Posts Tagged ‘science’

13 years after its description we spotted the dwarf puffer in wild for the first time.

YES!!! it was initially described using aquarium specimens.

imitator

Image of a female Carinotatraodon imitator. Photograph by Dr. Ralf Britz

 Some years back, while reading through the fish taxonomy literature, still as an early stage researcher, a brilliant (colourful and surprising) paper came into my attention (see citations for the link). It was about a new species of “dwarf” freshwater-puffer fish Carinotetraodon imitator. The species was being described, however from just “aquarium” specimen!! That was an important revelation to me. The paper also contained very minute details, great electron microscopy images, and osteological evidence to prove the case and distinguish it from its ‘look-alike’ the Carinotetraodon travancoricus.

 The first thought that crossed my mind was that – if I find the distribution location of this fish, it could make an interesting paper and a good addition to the literature. Years later…..

 Now during our collection trip in January, we spotted this fish in the wild. That too along with the scientist who originally described the fish in 1999. This record is now official and available for researchers, along with brilliant photographs taken by Ralf.

 This paper is important in many fronts:

  1. The conservation implications, were already evident when the species, very rare and often hard to spot among its look-alikes, was described.
  2. The location from where we located the fish is severely devastated due to sand-mining.
  3. The crucial role of aquarium fish traders: The fish description paper had acknowledged aquarium Glazer, for providing the fishes. This present paper thanks, Nikhil Sood from India Gills Bangalore for helping us to reach the spot and kindly taking us around. Aquarium traders really love the fishes and are keen to help researchers!!! So my colleagues if you find some aquarium people around you please look at them with respect from now on, at least some of them are not ‘against’ conservation in-situ (I have personally heard this many times) but FOR conservation!!

As a side note: This fish has been exported at least since 1999, thus many aquarium traders knew about it, and its origin from somewhere in Karnataka state in India, but none of them wanted to reveal the site for real in public, thus there are many ‘black sheeps’ around Glazers and IndiaGills!

Some researchers as well found this species in wild, albeit without any voucher specimen or photographs. Thus this publication in Ichthyological explorations of freshwaters, is the first one recording it in wild, and giving the information of the habitat in public. In a few years even if we lose the “hear-say” of traders’ knowledge, we have something in writing about the species. 

Readers of this Blog are invited to read the full paper and the original description paper (I can send an “authors'” copy of the former to interested parties). Fish taxonomy guys will benefit a lot by seeing how to go about doing a “description”.

Competing Interest: as evident I am an author of the paper which this post speaks about.

 References:

 Britz, R., Ali, A., Siby, P., Kumar, K. & R. Raghavan (2012). First record from the wild of Carinotetraodon imitator in Peninsular India (Teleostei: Tetraodontiformes: Tetraodontidae). Ichthyological Exploration of Freshwaters, 23: 105-109.

Britz, R. & Kottelat, M. (1999). Carinotetraodon imitator, a new freshwater pufferfish from India (Teleostei: Tetraodontiformes). Journal of South Asian Natural History, 4: 39-47.

Darwin in the first chapter of his treatise “On the Origin of Species By Means of Natural Selection” talks about variation in domestic animals. He starts the chapter by saying:

When we look to the individuals of the same variety or sub-variety of our [….] animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species [….] in a state of nature.”

Read it once more, YES!!! he said that there is more variation (breeds or varieties) among domesticated “species” like dog, cat, coconut palms etc., when compared to wild animals (or plants) like Lion (which has no breeds or varieties). He says (recognizes) that it is due to selective breeding. But how did this variety occur? He provide clues a few sentences later in the same chapter.

But I am strongly inclined to suspect that the most frequent cause of variability may be attributed to the male and female reproductive elements having been affected prior to the act of conception.”

Remember that no one knew about genes, and alleles as the basis of heridity at Darwin’s time. So his was a new observation, that guided us later. So is there any one out there fascinated about the variety among domestic animals those reproductive elements? You have a really great paper to read which shows the mechanism of evolution, the process of fixation of a variation and passing over of that variation by Schoenebeck and others. These kind of studies, does, not only study how a breed evolved but also shows us the greater picture of how evolution occurs. In a meticulously worked out paper, which should be a hard read for non-experts, they study dog breed skull shape variations.

