Tuesday, March 24, 2009

Intelligent Design is Boring


At a thread at another website discussing the idea that ID is "boring", an ID supporter wrote this:

"[ID] is boring to Will [Provine] I suspect (and to others for the same reason) because they rule out the possibility of an intelligent designer."

Actually, knowing Will Provine pretty well and hearing him say that ID is "boring" on several occasions, I can confidently state that the reason he finds it "boring" is that whenever something interesting in biology is discovered and somebody asks "Why is that thing the way it is?" Will hears most ID supporters answer "Goddidit". His opinion of ID is that it's a science-stopper because rather than suggesting new and interesting ways of trying to figure out how something came to be the way it is, he thinks that IDers simply throw up their hands and say "It's too complicated, so God / the Intelligent Designer must have done it".

Personally, I don't find ID boring for quite the same reason, as I don't always see ID supporters resorting to the "Goddidit" pseudoexplanation. No, the reason I tend to find most ID boring is it's relentlessly negative. That is, people like Michael Behe and William Dembski observe something marvelously complicated and say "That's Irreducibly Complex!" or "That's Complex Specified Information, so it couldn't have evolved via naturalistic means"...and then they leave it at that. No alternative means of creating the marvelously complicated thing is proposed (unless you credit Behe's "puff of smoke" pseudoargument).

Furthermore, I generally don't see ID supporters doing any original empirical research. In particular, I don't see any of them going out into the field (my favorite place to discover things) or into the lab and "getting down and dirty" with some biological phenomenon that they find absolutely fascinating.


My friend, Harry Greene (the world's authority on rattlesnakes) is my idea of a real scientist. He absolutely loves snakes, talks about them at the drop of a hat, has spent his entire professional life studying them in the field and in the lab, and has revolutionized our understanding of the ecology, ethology, and evolutionary biology of reptiles. To me, he's the epitome of an evolutionary biologist, because he has what we call "a feel for the organism" which goes far beyond simply studying it as an experimental subject.


And my friend, Lynn Margulis (the world's authority on endosymbiosis) is also my idea of a real scientist. She absolutely loves getting knee-deep in the mud of some tropical lagoon and scraping scum off of rocks to look at under the microscope. She's spent her entire professional life studying microorganisms in the field and in the lab, and has revolutionized our understanding of the evolutionary biology of microorganisms. Like Harry, she's the epitome of an evolutionary biologist, because she also "a feel for the organism" which leads her to discover things nobody ever thought to look for before, such as symbiotic bacteria embedded in the cell membranes of symbiotic protozoa from the guts of termites.

I have yet to meet or hear about or read about any ID supporter who does anything like what Harry and Lynn do. Yes, Michael Behe is a biochemist, but the things he does in his laboratory at Lehigh have little or nothing to do with ID. And William Dembski wouldn't know an actual living organism if it lunged out and bit him on the ankle.

Biology, and especially evolutionary biology, is that branch of the natural sciences founded and maintained by people who loved and were obsessed with nature and natural things. Darwin and Wallace and Fisher and Haldane and Wright and Dobzhansky and Mayr and Simpson and Stebbins and Hamilton and Trivers and Margulis and the two Wilsons (Edward O. and David Sloan): these are my heroes, and they are the "naturalists" (see how the word has another, much more positive meaning?) who have been the inspiration for my research, insignificant as it is compared with theirs.

And all that IDers can generally do is say "No, you're wrong, it can't happen that way, in fact it can't happen at all without a deus ex machina?" Ugh: boring, pointless, and most of all, no "feel for the organism".

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Tuesday, February 17, 2009

Macroevolution: Examples and Evidence


AUTHOR: Allen MacNeill

SOURCE:
Observed Instances of Speciation


COMMENTARY: That's up to you...

In honor of Darwin’s birthday, here is a response to yet another unsupported assertion by creationists and ID supporters, who often state (without evidence) that although microevolution might happen, there is no evidence for macroevolution.

The distinction between microevolution – the mechanisms by which evolution has occurred – and
macroevolution
– the large-scale pattern of change over time that has resulted from the operation of microevolutionary mechanisms – is as old as evolutionary theory. In the Origin of Species, Darwin himself argued for both microevolution (i.e. natural and sexual selection) and macroevolution (descent with modification), without using these terms. Following the publication of the Origin, Darwin’s theory of descent with modification was quickly accepted by virtually the entire scientific community. However, his proposed mechanisms of natural and sexual selection were not as widely accepted as the “engines” of descent with modification, falling into disrepute by the turn of the 20th century.

However, the founders of the “modern evolutionary synthesis” rehabilitated Darwin’s microevolutionary mechanisms by integrating them with Mendel’s theory of genetics and new discoveries in botany, ecology, ethology, historical geology, and paleontology. So successful was this synthesis that today all but the most committed young-Earth creationists accept that microevolution happens. However, it has become an article of faith among anti-evolutionists of all denominations, including “intelligent design” supporters, that there is no scientific explanation for macroevolution, and that in the case of the origin of humans, it didn’t happen.

There isn’t enough room in this post to address both of these misconceptions, so I will concentrate here on the first: that there is no evidence that macroevolution has happened, and that therefore it didn’t happen (or if it did, it required supernatural intervention). What follows is a brief sample of some examples of macroevolution and the mechanisms by which they have taken place, from the level of species up to the level of whole kingdoms. This is not an exhaustive sample by any means. However, it should give anyone with an open mind enough examples and evidence to form their own conclusions about the validity of modern macroevolutionary theory.

[I am particularly indebted to Joseph Boxhorn’s essay on the evidences for speciation (located at talk.origins.org) from which I have drawn many of these examples. Please go there to read more about them.]

MACROEVOLUTION AT THE LEVEL OF SPECIES

PLANTS


While studying the genetics of the evening primrose, Oenothera lamarckiana, de Vries (1905) found an unusual variant among his plants. Oenothera lamarckiana has a chromosome number of 2N = 14. The variant had a chromosome number of 2N = 28. He found that he was unable to breed this variant with Oenothera lamarckiana. He named this new species Oenothera gigas.


Digby (1912) crossed the primrose species Primula verticillata and Primula floribunda to produce a sterile hybrid. Polyploidization occurred in a few of these plants to produce fertile offspring. The new species was named Primula kewensis. Newton and Pellew (1929) note that spontaneous hybrids of Primula verticillata and Primula floribunda set tetraploid seed on at least three occasions. These happened in 1905, 1923 and 1926.


Owenby (1950) demonstrated that two species in the genus Tragopogon were produced by polyploidization from hybrids. He showed that Tragopogon miscellus found in a colony in Moscow, Idaho was produced by hybridization of Tragopogon dubius and Tragopogon pratensis. He also showed that Tragopogon mirus found in a colony near Pullman, Washington was produced by hybridization of Tragopogon dubius and Tragopogon porrifolius. Evidence from chloroplast DNA suggests that Tragopogon mirus has originated independently by hybridization in eastern Washington and western Idaho at least three times (Soltis and Soltis 1989). The same study also shows multiple origins for Tragopogon micellus.


