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Hi! - Speciation and Genome Evolution

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Previous Entry Hi! May. 22nd, 2005 @ 04:29 am Next Entry
My name is Nick Poyarkov, I am studying in Moscow State University (Russia) and currently I am interested in speciation and evolutionary biology of European Newts (Triturus) and related urodelian taxa.

What I want to ask you - I wonder if anybody discussed here the problem of subspecies definitions in zoology or biology generally? Actually nearly every biologist have heard about Biological Species Concept (Ernst Mayr's works etc., etc.) and it is a wide spread point of view that the SPECIES is the universal (species in zoology was thaught to be nearly the same as species in botany, for example) and the only "real" taxonomical category, while all lower (subspecies) and higher (genera, familis etc.) categories were considered to be not real but artificial categories for diversity systematization. However, several questions arise...

1) Rather phylosophical one - what means "reality" for a category? How can we determine if the taxonpomical category is real or not? What are suitable criteria?
2) If species is considered to be a "real" taxonomical category - we have individual organisms (they are "real" for sure), we have local populations (also seems to be real because they is limited gene flow among such clusters), we have geographical populations (real again, because we have nearly no gene flow among different geogrpahical popualtions in current time scale or what?), we have subspecies (mostly considered to be hypothetical categories not presented in reality) and we have real species? So, why subspecies are not real then?
3) If they are real - do you know any conceptual ways to separate "the real" subspecies and subspecies which were described only for practical needs?

I will highly appreciate any comments or advises! If you know any publications where the problem of taxonomical categories is discussed (especially some conceptual ideas concerning interspecific differentiation, phylogeography, subspecies criteria etc)- it would be great to get a reference!

Thanks in advance,
Yours sincerely,
NICK
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From:shalyndra
Date:May 23rd, 2005 01:39 am (UTC)
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It's funny you should ask.

I've been delving through an excellent book on the topic:

Speciation, by Jerry A. Coyne and H. Allen Orr (2004. Sinauer Associates, Sunderland, MA)

Here's a few articles that may be more relevant to my research than yours:

Barton, N. H., and G. M. Hewitt. 1989. Adaptation, speciation, and hybrid zones.Nature341:497-503.

Irwin, D.E., J. H. Irwin. 2002. Circular overlaps: Rare demonstrations of speciation. The Auk119:596-602.

Irwin, D.E., J. H. Irwin, and T. D. Price. 2001. Ring species as bridges between microevolution and speciation. Genetica.112-113:223-243.

Martin, P. R., and J. K. McKay. 2004. Latitudinal variation in genetic divergence of populations and the potential for future speciation. Evolution.58:938-945.

Matocq, M. D. 2002. Phylogeographic structure and regional history of the dusky-footed woodrat, Neotoma fuscipes. Molecular Ecology.11:229-242.

Wake, D. B. 1997. Incipient species formation in salamanders of the Ensatina complex. Proc. Natl. Acad. Sci. 94:7761-7767.

In my own opinion, I think that the taxonomic category it is prudent to call "real" depends on the questions you are asking. For example, in conservation, it may be important to adequately delineate as a species or subspecies some population which is particularly rare. In terms of plant diseases, sometimes it is useful to describe as "species" or "subspecies" morphologically and genetically similar pathogens which have different host specificities. Distinguishing subspecies within hybrid swarms in plant systems may only be significant if there is a variable ecological or genetic factor that you wish to look at.If, on the other hand, you are looking at the bigger picture, such as interpreting the fossil record, these finer distinctions may fall out in favor of larger taxonomic groupings that describe only the evolutionarily significant variation among groups. I also think that these kinds of descriptions only underscore the need for unified molecular-based phylogenies, so that everyone can communicate.

I'm sorry if that didn't make a lot of sense, as it was somewhat hastily written. Hope it helps.
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From:triturus
Date:May 23rd, 2005 03:07 am (UTC)

Thanks a lot!

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For the kind comment and refernces!

The book by Coyne and Orr is unknown for me - many thanks! I'll try to get a copy somehow.

As for the papers - I know those by Irwin & Irwin (2002) and david Wake's works of course! Other papers are also new for me - thank you very much!

