the phylogeographic challenge to creationism

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 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'm bumping this because Faith ignored these examples where genetic diversity did NOT decrease as a consequence of speciation since it occurred in sympatry...and not to pick on Faith, nobody else picked up on these examples either 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)quote:
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BMC Evol Biol. 2005 Feb 21;5(1):17. Related Articles, Links
Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes.Salzburger W, Mack T, Verheyen E, Meyer A.Lehrstuhl fur Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany. walter.salzburger@uni-konstanz.deBACKGROUND: 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.--------------------------------------------------------------------------------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,quote:
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Mol Phylogenet Evol. 2004 Dec;33(3):764-81. Related Articles, Links
Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex.Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH.Department of Biology, Boston University, Boston, MA 02215, USA. pollyc@bu.eduTaxonomic 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.--------------------------------------------------------------------------------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.This message has been edited by Mammuthus, 11-28-2005 03:50 AM

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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.

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This is false. The genetic combinations and their consequent phenotypic expression are not "suppressed" in the parent population at all. They may occur at a low frequency but that has nothing to do with suppression...evolution without mutation is also false and there are plenty of enzymatic and population studies to back this up.For example, here is the diversification of bacteria over 10 K generations.

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Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3807-12. Related Articles, Links

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Genomic evolution during a 10,000-generation experiment with bacteria.

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Papadopoulos D, Schneider D, Meier-Eiss J, Arber W, Lenski RE, Blot M.

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Abteilung Mikrobiologie, Biozentrum, CH-4056 Basel, Switzerland.

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Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

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Of note, one author ont he paper, Richard Lenski, helped demonstrate that adaptive mutations do not evolve to adapt and organism to its environment but that random mutations are selected and as crashfrog pointed out, mutations occur in every generation i.e. you have mutations that niether of your parents carry i.e. new mutations.Elena SF, Cooper VS, Lenski RE. Related Articles, Links
Punctuated evolution caused by selection of rare beneficial mutations.
Science. 1996 Jun 21;272(5269):1802-4.Here is a summary of the error rates associated with DNA polymerase (it is much higher for other replication enzymes like reverse transcriptase)

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Princess Takamatsu Symp. 1983;13:267-76. Related Articles, Links

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Infidelity of DNA synthesis as a cause of mutagenesis.

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Loeb LA, Liu PK, Das SK, Silber JR.

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The concept underlying these studies is that a major determinant of mutagenesis involves perturbations in the fidelity of DNA replication. i.e., the accuracy by which DNA polymerases copy DNA templates. To investigate this relationship, we have designed in vitro assays to measure the accuracy of DNA replication and used these systems to screen for and to quantitate factors that promote errors in DNA synthesis. Using DNA polymerase from bacteria, the frequency of mistakes with phi X174 DNA as a template approaches 10(-7) and is similar to the spontaneous mutation rates in bacterial cells. In contrast, DNA polymerases from animal cells are more error-prone. The differences in fidelity among mammalian DNA polymerases which lack error-correcting mechanisms suggest that these enzymes enhance accuracy by improving base-selection. Thus, mutants in DNA polymerase-alpha might be altered in base-selection. Chinese hamster V79 cell mutants selected by resistance to aphidicolin, a specific inhibitor of DNA polymerase-alpha, have been reported (Somatic Cell Genet., 7: 235-253, 1981). DNA polymerase-alpha was purified from mitochondria-free crude extracts of these mutants by sequential column chromatography using DEAE-cellulose and phosphocellulose. DNA polymerase-alpha purified from one of the mutants is 10-fold more resistant to aphidicolin than the same enzyme purified from the parental cells. Moreover, the apparent Km for dCTP is 1.0 +/- 0.4 microM for the mutant polymerase and 10 +/- 4 microM for the parental enzyme. These observed differences are in accord with the known competition between aphidicolin and dCTP, and provide a mechanism for the aphidicolin resistance of the mutant, i.e., the decrease in Km for dCTP. The elevated spontaneous and induced mutation rate exhibited by this mutant could be mediated by the alteration in DNA polymerase-alpha. With DNA replicating enzymes from a variety of sources, enhancement of mutagenesis has been demonstrated by alteration in precursor pools, damage to DNA templates, loss of nucleotide bases on DNA, metal ions that interact with nucleotide bases, and organic compounds that intercalate into DNA. The alterations of deoxynucleoside triphosphate pools also occur after treatment of animal cells with known mutagens. This observation may provide a new mechanism for mutagenesis by these agents independent of alterations in DNA.

