; though, this viability is subject to increasing the number of sequences in the reference library. According to our results, this increase should be performed focusing on the most frequently occurring species, as their presence in the reference library, even in a small percentage, is enough for an accurate gAMBI calculation.

Here, we have focused on the use of (meta) barcoding techniques to ease the first step for the calculation of AMBI: taxonomic identification. However, it could be possible to think about a new version of gAMBI based on total biodiversity metabarcoding profile that would not require finding a particular set of species previously defined. Therefore, besides working on increasing the gAMBI reference library, we are also focusing on comparing samples analyzed by visual taxonomy and by metabarcoding in order to explore more practical genetics based alternatives to AMBI.

Friday, March 7, 2014

Forest biodiversity

Lesser spotted woodpecker (Dendrocopos minor)
Production of marketed commodities and protection of biodiversity in natural systems are unfortunately very often in disagreement. Humanity is continuously expanding and so does the need for more goods and natural resources. On the other hand the conditions of our global ecosystems urgently call for strategies to resolve the conflict between production and protection.

Forest management is generally based on recommendations that are supposed to maximize economic revenues. However, in 40% of cases a better economic result would be achieved by neglecting some of the recommendations as a new study showed. This would also greatly benefit biodiversity.

Researchers from Finland studied a production forest landscape encompassing 68 square kilometers of land and more than 30,000 forest stands in Central Finland. Thy were interested in the potential of a forest landscape to simultaneously provide habitats for species and produce economic returns. More and more forest-owners become interested in not only earn money in the lumber trade but simultaneously retaining recreational values and habitats for species. This is the result of a change in humans's perception. People start paying attention to a variety of goods and benefits they may get from forests. For example, forests capture and store carbon from the atmosphere and thereby counteract climate change caused by human carbon emissions. 

The study shows that it is important to reconcile alternative uses of forests as they are not necessarily in a very strong conflict. Simultaneous consideration and optimization among alternative objectives can be beneficial. In the study, researchers of biological and environmental science collaborated with information technology researchers which work in the field of multi-objective decision making. The team projected forest growth 50 years into the future with alternative management regimes. The management regimes were compared from the point of view of six forest species - capercaillie (Tetrao urogallus), hazel grouse (Tetrastes bonasia), flying squirrel (Pteromyini), long-tailed tit (Aegithalos caudatus) and two woodpecker species (Dendrocopos minor, Picoides tridactylus). In addition habitats for six groups of dead-wood dependent red-listed species were examined. 

The research aimed at finding economical ways to maintain species habitats in a forest landscape and to reveal an optimal combination of management regimes that would maximize the habitat availability at a given level of economic returns. Small additional investments into biodiversity may yield large benefits. For example, increasing habitat availability for the capercaillie is relatively inexpensive but would go a long way. Providing dead-wood associated species with more habitats tends to be more expensive because it involve requires the reduction of harvest. A more economical measure could be the stop of silviculture thinning practices which would improve habitats for numerous species in production forests. Thinning is a method that artificially reduces the number of trees growing in a stand with the aim of hastening the development of the remainder.

Thursday, March 6, 2014

City biodiversity

The rapid conversion of natural lands to cement-dominated urban centers is causing great losses in biodiversity. Yet, comparative studies of urban biodiversity leading to robust numbers on the extent and information on the drivers of biodiversity loss in cities at the global scale are lacking. Previous urban biodiversity research has looked the local impacts of urbanization and did not consider overall impacts on global biodiversity.

Contrary to conventional wisdom that cities are a wasteland for biodiversity, a recent study involving 147 cities worldwide found that while a few species - such as pigeons (Columba livia) and annual meadow grass (Poa annua) - are shared across cities, overall the mix of species in cities reflects the unique biotic heritage of their geographic location. Surprisingly high numbers of plant and animal species persist and even flourish in urban environments:

We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.

