re: Shape based assignment as a multivariate measure

Jan ( Watermillman) can probably correct my presumptions about Kullander's species delineation work. He seems to have the historical details covered well.

It's unfortunate that Fishbase has deleted their "Occurrences" link for altum. However, even from the scalare "Occurrences" page, we can see that Kullander is aware of T Honslo ( and of course there were others) with finds at Orinoco locations such as Rio Inirida, Colombia.

Some of the deleted "Occurrences" , are listed on Ed's Altum Distribution Map.


re: Shape based assignment as a multivariate measure

It helps to run through Burgess 1979 article in the "Chronicles" section, titled "The Species of Angelfishes", to see how an interpretation of Schultz ( and perhaps Schultz ) is so hard to follow.

For starters, the fish from the uppermost Rio Negro are ID'd as altum in the end. Axelrod's new specimens are not so high in the counts.
However, from Schultz, these fish are all scalare, and so in the translation, there are difficulties, especially as it all translates into charts and maps with legends.

However, the problem with scale counts does not disappear, even taking into account any possible reconciliation of methods used. One problem is that sometimes at least, scale count is given as averages. Hence no raw data showing limits or range for the comparison and binning being done.
Last edited by rag on Sun Jan 02, 2011 6:12 pm, edited 5 times in total.

re: Shape based assignment as a multivariate measure

Burgess starts out interestingly, in mode much as we are in today, but more exclusive.

To us only Atabapo or true Orinoco sites could offer a guaranteed-sight-unseen, P altum. Burgess goes a bit further, saying the fish has only been found before, in the Orinoco basin.

Immediately thereafter, however, we find in his presentation of the map, that the upper Rio Negro specimens ( above or upstream of Axelrod's expedition locales), are included as altum ( black triangle). Axelrod's fish are thought possibly altum but the higher up Rio Negro locations are now classed as P altum. The provenance of these 6 upper Rio Negro specimens ( up as far as the Casiquiare Canal ) is not clear. They are not from Schultz. Perhaps they were purchased by Axelrod.

With this kind of shifting and changing landscape, and averages being used instead of lmits, it is easy to see how confusion arose and stays.

Here is abridged Burgess interpreting Schultz and giving his appraisal too at the same time, and overlaying his results and interpretation at times, as well.
Starting about Schultz's opinion...ending in Burgess' opinion..overlaid on the map in a mix and on that map we find Burgess now finds that the upper Rio Negro locales are P altum, even though it's supposedly only found only in the Orinoco basin.
..undoubtedly P altum represents P scalare type of angelfish in the upper Orinoco...having higher average fin and scale and vertebrae than scalare...however since altum has been taken only from Upper Orinoco basin, I prefer to species
Then we get to the counts.
When the average number of...fin rays and scales were plotted on a map... at the Igarape Anapichi and Apania...average soft ray dorsal count 26.2 anal fin ray 28.3 and scale rows 38.1.
the other 6 specimens from higher up the Rio Negro
average soft dorsal fin rays 28.0 anal fin 29.8 scale rows 40.3

when compared to counts for P altum from Orinoco ( dorsal 28.6 anal 29.7 and scale 42.6)
It must be remembered that there are possible method of counting differences between Schultz and Burgess, and between Burgess and the provider of the data on Orinoco altum.

So the map may have Schultz method and Burgess method (and others) all in one.

We see that the 6 specimens from up to the Cas. Canal exceed the Orinoco altum for average anal fin rays, come .6 from Orinoco on dorsal rays, and come 2.6 away from Orinoco on scale rows.

That is by Burgess, but the Orinoco specimens being compared to, may not have been examined by Burgess, and may have been counted by a different method.

As well, when checking the chart provided a bit further down, a different picture emerges than these averages suggests.

we see that the Axelrod specimens outnumber the others, and interestingly, mostly have HIGHER counts - in some instances the main bulk of the group is higher than ANY individual Orinoco altum.
When it comes to scales, unfortunately, it's been averaged. But it's close, indicating a good chance of overlap - or even Axelrod specimens exceeding P altum limits, there too.

