Bye, bye K2P

Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary process underlying the genetic data.

In a new study researchers from Honolulu assess substitution model adequacy for describing genetic variation and for estimating species richness from barcoding data. One of their main motivation for this is the almost ubiquitous use of the Kimura 2-parameter (K2P) model. Earlier studies have already shown that this is perhaps a poor choice because it doesn't always fit well at the species level and provided unreliable estimates of the number of OTUs.

What the colleagues did was first to assemble many (more than 2000) empirical data sets. For each of those they selected a ‘best fit’ model of molecular evolution and performed DNA barcoding analyses under both the chosen model and the K2P model to estimate the number of OTUs. For the latter they used either ABGD or hCluster. Finally, they conducted a Bayesian phylogenetic inference and posterior predictive simulation to assess the fit of each substitution model to each data set. 

Not surprisingly the more complex model seem to fit better. The most frequently selected model for the barcode data sets was GTR + Γ, followed by HKY + Γ. The model adequacy assessments showed that the K2P model was found to be within the 95% highest posterior density of only 3% of all datasets. 

But the more interesting find is that depending on the method and threshold employed, the total number of OTUs varied considerably (4%–31%) meaning that model choice has a substantial impact on the number of operational taxonomic units identified.

Take home message:

We demonstrate that the widely followed practice of a priori assuming the Kimura 2-parameter model for DNA barcoding is statistically unjustified and should be avoided. Using both data-based and inference-based test statistics, we detect variation in model performance across taxonomic groups, clustering algorithms, genetic divergence thresholds and substitution models. Taken together, these results illustrate the importance of considering both model selection and model adequacy in studies quantifying biodiversity.

Biodiversity protects fish

Biodiversity is more than a pretty face. Preserving biodiversity is not just an aesthetic or spiritual issue - it's critical to the healthy functioning of ecosystems and the important services they provide to humans, like seafood.

The accelerating loss and shifts of species across the globe have troubled scientists and the public for a while already. But, believe it or not, the question of whether biodiversity offers practical value - for humans and ecosystems - remained controversial. A new study, just published in the PNAS, offers the most comprehensive proof yet that preserving e.g. marine biodiversity can benefit people as much as it benefits the oceans.

Reef Life Survey is a comprehensive program that has conducted more than 4,000 underwater surveys of more than 3,000 fish species in 44 countries around the world. Many of the surveyors were volunteer citizen scientists, about a third of whom with no scientific background. Volunteer divers actually received training from some of the program's lead scientists at the University of Tasmania in order to enable them to collect data using standardized methods.

With this comprehensive global dataset on marine biodiversity involving standardized counts, the researchers tracked how 11 different environmental factors influenced total fish biomass on coral and rocky reefs around the world. Surprisingly, one of the strongest influences was biodiversity: Species richness and functional diversity enhanced fish biomass. The boost in fish resources provided by biodiversity was second only to that of warm temperatures.

Temperature showed a more complex relationship with fish biomass: Warmer ocean temperatures tended to boost fish biomass on average, while wider temperature fluctuations hindered it. But biodiversity made fish communities more resilient against changing climate. In communities with only a few species, fish biomass tended to increase with rising temperatures until seas warmed above 20°C, at which point biomass decreased. Communities with many species remained stable at these higher temperatures.

The researchers found a similar buffering effect of diversity against temperature swings. While both high- and low-diversity communities were less productive under fluctuating temperatures, high-diversity communities suffered only half as much as low-diversity ones. The researchers suspect communities with more species are better equipped to handle temperature changes because they have more of their bases covered. When temperatures fluctuate, a community with numerous species has better odds that at least a few species can thrive in the new normal.

This work is a critical step forward in linking insights from experiments in buckets and garden plots to the larger world. It shows that experimental ecologists have in fact been on the right track for 20 years, and that biodiversity is paramount to how natural systems work. The results demonstrate that preserving local biodiversity is not only an ethical directive with aesthetical and genetic insurance value, but that it is an imperative for human life,

Newsflash: 7th International Barcode of Life Conference

Just a brief newsflash on the next big DNA barcoding conference in 2017. More detailed info will come in the next Barcode Bulletin early June and through future posts.

