Posts Tagged ‘evolution’

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

Advertisements

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)

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…)

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.