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Finally, again related to cichlids, they speciate via hybídization in some cases and INCREASE their genetic diversity.

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Mol Ecol. 2002 Mar;11(3):619-25. Related Articles, Links

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Speciation via introgressive hybridization in East African cichlids?

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Salzburger W, Baric S, Sturmbauer C.

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Department of Zoology and Limnology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.

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Speciation caused by introgressive hybridization occurs frequently in plants but its importance remains controversial in animal evolution. Here we report a case of introgressive hybridization between two ancient and genetically distinct species of Lake Tanganyika cichlids that led to the formation of a new species. Neolamprologus marunguensis contains mtDNA haplotypes from both parental species varying on average by 12.4% in the first section of the control region and by 5.2% in a segment of the cytochrome b gene. All individuals have almost identical DNA sequences in the flanking regions of the single-copy nuclear DNA locus TmoM27, and show a mosaic of alleles derived from both parental lineages in six microsatellite loci. Hence, our finding displays another mode of speciation in cichlid fishes. The increase of genetic and phenotypic diversity due to hybridization may contribute to the uniquely rapid pace of speciation in cichlids.

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So, to clarify some points from all of this, Faith is making both some overly general statements and some false statements.First, we know about random mutation not only from evolutionary studies but from analysis of the enyzmatic processes themselves i.e. the biochemistry of DNA and RNA polymerases. Anyone who works in a lab will get a spec sheet with the Taq polymerase they purchase indicating the measured error rate. In any case, as crashfrog indicated, we know from in vivo studies that even in humans, every individual carries novel mutations not present in their parents due to polymerase errors (I am leaving recombination and retrotransposition out at this point).We know that genetically isolated populations (or species) can form without a decrease in genetic diversity so Faith is overstating the case that it always leads to a reducition of genetic diversity. Selection might reduce variation at a single or several loci but this does not generally reduce all variation in a population or species. The reductions she is talking about are associated with strong bottlenecks or founder events which admittedly do occur but are not the only mechanism of isolation and differentiation of populations to form species.Finally, I have no idea where Faith gets the idea that separating populations causes suppressed genes or phenotypes to suddenly appear. All populations have variants that are distributed in different frequencies i.e. the blood groups or any other trait you want to measure. A founder event does not lead to the end of suppression of a phenotype/genotype...it merely means that if you have a 100 variants and 1 goes on to found a new population, that the frequency in the new population is a 1/100th subset of the variation of the original population..but that 1 individual was not suppressed in the original population.If you add selection into the mix, selection does not just decrease variation, it can increase it as well i.e.

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Genetics. 2005 Aug;170(4):1897-911. Epub 2005 May 23. Related Articles, Links

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High-diversity genes in the Arabidopsis genome.

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Cork JM, Purugganan MD.

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Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.

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High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.

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Coming back to my elephant example, Loxodonta cyclotis and Loxodonta africana are two different species. They can form hybrids yet introgression of alleles from one group to the other is very rare i.e. they remain distinct gene pools and have for over 1 million years. Jump up a level to the genus level, African elephants and Asian elephants are interfertile (one hybrid was produced)..however, the two genera are completely distinct genetically and have not formed a single gene pool for 5 million years. Elephants and manatees are more closely related genetically (and morphologically) than either are to any other species. They are even more reproductively isolated than among elephant groups....so what is the difference between the microevolutionary event (among elephant group differences i.e. savannah African elephants and desert elephants both in the same species) and the macroevolutionary event, manatee differences from elephantids other thant he time that separates them?

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That is not so. What happened to Mendelian genetics if so? What does dominance and recessiveness mean if not something built into the population? It can't be something conferred willynilly by mutation. What does it mean to speak of numbers of alleles in a population? There are great numbers for some genes in some populations, small to even only one allele in others, and this has something to do with the built-in genetic picture as it gets worked on by the various Evolutionary Processes, not with random mutations.

