Variation in L260

[Suckermouth]

Hey guys,

I just recently purchased fish from pleco_breeder. Dom (pleco_breeder), please don't take offense for me asking questions about your fish, I'm prefacing this post by saying I am just being quite paranoid right now. Before purchasing he sent me this pic, but I was not very observant when I looked at it:



Now that I've seen the fish in person, my immediate reaction was that these fish are much more different than I expected. The male has way more spots and the female has more lines. The female looks like a typical L260 while the male has way more spots than I've ever seen, although in a pattern that appears consistent with other L260. Thoughts? I mean, my heart literally sank when I first saw the male being so different from the female because I thought it could be a misidentification, but after looking up L411 I realized that it couldn't be anything else but L260.

Let me know your thoughts, please! I think I'm being super paranoid now just because they're my fish, and also because when I first saw the photo the difference didn't jump out at me!

[MatsP]

Many of the Hypancistrus species vary quite a bit in pattern, so whether they have a bite more spots, or no spots is what I would call individual differences.

--
Mats

[Suckermouth]

Thanks Mats, I think I'm starting to come down from being on edge from my initial excitement. That makes sense, though I'm actually a little curious if there's geographical variation, or if this is how the lines develop on L260.

[pleco_breeder]

I'm not taking offense, but am curious if there is another pleco_breeder out there. I haven't sold any L260 in quite some time and checked all the website variations of my site I could find. Just looking for some clarification as I've had problems with other individuals claiming to be me in the past for everything from meeting lectures, to fish sales, to book sales. I would appreciate any info you can provide.

Thanks,

Larry Vires

[dconnors]

His aquabid handle is master_breeder, not pleco_breeder. Those are definately a nice pair of 260s, no ifs, ands, or buts. Hopefully I will get 4 juvies from Dom soon, I think it is getting warm enough to ship...

[racoll]

Those are definately a nice pair of 260s, no ifs, ands, or buts

This certainly does not assume that they are the same species.

Remember, an L number is just a picture in magazine, nothing more.

Milton, you have the molecular gear at Auburn right? Why not take a fin clip and get a COI or cytb sequence?

The Ward et al. (2005) COI primers should work. I've used these on Ancistrus.

[dconnors]

Those are definately a nice pair of 260s, no ifs, ands, or buts

This certainly does not assume that they are the same species.

Remember, an L number is just a picture in magazine, nothing more.

Milton, you have the molecular gear at Auburn right? Why not take a fin clip and get a COI or cytb sequence?

The Ward et al. (2005) COI primers should work. I've used these on Ancistrus.

I can agree with that. "A picture in a magazine"...That being said I would wonder what this fin clip sequence would tell us about L46/L98, or L66/L399/L400, or etc, etc I'm sure you get the idea. My point is my friend has blue eyes, blonde hair, and light skin-I have brown eyes, brown hair, and dark skin but we are both still Homo sapiens.

[racoll]

That being said I would wonder what this fin clip sequence would tell us about L46/L98, or L66/L399/L400, or etc, etc I'm sure you get the idea. My point is my friend has blue eyes, blonde hair, and light skin-I have brown eyes, brown hair, and dark skin but we are both still Homo sapiens.

These are but assumptions until someone actually tries.

[Suckermouth]

Ah, oops, mixed up the name of the seller! Sorry for the confusion!

Hey racoll, if the haplotypes between the male and female are different, it doesn't mean much since I don't know the amount of variation within a species, isn't that right? Perhaps I'll have to sequence some of the other Hypancistrus we have samples of (there should be samples of the four recently described species somewhere...) to get an idea of the amount of variation within and between Hypancistrus species.

Hey dconnors, I want to see pictures of the offspring so we can see what the resulting phenotype(s) are!

[racoll]

Hey racoll, if the haplotypes between the male and female are different, it doesn't mean much since I don't know the amount of variation within a species, isn't that right?

It depends how different!

It won't be terribly scientific, I agree, but it will give you a ball-park idea of how distinct they are.

