Archive for the ‘Ecology’ 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.

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.

As the title suggest, a new species of teleost has been found out, it was collected, “sort of” unearthed, from the sand bed of a small river in south western India, thus named “ammophila” which means “sand loving”.

The new eel-loach Pangio ammophila

This species is for now known only from this location, and grows not more than 3 centimeters. It is the tiniest fish that I have ever seen* and were it not for the authors of the study, Ralf Britz, Anvar Ali and Rajeev Raghavan, probably it would have stayed in the wilderness and would not have received this attention. Readers should recall that the lead author of this study is the same one who described the “smallest vertebrate” Paedocypris progenetica, thus this fish is rather “big” for him.

This find calls our attention to some important points:

  1. It is the fourth valid Pangio species from the Indian region, the congeners of which are all distributed in the South – South Eastern Asian region.
  2. This species has a remarkably different colour pattern from the hitherto identified species of the genus, and most similar to its geographically nearest species Pangio goaensis.

These two points leads our attention to the historical bio-geography of the region. How was the present distribution of animals, in particular fishes of South – South Eastern Asia formed. The disjunct distribution of these species with its congeners in the North Eastern India and South East Asia (a huge geographical barrier), is surprising. These authors have found out Dario urops which was described recently, which also has a similar disjunct distribution. So these findings should help advance our understanding of the historical bio-geography of the region as well as the pangean and gondwanan connections of the Asian fauna.

3. Another issue that this species brings to fore is conservation of fragile habitats. This location is the only place where the species is found and is thus important (also it should harbour other species).

The unprecedented economic growth in India and especially in the region means that indiscriminate sand mining occurs in this same stream. Imagine how many of these sand loving eel-loaches would have been mined out before being noticed by the authors? How do we balance the biodiversity conservation and economic growth?

*Competing interest: I was part of the collection team which found this species and is a collaborator at the Conservation Research Group.

Ralf Britz, Anvar Ali and Rajeev Raghavan (2012). Pangio ammophila, a new species of eel-loach from Karnataka, southern India (Teleostei: Cypriniformes: Cobitidae). Ichthyol. Explor. Freshwaters,, 23 (1), 45-50

Darwin built his theory of Evolution on two pillars, “heritable variations” and “survival of the fittest” by which occurs evolution by the means of natural selection. How did the heritable variations move from one generation to the next? The genes (we know that alleles) carry the variation in the parents to their offspring. Survival of the fittest, said that the organism with the most advantageous trait or character survived, at intra- and inter- population or species level. So what generates the variation and the chance of survival or adaptability?

At the molecular level we know about mutations, which are stabilized in the population or species ( then called substitutions), can be a reason for variation. We are aware about the neutral theory of evolution pertaining to the genome level or molecular level. Wherein we learned that most (deleterious) mutations are “purified”, and the variation at the genetic level is as a result of random fixation of mutations or random genetic drift. The evidence for this is that if natural selection was the reason for the genetic level variation then the key genes responsible for the functions would be evolving faster (fix more mutations/carry more substitutions since they are advantageous and are naturally selected) but this is not the case, key genes always are same between organisms say at an evolutionary scale of metazoa for example. We should not confuse that there is no positive selection or fixation of advantageous (?) mutations in key genes, it is present but to a smaller extent as opposed to the neutral (or nearly neutral) evolution, it can be episodic events in most cases for key genes.

Another set of variation at molecular level could be due to expression differences, in time (heterochrony), in cells (heterotopy) and in amount (heterometry). But are these the only source of variation? if so (so much variety) what we see, how could we explain it? We should understand that the variation in morphological traits, physiology and behaviour is guided by natural selection and that neutral theory (or nearly neutral theory) pertains only to the molecular level. Apart from these mutation and expression level variation, there are other sources as well, the epigenetic variations, the phenotypic plasticity and the symbiont variation that can be selectable and indeed heritable, which is what the paper of our interest today says.

If the symbiont or (microbiome) of the organism and its genome are in intricate connection (then they can be considered the holobiont) then evolution of the organism cannot be separated with the co-evolution and co-development of its microbiome. Nature has examples for horizontal and vertical transfer of symbionts between generations. The symbiotic association of the luminiscent Vibrio fischeri on the ventral side of the squid Euprymna scolopes is an example of horizontal transfer and association of symbiont. We know this association is crucial for the survival of the host (to avoid predators) and the symbiont benefits by getting a safe place to live in. The cases of Wolbachia in arthropods (wasps) are perfect examples of vertical transmission of symbionts wherein the eggs contain the bacteria and any egg (treated) without the bacteria perishes or fails to develop. As we look deeper, even human guts harbor these kind of symbionts without which we would not be able to survive and is transmitted vertically from mothers. So should be every case of each and every organism, but proof is lacking since investigations in that angle is just gaining momentum.

