DNA barcoding to prepare for the invasion

Puccinia psidii or better known as myrtle or guava rust is a fungus with a wide and expanding host range within the tree family Myrtaceae, with over 440 host species currently known, 250 of those were reported from Australia only. It is native to Brazil but since the late 1970s it has spread into continental US, most of the Hawaiian Islands, Japan, Australia, China, South Africa, and Indonesia. 

Unlike other plant pathogens, rust usually affects healthy plants. An infection may cause deformities such as growth retardation, witches brooms, stem canker, or formation of galls. Plants with severe rust infection may appear stunted and discoloured. Rusts are considered one of the most harmful pathogens to agriculture, horticulture and forestry, and they are very hard to treat.

New Zealand has been afforded the opportunity to prepare for a myrtle rust invasion. The Ministry for Primary Industries' (MPI) High Risk Site Surveillance programme is tasked with providing early detections of unwanted plant pests of tree species present in New Zealand, and the programme has been put on a myrtle rust alert. The identification of species of Myrtaceae by morphological means can be time consuming and often requires a combination of characters, which may not all be present at a particular time. The more rapidly species of Myrtaceae can be identified, the more rapidly surveying for myrtle rust and a response to an incursion can take place. Accurate surveillance of infected hosts will enable MPI to consider appropriate biosecurity measures in order to protect threatened plant species and vegetation communities and to reduce the risk of spread to new areas by workers and visitors.

In an attempt to prepare for a potential but also likely incursion to New Zealand a team of researchers has started to assemble a DNA barcode reference library for more than 100 species of Myrtaceae occurring in New Zealand. The team used the internal transcribed spacer (ITS), the external transcribed spacer (ETS) and the barcode standard marker matK. New Zealand has only 24 native species of Myrtaceae but a large number (386) of non-native cultivated Eucalyptus species that are very susceptible to this pathogen.

The Myrtaceae DNA barcode database will enable rapid identification of large numbers of myrtaceous specimens in the event of a myrtle rust incursion. This will help MPI to accurately survey the spread of the disease and thereby enable timely decision making and consideration of biosecurity measures in order to protect threatened plant species and reduce the risk of spread to new areas. 

Evolution of real glowfish

Bioluminescence, the production and emission of light from a living organism, is a fascinating phenomenon that is documented in over 700 genera of metazoans across the tree of life, with the vast majority living in the ocean. Among vertebrates, bioluminescence has evolved in cartilaginous (Chondrichthyes) and ray-finned fishes (Actinopterygii), and it is not observed in any lobe-finned fishes or tetrapods.

Bioluminescence is  a form of chemiluminescence produced in living organisms. The substrate luciferin reacts with oxygen and the enzyme luciferase and the reaction releases a photon:

A new study aimed to determine the number of independent evolutionary origins of bioluminescence in ray-finned fishes. The authors discovered that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Actually,  the colleagues showed that it has evolved independently 27 times in 14 major fish clades on of which includes the most abundant vertrebrate on Earth, the bristlemouth, numbering in the hundreds of trillions to quadrillions. 

There is a variety of ways bony fish can deploy bioluminescence, such as leveraging bioluminescent bacteria, channeling light though fiber-optic-like systems, or using specialized light-producing organs.  This shows how important bioluminescence is to vertebrate fish that life in the world's deep seas.

You have this whole habitat where everything that's not living at the top or bottom of the ocean or along the edges - nearly every vertebrate living in the open water - around 80 percent of those fish species are bioluminescent. So this tells us bioluminescence is almost a requirement for fishes to be successful.

The study also shows that once an evolutionary line of fish developed the ability to produce light, it tended soon thereafter to branch into many new species. The process is not fully understood and will require further study but there are some ideas:

Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.

Pristine landscapes are perhaps long gone

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets.

A new study is taking a new look at how the world's landscapes have been shaped by repeated human activity over many thousands of years. An exhaustive review of archaeological data from the last 30 years  reveals a pattern of significant, long-term, human influence on the distribution of species across all of the earth's major occupied continents and islands. It draws on new datasets using ancient DNA, stable isotopes, and microfossils, as well as the application of new statistical and computational methods.

