Phylogenetic relationships of Middle American cichlids

New cichlid species and taxonomy
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Bojan Dolenc
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Phylogenetic relationships of Middle American cichlids

Post by Bojan Dolenc » Fri Dec 05, 2008 1:41 am

Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini)
Říčan, O, R Zardoya & I Doadrio, 2008. Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. Molecular Phylogenetics and Evolution 49: 941–957.

Abstract

Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most genera has never been demonstrated, and many species groups are without applicable generic names after their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Říčan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91–110], and in the present study, we have added and analyzed independent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic hypothesis. We have analyzed a combined cytb-nuclear (RAG1 and two S7 introns) data set of 48 species representing main heroine lineages to achieve further resolution of heroine higher taxonomic levels and a combined cytb-morphological data set of 92 species to stabilize generic taxonomy. The recovered phylogenies supported the circumamazonian—CAM—Heroini (sensu Concheiro Peréz et al., 2007) as a monophyletic group, that could be divided into six main clades: (1) australoheroines (the southernmost heroine genus Australoheros), (2) nandopsines (the Antillean genus Nandopsis), (3) caquetaines (including the north western Amazonian genera Caquetaia and Heroina), (4) astatheroines (including Astatheros, Herotilapia and Rocio), (5) amphilophines (including Amphilophus and related genera), and (6) herichthyines (including Herichthys and related genera). Nuclear and mitochondrial data partitions arrived at highly congruent topologies. Suprageneric relationships were influenced mainly by the nuclear signal, as well as the most basal phylogenetic position of Australoheros within CAM heroines. The new phylogeny of the tribe Heroini provides robust framework to stabilize the taxonomy of the group and for future comparative studies on these morphologically and ecologically diverse freshwater fishes. Morphology was mostly informative at the genus level and aid in determining the monophyly and composition of heroine genera. Upon acceptance of all putative genera, as recovered in this study, the Heroini would be with 35 genera the most genus-rich clade of Neotropical cichlids.
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Re: Phylogenetic relationships of Middle American cichlids

Post by Dan Woodland » Fri Dec 05, 2008 7:17 am

I have the paper if someone is interested.... mojarra@cox.net...

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Re: Phylogenetic relationships of Middle American cichlids

Post by Bojan Dolenc » Fri Dec 05, 2008 8:34 am

I also have the paper: bojan.dolenc@aqua-vita.si
Change in habit, producing change of function, is the main cause of the production of change in living structure. F. Wood Jones (1953) Trends of life

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Re: Phylogenetic relationships of Middle American cichlids

Post by DRE » Tue Feb 03, 2015 2:14 am

Old, but still. The paper is also available here:
http://zardoyalab.com/pdfs/RicanMPE2008.pdf

I was wondering why is it that fishbase and Catalog of Fishes has not revived Astatheros? Why are cichlidae using Astatheros?

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Re: Phylogenetic relationships of Middle American cichlids

Post by Willem Heijns » Tue Feb 03, 2015 2:30 am

Maybe they are just a little bit slow. :wink:

It illustrates perfectly that generic assignments are a matter of opinion. Apparently (if the above doesn't go) the work of Rican et al. (2008) is not recognized and/or accepted and the current opinion is to follow CLOFFSCA.
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Re: Phylogenetic relationships of Middle American cichlids

Post by cichla » Thu Feb 05, 2015 5:59 am

Dear DRE, dear all,
there are two different kinds of contribution of zoological systematics: (1) phylogenetic analysis which provide the relationship of the recognized entities, and (2) papers about the taxonomy which provide the necessary diagnoses of the taxonomic units.

Usually, only taxonomic papers are used to change or to approve the classification (names). Since yet no comprehensive taxonomic paper about the Meso-American Cichlids is published. So, I think we need to wait until such contribution (published in a scientific, peer-reviewed journal) is available before we can use the 'new' names of genera for these cichlids.

