What is "Darwinism" and am I a "Darwinist"?

I don’t use the term “Darwinism” at all, any more than I would use the term “Newtonism” when referring to classical physical mechanics, “Einsteinism” to refer to relativity theory, “Bohr/Feinman/Heisenberg/Schroedingerism” to refer to quantum mechanics, or “Mendeleevianism” to refer to chemistry. What I and my colleagues (and friends) do is probably best described as “evolutionary biology”, and includes (at a bare minimum) the following:

1) the formulation and testing of a set of interconnected theories explaining the origin of biological diversity, consisting of descent with modification from common ancestors over deep geological time, describable via cladistic analysis, and supported by inference from multiple sources of empirical evidence, including comparative anatomy, biogeography, developmental biology, genomics, historical geology, and paleontology; and

2) the formulation and testing of a separate but related set of interconnected theories explaining the origin and modification of the phenotypic characteristics of living organisms, consisting (at a bare minumum) of the mechanisms of natural selection, sexual selection, genetic drift, and neutral molecular evolution in deep geological time, grounded (at least in part) in theoretical mathematical models of population genetics, depending on multiple sources of heritable phenotypic variation, and supported by inference from multiple sources of empirical evidence, including field and laboratory research in the fields of biochemistry, cell biology, comparative physiology, developmental biology, ecology, ethology, genetics, neurobiology, and physiological ecology.

Note that these two definitions of the principle domains of evolutionary biology correspond roughly to what are sometimes referred to as “macroevolutionary theory” and “microevolutionary theory” (in that order) and do not explicitly mention:

• theories of the origin of life from non-living materials, which are properly the purview of astrophysics, chemistry, and geology, not biology;

• the concept of “adaptation”, which has had a checkered past in evolutionary biology and is facing increasing challenges within the field; and

• teleology, which is almost never mentioned, except for those evolutionary biologists who have thought about it (which, in my experience, are relatively few), who generally assume that resort to teleological explanations in evolutionary biology is unnecessary. Not wrong, just unnecessary (not to mention unproductive as an empirical research hypothesis).

As philosophical concepts, both adaptation and teleology have a very long history, stretching back at least to Plato and Aristotle. However, recent developments in evolutionary theory, including (but not limited to) theories of epigenetics, exaptation, genetic drift/draft, neutral and nearly neutral molecular “drift” in deep evolutionary time, and punctuated equilibrium, have rendered the concept of “adaptation” as an increasingly marginal diversion rather than a central topic in evolutionary biology.

And teleology, rather than being considered “wrong” (when it is considered at all, which is seldom) is now increasingly being incorporated into new theories of “evolved agency”, especially in evolutionary psychology (my own field). I am currently working on a treatise on this latter subject, which I hope to finish before departing this veil of tears and laughter for that undiscovered country from whose bourn no traveller returns.

The Searchers

AUTHORS: William A. Dembski and Robert J. Marks II

SOURCE: Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA – October 2009, pp. 2647-2652

COMMENTARY: Allen MacNeill

First, congratulations to Drs. Dembski & Marks! Publication is the life blood of all career academics and the living heart of the intellectual process. It takes courage and hard work (and a little bit of luck) to get your original work published, and more of the same to weather the criticism that inevitably ensues. But, just as one cannot have a fencing match without an opponent, real progress in any intellectual endeavor cannot come from consensus, but only from the clash of ideas and evidence.

And so, to specifics:

I have no quibble with most of the mathematical analysis presented. Indeed, given the assumptions upon which the authors' Conservation of Information (COI) theory is based (with which I do not necessarily agree, but which are clearly presented in their paper), the analysis presented is apparently not completely outside the domain of No Free Lunch (NFL) theorems in general.

However, the same cannot be said for the application of these ideas to biological evolution. To be specific, consider the following quote [Dembski & Marks (2009) pg. 2651, lines 2-5]:

"From the perspective of COI, these limited number of endpoints on which evolution converges constitute intrinsic targets, crafted in part by initial conditions and the environment." [emphasis added]

This is indeed the crux of the issue vis-a-vis biological evolution. While it is clearly the case that Simon Conway-Morris asserts that there is an apparently limited number of biological "endpoints", it is neither the case that Morris' viewpoint represents the core of evolutionary theory, nor that his point is relevant to the analysis of COI presented in Dr. Dembski and Marks' paper.