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Faith, you have some deep misunderstandings about genetics and mutation. Mendelian genetics is the study of the segregation of mutations by hereditary transmission from one generation to another! Dominant and recessive is the phenotypic expression of a genetic mutation such that if one mutation is Dominant, the phenotype it confers will be expressed whether in the presence of the recessive mutation or in the presence of another identical sequence. Dominant and recessive traits are determined by mutations! Genetics has everything to do with mutation. Mendel only looked at traits that affected phenotype because at the time the basis of heredity was unknown.What does it mean to talk about number of alleles in populations? Simple, you have two copies of every nuclear gene in your diploid genome. If to copies of one gene differ by a point mutation, you have two alleles. The genes can differ in many different places. Each difference is an allele. For some genes, there are hundreds of different versions of the same gene in the population occurring at different frequencies. Population genetics and evolution measure how these frequencies change in response to selection, isolation, etc.You, me, crashfrog, all of us are "mutants" we carry errors that occurred as our parents DNA was being replicated during meiosis.There is no built in anything genetic except that DNA polymerases are very error prone and thus, every individual generates novel alleles in each generation. There is not built in variation...it increases and decreases depending on which is stronger, the selection against specific variations or the tolerance of a lot of errors. This can be measured in a test tube, in captive populations and in the wild...and even in human patient samples.

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This whole process can be understood without reference to mutation at all, but only to normal built-in Mendelian genetics, to dominance and recessiveness and others I havenh't learned well enough, that is, to genetic potentials

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Genetic potentials so not exist..and as explained, mendelian genetics is all about mutation..mick did not reference mutation because he assumed everyone knows that the variation he is talking about represents mutation events...there are no genetic variants without mutation..they are the same thing...this is Genetics 101.

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Yes, and this is because of the greatly reduced genetic diversity which severely limits or absolutely prevents the emergence of adaptive traits. Again, the more specialization, the more "speciation" in other words, the less genetic diversity, the less adaptability, the less capacity to "evolve."

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Except that every study from cichlids, to mice, to flies, to bacteria demonstrates exactly the opposite of what you state here. Richard Lenski has even demonstrated that specific mutations are selected for under experimental conditions which is followed by an explosion of genetic diversity within a mere 10,000 generations.

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I am convinced that macroevolution cannot occur, meaning that there are indeed fixed "Kinds" that can only vary --

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Not to be mean but considering you clearly do not have a background in any of the relevant biology, being "convinced" that something cannot occur is extremely premature and frankly insulting to those of us well versed in the subject...to put it in a way that you might understand, for sake of argument say I never read the bible. what if I told you that I am convinced that there is no mention of Jesus in the New Testament? I don't know anything about the Bible but I am still convinced my belief is correct. You would not find this arguement compelling would you? Well, you are making exactly this arguement with respect to macroevolution.

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Mick is the only one who seems to be able to think about these processes in terms of ordinary genetics without the addition of mutation

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Every variant in mick's paper, every allele, is a mutation....ORDINARY genetics is the study of how genes mutate and spread from one individual to another.

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Unique genotypes occur NATURALLY without mutations.

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Please show how...this would falsify Mendelian genetics if it could be shown and the several hundred thousand published studies on genetics and genomics have failed to demonstrate such an effect...Here are some websites to help you out.One on Mendelian geneticshttp://www.ndsu.nodak.edu/...lean/plsc431/mendel/mendel1.htmhere is another, pay attention to how mutations and alleles are definedhttp://www.athro.com/evo/gen/genetic.htmlhere is wikipedia
Allele - WikipediaNote, the only way to get an alternate DNA sequences is via mutation..thus all alleles are mutants whether they confer a negative or positive or neutral result on the phenotype of the organism.

Ok,
that mutations occur randomly and frequently is a measured biochemical property of all polymerases i.e. the enzymes that replicate DNA. That is one issue.Alleles are the result of this error prone replication mechanism, again measurable in the lab and in the wild.Selection can reduce the number of alleles in a population..but it can also increase it as in the case of cichlids and in bacteria. Evoltion is the change of allele frequencies over time within species, between species, and among higher taxanomic groups..whether macro or micro..the same process is at work.In any event, once two populations have become reproductively isolated, they continue to generate new variants with each offspring...we are all mutants for some locus or another. that is the point of Lenski's work on bacteria. It is also the point of the work on cichlids.the "usual Evolutionary Processes" means nothing to me. Care to elaborate?

Hi Faith,
I realize you are getting a bit piled on in this thread. Focus on the posts you wish to deal with and let the others slide as randman suggested. Also, most of us are not trying to belittle you. There are some basic concepts that you have misunderstood and aside from mick's OP, I am trying to help clear them up.

