Archive for the ‘Science’ Category

The Redline Torpedo Barbs have been proposed to be included in a new genus named Sahyadria. The two species of fishes (chalakkudiensis and denisonii) which were till date placed in the genus Puntius will now be under the new genus, Sahyadria – named after the Western Ghats mountain ranges to which these fishes are endemic to.


Sahyadria denisonii

There had been much uncertainty on the exact generic position of these fishes since the time they were described from Kerala, over a century and a half ago by the British naturalist Sir Francis Day. Taxonomists confused over its correct identity had placed these fishes under different genera like Barbus, Labeo, Puntius and Hypselobarbus.

A team of researchers, Rajeev Raghavan and Anvar Ali from the Conservation Research Group at St. Albert’s College, Kochi; Neelesh Dahanukar from the Indian Institute of Science Education and Research, Pune and myself carried out detailed osteological and molecular studies to finally clarify the riddle surrounding the exact identity of these fishes. The result of their study identifying and naming the new genus Sahyadria has been published today in the Journal of Threatened Taxa – an international journal of taxonomy and conservation.

 Recently, the same team of researchers had suggested that there is a huge undescribed diversity existing within the fishes currently known as Redline Torpedo Barbs, and had indicated the presence of at least six ‘evolutionarily distinct lineages’ apart from the two known species (Sahyadria denisonii and Sahyadria chalakkudiensis).

Redline Torpedo Barbs are extremely popular fishes in the international aquarium pet trade and their indiscriminate exploitation from the wild has led to their ‘Endangered’ listing in the IUCN Red List of Threatened Species.


Raghavan, R., S. Philip, A. Ali & N. Dahanukar (2013). Sahyadria, a new genus of barbs (Teleostei: Cyprinidae) from Western Ghats of India. Journal of Threatened Taxa 5(15): 4932–4938;

John, L., S. Philip, N. Dahanukar, A. Ali, J. Tharian, R. Raghavan & A. Antunes (2013). Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered Red-lined Torpedo Barbs – highly exploited freshwater fishes endemic to the Western Ghats Hotspot, India. PLoS ONE 8(7): e69741;

Raghavan, R., N. Dahanukar, M. Tlusty, A. Rhyne, K. Krishnakumar, S. Molur & A. Rosser (2013). Uncovering an obscure trade: threatened freshwater fishes and the aquarium pet markets. Biological Conservation 164: 158–169;

Recently our paper on the cryptic species among the red lined torpedo barbs (RLTB; Puntius denisonii and P. chalakkudiensis) have been published in plos one. The study identified 8 evolutionarily distinct lineages among the 12 different studied populations from its entire range.

At the molecular level, the study used mitochondrial DNA markers and employed species delimitation methods like the Bayesian Species delimitation method, the GMYC method etc, which identified 8 distinct lineages. At the morphological level CVA and MANOVA could distinguish all the populations as distinct.

However, taking into account both the results (from morphology and molecular methods), the minimum number of distinct lineages agreed by both methods is eight. Thus we conclude that the species has 8 distinct lineages that need separate conservation attention.

This study comes along with another study, which found that massive amounts of these barbs were being exported from India, after being collected from the wild. That means there are no regulations in India for the exploitation of this fish.

This fish is “endemic” to the Western Ghats of India. Now the finding that there are 8 distinct lineages that need separate conservation attention, calls for immediate action from the authorities, hobbyists and scientists, to generate an action plan and conserve this beautiful little fish.

Readers are invited to read this paper which is open access and downloadable at Plos One.


John L, Philip S, Dahanukar N, Anvar Ali PH, Tharian J, Raghavan R., and Antunes A. (2013) Morphological and Genetic Evidence for Multiple Evolutionary Distinct Lineages in the Endangered and Commercially Exploited Red Lined Torpedo Barbs Endemic to the Western Ghats of India. PLoS ONE 8(7): e69741. doi:10.1371/journal.pone.0069741

Recently our paper on the The phylogenetic position of Lepidopygopsis typus (Teleostei: Cyprinidae), a monotypic freshwater fish endemic to the Western Ghats of India has been published. This is an important work and a significant contribution to the Ichthyology of the Indian Peninsula, since it clears a longstanding misconception.

First of all, let me say that the species Lepidopygopsis typus a monotypic freshwater fish endemic to the Periyar Tiger Reserve (PTR) forests, is a relative of the Mahseers, and allied large barbs distributed in India, Pakistan, Afghanistan, Iran, Nepal and several North African regions.

It was until now confused to be a species within the “schizothoracinae”, which comprise the hill trouts or the mountain barbells of the Himalayas. The “disjunct distribution” has baffled ichthyologists and biogeographers at the same time.


Now we show that it is just a case of a “false disjunct” which arose due to improper systematic position of the species.

Here, using phylogenetic hypothesis testing, and using both mitochondrial DNA and nuclear DNA phylogenies we solve the puzzle. All are welcome to read the paper and comment on it. If the readers need a full text of the paper please feel free to mail me or one of my co-authors who will happily share it with you for non-profit/research purposes.



NEELESH DAHANUKAR, SIBY PHILIP, K. KRISHNAKUMAR, ANVAR ALI & RAJEEV RAGHAVAN, 2013. The phylogenetic position of Lepidopygopsis typus (Teleostei: Cyprinidae), a monotypic freshwater fish endemic to the Western Ghats of India, Zootaxa 3700 (1): 113–139.

A recent publication.

Rajeev Raghavan, Siby Philip, Neelesh Dahanukar, Anvar Ali, 2013. Freshwater biodiversity of India: a response to Sarkar et al. (2013). Reviews in Fish Biology and Fisheries, DOI 10.1007/s11160-013-9315-9.

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

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


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.


 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)

My paper “Fish lateral line innovationinsights into the evolutionary genomic dynamics of unique mechanosensory organ” has been published in Molecular Biology and Evolution. Data used for the analysis has been made public at figshare ( Any requests for PDF version of the advance access version should be directed to the corresponding author (see the journal abstract page) or to me “philipsiby” [at] gmail. I do not want to elaborate a lot about the paper here but invite you to read the paper and correct or discuss it here at zoospooks.