More changes in Danio phylogeny

[BillT]

I went to a talk on campus (at the U. of Oregon) by a graduate student on his new results on refining the evolutionary relationships among the fish of the Danio genus. It was pretty interesting (to me anyway). He expects to publish this in a few months.

Results (as I was able to reconstruct them from my notes):

[BillT]

Opps, hit the wrong button. Wanted to add more.

Disclaimer, disclaimer, disclaimer:
The relative times of the branch points are meaningless, since this is a drawing of a sketch one of his diagrams and I did not have time to make a detailed sketch.

This is  much better supported phylogeny than the previous ones since new molecular techniques allow him to look at way more markers and is also focused on the genus Danio not on larger groups which many other studies looked.

Points of interest: Danio aesculapis comes out as the closest relative to zebrafish in this study. The two forms of D. kyathit came out closely related to each other, but not as closely as D. aesculapis.
The larger Danios are farther away form D. rerio.

A lot of the species in Danio were not shown, including D. nigrofasciatus, which I know he has a lot of information.

Recent molecular surveys used something like 4,000 DNA bases of sequence data in 6 different genes.
McCluskey's new study started out with a huge amount of sequence (between 1.5 million to 220 million bases out of a genome of more than 2 billion bases), and then after selecting the more informative parts of the sequence for particular species comparisons, ended up with about 24,000 bases of sequence to compare.

[BallAquatics]

That's really interesting stuff Bill.  Just looking at the fish, you would think that D. nigrofasciatus would be closer to rerio than aesculapii.

Danio nigrofasciatus

Danio aesculapii

I can definitely see where Devario aequipinnatus and Devario pathirana are close.  Other than different markings, they have very similar body shapes. 

I would like to hear the latest on Danio meghalayensis.  For a while they thought Danio meghalayensis was a synonym to Danio dangila, but the two look nothing alike color or body shape wise.

Dennis

[BillT]

Just looking at the fish, you would think that D. nigrofasciatus would be closer to rerio than aesculapii.

Interesting point Dennis. I think that nigrofasciatus is closer in many or all the previous phylogenies. It was not in the data set that Braeden talked about for some reason. I know he has a lot of sequence data and the live D. nigrofasciatus fish, so hopefully the study will be expanded to include this and some other species.

Another obvious missing species is the pearl danio (Danio albolineatus). It has often been placed close to rerio in previous phylogenies. Sometimes pearl danios, to me, seem to be like a body double of aesculapii. However, I have animals called pearl danios that are either similar in size to zebrafish while other examples are much larger versions. I am not clear what is going with D. albolineatus, but it would not surprise me if there was actually an unrecognized diversity of species here (just like the case with D. choprae and D. flagrans that you posted about recently).

I know that when they get fish for studies, the lab guys are quite interested in the getting fish most directly from a single wild site as a sample, rather than fish resulting from crossing among different populations. This will give them many groups of fish (strains or lines) with a genome (meaning its collection of all the genes it carries) that does not have genetic elements mixed from possibly unrecognized separate species. This sounds like some of the killifish guys to me.

When given a choice to among different samples of a species, they would expect better (or less scrambled) results from a small specific population than in a line that was a big mix of genetics form a group of different populations. This to me (and probably most fish breeders) raises worries about getting an inbred, non-robust line of fish which would be difficult to maintain. This would be a long term concern, because these lines would have to be maintained as breeding lines which inevitably leads to inbreeding, reduced genetic variability and reduced viability.

My initial interest in breeding these fish has been in creating and selecting lines of different species that can be maintained in lab conditions that zebrafish are raised in labs. This will make them more useful in labs because they will be able to be bred in the conditions that are already present there. Its kinda like there is a nitche there (in the lab environment) where they fish can expand into if they are able to thrive there. It is a domestication process. This is probably best done by breeding together fish from different genetic backgrounds to get an increased genetic diversity, then letting selection find those genetic combinations that will survive in the particular environment and breeding situations. That means getting a lot of genetically different fish, throwing them into an environment and taking those that survive and breed in that situation and breeding them together for the next generation. I think this is a normal approach when first getting a species to breed in captivity.