The authors argue that it is wrong to assume that societies before the Industrial Revolution had little effect on the environment or diversity of species. They show that many living species of plants, trees and animals that thrive today are those that were favoured by our ancestors. Furthermore, large-scale extinctions started thousands of years ago due to over-hunting or change of land use by humans

One of the take home messages of the study is that pristine landscapes likely do not exist anywhere in the world today and, in most cases, have not existed for at least several thousand years. Consequently, the colleagues conclude that in light of their findings and other evidence of long-term anthropogenic change, we need to be more pragmatic in our conservation efforts rather than aiming for perhaps impossible natural states. I am sure that view will spark further discussions about what constitutes a natural state and and how far back in time we want to go to determine our efforts for restoration, conservation, invasive species eradication and so on. The main message of the paper is nicely summarized by the lead author:

Cumulative archaeological data clearly demonstrates that humans are more than capable of reshaping and dramatically transforming ecosystems. Now the question is what kind of ecosystems we will create for the future. Will they support the wellbeing of our own and other species or will they provide a context for further large-scale extinctions and irreversible climate change?

GBIF/GGBN survey

I received this from GBIF and I like to encourage all readers to do the survey. It actually takes less than 20 min of your time:

The Global Biodiversity Information Facility (GBIF) and the Global Genome Biodiversity Network (GGBN) are seeking expert opinions on how to link morphological and molecular biodiversity data, i.e. physical specimens, derived DNA, sequences, observations and other evidence of species' presence and abundance in space and time. This survey targets data users and providers of specimen and sequence information.

We know your time is extremely valuable, this survey should take about 25 minutes. We are particularly eager to receive early responses from those who are able to complete the survey by 15 June 2016, as we plan to report on preliminary results during workshop 9 of the SPNHC/GGBN conference, Documentation of environmental samples and eDNA on 20 June 2016.

To take the survey, please follow this link.

We encourage you to share the survey with your contacts and networks, especially with users and holders of molecular biodiversity data. The survey will run until 15 September 2016, and the final results will be reported at TDWG 2016 Conference in Costa Rica. If you have any questions about this survey, please contact Dmitry Schigel, Thanks in advance for your help.

Gabriele Dröge (GGBN), Siro Masinde, and Dmitry Schigel (GBIF).

Oh no! Researchers think DNA barcoding is dead.

A new week and a new paper I need to comment on. This one comes from one of DNA barcoding's old critics, Malte Ebach, and he and his co-authors take on Big Data and of course DNA barcoding although the latter it is not necessarily Big Data science yet. Actually the barcoding critique is pretty much out of context and as per usual incorrect: 

DNA barcoding has had minor impact in taxonomy, with some benefit for phylogeneticists, ecologists and conservationists; it has largely been superseded by technological advances, namely Next Generation Sequencing (NGS), in which whole genomes can now be routinely sequenced.

Were do I start? Well, DNA barcoding ain't dead and it had a big impact on taxonomy and still has. Actually, I think it is fair to say, that it became a regular tool in many taxonomist's toolbox. After reading the above statement I did a meta-analysis of the DNA barcoding literature searching for species descriptions that involved barcoding as diagnostic tool. I knew I would find some but I was surprised that I was looking at some 500 papers over the last decade. That is anything but a minor impact. 

Ebach also completely ignores other societal benefits of DNA barcoding, e.g. food authentication in his futile attempt to downplay a method he never liked. However, the best is his claim that new technology has superseded barcoding. Nope, that's not true. Actually both barcoding and high-throughput sequencing (HTS) complement each over very well and metabarcoding was probably DNA barcoding's most successful spin-off. Many colleagues around the world are already using HTS (that acronym will soon supersede NGS) in conjunction with organismal barcode reference libraries. 

All this doesn't sound like DNA barcoding's swan song to me.

However, this wasn't even the main story of the paper which is rather a diatribe on the use of Big Data in biology. I will not attempt to criticize the paper from a informatics standpoint. This should be done by an expert but it speaks volumes that Ebach's examples for what he refers to as "Big Data hubris" are 6 and 14 years old which in computer science are ages. Even worse, one is an opinion piece taken from Wired, and another one from the New York Times which today would trigger a lot of questions with respect to an almost homophobic connotation.

