Posts Tagged ‘fish’

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

My paper “Fish lateral line innovationinsights into the evolutionary genomic dynamics of 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.

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…)

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.