Don't get this wrong - overall, cities supported far fewer species (about 92 percent less for birds and 75 percent less for native plants) than expected for similar areas of undeveloped land. The process of urbanization has profound effects on biodiversity; cities worldwide contain substantially lower densities of species. However, cities are capable of retaining a unique regional flavor. That uniqueness is something that needs to be sustained. Conserving green spaces, restoring native plant species and adding biodiversity-friendly habitats within urban landscapes could, in turn, support more bird and plant species. If we act now and rethink the design of our urban landscapes, cities can play a major role in conserving the remaining native plant and animal species and help bring back more of them.

Wednesday, March 5, 2014

Moas and barcoding

Moas were the dominant herbivores in New Zealand's forest, shrubland and subalpine ecosystems for thousands of years, and until the arrival of the Māori were hunted only by the Haast's Eagle an extinct raptor which is still considered the largest true raptor that ever existed. It is generally considered that most, if not all, species of moa died out by A.D. 1400 due to overhunting by the Māori and habitat decline. As a consequence the Haast's Eagle disappeared as well as his predominant prey was not available anymore.

Today we know there were at least nine species of moa endemic to New Zealand, but because the flightless bird died out hundreds of years ago due habitat decline and overhunting, it is challenging to gain a complete understanding of the birds, some of which could stand as high as 3.6 m with their necks fully extended.

Moa species can be grouped into six genera. One of these, Euryapteryx, has been difficult to characterize into its constituent species for a long time due to the absence of substantial morphological, physiological, and behavioral data.

Some researchers from New Zealand have now used DNA Barcoding to show that two species were likely to have existed in the genus Euryapteryx, with the possibility of some subspecies. However they also encountered some problems that could be explained with repeated hybridisation events within the genus:

Individuals from other areas of New Zealand were unable to be clearly separated based on COI differences possibly as a result of repeated hybridisation events. Despite the accuracy of the COI barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus Euryapteryx, COI barcoding fails to provide a clear result, possibly as a consequence of repeated hybridisation events between these moa. A single control region SNP was identified however that segregates with the two general morphological variants determined for Euryapteryx; a smaller subspecies restricted to the North Island of New Zealand, and a larger subspecies, found on both New Zealand's North and South Island.

Tuesday, March 4, 2014

Coral fish biodiversity

Biodiversity reservoirs, coral reefs and associated ecosystems are in grave danger from natural and human-made disturbances and no one with any common sense would deny this fact but it becomes increasingly complex when we attempt to understand the process better and aim to predict how strong any impact is and how soon certain changes will show. It is almost impossible to keep track of all the alarming news and filter out those that are based on sound science and come with reasonable predictions. The latest World Resources Institute assessment for example is one of those alarming ones with 75% of coral reefs reported as endangered worldwide, a figure that may reach 100% by 2050. Such numbers are concerning, particularly as coral reefs provide sustenance and economic benefits for many developing countries and fish biodiversity on coral reefs partly determines the biomass available for human consumption. What is lacking is a more detailed insight into the relationship of human impact and loss of biodiversity.

In a new study researchers sampled 1553 fish communities through underwater surveys in 17 Pacific countries. They assessed the taxonomic, functional and phylogenetic diversity levels of a group of fish species fished along a human density gradient ranging from 1.3 to 1705 persons per sq. km of reef.. While taxonomic density is essentially known as species richness - the effective number of different species in a given region - the other two measurements are more representative of the entire community structure. Functional diversity refers to the variety of biological processes, functions or characteristics of a particular ecosystem (with multiple ways to calculate it) and phylogenetic diversity is a measure of biodiversity which incorporates phylogenetic relationships between species (has been used for a while already and even in barcoding studies). The aim of the study was to quantify the effect of human activities by using and comparing all three measurements, while decoupling the influence of biogeography and habitat along a gradient of human pressure.

Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional diversity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems.

The simple species count alone seems to be a rather poor indicator of anthropogenic pressure, while the two other biodiversity components are far more affected by human density. A strongly affected region might still be able to maintain a rather large and stable number of species but the for example the diversity of ecosystem function (and perhaps resulting ecosystem services) drops dramatically. This stresses how important it is to conserve all the components of biodiversity but also how crucial it is to look at more than one measure of diversity. Seems trivial but this study was the first that actually comparing these particular three measurements and how they are affected by disturbances.