Best, Cichla

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Re: Phylogenetic relationships of Middle American cichlids

Post by DRE » Thu Feb 05, 2015 10:21 am

Still it is used on cichlidae.com, right?
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Re: Phylogenetic relationships of Middle American cichlids

Post by Juan Artigas » Thu Feb 05, 2015 11:26 am

Yes correct we use it, you can read in the genus profile why
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Re: Phylogenetic relationships of Middle American cichlids

Post by Willem Heijns » Fri Feb 06, 2015 3:52 am

Ingo,
I wish there was such a clear distinction between phylogenetic and taxonomic papers. I have seen many phylogenetic studies with a paragraph "taxonomic consequences", containing concrete proposals for nomenclatural change. Also I have seen many taxonomic papers I could hardly describe as having the necessary diagnoses.
I'm afraid that if we hold on to this criterion in a (too) stringent way, many "old and forgotten" names would have to be treated as "valid" again.
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Re: Phylogenetic relationships of Middle American cichlids

Post by Rico Morgenstern » Sat Feb 07, 2015 7:32 am

I agree Willem, phylogeny and taxonomy are anyway interwoven since the emerge (and success) of phylogenetic systematics. A 'natural' classification has been sought since the discovery that organisms are naturally interrelated, even if the methods and concepts to acheive that goal have changed with time. Phylogenetics is the approach currently prefered to assess those natural interrelationships and to classify organisms accordingly. However, it is of course lamentable that taxonomic changes are often proposed en passant according to tree topology, but without (re)diagnoses or at least proper discussion of the taxa concerned. I hope this situation will be remedied soon. A (phenotypical) diagnosis, or better diagnosability, is clearly required at the species level (simply because indistinguishable species are non-observable, and thus useless except perhaps for some theoretical considerations) but should also remain an important criterion for recognizing genera, and be it only as a means to decide where to apply the genus category in a phylogenetic tree based on DNA analysis.
cichla wrote:So, I think we need to wait until such contribution (published in a scientific, peer-reviewed journal) is available before we can use the 'new' names of genera for these cichlids.
In spite of the above-said, I think that we should make use of the framework of molecular phylogenies in those cases where the results confirmed by various methods and datasets. We have the peculiar situation among CA cichlids that the most genera have never been properly defined and that any classification used during the last decades is decidedly tentative. CLOFFSCA is no exception, anyway I cannot repeat often enough that it is only a check list (and very useful as such) but not a revision; therefore it cannot be expected to provide a comprehensive rationale for the classification. The concepts of some genera as used there, especially Amphilophus and Vieja are not tenable, for those assemblages have been unambigously demonstrated to be polyphyletic. And polyphyletic taxa are 'forbidden' under any approach in systematics, unless perhaps you are a creationist. So I think there are sound and valid reasons for distinguishing between Amphilophus and Astatheros, even if we have no proper diagnosis for the former yet. For Astatheros, the definition given by Regan 1905 still holds and can be tentatively adopted, although it must be complemented by phylogenetically meaningful character states.
Juan Artigas wrote:Yes correct we use it, you can read in the genus profile why
Juan Miguel, your justification for recognizing Astatheros is essentially the same. However, based on the evidence you have used, the species calobrensis, nourissati and margaritifer must be removed. The former two clearly belong to other lineages (i.e. they would render Astatheros polyphyletic) and the latter has never been included in any phylogenetic study nor otherwise clearly demonstrated to be a member of this group. The criteria used by Bussing & Martin (1975) are admittedly superficial and do only partly apply to this species (if it is one at all and not a hybrid, which can by no means be ruled out), in fact it is currently not referrable to any genus.

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Re: Phylogenetic relationships of Middle American cichlids

Post by Juan Artigas » Sat Feb 07, 2015 11:49 am

Rico Morgenstern wrote:Juan Miguel, your justification for recognizing Astatheros is essentially the same. However, based on the evidence you have used, the species calobrensis, nourissati and margaritifer must be removed. The former two clearly belong to other lineages (i.e. they would render Astatheros polyphyletic) and the latter has never been included in any phylogenetic study nor otherwise clearly demonstrated to be a member of this group. The criteria used by Bussing & Martin (1975) are admittedly superficial and do only partly apply to this species (if it is one at all and not a hybrid, which can by no means be ruled out), in fact it is currently not referrable to any genus.
Thanks for the comments Rico, Jordan (1930) placed Heros margaritifer in Astatheros, I chose to accept that in the catalog for the time being. In any case, for all it has been written I would be very surprised if it does not turn out to be a synonym of Astatheros macracanthus.

About nourissati you are right, it shows in Astatheros in the catalog just for behavioral association with A. robertsoni with no reference. I have procrastinated moving it to Theraps where it is more properly placed in view of the available literature (although it does not behave like a Theraps at all). It seems that for all we know Allgayer was probably right after all (Even if his diagnosis of Theraps is wrong). I have come to think nourissati could be a natural hybrid of Theraps irregularis, in my opinion probably with Astatheros robertsoni.

