Posts Tagged ‘nature’

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)

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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.