the phylogeographic challenge to creationism

Maybe this is not the place, and I don't care what it sounds like, but I "fourth" the POTM-nomination.Very informative, and a great example, both of how micro- and macroevolution are actually just gradations of the same process, and of how to present a decent topic.Well done!

Just to add some more examples to the fine example presented by mick,

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Cytogenet Genome Res. 2002;96(1-4):85-96. Related Articles, Links

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Alps, genes, and chromosomes: their role in the formation of species in the Sorex araneus group (Mammalia, Insectivora), as inferred from two hybrid zones.

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Brunner H, Lugon-Moulin N, Hausser J.

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Institute of Ecology, Laboratory of Zoology and Animal Ecology, Lausanne, Switzerland.

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During the Pleistocene glaciations, the Alps were an efficient barrier to gene flow between isolated populations, often leading to allopatric speciation. Afterwards, the Alps strongly influenced the post-glacial recolonization of Europe and represent a major suture zone between differentiated populations. Two hybrid zones in the Swiss and French Alps between genetically and chromosomally well-differentiated species-the Valais shrew, Sorex antinorii, and the common shrew, S. araneus-were studied karyotypically and by analyzing the distribution of seven microsatellite loci. In the center of the Haslital hybrid zone the two species coexist over a distance of 900 m. Hybrid karyotypes, among them the most complex known in Sorex, are rare. F-statistics based on microsatellite data revealed a strong heterozygote deficit only in the center of the zone, due to the sympatric distribution of the two species with little hybridization between them. Structuring within the species (both F(IS) and F(ST)) was low. An hierarchical analysis showed a high level of interspecific differentiation. Results were compared with those previously reported in another hybrid zone located at Les Houches in the French Alps. Genetic structuring within and between species was comparable in both hybrid zones, although chromosomal incompatibilities are more important in Haslital, where a linkage block of the race-specific chromosomes should additionally impede gene flow. Evidence for a more restricted gene flow in Haslital comes from the genetically intermediate hybrid karyotypes, whereas in Les Houches, hybrid karyotypes are genetically identical to individuals of the pure karyotypic races. Genic and chromosomal introgression was observed in Les Houches, but not in Haslital. The possible influence of a river, separating the two species at Les Houches, on gene flow is discussed. Copyright 2002 S. Karger AG, Basel

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picture of a Valais shrew
http://www.konig-photo.com/Images/Sorant25.jpg
and common shrew
see it hereAgain, why would these two species not just collapse into one even though they can hybridize? Why do they show variation within their populations but can only minimally disemminate it between the groups? The micro and macro evolutionary processes are the same in both cases.Let's look at birds,

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Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16717-22. Epub 2005 Nov 7. Related Articles, Links

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From The Cover: Microevolution and mega-icebergs in the Antarctic.

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Shepherd LD, Millar CD, Ballard G, Ainley DG, Wilson PR, Haynes GD, Baroni C, Lambert DM.

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Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102904, NSMC, Albany, Auckland, New Zealand.

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Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adelie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.

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Now, what are the differences in the processes described in this among population comparison than in mick's examples from among populations, species, and genera? How about between the two species of Sorex?How about elephants?

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Science. 2001 Aug 24;293(5534):1473-7. Related Articles, Links

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Comment in:
Science. 2001 Aug 24;293(5534):1414.

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Genetic evidence for two species of elephant in Africa.

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Roca AL, Georgiadis N, Pecon-Slattery J, O'Brien SJ.

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Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.

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Elephants from the tropical forests of Africa are morphologically distinct from savannah or bush elephants. Dart-biopsy samples from 195 free-ranging African elephants in 21 populations were examined for DNA sequence variation in four nuclear genes (1732 base pairs). Phylogenetic distinctions between African forest elephant and savannah elephant populations corresponded to 58% of the difference in the same genes between elephant genera Loxodonta (African) and Elephas (Asian). Large genetic distance, multiple genetically fixed nucleotide site differences, morphological and habitat distinctions, and extremely limited hybridization of gene flow between forest and savannah elephants support the recognition and conservation management of two African species: Loxodonta africana and Loxodonta cyclotis.