The African Centre for DNA Barcoding, and the University of Johannesburg will be hosting the 7th International Barcode of Life Conference from 20 - 24 November 2017. This is the first time that this event will be held on the African continent and the venue chosen is the Nombolo Mdhluli Conference Centre, Skukuza, located within the heart of African wildlife, the Kruger National Park, South Africa. 

The conference website is not active just yet but I will make an announcement as soon as it is. For now some important dates:

Deadline for submission of abstracts: 01 July 2017

Notification of acceptance of abstracts: 20 September 2017

Deadline for early-bird registration: 30 September 2017

Deadline for online registration: 15 November 2017

How we are going to barcode that thing?

In low-oxygen environments, eukaryotes often possess a reduced form of the mitochondrion, but it was believed that some of the mitochondrial functions are so essential that these organelles are indispensable for their life.

Flagellated protozoa of genus Monocercomonoides are known for more than 80 years. They are distant relatives of the human pathogens Giardia and Trichomonas, comprised in the phylum Metamonada, whose members live exclusively in low-oxygen environments. Another interesting fact about them is that they apparently lack mitochondria. Originally they were considered among the most primitive eukaryotes, members of a lineage that diverged from the others before mitochondria appeared. However, they are now known to have lost mitochondria secondarily, and it was thought they retained functions and nuclear genes derived from them in some relic structures. 

In a new study, researchers from the Czech Republic and Canada sequenced the Monocercomonoides genome. They were surprised to find that this organism lacks all mitochondrial proteins. It seems to have gotten by without mitochondria thanks to a cytosolic sulfur mobilization system that they acquired from bacteria and that appears to be the substitute for essential mitochondrial functions. Through a unique combination of events including the loss of many mitochondrial functions and the acquisition of this essential machinery from prokaryotes this organism has found its own way of survival.

This amazing organism is a striking example of a cell which refuses to adhere to the standard cell biology text book, and we believe there may be many more similar examples in the so far hidden diversity in the world of microbial eukaryotes--the protists. It is very likely that the mitochondrion is absent in the whole group called oxymonads. We would like to know how long ago the mitochondria were lost.

From the inbox: eDNA workshop

Interdisciplinary workshop at the 2016 meeting of the Ecological Society of America

Sunday, August 7th,  2016 in Fort Lauderdale, Florida. 

Powerful genetic & genomic tools enabled the realization that all organisms shed molecular traces of their presence into their environment. In  ecology, use of extraorganismal “environmental DNA” (eDNA) gained prominence for detecting rare species. However, diverse disciplines also use and study extraorganismal DNA, including microbiology, fecal pollution tracking, forensics, hydrology, geology, and environmental biosafety. Despite methodological overlap between disciplines, interdisciplinary discourse has been limited. Thus, practitioners risk overlooking useful data and models, or worse, wasting resources on duplicative research.

In a recent open-access paper Cameron Turner and Matthew A. Barnes introduced the phrase "ecology of eDNA" to encapsulate the origin, state, transport, and fate of extraorganismal DNA-bearing matter. Understanding these properties and processes is critical for the rapidly- growing use of eDNA to infer organism presence/absence in our primary disciplines of ecology & conservation. Building on the relevant  research from other disciplines using extraorganismal DNA will undoubtedly benefit these disciplines, but we believe value can also go both ways. 

Bad barcoding

A tree that shouldn't be

In order to find new material for this blog and to stay on top of all things DNA barcoding I look at new publications on at least a weekly basis. Sometimes I come across some papers that cause reactions such as "Are you kiddin' me?" or other much stronger expressions that shouldn't be published in a blog like this one. Today was such a day.

Let me start with saying that is was disappointed to find such an article in a respected journal such as Mitochondrial DNA. I have published there myself and I can't understand how this article could make it through editorial and peer review.

So, let me introduce this one to you: 

Non-homologous COI barcode regions: a serious concern in decapod molecular taxonomy

This paper discusses apparent confusion of two different COI fragments as if this is actually a real problem. Let me give you an example: For decapod crustaceans, there are two major COI barcode regions (namely Folmer and Palumbi), which are non-homologous with limited overlaps. NO, there are not two major barcode regions used for decapods, there is just one - the Folmer one. The other is indeed a different region of the COI gene. That's not a big find. In fact this is known to everyone who does either DNA barcoding or molecular evolutionary studies. Such textbook knowledge does not warrant a full blown scientific study but here it is. The authors did not stop there and that's what makes the rest of the paper so bad even if the intentions were perhaps well meant. 