To be specific, the highlighted qualifier from the quote above – crafted in part by initial conditions and the environment – is precisely the issue under debate between evolutionary biologists and supports of intelligent design (ID).

Taken at face value, this qualifying simply phrase means that, given specific starting conditions and a specific time-varying environmental context, the various mechanisms of evolution (e.g. mutation, natural selection, genetic drift, inbreeding, etc.) tend to converge on a relatively limited set of genotypic and phenotypic "endstates" (i.e. what could be loosely referred to as "evolutionary adaptations").

This is simply another way of defining evolutionary convergence, and in no way constitutes evidence for intrinsic evolutionary teleology. On the contrary, it simply provides support for the hypothesis that, given similar conditions, similar outcomes result.

Furthermore, it assumes that virtually all characteristics of living organisms are adaptations (that is, genotypic/phenotypic characteristics that fulfill some necessary function in the lives of organisms). However, this is manifestly not the case, nor is it an absolutely necessary component of current evolutionary theory. On the contrary, many (perhaps the majority) of the characteristics of living organisms are not adaptive. This is certainly the case at the level of the genome, as evidenced by the neutral and nearly neutraltheories of molecular evolution.

Finally, Morris' (and, by extension, Dembski and Marks') position completely omits any role for historical contingency, which both the fossil and genomic record indicate are of extraordinary importance in macroevolution. As Dembski and Marks state, the "endpoints" (perhaps it would be more precise to refer to them as "way stations") of macroevolution depend fundamentally on initial conditions and the environment. But this is not fundamentally different from Darwin's position in the Origin of Species:

"The complex and little known laws governing variation are the same, as far as we can see, with the laws which have governed the production of so-called specific forms. In both cases physical conditions seem to have produced but little direct effect; yet when varieties enter any zone, they occasionally assume some of the characters of the species proper to that zone." [Darwin, C. (1859) Origin of Species, pg. 472, emphasis added]

Moreover, Dembski and Marks' analysis completely ignores the appearance (or non-appearance) of new genotypic and phenotypic variations, and on the accidental disappearance of such characteristics (via extinction), without regard to the adaptive value of such characteristics, or the lack thereof.

In other words, Dembski and Marks' analysis, while interesting from the standpoint of what could be called "abstract" search algorithms, completely fails to address the central issues of evolutionary biology: the source of evolutionary novelty (i.e. the "engines of variation"), the effects of changing environmental conditions on the actual forms and functions of living organisms, and the fundamental importance of historical contingency in the ongoing evolution of genotypes and phenotypes.

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

--Allen

A New Species of Finch in the Galapagos: So What?

Since the first reports of the origin of a new species of finch on the island of Daphne Major in the Galapagos archipelago appeared, there has been a flood of questions about just what exactly it was that Peter and Rosemary Grant observed, and how their observations relate to the larger question of macroevolution. As many evolutionary biologists (including me) anticipated, creationists and intelligent design ("ID") supporters have moved the goalposts, arguing that they have always accepted that speciation occurs, but that it does not necessarily mean anything for macroevolution, especially if one defines "macroevolution" as the origin of higher taxa (i.e. taxonomic categories above the level of species). So, what did the Grants observe, and how are their observations related to the larger question of the origin of higher taxa (i.e. macroevolution)?

The answer is that this long-term research project has provided direct evidence for the initial stages of macroevolution in the field. To be precise, what is at issue in the research reported by the Grants is what is known as “secondary contact”. This is what happens after a sub-population has become reproductively isolated from the population from which it was derived. According to Theodosius Dobzhansky and Ernst Mayr (two of the founders of the “modern evolutionary synthesis”), speciation is the result of genetic isolation resulting from geographic isolation: the members of two geographically separated populations of organisms no longer interbreed, and therefore genetic differences between the two populations accumulate over time.