Another more detailed chart later shows this to be true. The Rio Negro values for scale rows are at the 45 and 47 limit, whereas Orinoco altum is 43 !

Even Belem at the mouth of the Amazon, beats Orinoco altum on scale count.

Obviously the first item on a list for any study now is to set this out carefully and find out what happened, to put it all into context for the reader...and the into context for the study researchers themselves, since these counts are not going away......where Rio Negro fishes out-altum the Orinoco altum specimens. It's instead simply been "waved off".

There is an asterisk near the beginning of the Burgess article, indicating error in the corresponding TFH article in Position 2 on the map ( Axelrod site).
I don't think the whole thing has been clearly corrected for this article ( Since Burgess himself declares Orinoco altum higher in all counts, it's a claim unlikely to be found not to be self-contradictory )

I hate to do drone work, but I'm going to find the average mean of the figures given and see how they correspond within the Burgess article itself.

It just looks to me like bunches of Rio Negro fish specimens have higher counts on everything.

- but that is not the impression given once averaged, or the implication from Burgess.

Last edited by rag on Mon Jan 03, 2011 4:22 pm, edited 2 times in total.

re: Shape based assignment as a multivariate measure

Dirk, here are some mean average figures to compare Burgess with Burgess on Schultz, and with Burgess on Burgess on Schultz .

Orinoco P altum

soft dorsal fin rays
25, 25, 26, 26, 26, 27, 27, 27, 27 divided by 9 (specimens)= 26.2 mean average.

This number corresponds with Burgess on the Axelrod Igarapes collection
- not upper Orinoco ( which he previousy gave as 28.6 )

So I think we've found collation error at the base of the quagmire , Dirk. but there are more comparisons...maybe that chart is reflecting what Burgess reported about TFH error on the map...which remains unfixed in one of the charts.

Now to collate them plausibly properly, and take a look.

We have collections with 6, 9, and 25 individuals, from 3 locales. the six are mentioned as the uppermost Rio Negro collection, up to the Casiquiare.

The Axelrod collection is listed as 25 individuals at the Igarapes and listed dorsal mean average works out to 28.5

...close enough to be the altum from Orinoco at 28.6 ( 25 of them)

and the 9 specimens , listed as Orinoco altum with dorsal rays 27.8, those are Axelrod's Igarapes specimens with vaues taken from the Upper Rio Negro 6.

New collation of dorsal fin ray with anal fin ray figures

Orinoco altum 25 specimens
my mean average and Burgess
Dorsal 28.5 given as 28.6 Burgess
Anal 28.8 given as 29.7 Burgess

Upper Rio Negro 6 specimens
my mean averages and Burgess
Dorsal 27.8 given as 28 Burgess
Anal 29.8 given as 29.8 Burgess

Axelrod Igarapes 9 specimens
my mean averages and Burgess
Dorsal 26.2 given as 26.2 Burgess.
Anal 28.3 given as 28.3 Burgess

Which fits "the cline" hypothesis nicely, as Burgess notes.

However, we are not out of the woods yet. There is another chart with more confusing stuff...and there is the species limits ( any resulting overlaps) , rather than the averages, to consider. And the paradox of closeness of scale row figures on altum / scalare for Burgess, compared with Kullander.

Burgess, in text, confirms:

The Igarape collection has 9 specimens, at average 26.2 Dorsal Rays. Anal fin 28.3, Scales 38.1
The Upper Rio Negro 6 specimens are said to have 28, 29.8 and 40.3
The Upper Orinoco 25 specimens have average 28.6 Dorsal Rays 29.7 Anal Fin and 42.6 Scales
Last edited by rag on Sun Jan 02, 2011 11:41 pm, edited 7 times in total.

re: Shape based assignment as a multivariate measure

The next chart is on scale rows, and it says it is after Schultz, with addition from Burgess material on Axelrod's Igarapes collection.

It lists 16 individuals from upper Orinoco, and 10 individuals from upper Rio Negro, and 23 individuals from Axelrod's Igarapes collection.
Even if counting the upper Rio Negro 6 fish from before as from Axelrod, that adds up to only 6 + 9 = 15 individuals, vs. this new number of 23.

