Thursday, February 26, 2009

"Did Anyone Observe the Origin of Eukaryotes?"

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

A creationist asked the following pretty typical question on another blog:
"Have prokaryotes ever been observed become eukaryotes via endosymbiosis?" [sic]

If by "observed", one means directly observed, then of course the answer is "no". As far as we can tell, this probably happened more than a billion years ago. But if only things that have been directly observed are valid, then virtually all of science, if not almost all human intellectual endeavors, are invalid and pointless.

Did anyone alive today "observe" the decline and fall of the Roman empire? Of course not. So, how do we know it happened? We read about it, or were told about it. We might also have directly observed some ruins in Rome or elsewhere in Europe or Asia Minor, and made some inferences about where they came from and how old they are.

But if direct observation is necessary to validate an assertion, then each of us is trapped in a tiny world whose borders are the limits of our own unaided perceptual apparatus. Not even most forms of logic would survive such an absurd and self-destructive limitation.

However, if one allows for indirect observation and logical inference, then the answer is "yes". There are multiple sources of empirical evidence for the assertion that eukaryotic cells arose as the result of the serial endosymbiosis of several prokaryotic ancestors. You can read a summary of this evidence here (scroll down; it's toward the end of the article).

Furthermore, this inference is made using the most reliable (i.e. "strongest") form of logical inference known to us: consilience. There are multiple, independently discovered and derived lines of empirical evidence pointing to the serially endosymbiotic origin of eukaryotic cells. That is, the evidence for the serial endosymbiosis theory is based on consilience, which is much more reliable that induction, deduction, or even abduction alone.

As in any case having to do with a very complex universe, there are "gaps" in our current model of the serial endosymbiotic origin of eukaryotes. There is also empirical evidence that is not entirely consistent with the model as it now stands. However, as more and more empirical evidence has been discovered, the vast majority of it has supported Lynn Margulis' original theory.

So, which method of validation shall we choose? Shall we voluntarily blind ourselves to the only kind of evidence that can validate things that have happened outside of our immediate perceptual environment, or accept what virtually all thinking people accept – that we must, almost everywhere and at almost all times, accept the validity of empirical evidence that we have not ourselves immediately obtained?

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


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Monday, February 23, 2009

Chance and Necessity

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

One of the main disagreements between evolutionary biologists and "intelligent design" supporters is the role of "chance" (also called "randomness") in the origin of biological objects and processes (especially adaptations). In many cases, it seems that this disagreement is exacerbated by a disagreement about what the antonym of "chance" might be. In my experience, many people on both sides of the EB/ID disagreement think that the opposite of a "chance" event is an event that was "caused". However, this ignores the fact that many scientific explanations now include "chance" or "random" processes in causal explanations of natural objects and processes.

In this context, therefore, I propose that the antonym for "chance" is "necessity", as was first pointed out by Democritus of Abdera in the 4th century BC, whose two famous aphorisms were:

"All things are the fruit of chance and necessity"


"Nothing exists except atoms and the void".

The phrase "chance and necessity" is often used as a descriptive term in modern science. It means essentially "all natural/physical causes", or what one might consider to be the "Newtonian" world view. The reason that evolutionary biologists consider that Darwin founded the science of biology is that he proposed a theory of descent with modification and the origin of adaptations that was based entirely on "chance and necessity", thereby "unifying" biology with the other natural sciences.

However, it is clear that there is a myriad of objects and processes in the universe that are not entirely the "fruit of chance and necessity", just as there are clearly "things" that are neither "atoms" or "void". In purely physical terms, we now recognize at least three "things" in nature: mass, energy, and information. Only the first of these three qualifies under Democritus second aphorism, as neither energy nor information qualify as "things". Energy, of course, is interconvertable with matter according to Einstein's famous energy/matter equation. However, in the form of "pure" energy (such as electromagnetic radiation), energy is not detectable unless and until it interacts with matter (this is why outer space appears black, even though it is filled with light).

The "detectability" problem of energy is even more difficult in the case of information. It seems clear that all forms of information involve some sort of "translation", in which matter/energy relationships are "translated" into information, which can be stored and transmitted in forms that are not entirely reducible to the original matter/energy forms which they represent. As Korbzybski famously said, "the map is not the territory"; the representation (in the form of information) is not the "thing" represented".

