Evolution

Abstract

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Keywords: xxx

Introduction

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Direction in Evolution

In the sense that it has a direction, as opposed to being guided by some agency, evolution is directed. It does proceed from simple to complex - from primordial slime to hormonally-fuelled teen angst - though the advance may not seem at all worthwhile sometimes. This is elementary reasoning: complex things cannot exist without simple components from which to build them.

Evolutionary progress is like the two-gases-in-a-divided-box demonstration of entropy: although each individual interaction is purely random, in aggregate the result is as inevitable as it is irreversible. Certainly there are examples of simplification - a flea has lost its wings, a tapeworm has lost its gut - but it is not accidentally that we call such characters 'derived' and claim that possession of wings or gut are 'primitive.' Simplifications can represent progress, too. Finally, in many such cases, it is uncertain that the organisms' genomes are "simplified" in any meaningful sense.

Microevolution and Macroevolution

Biologists use the terms microevolution and macroevolution to dichotomize the tremendous diversity of evolutionary patterns and processes. Microevolution refers to change within populations of a species. In contrast, macroevolution is change above the species level, including speciation and the origin of broader taxa such as genera or even phyla. The terms recognize two basic approaches to studying biological evolution and diversity. Studies conducted by biologists with living organisms are limited to their own lifespans and perhaps the lifespans of their students. Even if they work with short-lived organisms such as annual plants or fruitflies, they can observe evolution for only a limited number of generations. This is a fine-grained, or microevolutionary, scale. In contrast, studies conducted by palaeontologists are limited only by the fossil record, which extends back a billion years or more.

This practical distinction about scales of observation becomes controversial because some macroevolutionists assert that they are studying different processes rather than simply the same patterns and processes over longer intervals of time. On the other hand, some biologists recognize only microevolutionary processes as the basis for all evolutionary change.

This broader agenda was apparent decades ago in the writings of palaeontologist George Gaylord Simpson. Simpson, who wanted to understand the origin of broad taxonomic groups such as birds with their feathered wings or angiosperms with their flowers and fruits, speculated about quantum evolution. Quantum evolution referred to the possibility that rapid and drastic biological shifts occur, and that such changes are fundamentally different from gradual changes that occur within species. Simpson’s colleague, Ernst Mayr, was apparently sceptical about this proposition, and suggested that species originate so rapidly within such small and local populations that speciation events tend to appear sudden only from the palaeontologist’s broader perspective. Eventually, these seemingly contradictory concepts would evolve into the idea of punctuated equilibrium, proposed by Niles Eldredge and Steven J. Gould in the early 1970s.

Despite the efforts of Simpson and Mayr, most evolutionary biologists evaded questions about a gap between microevolutionary processes and macroevolutionary patterns. They instead followed Darwin’s example in The Origin of Species, arguing that discontinuities in the fossil record are attributable to its incompleteness. Mechanisms other than the microevolutionary one Darwin proposed, gradual adaptive evolution by natural selection, are irrelevant and unnecessary. Ironically, Darwin himself was disappointed that the fossil record was so poorly studied. In The Origin of Species he admitted that a lack of information about past life forms was ‘probably the gravest and most obvious of many objections which may be urged against my views’.

Evolution of Major Clades

(maybe this should come before the previous section?)

In respect of evolution of the major clades, the custodians of present day neo-Darwinism have not discharged their duty well. Most students are guided unquestioningly to the belief that fundamental body plan differences between major taxa - such as the differences between an arthropod and a chordate - arise from the accumulation of many small (infraspecific) differences. That may not be the case.

Genes controlling major phenotypic outcomes, such as which end of an embryo is anterior (protostome vs. deuterostome), effect the earliest stages of development. Less major effects, such as the production of mammalian hair, occur later in embryonic development. <sidebar? p. 38, s. 2.3, first para, but read through to p. 40 for more ideas> The recognition of development issues "has important consequences for the neo-Darwinian view that major morphological differences between organisms from different higher taxa have been produced through the gradual accumulation of very small changes. Specifically, while in a non-developmental approach it seems plausible that many small changes can indeed accumulate to give a larger one, in a developmentally explicit approach it is clear that many late changes can not accumulate to give an early one. Thus, if taxonomically distant organisms differ right back to their early embryogenesis, as is often the case, the mutations involved in their evolutionary divergence did not involve the same genes as those involved in a typical speciation event, where usually the early embryogenesis of the daughter species concerned are virtually identical" (Arthur 1997, p. 22).

Arthur himself concedes "all sorts of complications to the argument" and it is not the intention here to promote his hypothesis (though the writer is personally captivated by it). The important point to note is that biology, evolutionary and paleontological books and educational curricula, the world over, typically gloss-over an important debate. Note that we do not have a case for special creation, here; simply a dropped stitch in the fabric of neo-Darwinian theory. Nevertheless, when an idea which has been credibly questioned continues to be presented as "the way it is," we have bad science.