This is the chart where both upper Rio Negro and The Igarapes Collection are higher in scale count in every way, to Orinoco.

Here the Rio Negro sites, all of them, have fish with more scales than Orinoco, higher scale counts in just about every way imaginable, from "least number of scales on any individual" to "most number of scales on any individual" and so on.

Let's see if anything pops out.

re: Shape based assignment as a multivariate measure

scale count averages and limits

Upper Orinoco 16 specimens mean average 38.1 lowest count 34 scales highest count 43 scales

Upper Rio Negro 10 specimens mean average 39.6 lowest count 36 scales highest count 45 scales

Igarapes 23 specimens mean average 43 lowest count 40 scales highest count 47 scales

Let's try reversing Orinoco and Igarapes again

mean averages

Orinoco 23 specimens average 43, range 40 to 47 scales
Upper Rio Negro 10 specimens average 39.6, range 36 to 45 scales
Igarapes 16 specimens average 38.1, range 34 to 43 scales

It fits the hypothesis better, but that's not the purpose. We do have a complete match on vaues for The Igarapes collection. We have none of them able to correspond completely to the previous chart on fins. that is, different numbers of specimens are given for this chart, as well as having the collation errors upon errors.

It fits with Kullander, but again, going by Kullander auto-defines Upper Rio Negro as a hybrid zone.

A further check can be done by seeing what Burgess says about further removed scalare locales and their counts, vs. altum or hybrid zone fish.

Burgess has Schultz or himself with lots of scalare over the 39 count for scale rows. Up to 44 in one instance. This conflicts with Kullander's 39 for scalare.

It's not that Kullander isn't right. it's about *what number of specimens, and range of fish locales*, did Kullander use, to count scale number and give that max length ?

[sigh] I can always read the Axelrod account again to see if he mentions something about numbers of fish.

OK Axelrod says they fished out about 8 angelfish that night on the Igarape, and even found P altum later ( which might mean he purchased some from upriver, those being the Upper Rio Negro fish. )

But there's still another way to compare Burgess with Burgess. Checking other locales for scalare to see if chart matches chart

it's useless.

Burgess says Axelrod extended the range to Humanita. First chart has Humanita with 32 specimens, second chart has it with 16.
Some locales match up, some are partially the same, some totally different, chart to chart.

There are the reversals in the collation, errors on errors in collation, and mathematical errors in averaging and rounding ( errors always upwards ). Finally nothing matches, or adds up.

The only troubling aspect left
after clearing the debris

is that all indications are, that many Orinoco altum do seem to have lesser scale counts than 46-48, by any permutation of Schultz through Burgess or Burgess on the new collection.

Whomever counted the Orinoco fish, counted some as high as 47, thus in the range of Kullander's upper limit of 48, and lending cromulence 8) to the lesser counts given for Orinoco ( because the scale counting method seems comparable or same here ) ...
...hence credence once more, to the notion of between-species overlap of values for the range of the quantitative characters.

The Kullander-inspired notion is that scalare "top out" at 39 scales. This might be challenged by some direct counts. Belem tops out at 44 and Manaus at 42 with Guyana at 40 according to Burgess and possibly Schultz.

With the addition of "species territory overlap", we have some possible solutions, of which more than one may be true:

a) "species overlap in territory"
b) "hybridization zone"
c) "overlap in range of quantitative characters for the 2 species"
d) "it's Axelrod publishing, and nothing should be taken seriously"*

* Maybe he also bought a few selections of fish and later they couldn't sort out which fishes were which. Since everything that could be mixed up, was mixed up, perhaps the specimens got mixed up, as well.


re: Shape based assignment as a multivariate measure

a) "species overlap in territory"
b) "hybridization zone"
c) "overlap in range of quantitative characters for the 2 species"
d) "it's Axelrod publishing, and nothing should be taken seriously"*
e) all of the above

If we imagine a researcher getting a batch of fish from a location with "a","b", or "c" or a comboof them :

In the box are altum, scalare, maybe hybrids , OR various combinations.
We sort by scale count. Anything 30-39 are scalare, and anything over 39 and under 46, are hybrids.