The paper starts saying that “dog breed skull shape diversity is a largely human created phenomenon (paraphrased)”, through artificial selective breeding.

What does the paper say about this skull shape variation? It says many things but importantly provide fascinating details about how a single mutation could lead to a prominent change in skull shapes. There are more details and it is not just about a mutation, although.

They looked at two extremes of skull shapes one with flat snouts and the second with long snouts. In essence they analyze, dog skull shapes, by grouping the Bulldogs, Boxers, Pitbulls, Pugs etc., in one extreme and the Collies, Greyhounds, Saluki etc., in the other extreme. Other breeds fell in between these extremes, for the skull shapes, of long snout (dolichocephaly) to flat snout (brachycephaly).

In a very rigorous analysis they found that the change in an amino acid (building blocks of proteins) on the 452nd position of the bone morphogenetic protein 3 (BMP3) gene of brachycephalic dogs have been the reason of their short snouts. It is easily said in a sentence, but the authors have put in a lot of details, they even show the a similar mutation when induced in the zebrafish, can make its cranio-facial morphology to go weird—similar to your pitbulls!!

Brachycephalic dogs have an amino acid named Leucine (L) at the 452nd position of the BMP3 gene, which is normally an amino acid called phynylalanine (F) in normal snouted dogs and other animals. So was it a “abracadabra” F452L that produced brachycephalic dogs? Yes and no, this mutation somehow formed in few dogs, which (dog) was seen by multiple independent breeders to develop such diverse brachycephalic breeds. Now these researchers see and present us the mutation as a story about what happened while selectively breeding such variants.

If you are not a science student, you should be exhausted by now, ok that is it remember F452L!!!! And remember next time when you play with your bulldog ask it about that Leucine!!!

For interested people read further or grab the freely download-able paper at the PloS Genetics Website.

They started analysing skull shapes of dogs, available in museums and private collections. The “shifts” in shape was examined by measuring more than 500 skulls from more than 100 different breeds of dogs. The 3D measurements were statistically analysed to explain the variation among the measurements between each breeds, and they found a sub-set of “promising” measurements that could explain the changes in skull shapes.

In the next step they used this “phenotype” data to do an association study, for the genotype data they generated. The paper explicitly says that the task was straightforward since pure-bred dogs would have a very strong visual phenotype, that would not vary, thus could be used to correlate the genotype data when generated from similar pure-bred animals. So they carried out genome-wide scans to detect any genotype association to a breed phenotype, using SNP datasets.

They found 5 promising Quantitative Trait Locii (QTL’s), for which there was strong association with the “flat snout-long snout” phenotype range. One of these QTL’s contained regions of genes BMP3 and PRKG2. They could zero down on the BMP3 gene or the bone morphogenetic protein 3 gene position 452. This position possess an amino acid called Leucine, in flat-snouted dogs, instead of another amino acid called phenylalanine which is found in normal snouted breeds.

NB: I would not mind, as a reader, if they had made the abstract and the introduction a bit longer 🙂

Jeffrey J. Schoenebeck, Sarah A. Hutchinson, Alexandra Byers1, Holly C. Beale, Blake Carrington, Daniel L. Faden, Maud Rimbault, Brennan Decker, Jeffrey M. Kidd, Raman Sood, Adam R. Boyko, John W. Fondon III, Robert K. Wayne, Carlos D. Bustamante, Brian C (2012). Variation of BMP3 Contributes to Dog Breed Skull Diversity PLoS Genetics, 8 (8)

ResearchBlogging.org

This recent paper (An update on DNA barcoding: low species coverage and numerous unidentified sequences; published in Cladistics) on an update of the Global DNA barcoding effort should be a real eye-opener to all people who love the NCBI Genbank and the process and openness of science, and especially to taxonomists.

DNA sequence based identification of organisms started during the 1980’s and is still an ongoing process. It is based on an idea that:

  1. If a hitherto identified specimen or organism gets its DNA portion sequenced and is made publicly accessible
  2. Other researchers could sequence their samples and check against the database to identify their sample, provided this second researcher lacks taxonomic expertise.

However this necessitates that the first researcher to know how to identify the specimen unambiguously.