The Russian cytologist Karpchenko (1927, 1928) crossed the radish, Raphanus sativus, with the cabbage, Brassica oleracea. Despite the fact that the plants were in different genera, he got a sterile hybrid. Some unreduced gametes were formed in the hybrids. This allowed for the production of seed. Plants grown from the seeds were interfertile with each other. They were not interfertile with either parental species. Unfortunately the new plant (genus Raphanobrassica) had the foliage of a radish and the root of a cabbage.


A species of hemp nettle, Galeopsis tetrahit, was hypothesized to be the result of a natural hybridization of two other species, Galeopsis pubescens and Galeopsis speciosa (Muntzing 1932). The two species were crossed. The hybrids matched Galeopsis tetrahit in both visible features and chromosome morphology.


Clausen et al. (1945) hypothesized that Madia citrigracilis was a hexaploid hybrid of Madia gracilis and Madia citriodora. As evidence they noted that the species have gametic chromosome numbers of n = 24, 16 and 8 respectively. Crossing Madia gracilis and Madia citriodora resulted in a highly sterile triploid with n = 24. The chromosomes formed almost no bivalents during meiosis. Artificially doubling the chromosome number using colchecine produced a hexaploid hybrid which closely resembled Madia citrigracilis and was fertile.


Frandsen (1943, 1947) showed that Brassica carinata (n = 17) may be recreated by hybridizing Brassica nigra (n = 8) and Brassica oleracea, Brassica juncea (n = 18) may be recreated by hybridizing Brassica nigra and Brassica campestris (n = 10), and Brassica napus (n = 19) may be recreated by hybridizing Brassica oleracea and Brassica campestris.


Rabe and Haufler (1992) found a naturally occurring diploid sporophyte of maidenhair fern (Adiantum pedatum) which produced unreduced (2N) spores. These spores resulted from a failure of the paired chromosomes to dissociate during the first division of meiosis. The spores germinated normally and grew into diploid gametophytes. These did not appear to produce antheridia. Nonetheless, a subsequent generation of tetraploid sporophytes was produced. When grown in the lab, the tetraploid sporophytes appear to be less vigorous than the normal diploid sporophytes. The 4N individuals were found near Baldwin City, Kansas.


Woodsia Fern (Woodsia abbeae) was described as a hybrid of Woodsia cathcariana and Woodsia ilvensis (Butters 1941). Plants of this hybrid normally produce abortive sporangia containing inviable spores. In 1944 Butters found a Woodsia abbeae plant near Grand Portage, Minn. that had one fertile frond (Butters and Tryon 1948). The apical portion of this frond had fertile sporangia. Spores from this frond germinated and grew into prothallia. About six months after germination sporophytes were produced. They survived for about one year. Based on cytological evidence, Butters and Tryon concluded that the frond that produced the viable spores had gone tetraploid. They made no statement as to whether the sporophytes grown produced viable spores.


Gottlieb (1973) documented the speciation of Stephanomeria malheurensis. He found a single small population (< 250 plants) among a much larger population (> 25,000 plants) of Stephanomeria exigua in Harney Co., Oregon. Both species are diploid and have the same number of chromosomes (N = 8). Stephanomeria exigua is an obligate outcrosser exhibiting sporophytic self-incompatibility. Stephanomeria malheurensis exhibits no self-incompatibility and self-pollinates. Though the two species look very similar, Gottlieb was able to document morphological differences in five characters plus chromosomal differences. F1 hybrids between the species produces only 50% of the seeds and 24% of the pollen that conspecific crosses produced. F2 hybrids showed various developmental abnormalities.


Pasterniani (1969) produced almost complete reproductive isolation between two varieties of maize (Zea mays). The varieties were distinguishable by seed color, white versus yellow. Other genetic markers allowed him to identify hybrids. The two varieties were planted in a common field. Any plant's nearest neighbors were always plants of the other strain. Selection was applied against hybridization by using only those ears of corn that showed a low degree of hybridization as the source of the next years seed. Only parental type kernels from these ears were planted. The strength of selection was increased each year. In the first year, only ears with less than 30% intercrossed seed were used. In the fifth year, only ears with less than 1% intercrossed seed were used. After five years the average percentage of intercrossed matings dropped from 35.8% to 4.9% in the white strain and from 46.7% to 3.4% in the yellow strain.


At reasonably low concentrations, copper is toxic to many plant species. However, several plants have been seen to develop a tolerance to this metal (Macnair 1981). Macnair and Christie (1983) used this to examine the genetic basis of a postmating isolating mechanism in yellow monkey flower (Mimulus guttatus). When they crossed plants from the copper tolerant "Copperopolis" population with plants from the nontolerant "Cerig" population, they found that many of the hybrids were inviable. During early growth, just after the four leaf stage, the leaves of many of the hybrids turned yellow and became necrotic. Death followed this. This was seen only in hybrids between the two populations. Through mapping studies, the authors were able to show that the copper tolerance gene and the gene responsible for hybrid inviability were either the same gene or were very tightly linked. These results suggest that reproductive isolation may require changes in only a small number of genes.

ANIMALS

Speciation through hybridization and/or polyploidy is now considered to be as important in animals as it is in plants. (Lokki and Saura 1980; Bullini and Nascetti 1990; Vrijenhoek 1994). Bullini and Nasceti (1990) review chromosomal and genetic evidence that suggest that speciation through hybridization may occur in a number of insect species, including walking sticks, grasshoppers, blackflies and cucurlionid beetles. Lokki and Saura (1980) discuss the role of polyploidy in insect evolution. Vrijenhoek (1994) reviews the literature on parthenogenesis and hybridogenesis in fish.

Dobzhansky and Pavlovsky (1971) reported a speciation event that occurred in a laboratory culture of Drosophila paulistorum sometime between 1958 and 1963. The culture was descended from a single inseminated female that was captured in the Llanos of Colombia. In 1958 this strain produced fertile hybrids when crossed with conspecifics of different strains from Orinocan. From 1963 onward crosses with Orinocan strains produced only sterile males. Initially no assortative mating or behavioral isolation was seen between the Llanos strain and the Orinocan strains. Later on Dobzhansky produced assortative mating (Dobzhansky 1972).


Thoday and Gibson (1962) established a population of Drosophila melanogaster from four gravid females. They applied selection on this population for flies with the highest and lowest numbers of sternoplural chaetae (hairs). In each generation, eight flies with high numbers of chaetae were allowed to interbreed and eight flies with low numbers of chaetae were allowed to interbreed. Periodically they performed mate choice experiments on the two lines. They found that they had produced a high degree of positive assortative mating between the two groups. In the decade or so following this, eighteen labs attempted unsuccessfully to reproduce these results. References are given in Thoday and Gibson 1970.