This process, commonly known as allopatric speciation, can be considered to consist of six discrete, successive stages:

1) Vicariance: A subpopulation (in this case, a couple of finches) becomes geographically isolated (on Isla Daphne Major) from its former panmictic conspecifics (i.e. the species Geospiza fortis on Isla Santa Cruz, a neighboring island);

2) Divergence: The genomes of the members of the vicariant subpopulation diverge from the genomes of the members of the panmictic source population as the result of various genetic mechanisms (for a list of such mechanisms, click here);

3) Reproductive Isolation: The reproductive anatomy, physiology, and behavior of the members of the vicariant subpopulation diverge from the reproductive anatomy, physiology, and behavior of the members of the original source population, resulting in reproductive isolation and (eventually...at least sometimes) reproductive incompatibility;

4) Secondary Contact: Successful hybridization between members of the diverging sub-population and the original source population decreases in frequency as the result of pre-zygotic and post-zygotic isolating mechanisms (for more, click here);

5) Reinforcement: Hybrids continue to decrease in frequency as non-hybrids increase in frequency as the result of microevolutionary mechanisms (i.e. mutation,natural selection, gene flow, genetic drift, and inbreeding depression), resulting in reinforcement of reproductive isolation and species boundaries; and

6) Maintenance: Species incompatibility is continuously reinforced via pre-zygotic and post-zygotic isolating mechanisms, resulting in continued genotypic and phenotypic divergence.

This is why Alfred Russell Wallace entitled his paper (which he mailed to Darwin in April 1858), “On the Tendency for Varieties to Depart Indefinitely from the Original Type”.

Note that none of these stages is absolutely defined; rather, they integrade in what Darwin characterized as an “insensible series”. Also note that stages 4 through 6 can be condensed into one stage (i.e. “reinforcement”), in which reproductive incompatibility increases steadily over time. Finally, some evolutionary biologists (most notably C. H. Waddington, Mary Jane West-Eberhard, Eva Jablonka and Marion Lamb) have proposed that stages 2 and 3 probably happen in reverse order (a process known as genetic assimilation).

This is the theoretical model; what actual empirical studies have shown is that diverging phylogenetic lines frequently become reintegrated, separating and then re-integrating more than once. Sometimes they become sufficiently reinforced that they remain separate and diverge continuously, and sometimes they “collapse” back into a single, panmictic “species”.

The importance of all of this to the theory of macroevolution is that divergence is divergence: phylogenetic divergence via reproductive isolation is macroevolution. Speciation is simply the first stage in the origin of all higher taxa.

Therefore, what is ultimately at issue between evolutionary biologists and creationists (including most ID supporters) is not speciation per se nor the mechanisms by which it occurs or is reinforced, but rather whether there are “natural” limits to the degree of divergence that can take place as a result of the mechanisms that comprise the “engines of variation”.

Despite much posturing on both sides, this is not a question that can be answered via pure theoretical (i.e. mathematical) speculation. However compelling a theoretical model may appear, it must be tested empirically to see if it conforms to the evidence from nature. This is what evolutionary biologists do all the time, and what ID theorists seem either unable or unwilling to do. Until this situation changes (if it ever does), no reputable empirical scientist anywhere will ever take ID seriously.

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

--Allen

Macroevolution: What Were the Evolutionary Ancestors of Whales?

ID supporters often assert that, although there is abundant empirical evidence for microevolution, there is no such evidence for macroevolution. One of the macroevolutionary transitions that they often cite is the evolution of whales from a land-dwelling ancestor. Which leads me to ask the following question:

What empirical evidence would verify (i.e. support) or falsify (i.e. undermine) the hypothesis that whales had evolved from a land-dwelling mammal? Please note that this is a hypothesis about macroevolution, not microevolution.

A basic principle of hypothesis validation in the natural sciences is that if one can find multiple lines of evidence, all of which support the hypothesis, then such evidence is much stronger than if there were only a single line of evidence. This is especially the case if the different lines of evidence are from very widely separated fields.

Until recently the main line of evidence for the evolution of whales (i.e. members of the mammalian order Cetacea) from even-toed ungulates (i.e. members of the mammalian order Artiodactyla) was anatomical. This anatomical evidence was derived from two sources:

1) similarities between the anatomy (especially skeletal anatomy) of living (i.e. "extant") Artiodactyls and Cetacea, and

2) an evolutionary phylogeny of the transition from terrestrial Artiodactyls to aquatic Cetacea, based on fossils.

