My paper “Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ” has been published in Molecular Biology and Evolution. Data used for the analysis has been made public at figshare (http://dx.doi.org/10.6084/m9.figshare.92411). 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.
Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organPosted: August 4, 2012 in Ecology, Nature, Science
Tags: Figshare, fish, lateral line, mechanosensory organ, Molecular Biology and Evolution
Tags: biogeography, fish, new species, ralf britz, taxonomy
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”.
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:
- 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.
- 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
Tags: Bioinformatics, Biology, evolution, fish, science, taxonomy, zoology
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.
- If a hitherto identified specimen or organism gets its DNA portion sequenced and is made publicly accessible
- 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:
- This project lived up to its initial speech act? (species coverage problem)
- 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
- Proper taxonomists (with proven credential) in each and every project (even if small) that they initiate.
- Deposit photographs of ALL the “barcoded” specimen in their website, individual researchers’ website and public access.
- Barcoders should put all their data in NCBI or make BOLD open access.
- Unwanted sequence deposition should be avoided (un-identified species).
- 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)
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
Tags: adaptation, co-evolution, ecological interaction, evolution, microbiome, selection, symbiosis and evolution
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.
Tags: mutualism, speciation, speciation by symbiosis, species concept, Symbiosis
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.
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.
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, dx.doi.org/10.1016/j.tree.2012.03.011
Tags: natural history museum london, nature, ralf britz, science, travel
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.
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.
Tags: Ecology, Interaction, nature, science, Symbiosis
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.
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.
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.