Crossley (1974) was able to produce changes in mating behavior in two mutant strains of Drosophila melanogaster. Four treatments were used. In each treatment, 55 virgin males and 55 virgin females of both ebony body mutant flies and vestigial wing mutant flies (220 flies total) were put into a jar and allowed to mate for 20 hours. The females were collected and each was put into a separate vial. The phenotypes of the offspring were recorded. Wild type offspring were hybrids between the mutants. In two of the four treatments, mating was carried out in the light. In one of these treatments all hybrid offspring were destroyed. This was repeated for 40 generations. Mating was carried out in the dark in the other two treatments. Again, in one of these all hybrids were destroyed. This was repeated for 49 generations. Crossley ran mate choice tests and observed mating behavior. Positive assortative mating was found in the treatment which had mated in the light and had been subject to strong selection against hybridization. The basis of this was changes in the courtship behaviors of both sexes. Similar experiments, without observation of mating behavior, were performed by Knight, et al. (1956).

Kilias, et al. (1980) exposed Drosophila melanogaster populations to different temperature and humidity regimes for several years. They performed mating tests to check for reproductive isolation. They found some sterility in crosses among populations raised under different conditions. They also showed some positive assortative mating. These things were not observed in populations which were separated but raised under the same conditions. They concluded that sexual isolation was produced as a byproduct of selection.

In a series of papers (Rice 1985, Rice and Salt 1988 and Rice and Salt 1990) Rice and Salt presented experimental evidence for the possibility of sympatric speciation in Drosophila melanogaster. They started from the premise that whenever organisms sort themselves into the environment first and then mate locally, individuals with the same habitat preferences will necessarily mate assortatively. They established a stock population of Drosophila melanogaster with flies collected in an orchard near Davis, California. Pupae from the culture were placed into a habitat maze. Newly emerged flies had to negotiate the maze to find food. The maze simulated several environmental gradients simultaneously. The flies had to make three choices of which way to go. The first was between light and dark (phototaxis). The second was between up and down (geotaxis). The last was between the scent of acetaldehyde and the scent of ethanol (chemotaxis). This divided the flies among eight habitats. The flies were further divided by the time of day of emergence. In total the flies were divided among 24 spatio-temporal habitats.

They next cultured two strains of flies that had chosen opposite habitats. One strain emerged early, flew upward and was attracted to dark and acetaldehyde. The other emerged late, flew downward and was attracted to light and ethanol. Pupae from these two strains were placed together in the maze. They were allowed to mate at the food site and were collected. Eye color differences between the strains allowed Rice and Salt to distinguish between the two strains. A selective penalty was imposed on flies that switched habitats. Females that switched habitats were destroyed. None of their gametes passed into the next generation. Males that switched habitats received no penalty. After 25 generations of this mating tests showed reproductive isolation between the two strains. Habitat specialization was also produced.

They next repeated the experiment without the penalty against habitat switching. The result was the same -- reproductive isolation was produced. They argued that a switching penalty is not necessary to produce reproductive isolation. Their results, they stated, show the possibility of sympatric speciation.


In a series of experiments, del Solar (1966) derived positively and negatively geotactic and phototactic strains of Drosophila pseudoobscura from the same population by running the flies through mazes. Flies from different strains were then introduced into mating chambers (10 males and 10 females from each strain). Matings were recorded. Statistically significant positive assortative mating was found.

In a separate series of experiments Dodd (1989) raised eight populations derived from a single population of Drosophila pseudoobscura on stressful media. Four populations were raised on a starch based medium, the other four were raised on a maltose based medium. The fly populations in both treatments took several months to get established, implying that they were under strong selection. Dodd found some evidence of genetic divergence between flies in the two treatments. He performed mate choice tests among experimental populations. He found statistically significant assortative mating between populations raised on different media, but no assortative mating among populations raised within the same medium regime. He argued that since there was no direct selection for reproductive isolation, the behavioral isolation results from a pleiotropic by-product to adaptation to the two media. Schluter and Nagel (1995) have argued that these results provide experimental support for the hypothesis of parallel speciation.


Less dramatic results were obtained by growing Drosophila willistoni on media of different pH levels (de Oliveira and Cordeiro 1980). Mate choice tests after 26, 32, 52 and 69 generations of growth showed statistically significant assortative mating between some populations grown in different pH treatments. This ethological isolation did not always persist over time. They also found that some crosses made after 106 and 122 generations showed significant hybrid inferiority, but only when grown in acid medium.

Some proposed models of speciation rely on a process called reinforcement to complete the speciation process. Reinforcement occurs when to partially isolated allopatric populations come into contact. Lower relative fitness of hybrids between the two populations results in increased selection for isolating mechanisms. I should note that a recent review (Rice and Hostert 1993) argues that there is little experimental evidence to support reinforcement models. Two experiments in which the authors argue that their results provide support are discussed below.

Ehrman (1971) established strains of wild-type and mutant (black body) Drosophila melanogaster. These flies were derived from compound autosome strains such that heterotypic matings would produce no progeny. The two strains were reared together in common fly cages. After two years, the isolation index generated from mate choice experiments had increased from 0.04 to 0.43, indicating the appearance of considerable assortative mating. After four years this index had risen to 0.64 (Ehrman 1973). Along the same lines, Koopman (1950) was able to increase the degree of reproductive isolation between two partially isolated species, Drosophila pseudoobscura and Drosophila persimilis.

The founder-flush (a.k.a. flush-crash) hypothesis posits that genetic drift and founder effects play a major role in speciation (Powell 1978). During a founder-flush cycle a new habitat is colonized by a small number of individuals (e.g. one inseminated female). The population rapidly expands (the flush phase). This is followed by the population crashing. During this crash period the population experiences strong genetic drift. The population undergoes another rapid expansion followed by another crash. This cycle repeats several times. Reproductive isolation is produced as a byproduct of genetic drift.

Dodd and Powell (1985) tested this hypothesis using Drosophila pseudoobscura. A large, heterogeneous population was allowed to grow rapidly in a very large population cage. Twelve experimental populations were derived from this population from single pair matings. These populations were allowed to flush. Fourteen months later, mating tests were performed among the twelve populations. No postmating isolation was seen. One cross showed strong behavioral isolation. The populations underwent three more flush-crash cycles. Forty-four months after the start of the experiment (and fifteen months after the last flush) the populations were again tested. Once again, no postmating isolation was seen. Three populations showed behavioral isolation in the form of positive assortative mating. Later tests between 1980 and 1984 showed that the isolation persisted, though it was weaker in some cases.

