A whole new whale

A whole new whale- genetic analysis supports the existence of a new whale species


In the mysterious dark waters of the deep seas, imaginative explorers have chased mythical creatures – from mermaids to kraken, creating an endless list of adventures. Even in the 21st century, we know very little about the creatures that inhabit these worlds. Now, a shy whale species comes into molecular spotlight as scientists use genetic tools to reveal its existence and decipher its relationship with better known cousins (1).


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The beaked whales are a mysterious and diverse family – characterized by teeth and a prominent beak. Very little is known about this family of whales because they live in remote oceanic habitats, dive deep and seem to be sparse (1, 2). The existence of a black beaked whale is long rumored among Japanese fishermen and was first described as a possible new species by Japanese researchers in 2013 (3). A type of beaked whale known as ‘Baird’s beaked whale’ are seen the north pacific (ranging from Japan to Mexico), these whales are slate-gray in colour. Rare sightings of smaller black whales have also been reported around these regions (only around Japan). Although the black whales are distinguished by their skin tone and smaller size, these criteria alone were not sufficient to to classify them as a new species. One explanation for example could be that the black whales were just the young juveniles of the slate-gray Baird’s beaked whale. A recently published study (1) uses mitochondrial DNA sequencing to show that the black beaked whales are genetically distinct from other beaked whales and are only distantly related to the slate-gray whales with overlapping geographical niches.

What did they do?

The team has analyzed the DNA sequence of a total 178 samples of Baird’s beaked whales. These samples were painstakingly collected  from the rare live animals captured across the entire north pacific range including  two  museum samples. Unsurprisingly, majority of these samples (170) belonged to the slate-gray forms and only 8 belonged to the suspected black whales. They compared the genetic sequence (haplotype https://en.wikipedia.org/wiki/Haplotype) of particular stretches about 450 base pairs (nucleotide lengths) of mitochondrial DNA of these whales. If indeed the 8 black samples belonged to a new species, then their DNA sequence is expected to be quite similar to each other and differ considerably from the slate-gray ones.

What did they find?

Genetic analysis showed that a particular stretch of  mitochondrial DNA from the black and slate-gray whale samples had only 6-7 differences within their own group but differed from each other in 16 positions. This compares with the difference of 12 nucleotides positions that the slate-gray whales have  with a different beaked whale species Arnoux’s beaked whale, a completely  different species found in southern hemisphere (a benchmark for genetic disparity the authors have used to validate the genetic differences-). This analysis in combination with the known physical characteristics of size and colour, positions the rare black whale as a new species. The presence of 6 nucleotide differences in the mitochondrial DNA of the 8 black whales suggests that there may be high diversity within the species as well.

Why is this important?

This work highlights how little we still know about the fascinating world around us. It uses relatively inexpensive, and widely available molecular methods (sequencing short stretches of mitochondrial DNA) to support the claim of a new species of whale in the North Pacific Ocean. This raises new questions about how this species lives and thrives in the remote oceans and how it is affected by human activity.



1.Morin, Phillip A., C. Scott Baker, Reid S. Brewer, Alexander M. Burdin, Merel L. Dalebout, James P. Dines, Ivan Fedutin, et al. 2016. “Genetic Structure of the Beaked Whale Genus Berardius in the North Pacific, with Genetic Evidence for a New Species.” Marine Mammal Science, July. doi:10.1111/mms.12345.

2. (http://www.beakedwhaleresource.com/aboutbeakedwhales.htm)

3. Kitamura, Shino, Takashi Matsuishi, Tadasu K. Yamada, Yuko Tajima, Hajime Ishikawa, Shinsuke Tanabe, Hajime Nakagawa, Yoshikazu Uni, and Syuiti Abe. 2012. “Two Genetically Distinct Stocks in Baird’s Beaked Whale (Cetacea: Ziphiidae).” Marine Mammal Science, September, doi:10.1111/j.1748-7692.2012.00607.x.

An interview with Dr. Phillip Morin

Q. You have performed analysis on 5 blacks and 8 gray beaked whales, how would you increase sampling? Would you deploy a dedicated team/ facility or co-ordinate more with the fishermen in the area to collect more samples? Does the constraints of sampling limit the interpretation of your finding?