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Yes I understand how Mendelian genetics work, and about alleles in the population and that should have been clear from many things I've said. you do not have to explain that. The difference is that now it is believed that there is no built-in coherent genetic picture that is segregated by hereditary transmission, it's all just tossed together by mutations and THAT's what's now considered to be segregated by hereditary transmission.

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The problem is you do not understand how Mendelian genetics works. Even Mendel recognized that new variants can spontaneously arise. His problem was that he could only look at variants that had a dramatic effect on the phenotype (in his case color or morphology) of the plants he studied. Currently, we can look at the changes in the DNA sequences that are responsible for the phenotypic changes. These changes in the DNA sequence occur at random by mutation. All transmissible variation in a population is due to mutation. An allele is a mutant version of a different allele. What we call wild type is usually the most frequent version of an allele like red eyes in Drosophila. It is an arbitrary designation...if you had started with a purple eye population of Drosophila, then wild type would be purple.

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The difference is that now it is believed that there is no built-in coherent genetic picture that is segregated by hereditary transmission

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It was never believed that there was build in coherent genetics. Even prior to molecular biology, new mutants appeared from pure stocks via mutations. It was recognized early on that radiation and chemicals that damage DNA can lead to a higher rate of the appearance of new variants because it changes the underlying DNA sequence. Genetics is the study of mutation and how it is passed on.
As to coherent genetics..no such thing...if you have kids, they represent novel mutants as they will carry novel alleles generated by mutation that do not occur in either your genome or that of your husbands.

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New phenotypes emerge as a result of the reproductive isolation and there is a corresponding reduction in genetic diversity in that new "species"/variety/breed.

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This is also incorrect. The phenotype did not emerge due to isolation. A rare phenotype may become common do to isolation but it may have been present in the original population. Otherwise, it would work like this, you have one population that gets split into two by geography or whatever. Gene flow between them is no longer possible. By random mutation in every generation, they will diverge from one another even without selection because every individual born carries new mutations. Since the populations cannot breed with each other, they will diverge and diverge to the point that even if they were to come into contact again, they would not be able to breed. This is observed in the lab and in the wild. There are other ways for speciation to occur but in this case, there would only be a reduction in genetic diversity if one of the two original populations was very small...and over time, as a small population grows, it gains diversity by random mutation...this has also been demonstrated in the lab and in the wild.

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Please read what Mick wrote in Message 29 as he didn't find it hard to agree with how I described this process. In fact he continues to explain it all to jar in terms that agree with me in subsequent posts. You may have a problem with my layman's language but he didn't. The concepts are clear enough I think, and I'm not reaching beyond the little I understand either.

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Mick is asking you to address a somewhat different issue. Not the origin of variation among populations, species, and higher taxonomic levels but rather what is the difference in the process. Why do you think and can you support that the processes that separate a rabbit from a chipmunk are different from those that separate two different chipmunks? I am explaining (at the nitty gritty level) that the processes and how they are measured are identical whether you are comparing to breeds of dog from a rabbit and an elephant.

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It has not been proved that mutation does all this, that there is no built-in genetic complement.

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In fact it has repeatedly been "proved". It is a known biochemical fact from the known replication error frequencies of all the polymerases known (and sold on the market for that matter). It has been observed and cataloged in bacteria, yeast, flies, humans, etc. etc. So you statement is just plain wrong. What has never been demonstrated is a build in genetic complement in any species.

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It has not been proved how much mutation is beneficial and how much disease,

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It really depends. It has certainly been shown in bacteria and in flies with mutation load studies. In humans there are specific cases which are quite well characterized such as malaria resistance and balancing selection for the sickle cell trait. But I may be misunderstanding you statement.

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it has not been proved that the rate of beneficial mutation could possibly explain the segregation by hereditary transmission of genes, into many geographically separated coherent subspecies of anything over a relatively short period of time.

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Actually, the beneficial mutation rate is relatively unimportant in this case. The markers analyzed are neutral markers that do not influence phenotype. And this has been successfully done in thousands of species.The study of beneficial mutations is more difficult and not as advanced. Mostly because beneficial is a relative statement. What is beneficial in one environment can be a catastrophe in another so that selection goes back and forth over time. In the lab it is much easier to show the effects of beneficial mutations than in the wild.Your post is fine as are your questions. But I would avoid making absolute statements of what scientists know or don't know until you are a bit more familiar with the field. One cannot pretend that thousands of studies just don't exist.Let me know if any of the explanations I posted are unclear.