Rather than summarize this comparative anatomical evidence here, I recommend that interested readers follow this link. What you will find is a fairly detailed summary of the evidence from comparative anatomy, all of it pointing to the conclusion that whales (i.e. Cetaceans) evolved from even-toed ungulates (i.e. Artiodactyls). It is this evidence that most evolutionary biologists have until recently cited as support for the macroevolutionary derivation of Cetaceans from Artiodactyl ancestors.

However, one can also ask the question Does the comparative genomics of Artiodactyls and Cetaceans support the same hypothesis? That is, are there observable DNA sequence similarities and differences that are similar in both scope and timing to the similarities and differences in the fossil record (and as reflected in the comparative anatomy of Artiodactyls and Cetaceans)?

This is an easily falsified hypothesis: If the genomic evidence does not support the Artiodactyl into Cetacean hypothesis — e.g. that Cetaceans evolved from some other clade, or that they had not evolved at all, but rather sprang into existence fully-formed and without genetic evidence of a macroevolutionary transition — then this evidence would not support the evidence from comparative anatomy and the macroevolutionary hypothesis based on comparative anatomy would be called into question.

So, what does the comparative genomic evidence indicate about the macroevolutionary relationships between the Artiodactyla and the Cetacea? Here’s a summary of the findings from comparative genomics:

The idea that whales evolved from within the Artiodactyla was based on analysis of DNA sequences. In the initial molecular analyses, whales were shown to be more closely related to ruminants (such as cattle and deer) than ruminants are to pigs. In order for the order name to reflect a real evolutionary unit, the term Cetartiodactyla was coined.

Later molecular analyses included a wider sampling of artiodactyls and produced a more complete tale. Hippos were determined to be the closest relative of whales, ruminants were related to a whale/hippo clade, and pigs were more distant. In addition to producing the controversial whale/hippo clade, these analyses debunked the idea that hippos and pigs are closely related. This had been a popular taxonomic hypothesis (Suiformes) based on similarities in morphological (physical) characteristics.

In addition to DNA and protein sequences, researchers tracked the movement of transposons called SINEs in the genome. A transposon is a DNA sequence that will occasionally make a copy of itself and insert that copy into another part of the genome. It is considered highly unlikely that SINEs will insert themselves into the exact same part of a genome by chance. The data indicate that several transposons inserted themselves at the same point in the genomes of whales, ruminants and hippos (sometimes referred to as "pseudoruminants" because although they have four-chambered stomachs like true ruminants, they do not chew the cud). This insertion point is not shared with camels and pigs.

This hypothesis has been tested with DNA sequences from a host of genes: the complete mitochondrial genome (as well as several of its genes independently), beta-casein, kappa-casein, von Willebrand factor, breast cancer 1, recombination activating genes 1 and 2, cannabinoid receptor 1, and several others. These sequence data and the transposons converge on the same conclusion that hippos and whales are more closely related to one another than either is to other artiodactyls.

Sequences analyzed in combined analyses with morphological characters have also produced the same results as sequences alone. Some have argued that the sheer number of characters (one for each nucleotide) in sequences swamps out the effects of morphology. There have been a few morphology-based studies that have suggested (weakly) the same results as the molecular results, but overall most morphological studies have conflicted with the whale/hippo hypothesis of Cetartiodactyla.

An important exception is a recent conducted by Boisserie et al. (2005). They examined 80 hard morphological characters of fossil and extant cetartiodactylan taxa. Their results suggest that hippopotamids evolved from within a clade of anthracotheres. That anthracothere/hippopotamid clade appears to be sister to the Cetacea and supports the molecular results.

[sources: http://en.wikipedia.org/wiki/Cetartiodactyla (summary article), where you can find links to many primary references]

Note that much of the genomic data (especially from transposon sequences) supporting the macroevolutionary hypothesis is based on non-adaptive DNA sequences. That is, DNA sequences that do not code for adaptive characteristics, and in many cases that do not code for anything at all. This is like figuring out which students have been copying the answers to test questions from other students by comparing their wrong answers. The right answers are the same for everybody, but wrong answers vary from student to student in virtually random ways. If two students have the same wrong answers, you can be reasonably confident that one of them copied the wrong answers from the other. You can then test this hypothesis by looking at seating charts, past test performance (cheaters are often identified by sudden increases in test scores without apparent increases in effort), and – often the last resort – asking them if they copied answers.