David Wake is a great person - I've got nearly all his articles concerning ring speciation in Ensatina and other salamanders. In Europe his articles (and articles by his lab gang) are considered to be a splendid example of phylogeographic studies. I am really fond of his works!!!

I am grateful for sharing your point of view.

Well, I absolutely agree that it's very difficult to delimitate any taxon borders when interpreting fossil data.

I completely agree also that it's important to be very careful with evaluation of taxonomical status of local populations if they are endangered. I am also trying to do the same thing here, with newts. But this is rather a matter of practical applicability, what do you think? Well, actually when we operate terms "useful" etc. it's difficult to see any general picture...

Actually, I think that the purpose of taxonomy is not to facilitate our understanding of diversity, but to describe it adequately. This means that when working with any group of organisms the scientist should have some conceptual ideas in his head and should not be too formal in his descriptions. As for me I am pretty doubtful that species is a universal "real" category, same for all organisms (as Mayr proclaimed)... If will try to elaborate a universal criterion for species delimitation - I guess we will have many troubles... For example it's evident that the criterion of "crossability" is completely unsuitable not only for organisms which lack sexual process, but also in many cases for allopatric populations of polytipic species (sic!)... And if we will take prokaryotes - it's completely impossible to use our understanding of taxa in their world...

Traditionally taxonomical categories were considered to be universal and common for all living things. However I am pretty sure that during the evolution the categories also somehow evolved - new kinds of taxonomical differentiation appeared... That's why it's very difficult to compare variation within different taxa of same categories, for example it's evident that differentiation within and among amphibian orders (Anura, Caudata, Gymnophiona) is much more pronounced than within and among orders of Birds. Same, I am not sure that species category in birds means the same level of differentiation as what we call species in amphibian taxonomy.

So I think that it's actually better to elaborate not universal criteria but more useful - for example, working with amphibians we can have an idea what were the major ways of evolution within the group, and we can try to get some general understanding what is for example subspecies or species within amphibians... This will be probably not so universal but much more applicable in practice.
From:pintofbovril
Date:May 24th, 2005 12:41 am (UTC)
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Wow, big topic!

I'd second getting hold of a copy of Coyne and Orr's Speciation book if you're interested in speciation in general, though there's not a huge amount about subspecies in there. The first chapter is entitled Species: Reality and Concepts and the appendix is A catalogue and critique of species concepts which are particularly relevent to the question here. The first chapter focuses largely on the Biological Species Concepts and issues with unisexual and uniparental organisms etc.

The appendix goes through a number of alternatives to the Biological Species Concepts (Coyne and Orr's concept of choice in more depth, discussing the ups and downs of each. See next comment....
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From:triturus
Date:June 24th, 2005 10:36 pm (UTC)

Gratitude

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Thank you very much for your kind answer with so impressive literature review!

Wow! I am impressed!

I see now that I should buy a copy of Coyne and Orr's Speciation and alos try to find some original articles following the references.

The only question arises - where should I buy them?

Probably anybody could advise me a nice book-shop in New York?

This year I am going to USA for two weeks (our University has a kind of exchange with SUNY, so a group of american students goes to Russia and we go to Cranberry Lake Biological Station), but only for 3-4 days in New York - this is a chance for me to visit the deposits of the American Natural History Museum, libraries and book-shops. I am not sure if I will be able to buy books using Amazon because I will stay in the hotel and I am not sure if I will have a card to pay with so I should better look for a good biological book-shop.

Thanks in advance and thanks a lot for help with literature...

NICK
From:pintofbovril
Date:May 24th, 2005 12:44 am (UTC)
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Here are the concepts from the appendix of Coyne and Orr (Coyne, J. A. and Orr, H. A. (2004) Sinauer Associates Inc., Sunderland, MA. ISBN 0-87893-089-2), the quotes they reference for each and some of the relevant literature for each - they cover some of the issues you've asked about:

Genotypic Cluster Species Concept:
"A species is a [morphological or genetically] distinguishable group of individuals that has few or no intermediates when in contact with other such clusters"

- Mallet, J. (1995). A species definition for the modern synthesis. J. Evol. Biol. 14:887-888.