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Mick understood what I meant by "suppressed" in terms of dominance and recession and didn't treat it as an invalid point. "Low frequency" is fine. Point is that when they are selected and reproductively isolated they generate a new race or breed or what evolutionists now call a species, and the very process of selection is the reduction of genetic diversity available to them.

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These are not technicalities. Suppressed in terms of dominant and recessive traits is incorrect and completely confusing terminology when then applied to speciation. Suppression has its own definition.The point is, sometimes during the formation of populations there is a reduction in overall genetic diversity of the population. Sometimes there is an increase i.e. hybridization, sometimes there is no change, i.e. sympatric speciation. Sometimes there is isolation of populations and no speciation. It is also wrong to say it is a reduction in the variation available to them..once you are born, that is all the variation you personally are going to get. As soon as reproduction occurs, new variants are produced by mutation that happens every step of the way.

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If the scientists insist on being scientifically exact I will give up or take the discussion to the religion side of the board. Snowing nonscientists under with scientific technicalities, burying the forest in the trees, and berating them for their failure to use scientific concepts as scientists do IS belittling them.

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I am sorry you feel that way. I have been reducing my explanations to a level I would use with high school students..and they usually get it. I am not trying to bury you in terms or technicalities. You might want to point out what it is you precisely don't understand from my posts. You have thus far made assertions about genetic diversity, genetics, and mutation that are false. When I explain it to you, you claim either that is over your head or I am burying you in technicalities but then proceed to claim you assertions are true. If I berated you (I don't believe I did) it is for making incorrect assertions and then claiming you are right while admitting you don't really understand the science.

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So why I can't get this one simple fact established here is a puzzle to say the least.

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I don't disagree with you. However, you then sometimes switch to making it a general case which is wrong. I was also trying to correct you more on your misconceptions about mutation and genetics as opposed to speciation. Your paragraph about a general trend of reduction DURING speciation often holds true...especially for domestic breeding where selection is very intense. My only point is that this is not the only situation found in nature and may not be the most common.

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The ideas that this process IS the process that generates all genetic material, or that it necessarily produces anything evolutionarily useful at all, still seem conjectural to me.

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I'm sorry that you feel it is conjectural but it is all established fact from the discovery of the DNA, the double helix, DNA polymerases and the study of their mutation rates. The direct genetic analysis of mutation events and their spread from parents to offspring and the segregation of mutations in populations. None of this is conjectural but is mundane lab work.

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I have been trying to be careful to avoid saying ALL and to acknowledge that there are some exceptions, saying only that the majority of the processes that select and isolate populations, that are labeled Evolutionary Processes, do have the effect of reducing genetic diversity.

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My only arguement with you here is whether or not it is the majority of cases. I do not see evidence for this.

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Who said it did? The point is the TREND. ANY reduction at all is a reduction.

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I can see why you would think this but bear with me, it is a bit complicated. In addition to base pair change mutations, during every meiosis (when you produce the half of the genes that you contribute to your offspring and your husband his half) recombination occurs and shuffles your chromosomes. Thus, if you have different alleles at a given gene on each chromosome, you randomize them somewhat in transferring them to your baby. If there is selection at one locus that prevents a certain allele from being passed on, it will have no affect at other loci farther away from it because they recombine and randomly transfer one or the other allele to the next generation. Thus, you could reduce diversity at one part of a chromosome (in a population) but still be overall more diverse everywhere else for the rest of the genome..so the trend would only apply to one locus but not overall. That was probably to complicated?