There is nothing wrong with cautioning users of the vast amounts of internet information sources, and Ebach actually nicely illustrates the issues of taking information provided by search engines such as Google Scholar at face value. Our new age of communication with ubiquitous information requires new critical thinking skills especially when it comes to the interpretation of such results but to me that is not an issue of the use of Big Data in science as proper research always questions results and correlations. It is actually our job as scientists to question them as much as possible and only if it endures such scrutiny a new scientific finding should be considered likely. And it is our job as educators to teach the new generation of students how to critically evaluate information and analytical results. So, if the intention was to write a piece that should caution us I am afraid that this publication failed to do so and the choice to include DNA barcoding can be at best considered mission-drift or at worst missionary.

New issue of the Barcode Bulletin

Here it is the newest issue of our Barcode Bulletin with the official announcement of the next International Barcode of Life Conference. If you can't wait - their website has a cool counter.

Enjoy reading!

Metabarcoding for honey authenticity

Let's start today's post with a question: Do you know what melissopalynology is? Perhaps not everyone can answer this question with a clear yes, of course. In short melissopalynology is the study of pollen contained in honey in particular to determine the source of the pollen. Not only is this used to determine the food sources and habitat range of bee colonies but also to combat fraud and mislabeling of honey. There are large value differences between honey derived from particular plants. Some monofloral honey can be much more valuable than honey derived from a mixture of plant species. Also, in the light of current threats to bee health it is crucial to determine if there is sufficient foraging habitat available as it is known that pollen diversity and quantity affect disease tolerance and longevity in bees.

Traditionally honey bee collected pollen is identified through morphological features revealed with light microscopy. However, this requires considerable skill and experience and in some plant families (Campanulaceae, Lamiaceae, Poaceae, Rosaceae) this is hampered by either a lack of characteristic features or high levels of morphological variation. It comes to no surprise that colleagues are looking into DNA-based alternatives such as metabarcoding. DNA barcoding of pollen collected by bees has been successfully done before but that pollen was directly sampled from the animals. 

Researchers from the UK compared DNA metabarcoding utilizing rbcL and 454 pyrosequencing with microscopic analysis for nine honey samples provided by domestic beekeepers in Wales and England (UK). Wales was the first nation in the world to have barcoded all of its native flowering plants and conifers, enabling the identification of any plant species in Wales from the tiniest fragment of leaf, seed or pollen grain. In total 98% of the Welsh native flora (1143 species) has DNA barcodes for rbcL and 90% for rbcL and matK. Such a reference library provides perfect conditions for a metabarcoding approach. I am happy to report that Wales is not alone anymore as DNA barcoding  of Canada's flowering plants is nearly completed as well.

The study results: There was 92% correspondence for the plant taxa that had an abundance of over 20%. However, the level of similarity when all taxa were compared was lower, ranging from 22–45%, and there was little correspondence between the relative abundance of taxa found using the two techniques. DNA metabarcoding provided much greater repeatability, with a 64% taxa match compared to 28% with melissopalynology. DNA metabarcoding has the advantage over melissopalynology in that it does not require a high level of taxonomic expertise, a greater sample size can be screened and it provides greater resolution for some plant families. However, it does not provide a quantitative approach and pollen present in low levels are less likely to be detected.

It is true that at this point metabarcoding is not suitable if one wants to determine pollen quantity and it a known fact that it fails to detect the rare species of a sample. There is some debate around those issues with some people claiming that especially PCR-based metabarcoding assessments can only provide presence-absence metrics while others think that this depends on the HTS platform used.

Anyway, I couldn't agree more with their final conclusion - DNA metabarcoding can be easily and widely used to investigate floral visitation in honey bees and can be adapted for use with other insects. It provides a starting point for investigating how we can better provide for the insects that we rely upon for pollination. I might add that the study clearly shows that we are capable to determine food sources of honey bees through analyzing pollen and other plant remnants in honey for food authentication and safety especially in countries where a large portion of the floral biodiversity has been barcoded.