Knowing that there are two different regions of the COI gene the authors went ahead 'validating' this by sequencing both from a decapod species and attempting some sort of phylogenetic analysis. But, unexpected results were drawn out as the COI gene tree exhibited reciprocal monophyly in its array, differentiating ‘‘Folmer’’ and ‘‘Palumbi’’ regions as two different entities. Really? A surprise? The only surprise to me is that they managed to align both of them. Well, that is not a surprise but rather a mystery as you can't properly align these two different parts. The overlap is minimal (<30bp). And, no matter what you throw at such a fundamentally flawed dataset (Maximum Likelihood, Neighbor joining, Minimum evolution) you will indeed get two very 'divergent' lineages in your resulting tree. The authors even went on to test the utility of both markers by generating trees from alignments that contained each set of sequences. You simply can not do that. 

How can such a study be published? First, the authors have not bothered to read the literature that clearly differentiates markers and with respect to the DNA barcode for animals clearly defines the region to be used. I have stated this repeatedly - you cannot call everything a DNA barcode. That is the opposite of standardization. Even worse, this study is a textbook example for comparing apples and oranges in the DNA analysis world. I still don't understand how they could take two different regions and attempted to align and analyse them. To show that it doesn't work? Well, then they shouldn't show a tree at all as any proper analysis fails much earlier in the process. However, the worst part of this story is the fact that it got published meaning it slipped through the entire peer review process. A reviewer should at least have pointed out the heavily flawed methods even if some of the conclusions are perhaps correct.

To be fair, in one case I have to agree with the authors of this study - there are some instances where sequences were uploaded to public databases such as GenBank and these are clearly not standard DNA barcodes but something else. They are not labelled properly and could cause confusion in case somebody does a name-based search and retrieves a mixture of different COI regions. However, that is not a problem of the method DNA barcoding but rather one of people that do not understand how it works.

The most popular reptiles

There is a debate in conservation as to whether the fact that we as humans like a particular species justifies conserving it, regardless of its importance from an ecological point of view. But although this idea of some species being "culturally valuable" has been around for some time, it has been difficult to measure and define. Whether or not we want to take these cultural variables into account when shaping conservation policy, we need data to support those decisions.

This is the rationale behind a new study by scientists from Oxford University and Tel Aviv University. The researchers looked at 55.5 million page views in the year 2014 for all of the 10,002 species of reptile accessed in Wikipedia. The ranked the world's most 'popular' reptiles, revealing the species that capture the public's imagination and providing valuable quantitative data towards the debate surrounding conservation priorities.

The network of online and cross-referenced information repositories known as Linked Data has allowed us to gather information about most known reptile species. We see potential in using data-driven approaches to study the cultural impact of global species through their online footprint. Wikipedia page-view counts are just one of many metrics that can be explored.

They found that venomous or endangered species, as well as those with higher body mass or posing a threat to humans, tended to be more interesting overall. There was also a bias towards species found in Wikipedia users' own regions -- for example, the Japanese pit viper was top of the Japanese-language rankings, while the green iguana was the most-accessed species among Spanish speakers. Taking all languages into account, the Komodo dragon was the most popular species overall, with 2,014,932 page views in 2014 (3.6% of total page views), followed by the common European adder and the saltwater crocodile.

Top 10 reptiles accessed on the English-language version of Wikipedia in 2014:

1. Komodo dragon

2. Black mamba

3. Saltwater crocodile

4. King cobra

5. Gila monster

6. Cottonmouth (viper)

7. American alligator

8. Leatherback sea turtle

9. Nile crocodile

10. Boa constrictor

Perhaps surprisingly, the study found that 'culturally interesting' reptile species in Wikipedia were widely distributed across the reptilian tree of life. If we only saved the top 5% of the most popular species in Wikipedia, we would cover 67% of the 88 reptile families.

Although the study was aimed solely at gathering data, the researchers speculate at the reasons behind the huge variations in public interest between species:

With notable exceptions such as the sea turtle or Galapagos giant tortoise, species that are venomous or otherwise dangerous to humans seem to capture people's imaginations more than others. The Komodo dragon is found in a geographical area probably the size of a small English county, yet it consistently attracts the most attention -- possibly because the idea of the dragon is so universal in myth and folklore.