Galina, et al. (1993) performed similar experiments with Drosophila pseudoobscura. Mating tests between populations that underwent flush-crash cycles and their ancestral populations showed 8 cases of positive assortative mating out of 118 crosses. They also showed 5 cases of negative assortative mating (i.e. the flies preferred to mate with flies of the other strain). Tests among the founder-flush populations showed 36 cases of positive assortative mating out of 370 crosses. These tests also found 4 cases of negative assortative mating. Most of these mating preferences did not persist over time. Galina, et al. concluded that the founder-flush protocol yields reproductive isolation only as a rare and erratic event.

Ahearn (1980) applied the founder-flush protocol to Drosophila silvestris. Flies from a line of this species underwent several flush-crash cycles. They were tested in mate choice experiments against flies from a continuously large population. Female flies from both strains preferred to mate with males from the large population. Females from the large population would not mate with males from the founder flush population. An asymmetric reproductive isolation was produced.

In a three year experiment, Ringo, et al. (1985) compared the effects of a founder-flush protocol to the effects of selection on various traits. A large population of Drosophila simulans was created from flies from 69 wild caught stocks from several locations. Founder-flush lines and selection lines were derived from this population. The founder-flush lines went through six flush-crash cycles. The selection lines experienced equal intensities of selection for various traits. Mating test were performed between strains within a treatment and between treatment strains and the source population. Crosses were also checked for postmating isolation. In the selection lines, 10 out of 216 crosses showed positive assortative mating (2 crosses showed negative assortative mating). They also found that 25 out of 216 crosses showed postmating isolation. Of these, 9 cases involved crosses with the source population. In the founder-flush lines 12 out of 216 crosses showed positive assortative mating (3 crosses showed negative assortative mating). Postmating isolation was found in 15 out of 216 crosses, 11 involving the source population. They concluded that only weak isolation was found and that there was little difference between the effects of natural selection and the effects of genetic drift.


Meffert and Bryant (1991) used houseflies (Musca domestica) to test whether bottlenecks in populations can cause permanent alterations in courtship behavior that lead to premating isolation. They collected over 100 flies of each sex from a landfill near Alvin, Texas. These were used to initiate an ancestral population. From this ancestral population they established six lines. Two of these lines were started with one pair of flies, two lines were started with four pairs of flies and two lines were started with sixteen pairs of flies. These populations were flushed to about 2,000 flies each. They then went through five bottlenecks followed by flushes. This took 35 generations. Mate choice tests were performed. One case of positive assortative mating was found. One case of negative assortative mating was also found.

Soans, et al. (1974) used houseflies (Musca domestica) to test Pimentel's model of speciation. This model posits that speciation requires two steps. The first is the formation of races in subpopulations. This is followed by the establishment of reproductive isolation. Houseflies were subjected to intense divergent selection on the basis of positive and negative geotaxis. In some treatments no gene flow was allowed, while in others there was 30% gene flow. Selection was imposed by placing 1000 flies into the center of a 108 cm vertical tube. The first 50 flies that reached the top and the first 50 flies that reached the bottom were used to found positively and negatively geotactic populations. Four populations were established:
Population A: positive geotaxis, no gene flow
Population B: negative geotaxis, no gene flow
Population C: positive geotaxis, 30% gene flow
Population D: negative geotaxis, 30% gene flow

Selection was repeated within these populations each generations. After 38 generations the time to collect 50 flies had dropped from 6 hours to 2 hours in Pop A, from 4 hours to 4 minutes in Pop B, from 6 hours to 2 hours in Pop C and from 4 hours to 45 minutes in Pop D. Mate choice tests were performed. Positive assortative mating was found in all crosses. They concluded that reproductive isolation occurred under both allopatric and sympatric conditions when very strong selection was present. Hurd and Eisenberg (1975) performed a similar experiment on houseflies using 50% gene flow and got the same results.

Recently there has been a lot of interest in whether the differentiation of an herbivorous or parasitic species into races living on different hosts can lead to sympatric speciation. It has been argued that in animals that mate on (or in) their preferred hosts, positive assortative mating is an inevitable byproduct of habitat selection (Rice 1985; Barton, et al. 1988). This would suggest that differentiated host races may represent incipient species.


The Apple Maggot Fly (Rhagoletis pomonella) is a fly that is native to North America. Its normal host is the hawthorn tree (Crataegus monogyna). Sometime during the nineteenth century it began to infest apple trees. Since then it has begun to infest cherries, roses, pears and possibly other members of the Rosaceae. Quite a bit of work has been done on the differences between flies infesting hawthorn and flies infesting apple. There appear to be differences in host preferences among populations. Offspring of females collected from on of these two hosts are more likely to select that host for oviposition (Prokopy et al. 1988). Genetic differences between flies on these two hosts have been found at 6 out of 13 allozyme loci (Feder et al. 1988, see also McPheron et al. 1988). Laboratory studies have shown an asynchrony in emergence time of adults between these two host races (Smith 1988). Flies from apple trees take about 40 days to mature, whereas flies from hawthorn trees take 54-60 days to mature. This makes sense when we consider that hawthorn fruit tends to mature later in the season that apples. Hybridization studies show that host preferences are inherited, but give no evidence of barriers to mating. This is a very exciting case. It may represent the early stages of a sympatric speciation event (considering the dispersal of Rhagoletis pomonella to other plants it may even represent the beginning of an adaptive radiation). It is important to note that some of the leading researchers on this question are urging caution in interpreting it. Feder and Bush (1989) stated:
"Hawthorn and apple "host races" of Rhagoletis pomonella may therefore represent incipient species. However, it remains to be seen whether host-associated traits can evolve into effective enough barriers to gene flow to result eventually in the complete reproductive isolation of Rhagoletis pomonella populations."



Gall Former Fly (Eurosta solidaginis) is a gall forming fly that is associated with goldenrod ( Solidago sp.) plants. It has two hosts: over most of its range it lays its eggs in Solidago altissima, but in some areas it uses Solidago gigantea as its host. Recent electrophoretic work has shown that the genetic distances among flies from different sympatric hosts species are greater than the distances among flies on the same host in different geographic areas (Waring et al. 1990). This same study also found reduced variability in flies on Solidago gigantea. This suggests that some Eurosta solidaginis have recently shifted hosts to this species. A recent study has compared reproductive behavior of the flies associated with the two hosts (Craig et al. 1993). They found that flies associated with Solidago gigantea emerge earlier in the season than flies associated with Solidago altissima. In host choice experiments, each fly strain ovipunctured its own host much more frequently than the other host.

Craig et al. (1993) also performed several mating experiments. When no host was present and females mated with males from either strain, if males from only one strain were present. When males of both strains were present, statistically significant positive assortative mating was seen. In the presence of a host, assortative mating was also seen. When both hosts and flies from both populations were present, females waited on the buds of the host that they are normally associated with. The males fly to the host to mate. This may represent the beginning of a sympatric speciation.


