Archive for the ‘Taxonomy’ 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.

Pdenisonii

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.

References:

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; http://dx.doi.org/10.11609/JoTT.o3673.4932-8

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; http://dx.doi.org/10.1371/journal.pone.0069741

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; http://dx.doi.org/10.1016/j.biocon.2013.04.019

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.

Reference:

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.

Lepi

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.

 

Reference:

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.

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.

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

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…)

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.

Reference:

Robert M. B., & S. R. Bordenstein, 2012. Speciation by symbiosis. Trends in ecology and evolution, dx.doi.org/10.1016/j.tree.2012.03.011