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Forest elephants and savannah elephants are interfertile. However, they only produce young rarely and thus form limited hybrid zones rather than forming a single population. This speciation designation is a macroevolutionary event...how is it different than the genetic differentiation among the different elephant populations studied? What is biologically different between the processes of micro and macro evolution that makes the former possible and the latter (as claimed by creationists) impossible?Creationists claim that they study the same data as us misguided scientists. Then, please, show me where the scientists responsible for these studies have misinterpreted the data.This message has been edited by AdminJar, 11-24-2005 12:09 PM

Hi Robin,Yep, that's exactly the point I'm trying to make. The initial title of the thread was "processes preventing the merging of species - a question for ID advocates". The basic question is what prevents these species hybridizing into a single unit if you do not accept that microevolutionary processes (including but not limited to reproductive isolation by geographic isolation) operate above the species level?You are right that creationists are not interested in the maintenance of genetic diversity but that is simply because they haven't got an explanation for it. They often complain that the origin of biological novelty (at "macroevolutionary" scales) cannot be observed in nature. But they fail to provide any explanation for the maintenance of biological diversity (at "macroevolutionary" scales) - which is a process that can be observed every day, right now!I just wanted to put the ball in their court for once.Mick

Hi Brad, Thanks for replying. I was getting a bit worried that no anti-evolution types would actually get involved in this thread, so I appreciate it!I like the phrase "determinant breaks". I think what my post is trying to show is that determinant breaks DO exist in nature at the limited level of genetic diversification, but in the cases I cited, the breaks are the result (at least in part) of geographic barriers to gene flow and not an intrinsic part of the microevoluationary process.For example the plains between the Rockies and the Coastal Mountains constitute a determinant break in the genetic diversity between subspecies or "varieties" of amoenus, but they ALSO consitute a determinant break in the genetic diversity between amoenus and minimumus. The geographic barrier appears to play a role in structuring populations both within a species and between species.So the microevolutionary process in itself is continuous, but its effects (in combination with the spatial differentiation of the environment) result in breaks at both microevolutionary and macroevolutionary scales.Flatow is correct to say that "IDers will make a difference between micro and macro evolution". As an anti-IDer I would ALSO be happy to accept that we might arrange genetic subunits in a hierarchical manner, and call the major subunits "macroevolution" and the minor subunits "microevolution". But that way of classifying things does not necessitate that the process underlying all these forms of diversification is not continuous.Cheers!Mick

Mick, do you understand this?

Its meaning is not immediately apparent... but:A graph is a collection of nodes which are connected by branches. A digraph is a collection of nodes which are connected by unidirectional branches. A cyclic digraph is a collection of nodes which are connected by unidirectional branches such that each node is connected to every other node by branches running in the same direction. A noncyclic digraph is a collection of nodes which are connected by unidirectional branches such that at least one node is not connected to at least one other node by a set of branches running in the same direction. A classical phylogeny is a binary noncyclic digraph. In other words, some node exists such that it is not directionally connected to some other node, and each node is directionally connected to either two or zero nodes. The parent to offspring ratio is the number of nodes which are directionally ancestral to a focal node divided by the number of nodes which are directionally descended from a focal node. (Ancestry versus descent is determined by the directionality of the graph).The confusion lies in the fact that I have absolutely no idea what a macrothremodynamic thermostat is.Mickadded in edit: a "causal graph" must be a digraph (causal in the sense that one node leads to the other in a directional maner)added in edit, again: an acyclic graph is the same thing as a noncyclic graphThis message has been edited by mick, 11-24-2005 05:07 PM

Thanks for the references! Even if no creationists post replies on this thread, I hope it will be a useful repository for information on the phylogeographic challenge to creationism.I'm currently putting together some data on island biogeography which tells a similar story, will report the results shortly.I've also got in touch with a geographer at my university who is an expert on the pacific northwest - with her help I hope to be able to explain what those precise but wavy lines on the species range maps for Tamias represent.Mick

Hi mick,
I'll try to do the same...there are some interesting studies on bats ,reproductive isolation and sympatric speciation that would be appropriate...and then of course cichlids. There is also a ton of literature on other fish species phylogeography. As you pointed out, if enough info is in this thread...we can always point back to it rather than re-referencing all the time.
Cheers,
MThis message has been edited by Mammuthus, 11-25-2005 04:17 AM