Halliburton and Gall (1981) established a population of flour beetles (Tribolium castaneum) collected in Davis, California. In each generation they selected the 8 lightest and the 8 heaviest pupae of each sex. When these 32 beetles had emerged, they were placed together and allowed to mate for 24 hours. Eggs were collected for 48 hours. The pupae that developed from these eggs were weighed at 19 days. This was repeated for 15 generations. The results of mate choice tests between heavy and light beetles was compared to tests among control lines derived from randomly chosen pupae. Positive assortative mating on the basis of size was found in 2 out of 4 experimental lines.


In 1964 five or six individuals of the polychaete worm, Nereis acuminata, were collected in Long Beach Harbor, California. These were allowed to grow into a population of thousands of individuals. Four pairs from this population were transferred to the Woods Hole Oceanographic Institute. For over 20 years these worms were used as test organisms in environmental toxicology. From 1986 to 1991 the Long Beach area was searched for populations of the worm. Two populations, P1 and P2, were found. Weinberg, et al. (1992) performed tests on these two populations and the Woods Hole population (WH) for both postmating and premating isolation. To test for postmating isolation, they looked at whether broods from crosses were successfully reared. The results below give the percentage of successful rearings for each group of crosses.
WH × WH = 75%
P1 × P1 = 95%
P2 × P2 = 80%
P1 × P2 = 77%
WH × P1 = 0%
WH × P2 = 0%

They also found statistically significant premating isolation between the WH population and the field populations. Finally, the Woods Hole population showed slightly different karyotypes from the field populations.

In some species the presence of intracellular bacterial parasites (or symbionts) is associated with postmating isolation. This results from a cytoplasmic incompatability between gametes from strains that have the parasite (or symbiont) and stains that don't. An example of this is seen in the mosquito Culex pipiens (Yen and Barr 1971). Compared to within strain matings, matings between strains from different geographic regions may may have any of three results: These matings may produce a normal number of offspring, they may produce a reduced number of offspring or they may produce no offspring. Reciprocal crosses may give the same or different results. In an incompatible cross, the egg and sperm nuclei fail to unite during fertilization. The egg dies during embryogenesis. In some of these strains, Yen and Barr (1971) found substantial numbers of Rickettsia-like microbes in adults, eggs and embryos. Compatibility of mosquito strains seems to be correlated with the strain of the microbe present. Mosquitoes that carry different strains of the microbe exhibit cytoplasmic incompatibility; those that carry the same strain of microbe are interfertile.

Similar phenomena have been seen in a number of other insects. Microoganisms are seen in the eggs of both Nasonia vitripennis and Nasonia giraulti. These two species do not normally hybridize. Following treatment with antibiotics, hybrids occur between them (Breeuwer and Werren 1990). In this case, the symbiont is associated with improper condensation of host chromosomes. For more examples and a critical review of this topic, see Thompson 1987.

MACROEVOLUTION ABOVE THE LEVEL OF SPECIES


Boraas (1983) reported the induction of multicellularity in a strain of Chlorella pyrenoidosa (since reclassified as Chlorella vulgaris) by predation. He was growing the unicellular green alga in the first stage of a two stage continuous culture system as for food for a flagellate predator, Ochromonas sp., that was growing in the second stage. Due to the failure of a pump, flagellates washed back into the first stage. Within five days a colonial form of the Chlorella appeared. It rapidly came to dominate the culture. The colony size ranged from 4 cells to 32 cells. Eventually it stabilized at 8 cells. This colonial form has persisted in culture for about a decade. The new form has been keyed out using a number of algal taxonomic keys. They key out now as being in the genus Coelosphaerium, which is in a different family from Chlorella.

Shikano, et al. (1990) reported that an unidentified bacterium underwent a major morphological change when grown in the presence of a ciliate predator. This bacterium's normal morphology is a short (1.5 um) rod. After 8 - 10 weeks of growing with the predator it assumed the form of long (20 um) cells. These cells have no cross walls. Filaments of this type have also been produced under circumstances similar to Boraas' induction of multicellularity in Chlorella. Microscopic examination of these filaments is described in Gillott et al. (1993). Multicellularity has also been produced in unicellular bacterial by predation (Nakajima and Kurihara 1994). In this study, growth in the presence of protozoal grazers resulted in the production of chains of bacterial cells.


The “species flock” of over 600 species of cichlid fish in Lake Victoria have all diverged within the past 15,000 years, according to Tijs Goldschmidt. Lake Victoria, the source of the Nile River in east Africa, was formed by block faulting in the African great rift valley. Geological evidence indicates that the lake was originally formed about 400,000 years ago, but dried out about 15,000 years ago. It subsequently refilled, and the 600+ species of cichlid fish have adaptively radiated during that period of time.

As the lake constitutes a single, although very large ecosystem, the adaptive radiation of the cichlid fish of Lake Victoria must be considered to have undergone a massive sympatric divergence. That this is the case is further supported by the observation that the extraordinary phenotypic variation seen among these fish has been accompanied by almost no genetic variation, except for a very small number of homeotic genes. Goldschmidt has suggested that the adaptive radiation of the cichlids of Lake Victoria has been driven by a combination of adaptation to a myriad of trophic niches, combined with sexual selection resulting from female choice (Goldschmidt, 1998).

MACROEVOLUTION AT THE LEVEL OF KINGDOMS


In 1970, Lynn Margulis proposed that the four kingdoms of eukaryotes (Protoctista, Fungi, Plantae, and Animalia, now combined in the domain Eukarya) originated from the endosymbiotic combination of four prokaryotic (i.e. bacterial) ancestors. The first step in this endosymbiotic partnership was the endosymbiotic incorporation of an aerobic bacterium with an acid-tolerant (probably Archaean) prokaryotic ancestor. The aerobic bacterium eventually evolved into what we now recognize as mitochondria. That this was the first step in the endosymbiotic origin of eukaryotes is supported by the observation that all eukaryotic cells (except such specialized cells as erythrocytes) have mitochondria, indicating that bacteria-derived mitochondria became associated with the ancestors of eukaryotes prior to the splitting of the eukaryotic clade into the plant, fungus, and animal kingdoms.

Margulis cites several lines of evidence supporting the hypothesis that mitochondria originated as endosymbiotic aerobic bacteria:

• Mitochondria have a double membrane. The outer membrane is very similar to the membrane of the vacuoles of eukaryotic cells, while the inner membrane is much more similar to the plasma membrane of bacteria.

• Like bacteria, mitochondria have circular DNA molecules, whereas the DNA molecules in the nuclear chromosomes of eukaryotes is linear.

• Also like bacteria, the circular DNA molecules of mitochondria are not complexed with histone proteins, whereas the linear DNA molecules in the chromosomes of the eukaryotic nucleus are tightly complexed with histone proteins.