If they come out at say >3% different, then it is more likely that you are looking at separate species.

[Suckermouth]

True enough, that is if I didn't screw it up and get myself some numts or COI-like sequence. I'll be starting my training with molecular techniques this summer so I'll throw some Hypancistrus samples in there if there's extra space. We'll be using cyt B for the project I'm helping with.

[MatsP]

Just to clarify the H. sapiens and it's great variation: Whatever feature of humans you take - say skin colour, you will find that there is the whole range from pasty white/almost blue to the darkest imaginable brown. There is no DISTINCT differential case where one particular feature is much different from others. Yes, people in Southeast Asia look different from those in Northern Europe, and both of these are different from people in Africa. But it is the same species. Domestic dogs are another example of "very different looks, but the same species". They are, however, by all definitions one species. In the case of dogs, the act of selective breeding done by humans has affected the "looks" quite a lot - same as with goldfish for example.

--
Mats

[racoll]

True enough, that is if I didn't screw it up and get myself some numts or COI-like sequence.

You should be okay. I've done over 500 COI sequences, and am yet to find an obvious numt (one that has weird amino acid code).

[Suckermouth]

Perhaps. I have just read the Buhay, 2009 (‘‘COI-LIKE’’ SEQUENCES ARE BECOMING PROBLEMATIC IN MOLECULAR SYSTEMATIC AND DNA BARCODING STUDIES) paper so it is fresh in my mind. If you haven't read it, take a look, it's got a funny, bogus phylogram she made to prove a point.

[racoll]

Perhaps. I have just read the Buhay, 2009 (‘‘COI-LIKE’’ SEQUENCES ARE BECOMING PROBLEMATIC IN MOLECULAR SYSTEMATIC AND DNA BARCODING STUDIES) paper so it is fresh in my mind. If you haven't read it, take a look, it's got a funny, bogus phylogram she made to prove a point.

Good paper that one.

If you do what she recommends, it should be quite easy to identify serious numts. They are probably also probably more prevalent in some groups more than others.

I prefer to check the integrity of sequences by eye, and assemble the contigs manually. This should reduce a lot of sloppy errors. For this I like to use Finch TV rather than Sequencher, which is too automated for my liking.

Here are some ways to avoid error and numts:

Manually assemble contigs
Get reading frame correct
Discard messy sequences
Don't sequence PCR products with crappy or multiple gel bands
Look for unusual amino acid changes, indels and stop codons
Compare to published mitogenomes
Extract only mitochondrion rich muscle tissue
Look at base compositional biases

[Suckermouth]

Extract only mitochondrion rich muscle tissue

Not on my live fish! ;) But your tips are noted, thanks!

[Mike_Noren]

Guys, do yourselves a favor and check out Geneious for the assembly, proofreading, BLAST'ing and editing of the sequences. I've used DNAstar and Staden, and for me Geneious is just in another division, almost another sport.
(Not affiliated with Geneious in any way, just a very satisified customer. To be brutally honest it's the first biomedical/phylogenetic software I've ever used that I consider to be of commercial-grade quality.)

[Jon]

Not gonna lie--manually assembling contigs sounds like a huge pain in the ass.

Automation is present and future. You can't fight it ;).

[Jon]

Also, it should be noted that most responsible breeders only spawn and or pair fish that have been caught in coordinated shipments from the same region. In my experience, even with this safeguard in mind, I have seen very pronounced polymorphisms in coloration between aforesaid co-captured individuals, not to mention differences in patterning between male and female members of the same, albeit loosely defined, species.

I wouldn't worry at all. And assuming they are both 260s, which they well appear to be, the likelihood that coQ sequences would differ to any degree would be low, even if they weren't captured from the same locality.

[racoll]

Guys, do yourselves a favor and check out Geneious for the assembly, proofreading, BLAST'ing and editing of the sequences.

Yeah, folks have been banging on about this here too.

Should really give it a go. Now, how to get it on my laptop?