But oddly, we have made no attempt to make a bin to take "hybrids".

What next ? We already locked ourselves into not having the 2 species overlap in counts. "Overlap in territory" doesn't help. The scale counts are are "in-between".

We conclude that because they are together, the altum might tend to look lke the scalare a bit phenotypically. And it's the water.

re: Shape based assignment as a multivariate measure

Hi Dave,

Thanks for your very thorough investigation of all of these counts, it shows up how complicated all of this gets and it also shows up that it is not so easy to classify angels based in these measurements, exactly what started off this thread.

I just wonder if anyone has investigated whether male and female fishes differ in these measurements. Why I ask this is because if I look at my scalare strains (I have three) then the females are always smaller than the males. If total size is one of the measurements performed, this could further complicate this issue.

Your thoughts?

Kind regards,

Somerset West, South Africa

re: Shape based assignment as a multivariate measure

With the modern camera and HD screens, we should be able to count scales and rays.
Which reminds me. Is this still The Stone Age, for scientists ?
Where are all the pics of those Santa Isabel, Boa Vista, and other scalares ?

What, not one photograph, in this day and age ?
Is this a bad joke, or what ?

Since in post-normal science we are not ever privy, it seems, to actual measurements ( even grey literature in the old days gave more), and we see only manipulated data points, pictorials, and conclusions, we have no way of knowing if Kullander's pointers are good enough to use, or not.

It's the method that is inadequate here, not the possible limits or limitations imposed by reality or Kullander, Burgess, or Schultz.

If 46 scales is really a hard minimum for Orinoco altum, that can easily be at least given a quick check. It may show us nothing but that probably most fall within Kullander's range, or it may show that there is a question.

The wide gap between 39 and 46 certainly seems definitive enough !

Or maybe it's not a hard limit at all. Just like "size'. He means "Not really".

Checking for scalare is harder because they might be hybrids.

There would seem to be enough sexual dimorphism to make some difference.
A female does not look quite like a small male. It's one of those things we do not have down to a formula on how to describe the whole picture. Domestics seem easier to discern the sex of, especially because the females are always bulging. :)

If the computer program that takes into account size, rotation, position, and "evens everything out", is blind to sex difference, it could skew the results, I'd think.

Sexual dimorphism sure would seem to be able to throw a curve into the outlines and angles, once the fish are "evened out" for size by the program.

...and if in these 3-step researches, the fish are presorted and then binned according to species ( i.e. size), then sex related size difference makes a difference.

Last edited by rag on Tue Jan 04, 2011 12:35 am, edited 3 times in total.

re: Shape based assignment as a multivariate measure

Dirk, an interesting question to me, is what to think of the situation for Science, if Kullander used only a few specimens of each species, maybe 20 ( however correctly chosen), in order to draw his species descriptions within the genus - and then later, everyone used those descriptions about a few individuals, to generalize and then to deduce ?

Raymond Smullyan on deduction and other things

re: Shape based assignment as a multivariate measure

Hi Rag,

I have just got home from watching a days cricket in Cape Town in a gloriously hot (too hot) day in Cape Toen and I have read your further comments.

I have not looked at the youtube clip yet and will do so after this, but I wanted to show you this recent publication on the Endler guppy. I include the summary and there you can see that they have defined these species with overlapping morphometric measurements but on the basis of the molecular analysis they have separated them into separate species. This sort of situation does not bode well for the definition of angelfish species based on morphometric measurements?

Kind regards,

You do not have the required permissions to view the files attached to this post.
Somerset West, South Africa

re: Shape based assignment as a multivariate measure

I would ask what happens when "overlap" becomes total and complete - when there is no "discernable physical difference" (except as shown by molecular study ).

Then there needs to be ( for us to conclude anything about "species" ), some other kind of observable difference - that is, a difference such as "behaviour". In my estimation, it is still not considered sufficient evidence, to make species distinctions, if the decision is based solely on molecular data. I believe a proposal to make a species split based only on the observations on one molecule, would be rejected - although I'm not sure it would be rejected on entirely reasonable grounds !