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I have carefully acknowledged that. Nevertheless the majority of them do have this effect -- natural selection, founder effect, bottleneck, migration etc. ONLY mutation and recombination (reintroducing populations to each other that are capable of interbreeding?) appear not to. And you say something else is going on with the cichlids but I can't follow it so until you translate it I don't know what the situation is there. What I can grasp of it -- it appears to be a discussion about separate clearly related populations that do not interbreed -- doesn't suggest anything in favor of macroevolution or any different kind of mechanism than we are discussing -- but since it is technically over my head you will have to break it down for me

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I'll try to break it down. A single population over time produces more and more variants due to mutation. In effect, every individual born is a novel variant. However, if the the population remains a single population and genes flow freely across the population (meaning there is nothing stopping an individual in one part of the population from breeding with another) they will stay a single species.This rule is broken in what is called sympatric speciation. In a large population with a complex environment (that is where cichlids come in), some individuals may become specialized by chance for a certain part of the environment that others are not specialized for. If there is selection for this specialization, over time, they may stop breeding with the general population even though they are in contact. Over time they cannot breed with the rest of the population and have speciated. This happens a lot in cichlids and has been observed in other species as well.African elephants (another one of my examples) is slightly different. Forest elephants are just that, a group of elephants that live in the forests of several countries in Africa. They are morphologically slightly smaller than the savannah elephants. They can breed with each other (forest and savannah). But the populations are genetically distinct and the limited breeding happens only where the two groups occassionally meet at the periphery of forests. But it does not diffuse forest genes into savannah elephants or savannah genes into forest elephants. So, although they can breed, they don't and the gene pools are very distinct. There are examples of this in baboons, crickets and lots of other species.Asian elephants are very different from African elephants. I promise you that if you look at them together, you will in about 5 seconds be able to tell which is which. They can also produce offspring when mated (it happened once) in a zoo though the calve died after 10 days. The gene pools of African and Asian elephants are as distinct as human and chimpanzee.Manatees are the most similar living species genetically to elephants. They don't look grossly similar and they cannot produce offspring. They do not inhabit similar environments.In each one of the cases I outline above, you have constant production of variants i.e. after speciation, the species does not stand still..it continues to vary with the birth of each individual. At different levels of separation, you get more and more restriction of gene flow whether it be restriction between different cichlid specialists, different types of elephants or different species entirely. At some point, there is no possibility for two populations to interbreed because they have become (and continue to become) so different from each other i.e. a elephants and manatees.The process of mutation, selection, drift, migration, etc. is the same in EACH case. It does not matter if you are looking at a population, a sub-species, species, genus, phylum, kindgom...the underlying process is identical. This is mick's point.

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And in the new population that 1/100 is going to become characteristic of it, and in order for that to happen the 99 other variants in the parent population have been eliminated, and THAT means there is sharply reduced genetic diversity in the new population -- in that trait anyway -- and correct me if I'm wrong, but when one trait is clearly selected by population isolation, surely many others are too.

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Not exactly correct. Think of it this way. You pack your suitcase with 1/10 of your clothes at random and fly to China. the other 9/10ths are not eliminated..but they are not in China. This has nothing to do with selection however. This would be called a founder event. Traits are not selected by population isolation. This is genetic drift. The random sub sampling of a larger population.If a small population moves into a new environment, they may come under new selection pressures. Take my forest elephant example. The Savannah elephants are enormous. They are bigger than woolly mammoths were. They are adapted to eating grass and living on open plains. Forest elephants are in a different environment entirely and due to selection, have some special adaptations for it. Most obvious, their size is greatly reduced compared to Savannah elephants since living in a forest restricts you overall size so the larger elephants of the original population would have been eliminated. Take it a step further out to mammoths. They lived on the arctic tundra. Their ears got small, so they would not lose heat, compared to African elephants that have huge ears. All newborn elephants are covered with hair..particularly Asian elephants...mammoths grew a thick covering of hair to protect them from the cold. All of this is because the new envirnoments they encountered would have applied very different selective pressures on the different populations once they separated. Over time, only the offspring that were best adapted would have survived to pass on their genes. Over time, this made the species very distinct from one another.Mick's chipmunks are showing the same thing. These are only a few examples out of thousands. The principles are always the same.

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I'm thinking along lines of a TREND, an overall reduction of genetic diversity throughout all populations or all life forms over all time. I know that in any particular formation of one population from another this may not occur, but the idea is to see if overall it occurs, as it seems to me it does. These processes either reduce genetic diversity or they more or less maintain the status quo, they don't increase it. Seems to me that the ONLY thing that increases genetic diversity is mutation. In the creationist way of thinking, hybridization doesn't add anything, it merely recombines parts of what is already the genetic allotment of a Kind. Thinking evolutionistically, mutation is continually adding genetic material -- but not everybody talks about it as a normal predictably beneficial process as you do.