Idea is old, but the name is new!

Recently during the early half of the last decade an international effort to “barcode” all organisms on earth has started based on the above said idea, which in turn is based on years of fine tuning by biologists and computer scientists (who developed BLAST and similar applications).

These researchers propose that sequencing a 650 base pair long region of the mitochondrial DNA could hold good to identify all the animals due to the peculiarities of the sequence. They claim to be the first ones to develop the idea, ignoring the efforts by earlier researchers, and their followers say that they have a “father of DNA barcoding”. I agree that they were the first ones to propose the NAME, but I wonder how it could be their NOVEL idea when the original BLAST algorithm (proposed in 1990) and the idea of sequence similarity was there already before this “barcoding” business.

Let’s come to the point

So the paper published in cladistics, looks at the claims of these “barcoders” and find some problems. They check whether:

  1. This project lived up to its initial speech act? (species coverage problem)
  2. Is it progressing scientifically? (“taxonomy” wise is it 100% percent right?)

Well, the answers are in the negative.

They find ~60,000 “metazoa” species’ barcodes in the NCBI database, which is well below the number of 10-20 million total species on earth (some claims are less but see the link). This is despite having substantial funding from the governments for the barcoding initiative. This paper says that they (Barcoding consortium) received $80 million from the Canadian government, we know about many other sources where every small barcoder gets tens of millions.

They (in this paper) looked for the keyword “barcoding” in the genbank records (of COI sequences) and remove all the COI records with that keyword, and find that only 16,000 (species) records get reduced from the list of 60,000 (species numbers not total COI records). This means that the rest are sequenced by general systematics projects and most probably not funded by any barcoding initiative.

Fishes and Birds had to be completely barcoded by 2012, according to their initial proposal, however when we look in the fish-bol website they say that barcoding for ~8500 have been completed, out of the ~31000 species in total. In the case of Fishes only ~4200 species are present in NCBI, so they have closed access to almost 4000 species.

The second distressing finding is that there are many “unidentified species” in the NCBI records. Out of 5,71,997 COI records in NCBI only 26% had proper names, or were identified up to the species level. That means a very high number of 74% were not identified to species level, so 3/4th of the barcodes produced are useless and squanders public money right*?

The paper highlights a case where a record of Diptera sp., has 1000 sequences with a genetic distance of 1% or less in the NCBI, which was produced by barcoding projects, what a waste of public money.

Readers of zoospooks are also requested to read that blog by Roderic M. Page, to understand the problem of having sequences without proper scientific names in public databases, and to get the idea about what these sequences without names means and how it is found out. He is one of the biggest scientists in my field and I am just a budding blogger/scientist, thus you would benefit better by reading his blog.

In short, DNA barcoding has performed below par, and their quest to barcode all species has failed at least until now. The main problems could be that they did not have trained taxonomists in their ranks. They are against taxonomy using morphological identification, thus these taxonomists distance themselves from barcoding, and barcoders know little taxonomy to correctly identify a species to its specific level. If barcoders say that they found cryptic diversity that was deposited as “sp.” in databases, then why 1000 specimens (with <1% identity), and I would also ask those people to read better about species delimitation methods.

To save itself, Barcoding needs

  1. Proper taxonomists (with proven credential) in each and every project (even if small) that they initiate.
  2. Deposit photographs of ALL the “barcoded” specimen in their website, individual researchers’ website and public access.
  3. Barcoders should put all their data in NCBI or make BOLD open access.
  4. Unwanted sequence deposition should be avoided (un-identified species).
  5. Sequencing unidentified specimen should be discouraged.

These are mere suggestions, by me, but for barcoding to be useful for public they need to clean up a lot, (1) use proper expertise and (2) open up their data and try for another 5 years and lets see what changes from this initial 5 year phase of their project. Regarding the title of this post, barcoding unidentified specimen and introducing errors to a precious database like NCBI should be discouraged and barcoders should understand that although it is a “people’s” choice technology, it has certain responsibilities towards the society and fellow scientists. Indeed I agree that it is very much useful to catalog the biodiversity, I also suggest that it should be done in a better way and in an open manner so that more people benefit and less human effort is lost. Also read my post on the new Pristolepis to see what happens when bad taxonomy and sequencing technology join forces.

