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Author Topic:   the phylogeographic challenge to creationism
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 1 of 298 (262504)
11-22-2005 5:17 PM


The term "genetic structure" is used to describe the amount of genetic differentiation within a population of individuals. A population that is extremely homogenous, or that exhibits a continuum of polymorphic alleles distributed randomly across its members, has little genetic structure. On the other hand, a population that comprises a number of differentiated subunits (i.e. races, strains, varieties), or that exhibits a continuum of polymorphic alleles distributed nonrandomly across its members, is genetically structured.
When evolutionary biologists claim that macroevolution and microevolution are the same thing, they mean that the processes resulting in genetic structure within a species are the same processes that result in genetic structure between species.
"Spatial genetic structure" is genetic structure that results from differences in the geographic parameters experienced by spatially-separated populations. It is a consequence of straightforward microevolutionary processes. For example, in the middle ages it was rare for a person of Western-European descent to mate with a person of Asian descent. This is simply a consequence of the fact that it was difficult to travel from Europe to Asia in the middle ages. In the age of relatively easy international travel, the spatial genetic structure of human populations has been reduced, resulting in novel genetic and cultural combinations as seen in the Metis people of Canada (link to information on Metis people). The most simple example of spatial genetic structure comes from individuals asking themselves, "How far am I willing to travel in order to find a mate?"
As a microevolutionary process, the origin of spatial genetic structure is easily seen in natural populations. I've attached below a phylogeny built from the genetic sequences of members of the species Tamias amoenus (commonly known as the yellow-pine chipmunk). There is also a map showing where each genotype of this single species is located. I've added colour to the picture so that spatial structure is more obvious, and I've also attached a picture of Tamias amoenus so you know what animal I'm talking about.
reference
Tamias amoenus appears to exist as a spatially structured population. According to the map, the "purple", "yellow" and "red" clades are quite distinct from each other, while the "blue" and "green" appear to be overlapping, but not by very much. This is not surprising, because according to the phylogeny, the "blue" and "green" clades are closely related sister taxa. Given that this phylogeographic data represents variation within a species, and that creationists generally accept "microevolution", it should be possible for evos and creos to agree on the significance of the data. We can base our understanding of this data on the microevolutionary principles that Tamias amoenus arise from a single common ancestor and that the descendants of that ancestor have spread across the range, accumulating mutations along the way which have been preserved in each geographical region by heredity. For example, one reasonable hypothesis about the radiation of Tamias amoenus across north-west america is that the earliest members of the species crossed the rockies from the east or north (these are the yellow and purple clades) and established themselves in the Columbia, Clearwater and Highland mountains. They then split into two subpopulations, one moving northwest into the Cascades (the red clade) and one moving southwest towareds Sierra Nevada (the blue clade). Finally, members of the southern population travelled along the Snake River plain and populated southern-central regions from Oregon Highlands to the Beartooth Mountains. That is what the data suggests to me. And we're only talking about microevolution at this point.
Tamias amoenus is not at all unusual in exhibiting this kind of spatial genetic structure. Below are cladograms and distribution maps for black bears, Ursus americanus, and the shrew Sorex monticolus showing similar geographical clustering of genotypes.
reference
reference
The molecular evidence strongly suggests that population genetic structure in at least some mammalian species results from geographic isolation between subpopulations. Do we find similar patterns at levels of analysis above the species? Does the pattern hold at macroevolutionary scales?
Let's get back to the chipmunk, Tamias amoenus. Members of the genus Tamias easily hybridize with each other, and are probably not subject to reproductive isolation by incompatibilities in reproductive physiology. The closest related species to Tamias amoenus is Tamias ruficaudus. Here's a picture of ruficaudus on the left and amoenus on the right:
Although the pictures looks virtually identical, you might just be able to see that ruficaudus has a red/brown tail while amoenus has a black tail (it's not a photographic artifact). In general, amoenus has slightly darker pigmentation (compare the density of black stripes in the two pictures; but bear in mind that the apparent presence of a black stripe beneath the arm in amoenus but not in ruficaudus might just be unusual in this individual - I don't think that's a diagnostic feature). The two species are genetically distinct populations (i.e. true species) but they hybridize at low frequency in the wild.
Here's a molecular phylogeny based on sequences collected from amoenus and ruficaudus, along with a distribution map and drawings of the baculum (penis bone) of selected clades. The species involved are labelled (as crosses, squares, circles, etc) according to baculum morphology. The distribution of each clade is laelled as a greyscale colour. (This is a more complicated diagram, you will have to look at it for a little while).
larger version (may be easier to read)
reference
Geographic isolation appears to play a significant role in the maintenance of species-level genetic structure, just as it played a role in the maintenance of population-level genetic structure within Tamias amoenus. In the north, we have "clade 1", Tamias amoenus (shown in dark gray on the map, and as filled diamond and 'x' on the phylogeny). In the south, we mainly have "clade 3", Tamias ruficaudus (shown as filled or unfilled triangles on the phylogeny or as light gray on the map). In between these two groups, we have "clade 6" and "clade 5", recently-evolved clades that comprise subgroups of each species (Tamias ruficaudus simulans and Tamias amoenus canicaudus), and are likely the result of hybridization (between ruficaudus ruficaudus, ruficaudus simulans and amoenus canicaudus), and long-term migration from south to north. Areas of hybridization are labelled as "introgression zones". Again, this data is entirely consistent with the idea that Tamias amoenus and Tamias ruficaudus share a common ancestor, and that the descendants of that ancestor have spread across the range, accumulating mutations along the way which have been preserved in each geographical region by heredity. The fact that hybridization occurs in the regions of overlap shows that geographical distance is a major factor in structuring the populations of these species rather than intrinsic isolation by reproductive phsyiological incompatibility. However it seems at least plausible that there is some degree of local adaptation and that perhaps assortative mating helps keep the hybrid zones relatively limited in size.
Does the phylogeographic pattern persist within a genus? Let's stick with Tamias.
Here's a graphic showing the distribution of five "species groups" (which consist of closely related species which may be a single species but simply differentiated by spatial genetic structure). Again, we find that genetic distance and spatial distance are remarkably consistent. I have added pictures of each species group; from left to right: townsendii, merriami, minimus, amoenus.
larger image - may be easier to read
reference
So the basic microevolutionary process of spatial genetic structure originating from geographic distance appears to account quite well for distinct genetic groupings within species (amoenus), between species (amoenus and ruficaudus) and within a genus (amoenus, minimus, townsendii, merriami).
If you accept microevolution but reject macroevolution, how do you account for the spatial genetic structure of the Tamias genus without using microevolutionary processes? What non-microevolutionary mechanism prevents these easily-hybridizable species from collapsing into a single unstructured unit?
Mick
This message has been edited by mick, 11-22-2005 04:48 PM