I think that a gene can be a phene, a genotype a phenotype, because they physically exist and are measurable.

Similarly, any molecule can be tested for, as can bird song - it is measurable. As is assortative mating.

Therefore there is no real philosophical problem with assigning clade splits along with either molecular lines or song lines. The question is: "Are they inherited ?" Are song and story lines inherited ? "Yes", one might say. Learned but inherited.

This notion of "learned but inherited" is yet another twist on the Lamarckian/Darwinian tango. Some might protest that the "inherited " part is not seen when the babies are raised away from the father. I'd comment that the "inherited" part is also not seen when a different father's sperm is the contributor to the genetics. : ) If you can take away one player in "inheritance" of an individual with a sweep of the arm, why not another ?

"Germ Line" obsession noisily has become the sole determinant of evolutionary tendencies, for our understanding. I'm proposing that "Story Line" is also valid code. I would go so far as to say that "Germ Line" is just another kind of Story Line.

In a flock of birds, researchers noted a DNA difference within samples from the flock.

They then banded or otherwise ID'd live birds which they DNA sampled, and so then they could study them further.
When they took a second look the found there was assortative mating going on amongst the birds in the flock, which was reflective of the DNA difference they had noted.

Seemingly the critters know the difference that we cannot see, and whether it be "scent" or "behaviour" ( perhaps like birdsong accent ), they know each other and choose their mate that way.

Here is the sticking point of this post: The above example seems OK. It's a real example. However what has NOT been PROVEN, is the physical link between the DNA difference, and the mate choosing.

Was it a scent difference ? A colour difference that we cannot see ? Was it even causally related to DNA at all ? Was it a learned, "inherited song" difference ?

Yet another fun twist here, is that humans can now know DNA, and human behaviour based on that knowledge is now influencing some mating choices, and DNA knowlege by dating couples may be a major player in evolution, soon enough. First use would be in avoidance of the expression of genetic disease, through bad mating combinations. So information being inherited through human culture is directly influencing mate choices, thus evolution, now with technically informed guidance from science.

Back to the birds...we actually still do not know if the DNA associated molecule, or the "gene product" is directly or indirectly causing the mate choices - or not at all. Therefore it MAY be case of spurious association.

However, the main point here is that we don't care. We don't care. We have successfully equivocated. We go ahead and say that because the DNA difference goes along with assortative mating, that it's "a hit". We go ahead and now we can use either DNA or mate choice equally, to bin these birds.

So we have progressed from seeing the mate selections as proof of species differences, to DNA correlation as proof. Either one of those will do, in order to to species "bin" the birds.

Here my point is that the birdsong may be every bit as strong a proxy for tracing the lineage as is a gene or a product molecule. Maybe the song is a better proxy in one way, in that it is strictly related to the birds, whereas a gene has it's own history.

Interestingly, from the recent Darwin's Finches hybridization investigations, it seeems that since the birdsong is taught by the male ( the father), then in case of hybridizaion , the hybrid species becomes "his" legacy.

The hybrid offspring males will be taught to sing the local songs, but with the foreign accent. This in turn plays out in mating availabilities and choices.

Any male bird of the hybrid emerging species, will be singing with an accent inherited from the foreign male ancestor of all the hybrids. Most of the mates of those males also will be of the hybrids.

Once such fine distinctions are raised however, there seems an arbitrarily imposed line being drawn, again: why wouldn't a religious cult which is mate-choice segregated, based on some specific behaviours passed down the lineage as learned behaviours, be a new species ?

Their DNA array would soon be different from others', and mate choice is highly correlated - caused apparently by something to do with DNA differences, but actually caused by the learned behaviour.

Furthering this notion, is the observation that religious cults might more enthusiatically engage in producing young, and teaching the survival codes, than secular groups. Often the codes might involve decimation and slight absorbtion, or obliteration of competing cults (or any secular populations).

This could lead to reduction or extinction of competing cults ( song/story lines) and secular populations.

That is a secondary behaviour difference correlated with the story lines, the genetics, and the assortative mating.