(*This is my opinion and has nothing to do with the paper cited)

Reference:

Shiyang Kwong, Amrita Srivathsan, Rudolf Meier. (2012). An update on DNA barcoding: low species coverage and numerous unidentified sequences Cladistics DOI: 10.1111/j.1096-0031.2012.00408.x

ResearchBlogging.org (more…)

Scientists have described a new species of fish from the Barapole tributary of the Valapattanam river of the Western Ghats. The scientists, Ralf Britz from the Natural history museum London, and Anvar Ali from the Conservation Research Group (CRG), St. Alberts College Ernakulam, and Siby Philip from the University of Porto, Portugal and CRG, found the species in a clear water stream, in Southern Karnataka, connecting to the Barapole tributary of the Valapattanam river. The study has been reported in today’s issue of Zootaxa, an international journal of zoological systematics.

Live Image of the new fish taken by Ralf Britz

The new species is named as Dario urops. The specific name (urops) is derived from Greek words ‘ουρά’ meaning ‘tail’ and ‘ὄψ’ meaning ‘eye’, denoting the conspicuous “eye-spot” on the caudal peduncle. This makes it the first discovery of badid fishes from the Western Ghats. Earlier 19 species of Badids were known from North-Eastern India, Bangladesh, Myanmar and South East Asia, and this find from the South of India, extends the distribution of this group of fishes as a whole south to the Western Ghats.

The new species measures a maximum up to 3 centimetres.  This attractive fish is has a background colour of yellowish beige, and the fins have a bluish-gray hue. The type material of the new species is housed at the museum of the Conservation Research Group, St. Albert’s College Cochin. Nikhil Sood, a Bangalore based aquarist and his Swiss friend, Benjamin Harink were the first people to discover the spot from where Dario urops was collected, and subsequently introduced the Indo-British Research Team to this location. Incidentally, Dario urops was first collected by Sir Francis Day more than 130 years ago from Wayanad and kept at the British museum, without formal description.

This find highlights the fact that the ichthyo-diversity of the Western Ghats is still not fully known and in general the importance of Western Ghats biodiversity hotspot. Researchers from the same group had identified another fish Pristolepis rubripinnis, which was published in yesterdays Zootaxa. Concerted and systematic exploratory survey for fishes in the Western Ghats are needed  to identify and preserve the valuable ichthyo-diversity.

References:

Ralf Britz, Anvar Ali & Siby Philip, 2012. Dario urops, a new species of badid fish from the western Ghats, southern India (Teleostei: Percomorpha: Badidae). Zootaxa, 3348: 63 – 68.

A group of predominantly Dutch scientists have revealed the reasons for the ecological success of seagrasses and in turn its associated organism the Lucinid molluscs. Seagrass meadows, as we know is an important kind of habitat for various organisms like coral reef fishes, reptiles (like turtles), waterbirds and mammals (dugongs, manatees), and is a basic environment for these organisms’ survivor-ship.

Sea-grass meadow and an associated puffer fish.

They survive till now, but as the paper points out it is a mystery how they do it. The sediments trap high organic matter content which in turn is fodder for some bacteria that revel in oxygen lacking environment and take up the sulfite present and produce sulfides as an end product of their metabolism. This sulfide is toxic to seagrass, so how do seagrass survive? This is the question asked by the researchers, they analysed data from world-wide, and formulated hypothesis and did experiments to prove their guess.

In their meta-analysis they found that a specific type of bivalve (Lucinidae) is associated with seagrass in more than 90% of the tropical and subtropical seagrass beds and in more than 50% of temperate seagrass meadows. This points that temperature-dependent sulfide deposition in tropics favours the association of the bivalve with the seagrass.

The bivalves harbours a symbiotic bacteria that metabolises sulfide and in turn benefits the mollusc, which sequesters sulfide and oxygen for the symbiont, by providing sugars. This association has been dated back to the Silurian (416 million years ago [Ma]; see the paper for detailed references), however the diversification of the mollusc and its associated symbiont is dated back only to the Cretaceous (145-65 Ma) when the seagrass emerged, the diversification of seagrass was in the Eocene but the symbiosis between them and the mollusc still continues, the probable diversification was aided by the help rendered by their symbiont mollusc to stabilize at first hand some 50 Ma .