Recognition Species Concept:
"Species are the most inclusive population of individual biparental organisms, which share a common fertilisation system"

- Paterson, H. E. H. (1985). The recognition concept of species. Pp.21-29 in E. S. Verba (ed) Species and Speciation. Transvaal Museum Monograph No.4, Pretoria.
See also
- Lambert, D. M. and Paterson. H. E. H. (1984). On bridging the gap between race and species:The isolation concept and an alternative. Proc. Linn. Soc. NSW 107:501-514.
- Lambert, D. M. et al. (1987). Are species self-defining? Syst. Zool. 36:196-205.
- Masters et al. (1987). The concept of species: Recognition versus isolation. S. Afr. J. Sci. 83:534-537.

Cohesion Species Concept:
"A species is the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms."

- Templeton, A. R. (1989). The meaning of species and speciation: A genetic perspective. Pp. 3-27 in D. Otte and J. A. Endler (eds) Speciation and its Consequences. Sinauer Associates, Sunderland, MA.

Evolutionary Species Concept:
"A species is a single lineage of ancestral descendant populations of organisms, whcih maintains its own identity from other such lineages and which has its own evolutionary tendencies and historical fate"

- Wiley, E. O. (1978). The evolutionary species concept reconsidered. Syst. Zool. 27:17-26.
modified from
- Simpson, G. G. (1961). Principles of Animal Taxonomy. Columbia University Press, New York.

Ecological Species Concept:
"A species is a lineage (or a closely related set of lineages), which occupies an adaptive zone minimally different from that of an other lineage in its range and which evolves separately from all lineages outside its range"

- Van Valen, L. (1976). Ecological species, multispecies, and oaks. Taxon. 25:233-239.

Phylogenetic Species Concept 1:
"A phylogenetic species is an irreducible (basal) cluster of organisms that is diagnosably distinct from other such clusters, and within which there is a parental pattern of ancestry and descent"

- Cracraft, J. (1989). Speciation and its ontology: The empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. Pp.28-59 in D. Otte and J. A. Endler (Eds) Speciation and its Consequences. Sinauer Associates, Sunderland, MA.
see also
- Wheeler, Q. D. and Nixon, K. C. (1990). Another way of looking at the species problem: A reply to Queiroz and Donoghue. Cladistics. 6:77-81.

Phylogenetic Species Concept 2:
"A species is the smallest (exclusive) monophyletic group of common ancestry"
- de Queiroz, K. and Donoghue, M. J. (1988). Phylogenetic systematics and the species problem. Cladistics. 4:317-338.
see also
- Rosen, D. E. (1979). Fishes from the uplands and intermontane basins of Guatemala: Revisionary studies and comparative geography. Bull. Am. Mus. Nat. Hist. 162:267-376.
- Mishler, B. D. and Brandon, R. N. (1987). Individuality, pluralism, and the phylogenetic species concept. Biol. Philos. 2:397-414.
- Baum, D. A. and Donoghue, M. J. (1995). Choosing among alternative phylogenetic species concepts. Syst. Bot. 20:560-573.
And also, I suppose some more of the debate in: de Queiroz, K. and Donoghue, M. J. (1990). Phylogenetic systematics and the species problem or Nelson's version of cladistics? Cladistics 6:61-75.
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From:triturus
Date:June 24th, 2005 10:50 pm (UTC)

Concepts

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Some comments and questions, if you mind:

Genotypic Cluster Species Concept:
"A species is a [morphological or genetically] distinguishable group of individuals that has few or no intermediates when in contact with other such clusters" - Do they mean a contact in time, or in space? The matter of "distinguishability" - is it an objective criterion? I mean am I right if I'll say that many depends of who is going to distinguish the groups?

Recognition Species Concept:
"Species are the most inclusive population of individual biparental organisms, which share a common fertilisation system" - I have read the Paternson's article. Unfortunatelly I found this idea to be a little bit not useful in practise - the problem of choice still is not solved. Especially when we compare a group of isolated allopatric populations, all of them are different from each other but we can not say anything if they are potentially inclusive population or not.

Evolutionary Species Concept:
"A species is a single lineage of ancestral descendant populations of organisms, whcih maintains its own identity from other such lineages and which has its own evolutionary tendencies and historical fate" - A very famous definition! Mostly because of Simpson was one of the authors... His book was even translated in russian. I like it very much.