• The DNA molecules of mitochondria (like the DNA of bacteria) do not include intron sequences, whereas the DNA molecules in the chromosomes of the eukaryotic nucleus generally include at least one, and often many intron sequences.

• Most of the genetic components of the mitochondrial genome, including such genetic “machinery” as promoter sequences and terminator sequences, are coded in the same way as in bacteria, and are significantly different from the genetic “machinery” in the DNA in the chromosomes of the eukaryotic nucleus.

•Mitochondria have their own ribosomes, which are virtually identical with bacterial ribosomes, but very different in size and structure from the ribosomes in the cytosol of eukaryotic cells.

• Mitochondria reproduce independently inside their host cells via binary fission, the same mechanism by which other bacteria reproduce, and very different from the process of mitosis by which eukaryotic cells divide.

The second step in the endosymbiotic origin of eukaryotes was the incorporation of motile, microtubule-containing bacteria similar to spirochaete bacteria into the mitochondrion-containing eukaryotic ancestor. Margulis proposed that these bacteria evolved into the cilia and flagella of eukaryotic cells (called undulapodia), which eventually evolved into the mitotic spindle apparatus by which all eukaryotic cells divide. She predicted that the basal bodies of cilia and flagella would have their own DNA, a prediction that was verified by researchers who (ironically) were trying to disprove her hypothesis. Another observation supporting Margulis’s hypothesis about the endosymbiotic origin of undulapodia is the fact that, like mitochondria, cilia and flagella reproduce independently of the cells to which they are attached, via a mechanism similar to binary fission. That the incorporation of spirochaete-like bacteria into the ancestors of all eukaryotes was the second step in the endosymbiotic origin of eukaryotes is supported by the observation that almost all eukaryotic cells (except a few very primitive species) reproduce via mitosis, indicating again that the undulapodia-derived spindle apparatus became associated with the ancestors of eukaryotes prior to the splitting of the eukaryotic clade into the plant, fungus, and animal kingdoms.

The final step in the endosymbiotic origin of eukaryotes was the incorporation of photosynthetic bacteria similar to cyanobacteria into the mitochondria-and-undulapodia-containing eukaryotic ancestor. These photosynthetic bacteria evolved into the chloroplasts of eukaryotic algae and plants. Like mitochondria, chloroplasts have a number of structural and functional similarities to photosynthetic bacteria that point to their endosymbiotic origin:
• Like mitochondria, chloroplasts have a double membrane. The outer membrane is very similar to the membrane of the vacuoles of eukaryotic cells, while the inner membrane is much more similar to the plasma membrane of bacteria.

• Like bacteria and mitochondria, chloroplasts have circular DNA molecules, whereas the DNA molecules in the nuclear chromosomes of eukaryotes is linear.

• Also like bacteria and mitochondria, the circular DNA molecules of chloroplasts are not complexed with histone proteins, whereas the linear DNA molecules in the chromosomes of the eukaryotic nucleus are tightly complexed with histone proteins.

• The DNA molecules of chloroplasts (like the DNA of bacteria and mitochondria) do not include intron sequences, whereas the DNA molecules in the chromosomes of the eukaryotic nucleus generally include at least one, and often many intron sequences.

• Most of the genetic components of the chloroplast genome, including such genetic “machinery” as promoter sequences and terminator sequences, are coded in the same way as in bacteria, and are significantly different from the genetic “machinery” in the DNA in the chromosomes of the eukaryotic nucleus.

•Like mitochondria, chloroplasts have their own ribosomes, which are virtually identical with bacterial ribosomes, but very different in size and structure from the ribosomes in the cytosol of eukaryotic cells.

• Like mitochondria, chloroplasts reproduce independently inside their host cells via binary fission, the same mechanism by which other bacteria reproduce, and very different from the process of mitosis by which eukaryotic cells divide.

• If separated from their eukaryotic host cells, chloroplasts can grow and reproduce on their own, looking and acting for all the world like photosynthetic bacteria.

That this was the final step in the endosymbiotic origin of eukaryotes is supported by the observation that only plant cells (and some protists) have chloroplasts, indicating that bacteria-derived chloroplasts became associated with the ancestors of eukaryotes after to the splitting of the eukaryotic clade into the plant, fungus, and animal kingdoms. This suggestion is strengthened by recent research indicating that fungi and animals are more closely related to each other than either are to plants, indicating that the split between photosynthetic eukaryotes (i.e. algae and plants) and heterotrophic eukaryotes (i.e. fungi and animals) happened before the incorporation of endosymbiotic photosynthetic bacteria in the ancestors of algae and plants.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Sunday, April 27, 2008

Serial Endosymbiosis and Intelligent Design



AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

It's very gratifying to see Lynn Margulis finally getting the recognition that she deserves. As the most effective exponent of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn's work provides an excellent example of how ID should (but currently doesn't) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).

Her theory was greeted with contempt and scorn by almost all evolutionary biologists (sound familiar?), who believed at the time that all eukaryotic cellular organelles evolved by gradual elaboration of invaginations of the plasma membrane. But Lynn didn't give up, or continue to simply restate her original theory (sound familiar?). Instead, she continued to do extensive field and laboratory research, publishing hundreds of papers and dozens of books in which she presented the accumulating empirical evidence supporting her theory. With time, other researchers (encouraged by the success of her field and lab research) began to test her hypotheses themselves, and discovered yet more empirical evidence supporting her theory.

And so today, Lynn Margulis's SET has become the dominant theory explaining not only the origin of eukaryotes, but also the origin of evolutionary novelty at dozens of different levels in biology (see her book, Acquiring Genomes for a comprehensive review). So well accepted has her work become by evolutionary biologists that finally, after almost four decades, creationists and ID supporters have begun to attack her theories. As she said at our Darwin Day celebration at Cornell this past February, no greater affirmation of one's "having arrived" as a major theorist in evolutionary biology could be imagined.

The point here is that, if ID wants to become accepted as part of evolutionary biology in the same way that Lynn Margulis's SET has become accepted, then ID supporters have to do the same thing she did: get out in the field and get your hands dirty, and get into the lab and do the same thing. Her ideas were just as unorthodox and unacceptable in 1969 as ID is now. However, she didn't put all of her effort into public relations and political propaganda. No "Symbiosis Institute" dumped millions into the production of deliberately distorted press kits and one-sided propaganda films. Legions of self-appointed experts whose only exposure to biology was in high school classes or what they read on Answers in Genesis or Uncommon Descent bloviated on SET and declared themselves experts after a week of superficial study of articles on Wikipedia.

No, Lynn and her colleagues did the hard work of finding the empirical evidence that eventually carried the day and established her SET as one of the bedrock foundations now worthy enough of respect as to earn the ire of the creationists and IDers. Her ideas are still radical, and still raise the blood pressure of many evolutionary biologists. Her dismissal of the "modern evolutionary synthesis" in particular is not popular among many evolutionary biologists, who are largely still mired in paradigms that are at least four decades of out of date. She has said some things about the "modern synthesis" that have brought smiles to the faces of the creationist quote-miners. The difference between her and them is that they can't even begin to claim any credibility in science; their "work" is entirely parasitic on hers, and deserves nothing but contempt.