Eventually, and probably quickly, some genetic change will occur which is in the same vein as the behavioural difference...and a genetic "accommodation" has occurred. That is, if esteemed behaviour of a religious group is to study code, even as a profession, then any mutation furthering that ability will be immediately beneficial under natural selection. If esteemed behaviour learned from the song is to decimate other cults, then aggressive warriors will be the emerging phenome.

A genetic change which ordinarily, or to the general population would NOT be very beneficial, or might even be deleterious, might be advantageous. A change that IS deleterious can be retained if it offers any advantages that well complement the song's evolutionary direction.

In this picture, we see that randomly generated genetic change is only allowed to be retained because of preceeding behavioural change. What would not be allowed genetically under natural selection is now not only allowed but the landscape where it would work, is already in place.

"Learned behaviour", acquired characteristics, leading to speciation - which is leading us to Lamarckism.

Allow me to preempt rebuttal point that songs may not be inherited at time of gamete meeting gamete.

What exactly is the determinant of the precise time span allowed ( time span during which all information must be transmitted to the "offspring") in order for information to be considered "inherited" ? Why is it tied to the DNA only ? Answer: it is isn't.

Through epigenetics we know inheritance is not only about genes.

On the other hand, even though we know inheritance is not only about genes, one kind of accommodating genetic change may be compared to cementing a previous change in place by encoding for it. Encoding for what has already phenotypically been in place for some time - and is indistinguishable morphologically.

We know that the phenome of offspring and grand-offspring can be drasticlally changed due to epigenetic effects. Learned code/song could bring behaviour that offers an environment which is an epigenetic factor. e.g. enforced choice of menu .

Thus the offsprings' "inheritence", as with the famous agouti mice ( a phenome difference caused 100 % by environment, 0 % genome difference), can be a product of the song, learned behviours, environmental influences. Spuriously or temporarily associated inheritance, at worst - but not nonsensically. 8). After all it's inherited phenomic difference which happens to be 100 % associated with "song" difference and NOT associated in any way, with a gene difference.

Here I plead thusly: Once again, "we don't care." We already admit to our automatic behaviour of accepting EITHER any of the presence/absence, gross amount, relative amount, balance, ratios of the product molecule , OR the
mate choice
, as equally weighty evidence of the same thing ( speciation event).

We are accepting these things as equal and cannot then logically refuse, out of hand, to accept others as equally valid, if equally proven ( in this NOT proven but still accepted )

The study of inheritance of song and information does not stop there. One could trace the trees of the lineages of phylogeneticists, complete with all the same evolutionary terms ... regression, hybridization, and so on. You'll use the terms, words, phrasings, of your clade.

The aura of exclusivity about Evolutionary Biology, does not seem to justify treating the events of biological inheritance as different in kind from any other inheritance event.

Dirk, it seems it's always back to Square One. How were these fish "Kullander binned" ?

What does the "Standard" part of "Standard Length", stand for ?

What does that mean, precisely ?
Last edited by rag on Wed Jan 05, 2011 9:56 am, edited 7 times in total.

re: Shape based assignment as a multivariate measure

Hi Dave,

I think that you have now just about exhausted this topic, and I think that we should try to sum up where we stand with all of this with regard to P scalare and P altum and whilst we are about it we should actually include P leopoldi.

Could you perhaps put together a comparison of the morphometric measurements of these taxa including the Rio Negro fishes so that we can say that this is state of affairs as we have it at the moment.

Your extensive discussion of this topic shows us that species concepts or the definition of what we define in this case as an angelfish species is subject to interpretation and that it is not entirely a crisp clear cut scientific assessment. Species definitions are assisted by morphometric measurements, DNA assessments, and even behaviour and habit assessments and last but not least cytogenetic considerations (chromosome counts for the non-scientists amoungst us)(I cannot assess the last thesis because of the fact that I do not speak Portuguese). This also means that as we add new scientific data to what we know we may change our opinions of what constitutes one of the angelfish species.

My personal opinion is that DNA data will be able to give us another set of important insights into how the different angelfish are related and then we will again have to assess where all of this brings us.

Kind regards,

Somerset West, South Africa