Replies to this message:
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 7 of 298 (262554)
11-22-2005 7:55 PM
Reply to: Message 6 by robinrohan
11-22-2005 6:17 PM


Hi robin,
I'm not specifically talking about speciation (a supposedly macroevolutionary process). I'm talking about the genetic differentiation of populations (a supposedly microevolutionary process).
I'm trying to show that a microevolutionary mechanism ("i only mate with individuals I can access geographically, and my offspring will therefore have geographically-distinct karyotypes") can (at least in principle) be responsible for the genetic structure of populations, species and genera. In other words, microevoluationary processes can account for the maintenance of macroevolutionary structures (such as the genetic structure of Tamias).
I originally intended this thread to go into the ID forum. I invite people who believe in microevolution but reject macroevolution to explain how the spatial genetic structure of Tamias and other taxa is maintained, without making use of microevolutionary processes.
The genetic structure of populations within species (Tamias ameonus) and between species (the Tamias genus) is consistent with the idea of common descent and heritable genetic variation. For example if you get out an atlas you will be able to draw in geographic entities such as Snake River and the Northern Rockies, and see that the genetic delineation of populations both within and between species follow such entities precisely (I'll try to do this in a later post - at the moment I'm looking for a decent hi-res map of north america available online).
It would be interesting to know why macroevolution is supposed to be impossible, given that its phylogeographic patterns are 100% consistent with microevolutionary processes.
I'll post some maps tomorrow.
AS a side note, I believe that speiaction in Tamias has occured allopatrically due to geographic isolation, but that's not precisely what I want to talk about here.
Mick