Ecological Species Concept:
"A species is a lineage (or a closely related set of lineages), which occupies an adaptive zone minimally different from that of an other lineage in its range and which evolves separately from all lineages outside its range" - and what should we do if isolated but similar populations occupy really different adaptive zones (niches)? There are many examples of such situations. Are they different species or not?

Phylogenetic Species Concept 1:
"A phylogenetic species is an irreducible (basal) cluster of organisms that is diagnosably distinct from other such clusters, and within which there is a parental pattern of ancestry and descent" - this one is at least a simple one. It seems that it is possible to check it. I like it.

Phylogenetic Species Concept 2:
"A species is the smallest (exclusive) monophyletic group of common ancestry" - this one is at least a simple one. It seems that it is possible to check it.
From:msbarker
Date:June 5th, 2005 11:55 pm (UTC)

My two cents and some books

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I want to keep this comment short because could go on for way too long. In botany, subspecies are alomst always used to delineate a portion of a species that is both geographically and morphologically differentiated from other parts of the species. The distinction between subspecies differences and species differences is that the subspecies differences are not as pronounced as the species differences for that particular genus. Further, I think these are usually real difference, and their description can be used to accurately describe the diversity. In zoology, I don't think the use of subspecies is so well codified and I am not sure that the category is used similarly across animal taxa. But I am no zoologist. However, the philosophical questions about species reality are sort of moot for studying species. If they are not real, then you can not study them, correct? So, I operate on the premise that they are real and evaluate hypotheses to demonstrate discontinuities in nature; be it morphological, genetic, or phylogenetic discontinuities. But if you want to read more about the philosophical questions, you should check out:

"Species: New multidisciplinary essays" edited by R. A. Wilson, 1999, MIT Press. - Tons of philosophical discussions on species reality.

I would also suggest the following book as well:

"Species Concepts and Phylogenetic Theory: A Debate" edited by Quentin D. Wheeler and Rudolf Meier,2000, Columbia University Press. - A big long fight between different authors replying to each others attacks on their pet species concepts. The last few attack replies are a lot of fun.

If you are interesting in speciation genetics, two books in addition to Coyne and Orr are good reads: Dieckmann, Doebeli, Metz, and Tautz's "Adaptive Speciation" 2004, Cambridge University Press is worth some time. As is Sergey Gavrilets' "Fitness Landscapes and the Origin of Species" 2004, Princeton University Press. Both are heavy on modeling and math, so beware.

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From:triturus
Date:June 24th, 2005 11:02 pm (UTC)

Re: My two cents and some books

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Thanks a lot for your comment and useful references.

I absolutely agree with you that subspecies are real, this is an important category which helps us to describe the diversity. Unfortunatelly during last ten years in zoology at least there were some publications where the reality of subspecies as a 'real' category or even as a useful concept was questioned. As I am absolutely sure (basing on my personla studies of my group of taxa) that they are real I would like to write a sort of "reply" to those guys which were in doubts if subspecies is real category or not.

That's why I am really grateful for your comments and refernces.

Surely subspcecies are important for studying biodiversity - just every subspecies marks a bifurcation of the evolutionary tree and is in an evolutionary perspective a kind of new species in future and also the diversity of subspecies and different adaptive forms within a species makes the whole species a bit more stable unit in evolutionary perspective, in future some subspecies will survive, some not, so the diversity within the species somehow marks also it's own stability I think.

I think that actually subspecies in zoology is not less useful category than in botany, however sometimes it markes a bit different levels of differentiation because of fantastic diversity of animal life... Subspecies in salamanders and newts, birds, mammals seem to be a bit similar categories, but subspecies in insects, crustaceans, or even infusoriae are not the same.

The book by Wilson! It's great! Exactly what I need! Is it still possible to find it (6 years after print)?

With respect,
Nick Poyarkov
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From:triturus
Date:June 24th, 2005 11:05 pm (UTC)

By the way!

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A new article where the problem of specific- and subspecific boundaries is touched was published:

Babik, W., W. Branicki, J. Crnobrnja-Isailović, D. Cogălniceanu, I. Sas, K. Olgun, N. A. Poyarkov, M. Garcia-París & J.W. Arntzen (2005) Phylogeography of two European newt species — discordance between mtDNA and morphology. Molecular Ecology, 14, pp.: 2475-2491.

Nick Poyarkov
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