Conclusion: The empirical evidence from comparative genomics closely matches the empirical evidence from (both extant and fossil) comparative anatomy.

Is that all, or is there yet another line of evidence that might be pursued to verify or falsify the Artiodactyl into Cetacean hypothesis? Yes, there is. Consider the observable fact that whales reproduce much more slowly than even-toed ungulates (such as deer and hippos). Indeed, there is a general principle in zoology that the larger the members of a species are (on the average) the fewer offspring they have, the more widely spaced those offspring are in time, the fewer offspring they can have over their lifetime, and the longer the average lifespan of individuals.

For example, deer can have offspring every year, and under good conditions can sometimes have twins or even triplets in one reproductive cycle. By comparison, baleen whales can only have offspring every few years (it can take up to two years for one pregnancy in large baleen whales), they virtually never have more than one calf at a time, they have only a few reproductive life cycles per lifetime, and they have much longer lifespans than deer.

This means that, if Cetaceans evolved from Artiodactyls, one might be able to find empirical evidence that the rate of the macroevolutionary transition from Artiodactyl ancestors into Cetacean descendants had slowed down as the result of the increase in size, decrease in number of offspring per reproductive cycle, decrease in total number of offspring per lifetime, and increase in average lifespan. In brief, there might be evidence that the macroevolutionary “clock” slowed down as Cetaceans evolved larger and larger size.

Here’s the latest genomic evidence vis-a-vis this hypothesis:

Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti).
Molecular Biology and Evolution. 2009 Nov;26(11):2427-40. Epub 2009 Jul 31.
Jackson JA, Baker CS, Vant M, Steel DJ, Medrano-González L, Palumbi SR.
Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, OR, USA.

ABSTRACT: Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes approximately 34 million years ago (Ma), between the balaenids and balaenopterids approximately 28 Ma, and the time to most recent common ancestor within the Balaenopteridae approximately 12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1-15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human-chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21-0.37%/My across a range of studies).

CONCLUSION: The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome. [emphasis added]

So, there are indeed empirically falsifiable hypotheses for the macroevolution of whales from land-dwelling ancestors. If whales (Cetacea) evolved from even-toed ungulates (Artiodactyla), then the following predictions should be supported by the observable data:
• that there should be anatomical similarities between extant Artiodactyls and Cetaceans,
• that there should also be anatomical similarities between fossil Artiodactyls and Cetaceans,
• that there should be shared similarities and differences between the genomes of extant clades of Artiodactyls and Cetaceans, and that the overwhelming majority of these similarities and differences would mirror the comparative anatomical evidence for the macroevolutionary origin of the various clades of the Cetartiodactyla, and
• that the inferred slowing of macroevolutionary change during the transition from Artiodactyl ancestors to Cetacean descendants should also be consistent with the hypothesis that the rate of this transition would have slowed as the result of increasing body size, increasing reproductive spacing, decreasing numbers of offspring per life cycle, and increasing longevity.

And it is.

Clearly, an ID supporter might then ask for specific empirical evidence on how the various transitions occurred at the genetic and developmental level, and if these details could unambiguously distinguish between natural and supernatural causes for such genetic mechanisms. Evolutionary developmental biologists are currently working on answers to the first part, but I personally cannot imagine how one could empirically test the second part. Furthermore, it seems to me that invoking a supernatural cause for the macroevolutionary transition from Artiodactyls to Cetaceans would be unnecessary, and would add nothing whatsoever to our understanding of the mechanisms by which this transition occurred.

Ergo, if I were doing this research and publishing my results I wouldn’t mention it, as it would be completely unnecessary for a scientific explanation of this phenomenon.

Just out of curiosity, ask yourself how one might use any of the foregoing as positive or negative empirical evidence for the existence of God. I mention this because some evolutionary biologists believe they can use the data of evolutionary biology to disprove the existence of God, and some ID supporters believe they can use the data of evolutionary biology to prove the existence of God. Personally, I believe both attempts are misguided, pointless, and ultimately futile. That’s why I don’t make such attempts, and wonder why anyone would.

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

--Allen

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