The authors hypothesised that the association between the mollusc (with the endosymbiont which metabolises sulfides), could have helped in the survival of the seagrass which would otherwise have perished due to the high sulfide content in the sediments. The do experiments and prove that is the case.

We read yet another paper which really observes, hypothesizes and proves. It provides evidence of diversification of the mollusc and seagrass were interdependent, while 11 out of 12 seagrass genera harboured associated molluscs 18 genera (~50% of Lucinidae genera) of the molluscs are associated with seagrass. Basic research like this would help the restoration programs for sea-grasses which is not yet a big success.  Such basic research into the function of the ecosystem, its components, interactions etc. are the need of the hour.

Reference:

Tjisse van der Heide, Laura L. Govers, Jimmy de Fouw, Han Olff, Matthijs van der Geest, Marieke M. van Katwijk, Theunis Piersma, Johan van de Koppel, Brian R. Silliman, Alfons J. P. Smolders, Jan A. van Gils, 2012. A Three-Stage Symbiosis Forms the Foundation of Seagrass Ecosystems. Science, 336:6087, 1432-1434.

Today Zootaxa, the mega journal of Zoological Systematics, published the details of a new Pristolepis fish from the Western Ghats biodiversity hotspot. The new fish is named as Pristolepis rubripinnis, and as the name suggests has “red-orange” shade on it “fins”.  The authors have put in a lot of detail in describing this species and is a must read for naturalists, students and researchers with an interest in the ichthyo-diversity of the Western Ghats.

Pristolepis rubripinnis

In this age when science means just hunting for Impact Factors, scientists often resort to tell the “story behind their publications” elsewhere, as seen in the TreeOfLife blog. I think that scientists really enjoy the process of science and that it is a real motivation for many scientists (i.e., to follow the process after a hypothesis is formulated). However, this pleasure and the process and details is not always evident while reading majority of the scientific publications.

Whereas when you read a real TAXONOMIC work you really read the hypothesis, the process, it is a beauty. Here it started after finding a “marked colour variant of Pristolepis” and recollecting the confusion in the taxonomic literature about Pristolepis species of Western Ghats, which helped them to formlate a hypothesis seeking to answer the question “is it a species new to science”? and the answer was YES!!!!!

Earlier in 1849 Jerdon had described the first ever Pristolepis species from North Kerala “above the Palakkad Gap” as this paper says. Then Günther described Catopra malabarica in 1865. However, it was found to be a junior synonym of Pristolepis marginata by Jerdon himself the next year (see the present paper by Britz et al., for an interesting read on all these). So there was only one recognized Pristolepis from South India.

However, some authors cited both P. marginata and P. malabarica to be present in India, some others said P. marginata was the only species in India, some authors also said that P. marginata and P. fasciata were present in India. It is noteworthy that P. fasciata was described from South East Asia and its type locality is in Borneo and it has stripes on its body. No Pristolepis in India has stripes (at least until now). Another funny fact is that Indian authors have “sequenced” P. fasciata from India, when this species is absent from India, just see NCBI genbank.

So this study puts to rest a lot of confusion about Pristolepis in India. It highlights the importance of proper taxonomy before phylogeny or sequencing studies. It also takes back the readers to the real science where observation is made hypothesis is formulated and it is proved right or wrong, the writing style illustrates the process (thought process) behind the find, which should be educating for young researchers. Finally we have a new species of fish that was unknown until yesterday.

References:

1) Ralf Britz, Krishna Kumar & Fibin Baby, 2012. Pristolepis rubripinnis, a new species of fish from southern India (Teleostei: Percomorpha: Pristolepididae). Zootaxa 3345: 59–68

2) Jerdon, T.C. (1849) On the freshwater fishes of southern India. Madras Journal of Literature and Science, 15, 139–149.

3) Günther, A. (1864) Descriptions of three new species of fishes in the collection of the British Museum. The Annals and Magazine of Natural History, 3rd Series, 14, 374–376.

4) Jerdon, T.C. (1865) On Pristolepis marginatus. Annals and Magazine of Natural History, 16, 298.