Ok, here come the cichlids,
Note, going from the arguement in the OP, why do cichlids form populations/species that no longer exchange genetic information with one another even though the populations occur in the same lakes i.e. sympatric speciation? This is a nice example of macroevolution that is observable at the genetic level...what is the difference between what we observe between cichlid species as opposed to within cichlid populations? (Note: most of these articles are open access and anyone who want to, can read them)

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BMC Evol Biol. 2005 Feb 21;5(1):17. Related Articles, Links

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Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes.

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Salzburger W, Mack T, Verheyen E, Meyer A.

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Lehrstuhl fur Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany. walter.salzburger@uni-konstanz.de

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BACKGROUND: The adaptive radiations of cichlid fishes in East Africa are well known for their spectacular diversity and their astonishingly fast rates of speciation. About 80% of all 2,500 cichlid species in East Africa, and virtually all cichlid species from Lakes Victoria (approximately 500 species) and Malawi (approximately 1,000 species) are haplochromines. Here, we present the most extensive phylogenetic and phylogeographic analysis so far that includes about 100 species and is based on about 2,000 bp of the mitochondrial DNA. RESULTS: Our analyses revealed that all haplochromine lineages are ultimately derived from Lake Tanganyika endemics. We find that the three most ancestral lineages of the haplochromines sensu lato are relatively species poor, albeit widely distributed in Africa, whereas a fourth newly defined lineage - the 'modern haplochromines' - contains an unparalleled diversity that makes up more than 7% of the worlds' approximately 25,000 teleost species. The modern haplochromines' ancestor, most likely a riverine generalist, repeatedly gave rise to similar ecomorphs now found in several of the species flocks. Also, the Tanganyikan Tropheini are derived from that riverine ancestor suggesting that they successfully re-colonized Lake Tanganyika and speciated in parallel to an already established cichlid adaptive radiation. In contrast to most other known examples of adaptive radiations, these generalist ancestors were derived from highly diverse and specialized endemics from Lake Tanganyika. A reconstruction of life-history traits revealed that in an ancestral lineage leading to the modern haplochromines the characteristic egg-spots on anal fins of male individuals evolved. CONCLUSION: We conclude that Lake Tanganyika is the geographic and genetic cradle of all haplochromine lineages. In the ancestors of the replicate adaptive radiations of the 'modern haplochromines', behavioral (maternal mouthbrooding), morphological (egg-spots) and sexually selected (color polymorphism) key-innovations arose. These might be - together with the ecological opportunity that the habitat diversity of the large lakes provides - responsible for their evolutionary success and their propensity for explosive speciation.

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more references,Baric S, Salzburger W, Sturmbauer C.
Phylogeography and evolution of the Tanganyikan cichlid genus Tropheus based upon mitochondrial DNA sequences.
J Mol Evol. 2003 Jan;56(1):54-68.Ruber L, Verheyen E, Meyer A.
Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika.
Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10230-5.Here are some bat references,

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Mol Phylogenet Evol. 2004 Dec;33(3):764-81. Related Articles, Links

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Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex.

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Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH.

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Department of Biology, Boston University, Boston, MA 02215, USA. pollyc@bu.edu

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Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.

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more references
Pestano J, Brown RP, Suarez NM, Fajardo S. Related Articles, Links
Phylogeography of pipistrelle-like bats within the Canary Islands, based on mtDNA sequences.
Mol Phylogenet Evol. 2003 Jan;26(1):56-63.Ditchfield AD. Related Articles, Links
The comparative phylogeography of neotropical mammals: patterns of intraspecific mitochondrial DNA variation among bats contrasted to nonvolant small mammals.
Mol Ecol. 2000 Sep;9(9):1307-18.

I don't think the creationists see the significance. I'm having a problem myself. What is the relationship between microevolutionary processes maintaining a status quo and "macroevolution"?

I agree Robin. I read through the OP, and it is impressively thorough and thoughtful, but I fail to grasp how it is in any way a challenge to creationism.I've avoided this thread because I'm afraid it would just bury me in a morass of semantic distinctions, but I guess I'll risk saying this much.