This message is a reply to:
 Message 6 by robinrohan, posted 11-22-2005 6:17 PM robinrohan has replied

Replies to this message:
 Message 8 by robinrohan, posted 11-22-2005 8:05 PM mick has replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 9 of 298 (262564)
11-22-2005 8:28 PM
Reply to: Message 8 by robinrohan
11-22-2005 8:05 PM


robinrohan writes:
OK, I get this. But didn't you say that these different species within the genus Tamias interbreed? How then can we call them distinct species? What's the rationale?
Members of speciose genera of rodents frequently do not fulfill the requirements of the biological species concept. But the BSC is based on the idea of gene flow, and since gene flow between populations within a species is almost always more than 0% and is always less than 100%, I think it is reasonable to consider the BSC as a gradient rather than as a binary classification system. It is usually operationalized as a binary system, but that is simply the most conservative view of "species" that we can have when we do experiments.
Although there might be some debate about whether amoenus and ruficaudus are "true species" according to the BSC, there is no doubt that the level of genetic diversification within Tamias is similar to that within other genera. Their species status is established on the basis of diagnostic systematic traits an on cladistic analysis. There hasn't been enough research to know whether hybrids of each species (or species group) suffer a reduction of fitness.
Hybridization in mammals is actually extremely common (and much more common in amphibians and birds, where hybridization not between genera but between families is not unheard of). More pertinent than the BSC is the genetic structuring of sympatric populations and the nature of "introgression zones". Life's just a big tree, after all.
Mick
in edit: you can find examples of inter-family hybridizations at http://www.bird-hybrids.com (I don't have time to search for them for you, but I guarantee they are in there)
This message has been edited by mick, 11-22-2005 08:37 PM

This message is a reply to:
 Message 8 by robinrohan, posted 11-22-2005 8:05 PM robinrohan has replied

Replies to this message:
 Message 10 by robinrohan, posted 11-22-2005 8:51 PM mick has replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 18 of 298 (262937)
11-24-2005 12:31 PM
Reply to: Message 10 by robinrohan
11-22-2005 8:51 PM


Re: Divergence
robinrohan writes:
What your example shows us is that these variant races of chipmunks, or different specie, or however we wish to label them, get "maintained." They don't over time get all mixed up together again and become like they were before this separation happened, right?
But I would not think that creationism would be concerned with maintenance of the status quo but with further divergence.
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

This message is a reply to:
 Message 10 by robinrohan, posted 11-22-2005 8:51 PM robinrohan has not replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 19 of 298 (262946)
11-24-2005 12:59 PM
Reply to: Message 11 by Brad McFall
11-22-2005 9:44 PM


Re: Divergence
Hi Brad,
brad mcfall writes:
After thinking about this I thought this morning that in truth these evos had not thought about the process hard enough. I can write a sentence next which might be a true "law of nature." If it is then it would enable one to show determinant breaks.
The sentence is, Brad said, "There is a direct correlation between causal acyclic graph representations of macrothremodynamic thermostats and parent to offspring ratios per clade."
Now if this is true it would also have something to say about spatial patterns of speciation statistically. I am not prepared to engage Mick on this, so I hope my interjection is not taken badly.
From this perspective I can see indeed that a creationism reply is suffiently outside Alvin and his yellow submarine band, but to be fair, I would have to engage Mick not at my hyper velocity but his more paced and deligthful posts.
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

This message is a reply to:
 Message 11 by Brad McFall, posted 11-22-2005 9:44 PM Brad McFall has replied

Replies to this message:
 Message 20 by robinrohan, posted 11-24-2005 1:07 PM mick has replied
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 21 of 298 (262979)
11-24-2005 3:30 PM
Reply to: Message 20 by robinrohan
11-24-2005 1:07 PM


Re: Divergence
"There is a direct correlation between causal acyclic graph representations of macrothremodynamic thermostats and parent to offspring ratios per clade."
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.
Mick
added 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 graph
This message has been edited by mick, 11-24-2005 05:07 PM