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In the interest of time, I will keep this response short. There is certainly not a trend of overall reduced genetic diversity. In some species there is..especially those that are threatened with extinction. In humans, our diversity is increasing and their are lots of studies that show this. In many other species this is also the case. There is simply no "genetic allotment". That concept can be easily refuted, and has. In fact, you and I probably have entire pieces of DNA that differ from each other and are entirely new due to a phenomenon known as retrotransposition. However, I will point out one thing that may not have been clear, I don't mean to indicate that every mutation is successful. There are mutants that are born sterile or otherwise unable to reproduce that basically become extinct. Mutation is countered by selection. The vast majority of mutations wind up as miscarriages.I was not trying to insult you with the high school comment. I am just indicating I am watering down the technical jargon a great deal. My only way to know what you do understand or don't is by you pointing it out specifically. You will have to keep in mind that I am not used to talking about genetics with non-biologists. I am used to talking about it with other molecular biologists...so we basically have to teach each other how to communicate with each other

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I have had less time to think about all this in the last few days, a situation which will continue for a few more days, and what there is to think about is more than usual, so I'm lagging behind, but I wanted to answer that much of your post.

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Take all the time you need Faith. The advantage of a forum like this is that the post won't disappear and you don't need to answer in haste.Cheers,
M

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Hybridization, sexual recombination etc. Not a genuine increase according to a creationist, simply a way the trend to reduction is masked in a large gene pool.

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But that is not what I am talking about. I am talking about NEW mutations. Also recombination can produce large scale mutations that never existed before since it does not always work properly either. My point about hybridization is that speciation does not require reduction in genetic diversity.

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According to my conjectures, it is in species that are threatened with extinction where this trend of genetic reduction reaches its final extreme, that's why it is noted at that point, and those extremes do tend to be where "speciation" has recently occurred, no? In any case, I am convinced those extremes prove the overall trend, "the way of all flesh" as it were.

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I mean something very different. A species on the verge of extinction has been reduced to a very small number of breeding individuals. Thus, the population will be very homogeneous. And small numbers and lack of diversity (particularly of the genes controlling the immune system) puts the species at risk of complete collapse. A bottleneck during speciation does not have to be so extreme...a very diverse and large population could be cut in half...both halves would still have a lot of diversity and could still speciate...like in cichlids.

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I am certain there is a genetic allotment so your flat assertion that it's been disproved doesn't deter me

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I made a flat assertion because you complained that I was going over your head. I could very easily link you to the scientific studies that refute the concept of genetic allotment. It is not a new find. Denying it is simply denying reality.

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It is a terrible handicap to have no experience of talking biology with a nonbiologist. I don't know if it's possible to overcome that.

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But I guess it is fun to try or we would not be posting to each other in this thread

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Thanks for the acknowledgment that most mutations are unsuccessful. How sure are you that that leaves enough useful ones to counteract the genetic reduction effects of selection, migration, bottleneck and so on? What kind of data/statistics could even be available about this?

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Because we observe mutations in each generation that have not been aborted. As I said, every single one of us has novel mutations that do not occur in our parents. Have you heard of PCR the polymerase chain reaction where you can amplify DNA from a single copy to millions in a test tube? Even here, you can find polymerase errors in your sequences due to its lack of fidelity. Companies spend big bucks trying to make error free polymerases....our bodies don't.I also want to point out since you have mentioned this in two posts now, migration does not reduce genetic diversity. In fact, migration is a good way to keep gene flow constant over distant populations. Two groups will not diverge if they keep migrating into each other...migration is a great way to reverse trends towards speciation.

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Thanks for keeping your post short.

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No problem...I also have limited time (should be working on grants )
and mick and others have posts that are worth you time as well...so I will try to avoid excessively long posts.

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Isn't sympatry just a version of reproductive isolation between members of the same species? If so, this isn't a different example and of course genetic diversity decreases as the genes of the parent population are left behind and fewer genes are maximized in the new population. If it is, I will try to get how it's different.

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Speciation in sympatry leads to reproductive isolation without any physical barrier to gene flow being involved. It does not necessarily lead to reduction in genetic diversity if the breeding population of the two groups is the same when speciation occurs. Also, once speciation occurs, mutation and evolution do not stop...even after a bottleneck, over time you might find the smaller population has greater diversity than the original larger population.In fact, if two species hybridize and the resultant hybrid can no longer breed with either parent species, then speciation has lead to a dramatic increase in genetic diversity in the new species compared to the separate original species.