As for calobrense again, I placed it in Astatheros for morphological association following Bussing & Martin (1975:37) admittedly by them "very superficial appraisal", nevertheless, it seems somehow tentatively more consistent with its morphology and coloration than to place it in Amphilophus.

This being said, there is the case of bocourti, following phylogenetic data should probably be in Vieja for association with V. pearsei. I have adopted an orthodox position in its regard waiting for a taxonomic reference to do the move, that attitude now seems inconsistent with some other catalog decisions and admittedly confusing. I have being suggested several times (recently by Willem) to move it to Vieja and I have decided to do so as soon as I get to prepare a paragraph with the reasons to do so, to be posted in the CRC announcements.
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Re: Phylogenetic relationships of Middle American cichlids

Post by Willem Heijns » Sun Feb 08, 2015 5:06 am

A very interesting issue is emerging here. The position of phylogeny in relation to taxonomy.

In my view phylogeny is the study of history. Where does diversity come from and how are organisms related (in terms of descent)? Taxonomy is classification. How do we classify organisms into taxa (be it genera or species or any other level)?

Phylogenetic classification is a term uniting the two fields. In the old days classifications were based on (phenotypic) similarities; nowadays they are more and more based on phylogenetic relationships. And rightly so. Phylogenetic relationships are increasingly discovered using molecular analyses.

And here's the dilemma: to transform these phylogenetic trees (based on DNA) into taxonomic classifications (species, genera), we apparently need observable (i.e. phenotypic) characters, to be presented in a diagnosis. Rico says: "indistinguishable species are non-observable and thus useless". At least for us hobbyists.

Aside from the fact that it is much more trendy to publish new phylogenetic trees than it is to write thorough diagnoses, molecular characters are not far from being included in these diagnoses. Říčan (pers.comm.) is about to do precisely this. And if he doesn't, someone else will, eventually.

Imagine two genera being diagnosed with mainly (or exclusively) molecular characters and given available names, do we recognise these?
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Re: Phylogenetic relationships of Middle American cichlids

Post by Juan Artigas » Sun Feb 08, 2015 8:17 am

Willem Heijns wrote:Imagine two genera being diagnosed with mainly (or exclusively) molecular characters and given available names, do we recognise these?
I think you should consider the fact that differences in genotype should express in differences in the phenotype, visible (and measurable), for the aquarist or the taxonomist (if it requires dissection). How can you give such a weight to genotypic differences that do not express? Isn't the genotype a code to express in the phenotype with the purpose to survive and reproduce?
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Re: Phylogenetic relationships of Middle American cichlids

Post by Willem Heijns » Sun Feb 08, 2015 9:23 am

I recently read a paper (but I seem to have lost it) with an interesting discussion about species showing phenotypic and/or genetic variation. The subject was adaptive radiation, where few genetic changes (lack of time) result in many different phenotypes. The flipside of this is many genetic changes resulting in few changes in phenotypes, because of convergence. The extreme of this is the phenomenon of cryptic species.

Be that as it may, if we (hobbyists) need observable characters to distinguish between species, how do we go about diagnoses based on molecular characters? Genetic differences may be expressed in phenotypes, but I can imagine situations where these are not included in published diagnoses, because the DNA is considered enough to define the species.
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Re: Phylogenetic relationships of Middle American cichlids

Post by Bas Pels » Sun Feb 08, 2015 2:46 pm

I once read that, going form somethnig like a chimpansee, we only needed to change a few regulatory genes, that is, we needed to keep some bones growing for a longer duration and others not.

2 % of our DNA is different, but a lot of these differences are related with non coding DNA, or genes coding for proteins which both function well. I therefore would say the differences between our DNA is highly irrelevant for our genotype.

The same would go for the differences between say a citrinellum and a dovii. Most of the differences in the DNA does not relate to the bodyshape.

Measuring more than one part of the genome has resulted in more than one phylogenetic trees, which differ greatly on the species level, but not that much on the higher levels. As DNA consists of 4 letters, and C and G often exchange each other, just as a T is most often replaced by an A (and not a C or G) we can, by measuring a difference, not say how often the A has been replaced by a T and vice versa.

Therefore I think we should measure more genes, and than try to combine the results.

I think this will not change the say Petenia from an Amphilophine cichlid into a Herichthyne cichlid, but it might solve, for instance the place where H calobrense ends up within the Amphilophines.

Far too much is uncertain yet

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