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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 22 of 298 (262985)
11-24-2005 5:14 PM
Reply to: Message 17 by Mammuthus
11-23-2005 5:56 AM


Thanks for the references!
mammuthus writes:
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.
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

This message is a reply to:
 Message 17 by Mammuthus, posted 11-23-2005 5:56 AM Mammuthus has replied

Replies to this message:
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 Message 25 by robinrohan, posted 11-25-2005 10:18 AM mick has replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 28 of 298 (263370)
11-26-2005 4:31 PM
Reply to: Message 25 by robinrohan
11-25-2005 10:18 AM


Hi Robin
robinrohan writes:
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 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.
Mick
in 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

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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 29 of 298 (263372)
11-26-2005 4:51 PM
Reply to: Message 27 by Faith
11-25-2005 2:48 PM


Hi Faith,
First of all, thanks for posting.
Faith writes:
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.
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?
Mick
ps. 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

This message is a reply to:
 Message 27 by Faith, posted 11-25-2005 2:48 PM Faith has replied

Replies to this message:
 Message 31 by jar, posted 11-26-2005 5:34 PM mick has replied
 Message 34 by Faith, posted 11-27-2005 3:45 AM mick has replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 30 of 298 (263373)
11-26-2005 4:59 PM
Reply to: Message 24 by Mammuthus
11-25-2005 4:16 AM


Thanks!

This message is a reply to:
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 32 of 298 (263406)
11-26-2005 7:08 PM
Reply to: Message 31 by jar
11-26-2005 5:34 PM