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Whatever isolates the populations, the same mechanisms are at work: each population has a portion of the original gene pool and expresses it phenotypically to the exclusion of the genetic types in the other pool. So, as with Mick's chipmunks, you get two separate varieties of the same species that either have no opportunity, no ability or no interest in interbreeding. And in all these cases genetic diversity IS reduced as in order for the differences in traits to emerge, the alleles for the other forms of those traits must have been eliminated or significantly reduced in the new population or "species."

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Interesting, but you seem to be admitting that speciation can happen. Your statement is largely correct except for the expressing of phenotypes that are present in the new population part. The new phenotypes evolve in separation. At the moment when two populations are separated, they are just a subset of the original population. They may have genotype/phenotypes that are present in both populations but the frequencies are different. It is only after time that they will start to adapt and diverge...the absence of gene flow between the two populations will insure that they start becoming phenotypically divergent.How is this different than say the processes that separate bears from dogs..elephants from manatees?

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Or were possibly recessive until the dominant forms were eliminated and allowed them to come to expression in the phenotype. Or were produced by genetic drift or whatever, again all processes that involve the reduction of genetic diversity in the service of developing new phenotypes, traits, characteristics, "species."

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This again makes no sense. If there are 8 blue balls and 2 red ball in a population and one red ball goes on to found a new population, the red phenotype is not surpressed in the old population. It is at a lower frequency. After a few hundred generations, maybe there are no red balls left in the original population by chance or selection..but the red ball population has grown and has new mutants, say purple. Now you have two populations, one all blue, and one with red and purple...this is what we observe. Not that if you are suddenly isolated you just grow a new phenotype. What you are proposing is basically Lamarkism which was refuted long ago.

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You are giving new examples but there's no difference in the genetic picture that I can see --

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This is the point...there is no difference between generation of a new population, species, genus, family, order etc. the process is the same. The only difference is the length of time involved. Two closely related species may be equally genetically diverse because since they speciated, they have built up genetic diversity after the reduction. This is directly observable. This is what we see. Evolution is change over time..the more time, the more change..it is exactly what we see looking at genetics and and to some extent, morphology, no matter what taxanomic level we are considering.

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I'm not sure what this focus on lineages is intended to prove, but as with the above, I expect variation within species and nothing about it contradicts creationist expectations so if you think it does I hope you will be more specific.

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It contradicts creationist expectations because in all cases it contradicts the concept of immutable kinds. The fact that every individual is born with novel mutations contradicts "genetic allotment". Everything from the biochemistry of DNA, RNA and proteins to the study of mutations segregating in families, groups, populations, species, genera, etc. demonstrates that evolution occurs. Where it cannot be directly measured (over millions of years) it leaves behind footprints exactly like those we observe today. Even ancient DNA lets us directly observe the process over vast time spans.What creationists fail to do is show how the different levels of divergence in mick's example, or any example are different biologically i.e. what is the difference between dogs and cats diverging as opposed to house cats from cheetah's? Every piece of evidence ever gathered says there is no difference in the underlying process. Creationism is the denial of this evidence. Creationism denies that mutations increase diversity even within a species. But other than arguments about contradicting faith or personal beliefs and asthetics, creationism does this with no supporting evidence and loads of evidence that contradicts it.

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Mutation introduces changes that are called mistakes -- mistakes in DNA replication. MOST of them as Mammuthus just acknowleged, abort

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I don't want to draw the thread off topic but I was grossly oversimplifying here. I was talking about mutations that affect phenotype. Most DNA is non-coding so most mutations are neutral or slightly deleterious. But I did not want to drag the entire topic into mutation analysis

Hi Mark,
maybe it would be worthwhile to start a thread on mutations for Faith? I am having enough trouble keeping up these days and am heading off to give a lecture next week so I would like to leave it in your hands
Cheers,
M

Hi mick
Let me know if any of my posts (aside from this one maybe) contribute to derailing the thread...even if the topic of the derailment is interesting. Feel free to boot me out of it. I rather see progress on the topic than contribute since I have been trying for years to get a creationist to engage in exactly this topic. Faith has taken it up so I don't want her to leave in frustration because of distractions.
cheers,M