Archive for June, 2012

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.

References:

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.

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

 


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.