faith, diversity, f-statistics and sticklebacks
Hi Jar,
You're dead right to pick me (and Faith) up on those points because they rely on a lot of unstated assumptions. It's a very good question. But I think Faith's words are basically okay.
Jar writes:
Does the parent population have greater genetic variability and does such a statement even have meaning?
Can I explain it in a straightforward way, at the risk of sounding a bit patronising?
We're talking about populations of individuals who differ very slightly in their genetic makeup. Let's consider one gene (say, the gene that codes for insulin). Every individual has an insulin gene, but within the population there are a variety of different versions (alleles) of insulin. They vary by one or two amino acids, or by one or two nucleotide changes that aren't even expressed in the protein. But although the insulin sequences and the insulin proteins might vary slightly, they're all still recognizable as insulin. If we're talking about diploid organisms, then each individual has two copies of the insulin sequence (one from the mother, one from the father) and these might be identical or they might be slightly different.
Let's say you start with a "large" population of individuals on the east side of a mountain range. There is a creek running between mountains that is full of ice and snow and the winter, and is flowing in the summer. At some point in one unusually warm spring, when the ice has started to thaw but the river hasn't filled up with water yet, some "small" number of migrants manages to cross the mountain range by moving down the side of the creek. It then establishes itself on the west side of the mountains as a new population.
Given that none of the individuals have given birth on the way down the creek, in genetic terms the migrant population is a pure subset of the ancestral population. There is no way that the migrant population could be carrying alleles that were not present in the ancestral population. If we measure "genetic diversity" as the number of alleles present in a population, then the "genetic diversity" of the migrant population must be equal to or less than the "genetic diversity" of the ancestral population.
faith writes:
by removing some genetic potentials
When faith says that, she is assuming that we measure genetic diversity by the number of alleles present in the migratory population compared to the number of alleles present in the ancestral population. If the ancestral population is "very large" and the migrant population is "very small" then it stands to reason that the migrant population, as a subset of the ancestral population, will have fewer alleles and less genetic diversity. It's possible that the migrant population will happen to contain all of the alleles of the ancestral population, but it's unlikely to the extent that the former is smaller than the latter. And it's impossible that new alleles were generated along the way.
This is the "bottleneck" effect.
[AS a side note, the founder effect comes from a different idea. Let's say the ancestral population has three different insulin alleles (A,B and C). Of all the alleles in the ancestral population, 90% are of type A, 4% are of type B and 1% of type C. It is possible that, just by chance, the migrant population has completely different frequencies of each allele. In the migrant population, 30% has allele A, 35% has allele B and 35% has allele C. The migrant population would then have a greater proportion of previously rare alleles, but the alleles wouldn't be "more diverse".
]
Best of all, if you are dealing with sexual species, you could measure genetic diversity in a more concrete way by calculating the frequency of heterozygotes, which gives rise to the celebrated "F-statistics". A heterozygote is an organism that inherited an allele from one parent that differs from the allele inherited from the other parent.
Under conditions of completely random mating, large population size, no natural selection, no migration, etc., the expected frequency of heterozygosity in a polymorphic allele within a population can be calculated analytically (see Hardy-Weinberg equilibria for more than two alleles). The F statistics are a measure of how much the frequency of heterozygotes departs from these model conditions due to nonrandom mating, migration, selection or whatever, and are reported as a measure of the reduction in heterozygosity due to non-hardy-weinberg conditions (minimum of 0 = all alleles are mixed randomly between populations, maximum of 1 = each population has a different allele ; see here and a population genetics textbook)
There are also some straightforward (but dubiously useful) ways of estimating genetic diversity in this context, such as spatial autocorrelation, which are borrowed from geography but aren't necessarily all that informative on biological matters.
The short of it is that it's not a meaningless question, and Faith is correct to say that colonization of a new habitat by a minority from a large ancestral population will generally involve a reduction of diversity, whether it is measured as the reduction of the number of alleles present in a single population, or a relative reduction of heterozgosity measured across both ancestral and colonizing populations.
faith writes:
bringing new genetic combinations to phenotypic expression that were suppressed in the parent population
Faith must be talking about dominance here; if heterozygosity if reduced by nonrandom mating then the frequeny of (previously rare) homozygotes increases in the new population, and you get homozygous-recessive phenotypes in the colonizing population that are not expressed in the ancestral population. Right, Faith?
Mick
in edit:
Sorry, after all that I forgot to answer your last question:
jar writes:
Do newly seen traits result from simply removing some genetic suppression mechanism, and if so, what is that mechanism?
Insofar as one genetic suppression mechanism is dominance, then yes that's one way you could get novel traits that were never before seen in the ancestral population. But obviously it's not the only way, and the whole idea of dominance is a very blunt instrument when we're talking about fine scale tuning of the phenotype.
But it certainly wouldn't surprise me to find that novel traits are "released" during colonization episodes - in fact that may well be how the different coloration patterns of the chipmunks came to be fixed in each population.
A number of biologists are currently investigating the idea that genetic diversity is maintained at a low level in large, random-mating "hardy-weinberg-like" populations and repeatedly introduced into geographically isolated areas through rare colonization events. One is Dolph Schluter (http://www.zoology.ubc.ca/~schluter/lab.html). He studies these little stickleback species which live both in the ocean and in freshwater. He has found that alleles favouring freshwater life are found as recessive alleles in ocean populations, and that recurrent migrations from ocean to freshwater streams up and down continental costalines have "released" these alleles repeatedly. He calls the ocean a "molecular conveyor belt" leading rare alleles from a large ocean population to smaller, isolated freshwater streams. The relevant link is here. The EDA research deserves a thread of its own!
Here's a quick taster:
quote:
This finding shows that while the morphological change is large, the underlying genetics are simple," Kingsley told The Scientist. Marine water fish carry the genetic change at such a low frequency that individual animals do not carry homozygous alleles for the gene, a condition required for the development of low-plated fish, he said. But when these marine fish move to a new freshwater environment, the low-plated phenotype has a selected advantage, and the low-plated fish can appear quickly through natural selection at a higher frequency of the preexisting genetic change.
This message has been edited by mick, 11-26-2005 09:13 PM
This message has been edited by mick, 11-26-2005 09:17 PM

This message is a reply to:
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Replies to this message:
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 100 of 298 (263933)
11-28-2005 8:42 PM
Reply to: Message 34 by Faith
11-27-2005 3:45 AM