When the history of evolutionary biology in the 20th century is written (I hope to contribute to it myself, if I live long enough), the work of Lynn Margulis will rank right up there with the work of Fisher, Haldane, Wright, Dobzhansky, Mayr, Simpson, Stebbins, Gould, Lewontin, Kimura, Williams, Hamilton, Trivers, and the two Wilsons. And unless and until IDers decide that it's finally time to stop doing agitprop and start doing science, they and the creationists will at best be a trivial footnote.

Comments, criticisms, and suggestions are warmly welcomed!

--Allen

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Friday, February 10, 2006

A Third Way: James Shapiro and the Post-Modern Synthesis



AUTHOR: James A. Shapiro

SOURCE: The Boston Review

COMMENTARY: Allen MacNeill (following the article)

The recent reviews in your columns of books by Dennett, Dawkins, and Behe are testimony to the unflagging interest in controversies about evolution. Although such purists as Dennett and Dawkins repeatedly assert that the scientific issues surrounding evolution are basically solved by conventional neo-Darwinism, the ongoing public fascination reveals a deeper wisdom. There are far more unresolved questions than answers about evolutionary processes, and contemporary science continues to provide us with new conceptual possibilities.

Unfortunately, readers of Boston Review may remain unaware of this intellectual ferment because the debate about evolution continues to assume the quality of an abstract and philosophical "dialogue of the deaf" between Creationists and Darwinists. Although our knowledge of the molecular details of biological organization is undergoing a revolutionary expansion, open-minded discussions of the impact of these discoveries are all too rare. The possibility of a non-Darwinian, scientific theory of evolution is virtually never considered. In my comments, then, I propose to sketch some developments in contemporary life science that suggest shortcomings in orthodox evolutionary theory and open the door to very different ways of formulating questions about the evolutionary process. After a discussion of technical advances in our views about genome organization and the mechanisms of genetic change, I will focus on a growing convergence between biology and information science which offers the potential for scientific investigation of possible intelligent cellular action in evolution.

The past five decades of research in genetics and molecular biology have brought us revolutionary discoveries. Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated. The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics.

Four categories of molecular discoveries are especially important in opening up exciting new ways of thinking about the biological processes that underlie evolutionary change.

(1) Genome Organization. Our current ideas of genome organization are completely different from the "beads on a string" view that dominated genetics in the 1940s and 1950s. At that time genes were "units" which corresponded to individual organismal traits, and the "one gene-one enzyme" hypothesis told us that the essential business of each gene was to encode a specific protein molecule linked to a particular phenotype. We have now deconstructed each genetic locus into a modular assembly of regulatory and coding motifs. Most of these motifs are shared among many loci, suggesting that genomes are assembled Lego-like from a repertoire of more basic sequence elements, many of which do not encode proteins but determine other important functions (transcription, translation, RNA processing, DNA replication, chromatin condensation, etc.). As we analyze genome expression during cellular proliferation and multicellular development, we have learned that diverse genetic loci are organized hierarchically into interconnected genome-wide networks which function dynamically. Not confined to a single pathway, many genetic loci are active at different times, participating in the expression of more than one phenotypic trait. Comparisons of genomes in different organisms have revealed unexpected patterns of evolutionary conservation across large taxonomic distances, while closely-related genomes frequently differ significantly in the arrangement of repetitive DNA elements which do not encode proteins.

How all of this modularity, complexity, and integration arose and changed during the history of life on earth is a central evolutionary question. Localized random mutation, selection operating "one gene at a time" (John Maynard Smith's formulation), and gradual modification of individual functions are unable to provide satisfactory explanations for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for.

Studies of the molecular sources of genetic variability have taught us two major lessons about how cells take care of their genomes--one about self-protection, the other about self-reorganization.

(2) Cellular Repair Capabilities. First, then, all cells from bacteria to man possess a truly astonishing array of repair systems which serve to remove accidental and stochastic sources of mutation. Multiple levels of proofreading mechanisms recognize and remove errors that inevitably occur during DNA replication. These proofreading systems are capable of distinguishing between newly synthesized and parental strands of the DNA double helix, so they operate efficiently to rectify rather than fix the results of accidental misincorporations of the wrong nucleotide. Other systems scan non-replicating DNA for chemical changes that could lead to miscoding and remove modified nucleotides, while additional functions monitor the pools of precursors and remove potentially mutagenic contaminants. In anticipation of chemical and physical insults to the genome, such as alkylating agents and ultraviolet radiation, additional repair systems are encoded in the genome and can be induced to correct damage when it occurs.

It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. By virtue of their proofreading and repair systems, living cells are not passive victims of the random forces of chemistry and physics. They devote large resources to suppressing random genetic variation and have the capacity to set the level of background localized mutability by adjusting the activity of their repair systems.

(3) Mobile Genetic Elements and Natural Genetic Engineering. The second major lesson of molecular studies into the origins of genetic change is that all cells possess multiple biochemical agents for natural genetic engineering--processes that include the cutting and splicing of DNA molecules into new sequence arrangements. Most frequently, natural genetic engineering capabilities reveal themselves through the activities of mobile genetic elements--DNA structures found in all genomes that can move from one position to another. Mobile genetic elements are the most fluid components of the genome and also the most taxonomically specific. In human cells, mobile elements include retrotransposons, like the half-million or more Alu sequences dispersed over all our chromosomes, as well as the inherited gene fragments which our lymphocytes assemble daily to form active genetic loci encoding the key antigen recognition molecules of our immune system. The biochemical agents of DNA restructuring include the enzymes used in our own genetic engineering for research and biotechnology (nucleases, ligases, reverse transcriptases and polymerases) as well as other proteins that combine to form molecular machines capable of mobilizing different genomic components.

The existence of cellular biochemical activities capable of rearranging DNA molecules means that genetic change can be specific (these activities can recognize particular sequence motifs) and need not be limited to one genetic locus (the same activity can operate at multiple sites in the genome). In other words, genetic change can be massive and non-random. Some organisms, such as the ciliated protozooan Oxytricha, completely reorganize their genetic apparatus within a single cell generation, fragmenting the germ-line chromosomes into thousands of pieces and then reassembling a particular subset of them into a distinct kind of functional genome. Furthermore, natural genetic engineering systems can operate premeiotically during the somatic development of tissues that will ultimately produce gametes. This means that major chromosome reorganizations can be present in multiple gametes. Consequently, the appearance of new genome architectures during evolution is not necessarily limited to isolated individuals.