How does the OP demonstrate that micro and macro evolution are just gradations of the same process? It is merely a description of the effects of isolating portions of a population which is hardly unknown to creationists. It is what happens in the development of races of human beings too. That is, subgroups of a population take a portion of the gene pool with them, reducing their genetic variability in relation to the parent population, and this develops distinctions in the group from the parent group and from other isolated groups.This occurs in all the forms of "evolutionary processes." It occurs in natural selection and it occurs in artificial selection (breeding), it occurs for geographic reasons and it occurs for behavioral reasons etc. etc. etc. It occurs wherever a part of a gene pool is isolated reproductively from the larger gene pool, in any way whatever and for any reason whatever, by removing some genetic potentials and bringing new genetic combinations to phenotypic expression that were suppressed in the parent population with its greater genetic variability.This message has been edited by Faith, 11-25-2005 08:20 PM

Hi Robin I am not talking about "maintaining the status quo". I am talking about the origin and maintenance of genetic structure. The word "maintenance" does not mean that nothing of evolutionary interest is happening. Individuals are still travelling around and mating, but a level of genetic structure above the individual persists. Even "stasis" is a dynamic evolutionary process simply because animals are born, move around, mate selectively, then die ad are replaced by their offspring.I'm saying that disjointed patterns between genes and geography are in a continual process of being regenerated. I am not suggesting that the phylogeographic patterns in chipmunks are fixed and permanent, and evolutionary processes just maintain them. Wait till the sea rises a bit, or the climate changes, and the genotypes of these different species will recombine in new and interesting ways.To reiterate:Creationists claim that evolutionary processes only operate "within kinds". They are correct that at least one evolutionary process (reproductive isolation by geographic distance) is responsible for the diversification of populations within a species.Creationists further claim that evolutionary processes do not operate at macroevolutionary scales. I (and many others) have made repeated attempts to clarify what distinguishes "micro" from "macro" evolutionary scales but the response has not been forthcoming.In the examples I posted, I assumed that evolution above the species level is the working definition of macroevolution. I tried to show that the mechanisms giving rise to reproductive isolation and genetic structure below the species level are also giving rise to reproductive isolation and genetic structure above the species level.The challenge is for creationists who accept microevolution but reject macroevolution to explain why evolutionary processes that THEY ACCEPT operate below the species level are supposed to evaporate above the species level.If creationists do not accept that evolutionary processes operating above the species level are "macroevolution" then it is perhaps time for them to give a definition of what they mean by "macroevolution" once and for all.However I'm still putting together some stuff on island biogeography which will cover adaptive radiations of novel genera in isolated geographic areas, so perhaps that will be satisfactory as far as micro-vs-macro is concerned. I mean, if the origin of a new genus is not macroevolution then a creationist will really need to enlighten me.Mickin edit: maybe I'm using the word "creationist" incorrectly? When I say "creationist" I mean specifically those creationists who reject macroevolution. There are plenty (like Jar) who are creationists but accept macroevolution. Sorry about that.This message has been edited by mick, 11-26-2005 04:33 PM

Hi Faith,First of all, thanks for posting. Well we agree on all of that. Can I just clarify?Do we agree that, at least in principle, different species of Tamias have different alleles, and different allele frequences, because of phylogeographic processes as you have described them?Do we agree that these alleles are responsible for the existence of divergent phenotypes in each species (And subpopulation)?Do we agree that some of these phenotypic differences (such as changes in body size, coloration, etc) are diagnostic of the different species?Do we agree that differences in mating preference (if any) might result from such processes?Do we agree then that the diversification of species can be explained with reference to microevolutionary processes?Finally: can these diagnostic differences between Tamias species be considered "macroevolution" and if not, why not? What magnitude of phenotypic change above the origin of species is necessary for you to admit that macroevolution has occurred?Mickps. I'm asking the last question just because I am gathering more data right now, and if you could be more explicit as to what you'd want to see as evidence of macroevolution through phylogeographic processes, I could try to find it for you.This message has been edited by mick, 11-26-2005 04:52 PM

Thanks!