Danio classification is, in some ways, really confusing. The number of described species has at least doubled in the last 15 years. The same is probably true of the Devarios and other groups in other related groups of fish. Probably this is because there have been several people who have focused on studying these fish which resulted in not only finding new species, but also looking at greater detail at the different species, making better comparisons, and coming up with better phylogenies. This stuff is like an ongoing detective story if you get into the details. This is part of what interests me. Order from chaos.

I can definitely see where Devario aequipinnatus and Devario pathirana are close.  Other than different markings, they have very similar body shapes.

I would like to hear the latest on Danio meghalayensis.  For a while they thought Danio meghalayensis was a synonym to Danio dangila, but the two look nothing alike color or body shape wise.

I completely agree. When I first look at these fish, the most striking basis of comparison for me is the general body shape. In particular, when comparing Danios and Devarios I look at the body shape. Danios have a more rounded cross-section and look torpedo shaped to me. Devarios look more blade-like in cross section to me (narrow at the bottom, thicker at the top). The larger Devarios at least, seem to live in faster flowing water and can really zip if they want to (for that they need a larger tank).
I am thinking of getting some Opsarious (maybe spelled right). They look somewhat like a Devario but are a different genus, with a Devario-ish body but with some differences.

I do not give body markings a lot of weight in these fish. There are lots of genetic based differences in zebrafish that change both colors and patterning due to single mutations. This would include: normal, albino, golden, a bluish version, a highly reflective version, leopard (small spots), various larger sizes of spots, fewer stripes, thicker stripes, thinner stripes. These relatively short term changes based on breeding makes me expect that markings would be easy to change, in larger populations, over longer evolutionary periods.

D.meghalayenesis:
I mentioned to Braeden and his adviser (boss) that I just got some D. meghalayenesis from you. He was excited and wanted to get some DNA. I told him I wanted to breed them before he mushed them up for DNA. He said he could come over and do a fin clip (knock out the fish, cut off some of the tail fin with a razor blade for later DNA extraction) or could probably get DNA out of any recently dead fish if I threw them in the freezer. The boss won't send him to the sub-continent to collect fish himself (life is tough).

This maybe one of those few cases where one could sell someone a dead fish and they would be happy. Well, I guess that would also work for restaurants, or a taxidermist...

[BallAquatics]

Another obvious missing species is the pearl danio (Danio albolineatus). It has often been placed close to rerio in previous phylogenies. Sometimes pearl danios, to me, seem to be like a body double of aesculapii. However, I have animals called pearl danios that are either similar in size to zebrafish while other examples are much larger versions. I am not clear what is going with D. albolineatus, but it would not surprise me if there was actually an unrecognized diversity of species here (just like the case with D. choprae and D. flagrans that you posted about recently).

I think that is it exactly Bill.  There are several fish that exhibit differences in colour and patterning depending on where they were collected, and I think it's very likely that the species as currently-recognised will turn out to represent a group of closely-related fishes.  I currently keep both D. albolineatus and D. roseus and on any given day they are indistinguishable from one another.  I also kept D. albolineatus var. tweedei in the past.  The Seriously Fish site has some good info, http://www.seriouslyfish.com/species/danio-albolineatus/.

A recent issue of Practical Fishkeeping had a two part series on Danios by Heiko Bleher.  He had photos of maybe 6 different fish that were wild caught that looked like Zebra Danio, but you could tell they were not what we know as Zebra fish.

When I first look at these fish, the most striking basis of comparison for me is the general body shape. In particular, when comparing Danios and Devarios I look at the body shape. Danios have a more rounded cross-section and look torpedo shaped to me. Devarios look more blade-like in cross section to me (narrow at the bottom, thicker at the top). The larger Devarios at least, seem to live in faster flowing water and can really zip if they want to (for that they need a larger tank).

Well just as you say that, there are exceptions.  My Devario xyrops have bodies shaped just like Danio dangila, but then Danio choprae have the blade-like Devario body that you mention.  LOL

I am thinking of getting some Opsarious (maybe spelled right). They look somewhat like a Devario but are a different genus, with a Devario-ish body but with some differences.

I kept a close relative to these guys several years ago.  Very beautiful fish and very active.....

This maybe one of those few cases where one could sell someone a dead fish and they would be happy. Well, I guess that would also work for restaurants, or a taxidermist...

That's great!  There are many people that sell dead computer hardware for parts or repair.  I just might need to look into selling dead fish on AquaBid for scientific study.  LOL

Dennis