Selection (natural selection) of the symbionts associated with the host due to environmental cues are presented in the paper as well. They present the case of coral-zooxanthillae symbiosis and selection of a specific strain of the microalgae in response to elevated temperatures to form the dominant community. The temperature tolerance of desert plants (and many other plants) and the inhibition of the HSP 90 (for temperature tolerance) is provided by external cues provided by symbiotic fungi, the paper provides a strong case of selection of the holobiont in response to the environmental cues. The aphid thermal tolerance is also an interplay between its symbionts (Buchnera being prominent), and this interaction can be disrupted by mutations, showing that the interaction is really selected for.

Reading the paper enables us t0 appreciate the importance of the symbiont in the development and evolution of organisms. Evolution and development is related to the environmental conditions the ecological interactions, the opportunities in environment can lead to adaptions, symbionts fits in nicely as a co-evolving component stressing the view that organisms are not individual units but interdependent. The molecular level selection forms the micro-level, the symbiont and selection forms the intermediate level and ecological interactions and external cues forms the macro-level, of adaptation, developmental variability and eventually evolution.


Scott F. Gilbert, Emily McDonald, Nicole Boyle, Nicholas Buttino, Lin Gyi, Mark Mai,Neelakantan Prakash, and James Robinson, 2010. Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy. Phil. Trans. R. Soc. B, 365:1540 671-678.

A recent review on this topic by Robert Bucker and Seth Bordenstein, directed my attention to this little, taught and debated, fact. We consider that the process of speciation to be, one which divides an existing single species into two, or more clearly, the emergence of a new species. Biological species concept is one of the most favoured ones, but others are not uncommon and each has its own arguments making you wonder why these many species concepts. However, all the species concepts agree at one point that a new “species” is formed, through reproductive isolation (biological species concept), or a lineage evolving separately (as in the evolutionary species concept and which is true even for asexual beings), even the phylogenetic species concept advocates monophyly of a group to consider it a species where again a species is formed. Our peek today is not into the species concepts but one of the least appreciated and more important causes of speciation, an organism’s associated microbial community or symbionts.

Clownfish-Sea Anemone mutualism: if the host and symbiont has a specific preference could it lead to ecological divergence and thereby speciation?

The idea of symbiosis as an integral part of speciation, be it in reproductive isolation (sensu Biological Species concept and many others ), or in niche divergence (sensu Ecological species concept), can be easily comprehended. This review paper addresses the importance of symbionts in the whole process of speciation. We all know that changes in the genes (mutations) are fixed in the genome if advantageous (substitutions), which leads to adaptive divergence of the population and this slow process (millions of years) could lead to speciation. However, the authors argue here for another “genetic” component other than the nuclear genes the “symbionts”.

It is known that symbionts/microbes are omnipresent among the eukaryotes, which we recently come to call as microbiome, and is often clubbed together with the genome as called the hologenome of the organism. Here we need to recognize that microbial community of the organism can be decisive in determining the reproductive isolation between its sister (isolated) population harboring a different microbiota. While reading the paper we are convinced that the immune genes that are constantly facing adaptive evolution do so due to also the influence of the pathogen/microbial community of the organism as one of the factors. Thus, considering the immune genes as reproductive isolation locii could lead us to appreciate the importance of symbionts.

This paper cites different examples of Wolbachia symbionts (and many others) in the arthropods and the adaptive divergence and reproductive isolation between populations, and even ecological and behavioral isolation. The authors also point out that the hybrid incompatibilities caused due to symbionts are a “third” genetic factor. Cytoplasmic incompatibility between hybrids is a reality when we look at vertical transfer of symbionts or pathgens. In short, symbiotic association can be akin to allopatry in one sense, and aid speciation. The figure in this post (nemo) could be misleading and is just an example of mutualism, and is different from microbial association and speciation, the readers are directed to read the “trends review for better comprehension of the problem.

Wolbachia, a major symbiont of arthropods and touted to be involved in speciation by symbiosis one among a long list of microbial symbionts/microbiome.

The review synthesizes the symbiont reproductive incompatibility issue its extent its frequency and the hybrid incompatibility angle, OR pre and post reproductive isolation by symbionts. It is a good read, and an educating review of literature and introduction to concepts for students of evolutionary biology.


Robert M. B., & S. R. Bordenstein, 2012. Speciation by symbiosis. Trends in ecology and evolution,