They are still Tamias....
Hi Faith,
faith writes:
Yes. But I have a problem with the term "species."
faith writes:
Don't like that term "species"
faith writes:
Problem with term "species."
Faith writes:
They are still Tamias.
The problem with all of that is that it is an argument that leads nowhere. The whole argument "they are still Tamias" is just a red herring. It's a way of avoiding the question.
Let's say we take Tamias amoenus (everybody must be bored of this stripy fellow by now) and Oryctolagus cuniculus (the rabbit). Let's see how far "they are still" can take us.
Presumably you would accept that they are "different". One's a chipmunk and one's a rabbit, after all.
Starting from the chipmunk we could say:
1. Comparing Tamias amoenus in the north and Tamias amoenus in the south: They are still "yellow-pine chipmunk"
2. Comparing Tamias amoenus and Tamias straitus: They are still chipmunk. Picture of striatus below.
3. Comparing Tamias amoenus and the genus Funisciurus: They are still "sciurinae". Picture of Funisciurus below.
4. Comparing Funisciurus and the genus Glaucomys: They are still "sciuridae". Picture of Glaucomys volans below.
5. Comparing Glaucomys with the genus Dipodomys: They are still "sciurognathi". Picture of Dipodomys spectabilis below.
6. Comparing Dipodomys to the genus Octodon: They are still "rodents". Picture of Octodon degus below.
7. Comparing Octodon to the genus Oryctolagus: They are still "glires". Picture of oryctolagus below.
8. Comparing Oryctolagus cuniculus with the genus Sylvilagus: They are still "rabbits". Picture of Sylvilagus floridanus below.
9. Comparing Sylvilagus with Lepus (the hare): They are still "leporidae". Picture of Lepus capensis below:
10. Comparing Lepus with the genus Ochotona: They are still "lagomorpha". Picture of Ochotona princeps below.
11. Comparing Ochotona princeps with Tamias amoenus: They are still "glires"........ Picture of Tamias amoenus below.
So the "They are still..." argument allows us to travel between species, genera, subfamilies, families, orders, and superorders without ever accepting that "macroevolution" has taken place.
It's a useless argument, it leads nowhere.
Mick
in edit: to clarify:
Tamias amoenus and Tamias striatus are different species, but the same genus.
Tamias and Funisciurus are different genera, but the same subfamily.
Funisciurus and Glaucomys are different subfamilies, but the same family.
Glaucomys and Dipodomys are different families, but the same suborder.
Dipodomys and Octodon are different suborders, but the same order.
Octodon and Oryctolagus are different orders, but the same superorder.
Oryctolagus and Sylvilagus are different genera, but the same family.
Sylvilagus and Lepus are different families, but the same order.
Lepus and Ochotona are different suborders, but the same order.
Ochotona and Tamias are different orders, but the same superorder.
One of these pairs of species MUST represent macroevolution even in the eyes of a creationist. Unless they are all "the same kind", in which case the question goes back to the opening post: where does the genetic structure between these pairs come from if it does not come from through microevolutionary processes?
This message has been edited by mick, 11-28-2005 09:21 PM
This message has been edited by mick, 11-28-2005 09:24 PM
This message has been edited by mick, 11-28-2005 09:25 PM

This message is a reply to:
 Message 34 by Faith, posted 11-27-2005 3:45 AM Faith has replied

Replies to this message:
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 122 of 298 (264460)
11-30-2005 1:20 PM
Reply to: Message 111 by Faith
11-29-2005 5:09 PM


keeping things civil
Hey can we all be polite, cut out the swearing and name-calling etc. and not worry about who started it.
I appreciate Faith making the effort to engage in this thread, and I appreciate the contributions of others too. I this thread is doing a reasonable job of making us examine and justify our assumptions so let's keep it going in a friendly manner.
Mick

This message is a reply to:
 Message 111 by Faith, posted 11-29-2005 5:09 PM Faith has not replied

  
mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 128 of 298 (264485)
11-30-2005 2:09 PM
Reply to: Message 106 by NosyNed
11-29-2005 2:55 PM