No one, including hard-core "naturalists", suggests that information doesn't exist. The problem (and this is where EB and ID run into serious difficulty), is how (and perhaps by whom) information can become "translated" in the first place. It is not even completely clear that simple "natural" processes (such as the photoelectric effect) do not include an exchange of "information" as well as an exchange of energy (in the form of a photon, for example). In quantum electrodynamics, does the exchange of a photon (or, even worse, a virtual photon) constitute an exchange of "information" between the interacting particles?

In classical physics, there is no "arrow of time". Newtonian mechanics can be run forward or backward in time, with no contradictions (and no way to tell which way the process is happening). However, in those branches of modern physics in which random processes play a part (statistical mechanics, thermodynamics, and quantum mechanics), randomness is necessarily tied to "time's arrow". The same is apparently the case with information, at least in its Shannon form.

Ergo, it seems to me that the problem of information is one that is necessarily tied with the concept of "chance". Indeed, I have come to think that information is a manifestation of one of the operations of "chance" in nature; without information, chance overwhelms everything and the universe disintegrates into permanent incoherence.

This is clearly the case in biology. The "fixing" of information in the physical form of the genetic material is the only thing that makes biology possible. Without such "physicallization" of information (in the form of DNA, RNA, proteins, etc.) biological systems would be impossible, as they would disintegrate into incoherence.

Ergo, the transition from purely physical (i.e. mechanical/Newtonian) processes that do not include the translation and transfer of "translated" information to biological processes that necessarily involve the translation and transfer of "translated" information is the central problem of both biology and the physical sciences. As I have written before, I am not sanguine about our ability to answer this problem using historical information, as the transition occurred at a time (and perhaps in a place) which has left no traces from which we can infer its dynamics.

This leaves us with theoretical models, which are of course based on metaphysical assumptions about reality. I believe it would be fair to say that IDers assume that information can exist without a physical referrent (i.e. something that "carries" or "transmits" the information), whereas EBers (along with most other natural scientists) assume that information must have a physical referrent (i.e. it cannot exist in purely "disembodied" form).

Furthermore, it seems clear from previous discussions in this forum that IDers assume that information can be "foresighted"; that is, it can somehow anticipate future outcomes, not by "induction" from the past but by some kind of "deduction" from the future. EBers (again, like most other natural scientists) assume that "time's arrow" cannot point backward, and that the future is therefore relentlessly driven by the past.

It seems to me that the foregoing lays out the problems which which any scientific theory of "origins" must come to grips:

• whether information can exist in purely "disembodied" form in nature, without a physical referrent

• whether the origin of the "translation" of information into physical form (i.e. the origin of the genetic translation machinery of living organisms) cannot take place without an input of "disembodied" information

• whether any form of information transfer can be genuinely "foresighted" (i.e. can be modified by events that have not yet happened, rather than simply predicting future events based on events that have happened in the past).

Evolutionary biologists (and the vast majority of all natural scientists) begin with a metaphysical world view in which their starting assumptions answer these three questions with NO. By contrast, most of the ID supporters with whom I have had such discussions begin with a metaphysical world view in which their starting assumptions are exactly the opposite: they answer these three questions with YES.

Personally, I believe that the metaphysical world view of most scientists is easier to work with, as it requires fewer "YES" answers to these questions (i.e. it requires fewer unverifiable assumptions about things that must exist for the universe to work). However, I freely admit that this belief is on a par with my acceptance of "Occam's razor" as a basic principle of scientific explanation. That is, "Occam's razor" clearly isn't "true", it's just useful as a rule of thumb in doing science.

So, where does this leave us? I think it explains why most scientists are uncomfortable with the word "design" being applied to biological objects and processes. As I have pointed out, Ernst Mayr argued for the legitimacy of the concept of design in biology, when what was meant by that term was the idea that organisms are "designed" by the information encoded in their genomes, interacting with the information obtained from interactions with their environments. This is because this view of biological "design" conforms to the three answers to the three questions listed above as answered by most scientists.

However, Mayr (and virtually all other evolutionary biologists) was uncomfortable with the idea that the process by which genomes and environments came into being was also "designed" - that is, that there was some foresighted process in which intention played a part in the bringing into existence of the physically embodied objects and processes in biology. Again, this is because this view of biological "design" does not conform to the three answers to the three questions listed above as answered by most scientists.

Where do we go from here?

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


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Tuesday, February 17, 2009

Macroevolution: Examples and Evidence

AUTHOR: Allen MacNeill

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
– 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 from which I have drawn many of these examples. Please go there to read more about them.]



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.


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.


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).


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!


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Thursday, February 12, 2009

Charles Robert Darwin, Born 12 February 1809

AUTHOR: Charles Darwin

SOURCE: Origin of Species

COMMENTARY: Allen MacNeill (following the excerpt)
"In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation. Light will be thrown on the origin of man and his history.

"Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Silurian system was deposited, they seem to me to become ennobled. Judging from the past, we may safely infer that not one living species will transmit its unaltered likeness to a distant futurity. And of the species now living very few will transmit progeny of any kind to a far distant futurity; for the manner in which all organic beings are grouped, shows that the greater number of species of each genus, and all the species of many genera, have left no descendants, but have become utterly extinct. We can so far take a prophetic glance into futurity as to foretell that it will be the common and widely-spread species, belonging to the larger and dominant groups, which will ultimately prevail and procreate new and dominant species. As all the living forms of life are the lineal descendants of those which lived long before the Silurian epoch, we may feel certain that the ordinary succession by generation has never once been broken, and that no cataclysm has desolated the whole world. Hence we may look with some confidence to a secure future of equally inappreciable length. And as natural selection works solely by and for the good of each being, all corporeal and mental endowments will tend to progress towards perfection.

"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."
- Charles Darwin,
On the Origin of Species
[pages 488 to 490]


Today is the 200th anniversary of the birth of Charles Darwin (and Abraham Lincoln). Just a few comments about this anniversary and about the passage, above (from the end of the first edition of the Origin of Species).

• Here is how Darwin felt on the morning of 12 February 1859 (the year the Origin of Species was published), according to a letter he wrote to W. D. Fox:
"I have been extra bad of late, with the old severe vomiting rather often & much distressing swimming of the head…

Doesn't sound much like a man who was about to turn the whole world upside down, does it? Darwin was a chronic hypochondriac, and this account of a "bad morning" was pretty typical.

• Years ago I created, directed, produced, and starred in a one-man play called "An Evening with Charles Darwin," based on excerpts from Darwin's correspondence and autobiography. In it, I had the character of Darwin (in the last year of his life) talk about the coincidence of his birthday falling on the same day as that of Abraham Lincoln. This coincidence is significant from a biographical and historical standpoint because Darwin and his family were firm and outspoken abolitionists, and counted Abraham Lincoln among their moral and political heroes. Although I am not aware that Darwin ever mentioned this coincidence, I found it useful for his character to mention it in the play, as it illustrated a facet of Darwin's personality that is rarely mentioned in popular biographical treatments of his life and character.

• In predicting the future impact of his theory, Darwin mentioned specifically only psychology and human evolutionary history. As a partisan for evolutionary psychology, I find this both gratifying and curious. Gratifying, because we really are beginning (finally!) to base psychology on "a new foundation" (i.e. comparative human ethology) and are starting to investigate how (and even, in some cases, when) "each mental power and capacity" was acquired. It's an exciting and very productive time to be working on these subjects!

• Sharp-eyed readers will note the lack of reference to "the Creator" in the final paragraph. This passage is taken from the first edition of the Origin, published in 1859. In that original edition, Darwin wrote
"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one..."
Poetic, but more to the point, clearly not theological, as asserted by some creationists, who are motivated to show that even Darwin refers to creation in the Origin.

• However, Darwin does refer to the Creator, even in this first edition:
"To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual."

From this passage, it is clear that the full extent of the intervention in nature by the Creator was to establish the natural laws that govern what happens in nature. Throughout the Origin, Darwin makes it clear that it isn't necessary to ascribe any other kind of intervention into by Creator, for any reason. Therefore, the Creator cited by Darwin in this concluding passage is clearly the kind of God venerated by Deists. And Deism, as Will Provine and others have repeatedly pointed out, is functionally equivalent to atheism. A Creator that is, by His own choice, constrained to function entirely through the laws of nature (which He Himself created) is unnecessary for the creation and implementation of "secondary causes" (i.e. everything that happens after the universe and its governing laws have been created).

• Think of the courage it must have taken for Darwin to publish the Origin:
"Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created." [emphasis added].

Despite his modest fame among the educated public as author of the
Journal of the Voyages of HMS Beagle
and his reputation among naturalists as the author of four monographs on barnacles, Darwin was essentially an amateur naturalist who dared to propose a theory that was in direct opposition to the publicly stated positions of the most admired professional naturalists and scientists of his time, not to mention two millennia of European history and politics.It is a measure of his confidence in the truth of his own ideas and observations that he went ahead and published the Origin. After that, writing and publishing The Descent of Man... would have been a relative cakewalk.

So, happy birthday, Charles Darwin (and all of his admirers out there in cyberspace) – Many happy returns!


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