Actually, we have sampled 5 of the new black form, included DNA sequences from the 3 that were previously analyzed in Japan, for a total of 8 of the black form. We included 170 of the gray form in our study, ranging from Japan to Mexico across the North Pacific. We would certainly like to have more samples of the black form, and hope that researchers who have data on additional beached whales that they think may be the black form will contact us, and that researchers, fishermen and others who see live beaked whales can help us to find where they spend their time when they are alive. At the moment we do not have funding to commit to this type of study, but if we are able to get a better idea of where to look for them, that could help us develop a more specific (and less expensive) study. Although the sample size is fairly small, the fact that samples are from both Japan and the Bering Sea strengthens the result, and the fact that we have sampled across the known range of Baird’s beaked whales (the gray ones) also strengthens our interpretation of 2 separate species in the North Pacific.

Q. What do we know about the behaviour of the black whale – are they solitary or social? Are they hunter carnivores or live on krill? Usually food is abundant in the shallow sea near the coast and in deeper sea basins the food becomes scarce, do we know something about their dietary habit that allows them to survive? Is the restriction of their abundance in particular geographical locations is because of a known nutrient gradient around your sampling sites?

There are 22 known species of beaked whales, and to my knowledge all of them live primarily in deep waters and feed on squid and/or fish at depth, and are naturally not abundant, probably due to this dietary specialization, high energy needed to obtain sufficient food, and patchiness of food sources. All are also typically found in smaller groups, though Baird’s beaked whale is known to travel in larger groups of 30 or 40 at times. Although we don’t know anything about the behavior or habits of the new species, we can infer that, like other beaked whales, it feeds at depth on squid or deep/bottom fish, and probably travels in small groups (a few individuals).

Q. Mitochondrial DNA versus genomic DNA for phenotyping – what are the challenges of using complete genomic sequences – What would the advantages of doing complete genome sequencing be?

Genome sequencing remains relatively expensive and requires quite a lot of high-quality DNA. For the purposes of determining whether there are 2 species, short sequences of mitochondrial DNA are actually very diagnostic (and therefore adequate), very inexpensive, and can be generated even from bone specimens in museums. We will very likely do some additional sequencing from the nuclear genome to get a more precise estimate of the amount and timing of divergence among the 3 species in the genus Berardius, but full genome sequencing is unlikely to contribute much in the absence of more information on the biology, life history, behavior, etc. of the species, so that is were we are better off putting our research time and effort.

Q. When do you call something a new species ?Can you tell us a little bit more about how haplotypes are used to infer distance and diversity? What other lines of evidence would further strengthen the black beaked whale as new species?

That’s a difficult question, as evolution is a continuous process, and taxonomy (the process of describing species and higher taxa) is an artificial hierarchy imposed on evolution to help us understand and describe biodiversity. We are using a species concept that infers species when genetic evidence indicates that they are evolving along independent evolutionary trajectories, e.g., they do not significantly interbreed and have not for long enough that they have evolved different ecosystem niches and functions (e.g., different food sources or feeding behaviors, habitat use, mating systems, acoustics, etc.). The mtDNA data strongly suggests that this is the case, as there are only very small differences between haplotypes of individuals within each form (≤5), and much larger differences between haplotypes of the two forms (16-26). The fact that the 2 adult specimens of the black form from which we have measurements are only about 2/3 the size of adult Baird’s beaked whales (far outside the normal size range for adult Baird’s whales), and that they have darker skin and several other recognizable (to experts) physical differences also indicates that they are different species, not just variation within a species.

Q. Do you see yourself as a sort of molecular explorer? How would you go about naming the new black whale?

This study has very much been like molecular exploration! We’ve used genetics to help us identify specimens that were previously identified as Baird’s beaked whales, and then been able to follow up with additional studies on those specimens. We use genetics that way frequently for marine mammals because it is so difficult to study them in their natural habitats. Official naming of the new species is done by publishing a complete description of the species (as complete as the specimens will allow), including some skull morphology if possible, and identification of a type specimen (the “holotype”) that will mostly likely be a skull in the Smithsonian Museum that was collected in 1948, but previously thought to be from a small Baird’s beaked whale. There is a team of researchers from Japan that are currently working on that publication and will most likely propose a scientific name. They were the first to indicate that this might be a new species in 2013 based on the 3 specimens from Japan, so that is why they have taken the lead in describing and naming it.

Q. What are the implications of your findings for whaling and conservation?

Baird’s beaked whales and several other toothed whales and dolphins are still commercially hunted in Japan, so it will be important for the whaling industry and scientists there to monitor the hunts to make sure that the new species, which appears to be much more rare than Baird’s beaked whales, is not taken. There are also other potential human impacts that could endanger this species, including seismic exploration, navy sonar, increasing ocean noise from other sources, pollution, entanglement in fishing gear, competition with humans for food, and climate change. Now that we know it’s there, we can work to learn more about it and, hopefully, how to protect it from these potential impacts