The discovery that genome reorganization is largely a biological process traces back to Barbara McClintock's pioneering studies of mutation and chromosome rearrangement in maize from the 1940s through the 1960s. She linked these genetic events to changes in the regulation of gene expression programs during plant development. We can now appreciate her tremendous wisdom and foresight by seeing how the Lego-like patterns of integrated genome organization mentioned above could be created by the activity of cellular natural genetic engineering systems. Because, like all cellular functions, natural genetic engineering systems are subject to control circuits, they can be held in abeyance for long periods and then called into action at certain key times. Sometimes these activations can be regularly programmed, as in the development of our immune systems, and sometimes activations can occur in response to crisis, as McClintock documented in maize.

The point of this discussion is that our current knowledge of genetic change is fundamentally at variance with neo-Darwinist postulates. We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures. Inevitably, such a profound advance in awareness of genetic capabilities will dramatically alter our understanding of the evolutionary process. Nonetheless, neo-Darwinist writers like Dawkins continue to ignore or trivialize the new knowledge and insist on gradualism as the only path for evolutionary change.

(4) Cellular Information Processing. While it is easy to see how advances in our understanding of genome organization and genetic change will impact theories of evolutionary processes, another development in contemporary biology is of less obvious but even more basic relevance. This is the growing realization that cells have molecular computing networks which process information about internal operations and about the external environment to make decisions controlling growth, movement, and differentiation. This realization has come, in large measure, from detailed genetic analysis of cellular processes and multicellular development. The inducible repair systems mentioned above provide a relatively simple, well-studied example. Bacterial and yeast cells have molecules that monitor the status of the genome and activate cellular responses when damaged DNA accumulates. The surveillance molecules do this by modifying transcription factors so that appropriate repair functions are synthesized. These inducible DNA damage response systems are sophisticated and include so-called "checkpoint" functions that act to arrest cell division until the repair process has been completed. When the checkpoints do not function, cell division proceeds before repair is completed, and the damaged cells die or produce inviable progeny. One can characterize this surveillance/inducible repair/checkpoint system as a molecular computation network demonstrating biologically useful properties of self-awareness and decision-making.

There are many other cellular systems that display comparable information-processing capabilities. Fro example, it is now common among molecular biologists who study the cell cycle to speak of various checkpoints (Is DNA replication complete? Are the chromosomes properly condensed and aligned on the metaphase plate?) and decision points (e.g., when to initiate chromosome movement and cytokinesis).

A recent special issue of Scientific American [1] describes beautifully how cancer is now seen as a disease of the molecular information processing routines that ensure orderly cell growth and behavior in the healthy organism. Aberrant tumor cell growth appears to result from at least two kinds of malfunction: the loss of checkpoint controls, or the failure of decision-making routines that dictate programmed cell death (apoptosis) for cells in inappropriate surroundings. During embryonic development, cells make decisions about differentiation based on multiple molecular signals picked up from their environment and from their neighbors by means of surface receptors. These receptors are linked to intercellular molecular cascades called "signal transduction pathways" which integrate the inputs from the receptors to generate appropriate patterns of differential gene expression and morphogenesis of specialized cell structures.

Signal transduction is not limited to multicellular development. We are learning that virtually every aspect of cellular function is influenced by chemical messages detected, transmitted, and interpreted by molecular relays. To a remarkable extent, therefore, contemporary biology has become a science of sensitivity, inter- and intra-cellular communication, and control. Given the enormous complexity of living cells and the need to coordinate literally millions of biochemical events, it would be surprising if powerful cellular capacities for information processing did not manifest themselves. In an important way, then, biology has returned to questions debated during the mechanism-vitalism controversy earlier this century. This time around, however, the discussion is informed by two new factors. One is that the techniques of molecular and cell biology allow us to examine the detailed operation of the hardware responsible for cellular responsiveness and decision-making. The second is the existence of computers and information networks, physical entities endowed with computational and decision-making capabilities. Their existence means that discussing the potential for similar activities by living organisms is neither vague nor mystical.

What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?

Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.

A sounder perspective on the history of science would be very helpful to all concerned. For example, a parallel has been drawn by Allen Orr and others between criticisms of Darwinian orthodoxy and assaults on the Law of Gravity, presenting them as equally deplorable examples of anti-science obscurantism. Yet, if truth be told, gravity is far from a settled matter. The relativistic Law of Gravity at the end of the 20th century is not the same as the classical Law of Gravity at the end of the 19th century, and discovering how the continuous descriptions of general relativity can be integrated into a single theory with the discrete accounts of quantum physics is still an active field of research. From a scientific point of view, then, the Law of Gravity has quite properly been under continuous challenge. Dogmas and taboos may be suitable for religion, but they have no place in science. No theory or viewpoint should ever become sacrosanct because experience tells us that even the most elegant Laws of Nature ultimately succumb to the inexorable progress of scientific thinking and technological innovation. The present debate over Darwinism will be more productive if it takes place in recognition of the fact that scientific advances are made not by canonizing our predecessors but by creating intellectual and technical opportunities for our successors.

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NOTES:

[1] Robert Weinberg, "How Cancer Arises," Scientific American 275, no. 3 (September 1996), pp. 62-70.

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COMMENTARY:

In general, I agree with Shapiro: the paradigms established during the "modern evolutionary synthesis" of the 1930s-50s are by and large defunct. In particular, the idea that evolutionary change is necessarily gradual has been under fire since at least 1972, and the evidence available now is leaning toward what Ernst Mayr once called "evolution by jerks" - that is, punctuated equilibrium. And new work in the field of evolutionary developmental biology ("evo-devo") has provided a new paradigm for the production and evolution of variation at speeds and in degrees that are largely incompatible with the "modern synthesis."

But this doesn't mean, by any stretch of the imagination, that current evolutionary theory now needs to have "intelligent design theory" incorporatd into any of its newly emerging paradigms. On the contrary, the new empirical studies in evo-devo, paleontology, and especially evolutionary genetics have provided us with new explanations for the sources of variation in natural and laboratory populations, and new explanations for the mechanisms by which that variation can be fixed and modified in evolving populations. Nowhere in this exciting ferment of laboratory and field research has anyone found any need to invoke any supernatural "intelligent designer" to explain where this variation comes from, or where it is going.

"Intelligent design theory" isn't a forward-looking science at all; it's a rear-guard action in a "long twilight struggle" against the startling and overwhelming successes that evolutionary biologists have had recently in explaining the origin and evolution of life on Earth. We biologists have indeed begun to give up our tired old "modern" paradigms, but unless the supporters of "intelligent design theory" are ready to do the same, they will almost certainly fade into a footnote in the history of science.

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ORIGINAL PUBLICATION REFERENCE:

Location Online:
The Boston Review
URL: http://www.bostonreview.net/br22.1/shapiro.html

Original posting/publication date timestamp:
February 1997

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