Re: Snowing under
given that Faith is the only creationist other than Brad who has participated in the thread, and the Faith is a YEC, then it's a bit harsh for her to be attacked by dozens of biologists at once. I know these are the rules of the biology forums, but I have seen lots of decent threads killed with this kind of argument. I expect (and the EVC rules require) that all posters who disagree with Faith provide substantive evidence for their position or evidence against Faith's position.
I'm a bit irritated to find a thread I started with a great deal of effort degenerate over 24 hours like this. I (and Mammathus, and robinrohan (and, dare I say it, Faith)) have put some effort into our posts on this thread and it's being spoiled by completely irrelevant bickering with no substantive points being made.
(Not meaning to pick on you in particular, NosyNed. This is aimed at a lot of short content-free posts that appeared recently).
For example:
crashfrog writes:
Ask her. Or did you not notice that I was repeating her remarks to me? If you're concerned about the direction the tone of the thread is taking, look to the one that instigated it, not me.
nosyned writes:
You are the one making firm statements about what is and isn't true. If anyone is belittling you it is for doing that when you know only very, very little about the subject and some of what you "know" is completely wrong.
crashfrog writes:
And if she insists on lowering a previously-civil thread to a personal level as she did, I'll respond in kind, as I have. I've never demanded that Faith reply to my posts. She's never been forced to. If she doesn't want to talk to me, that's fine.
faith writes:
YOu keep saying this but I have no idea how I was uncivil. I asked you to make an effort to get what I'm saying as it seems to me all you were doing was objecting and objecting and correcting and correcting and taking the topic everywhere except what I was focused on, never made the slightest concession to anything I'd said, and that gets very wearing and I finally said so. The only incivility in the whole exchange came from you.
faith writes:
Since the explanations are "simplified, digested and made easy" for my sake, yet are way too much for me to digest in a reading or in some cases ever, due to my ignorance, certainly; and since it is all so clear and simple to you, I wonder if you would be so kind as to explain to me briefly in your own words exactly what my opponents have collectively been saying to me over the last, oh, 60 to 70 posts.
crashfrog writes:
You're hopeless. Almost every thread where I engage with you winds up in the same place - you're unable to defend your arguments, so you attack me personally. I keep your best example of your personal vitriol against me on a bookmark; it's hilarious.
AdminNWR writes:
It might be possible that you have a problem (bad data) in one of the forum saved cookies in your browser. You can try to logout, then login again. Click on the "logout" link near the top of the forum page. Make sure you have your password handy, since that will be needed to login again.
None of these post provided any useful data, any useful insights or any interesting arguments.
JUST STOP IT! YOU'RE FUCKING UP MY THREAD! AND I PUT A LOT OF EFFORT INTO IT!
Mick
This message has been edited by mick, 11-30-2005 02:23 PM
This message has been edited by mick, 11-30-2005 02:25 PM
This message has been edited by mick, 11-30-2005 02:26 PM

This message is a reply to:
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Replies to this message:
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mick
Member (Idle past 5016 days)
Posts: 913
Joined: 02-17-2005


Message 131 of 298 (264541)
11-30-2005 4:29 PM
Reply to: Message 130 by crashfrog
11-30-2005 3:51 PM


Re: Snowing under
crashfrog writes:
YEC's like Faith don't substantially respond to points or bother to correct their misapprehensions unless you drill them with it. That doesn't seem to be something you're prepared to do.
Please read through my posts in this thread and tell me that I'm
"not prepared" to correct people's misapprehensions or to challenge creationists. I am just one of the few people here who respond to posts by people like Faith and Brad in a way that is similar to how I'd expect to have my own posts addressed by others.
I just want people here to talk about phylogeography and crationism, and not whether Faith is stupid or crashfrog is uncivil...
Mick
in edit: if you look at the top of the page, you see a list of registered members who are logged in, and a list of "guests" (unregistered vistors who are just popping by). At the time of writing, there are 22 registered members, and 79 visitors. I have seen a situation where there are about 5 registered members, and 99 visitors. Those visitors are people who are interested in the EvC debate, and might be tempted by the title "the phylogeographic challenge to creationism"; but when they click on the link to this thread they find that half of it is pointless infighting between cliques, and there is no real debate going on at all.
in edit, again: mind you, after 10,000 posts, I might be pretty grouchy as well...
This message has been edited by mick, 11-30-2005 04:43 PM
This message has been edited by mick, 11-30-2005 04:47 PM

This message is a reply to:
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Replies to this message:
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