New Headings Required

Maybe under systematics: This adaptive scenario is consistent with the concept of anagenesis, a single species changing directionally through time. Anagenesis, from the Greek words meaning ‘the same branch again’, may be either gradual or abrupt (Figure 1). Sometimes, if a population is sufficiently different from the ancestral population, a new name may be assigned and the new taxon is referred to as chronospecies. Anagenetic processes leading to chronospecies are often referred to as phyletic speciation or phyletic evolution. Phyletic speciation is distinct from cladogenesis, a true speciation event that involves the branching of one species into two. Cladogenesis, a word derived from the Greek for ‘origin of a branch’, is essentially synonymous with speciation.

Finally, one of the most important debates about macroevolution involves the concept of punctuated equilibrium, proposed by Eldredge and Gould in 1972 on the basis of two observations. First, most fossil species appear to originate instantaneously and coexist thereafter with their progenitors. Second, the changes observed at cladogenesis are rapid and exceptional; species otherwise appear unchanged for millions of years. These twin observations cast doubt on the concept of phyletic gradualism. They are also consistent with a scenario of speciation known as the peripheral isolate model, originally proposed by Ernst Mayer. The peripheral isolate model proposes that speciation commonly involves divergence of populations that are isolated from each other geographically. After speciation, if geographic isolation is overcome, the two species can coexist without interbreeding. Any speciation event that conforms to this model might not be preserved in the fossil record at a single site.

One criticism of this approach is that selection pressures in laboratory environments are extremely artificial in comparison to selection regimes operating in nature. To counter this criticism, studies were initiated during the 1980s and extended into the 1990s to determine how quickly evolution can occur in response to natural selection in the field. A series of thorough and relatively long-term studies of Trinidadian guppies (Poecilia reticulata) have convincingly demonstrated rapid microevolutionary change in the field. These guppies live either in predator-free river drainages or in river drainages where predation rates are substantially higher. Since waterfalls or rapids often restrict the movement of both the guppies and their predators, the two contrasting types of guppy populations and guppy habitats are isolated from one another. When guppies from the two types of populations are reared side by side in the laboratory, those from high-predation habitats mature at an earlier age and smaller size. This is consistent with an adaptation to obviate the impact of predators, who preferentially attack larger fish. The researchers therefore predicted that they could select for fish that mature later and at a larger size if they transplanted them from high-predation to low-predation portions of the river. Transplantation studies that spanned more than 11 years compared the original, control populations with transplanted populations and found that transplants evolved as predicted: they reached maturity later and at a much larger size.

The guppy studies do convincingly demonstrate that natural selection can cause rapid evolutionary change. Moreover, in the absence of other well-tested mechanisms that can account for rapid evolutionary change, it is parsimonious to conclude that microevolution can account for evolutionary change in the fossil record. However, these studies do not rule out the possibility that novel macroevolutionary mechanisms exist. They are also frustrating for two additional reasons. First, because they do not result in cladogenesis, they cannot really claim to be relevant to questions of speciation and macroevolution. They also raise a second question: why does evolution in the fossil record occur so slowly, when it is possible for it to occur much more rapidly? The guppy researchers suggest that environmental variables change erratically, resulting in natural selection regimes and responses to selection that may also vary over time, but result in no net change.

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The two examples of an apparent molecular clock, and the high level of genetic diversity within species, came from these new molecular data, and clearly required an explanation. This came quite quickly, still in the 1960s, and resulted in a major new theoretical development – Motoo Kimura’s neutral theory of molecular evolution. His basic conclusion was that most amino acid (or nucleotide) changes that had occurred during evolution were neutral – ‘neither beneficial nor injurious’ in Darwin’s words. As described later, the neutral theory explained both the molecular clock and the high genetic variability by predicting that mutations were occurring continuously – regardless of any ‘needs’ of the organism – a strong confirmation of a darwinian view of evolution. Thus the early molecular evolution studies showed the continuum from neutral genetic changes to those leading to genetic disease. It led to a major enrichment of evolutionary theory that is considered in more detail later.

The proposed explanation was that the original haemoglobin was a single chain – if its gene duplicated there would be two copies in the same nucleus. Over time the two copies could be recruited into slightly different functions. In the haemoglobin case the two chains interacted with each other; otherwise their functions were much the same. Haemoglobins were thus a family of proteins, and soon many other families were found. The mechanism of gene duplication and divergence gave a mechanism that could account for the increasing complexity of organisms through time.

In 1982, Penny et al. showed that it was possible to test quantitatively the prediction that different proteins from the same mammalian species should give highly similar evolutionary trees; for example, trees from two proteins for 11 mammals were so similar that there was only one chance in about 100 000 that the trees were selected randomly. Here was a test of the theory of evolution itself – it led to predictions about trees that could be tested. There was no longer a need for special pleading that ‘evolution was harder to demonstrate because it happened so long ago’. It could be subjected to the same type of testing as any other scientific theory.

Alternative (nonevolutionary) hypotheses can also be tested using molecular data. For example, it could be argued that under a theory of special creation the protein in hairs of a polar bear and a snow rabbit would be similar for functional reasons (insulation), at least when compared to either a Sun bear or to a rabbit from a warmer climate. In contrast, the theory of descent predicts that the two bears share a more recent common ancestor and thus their protein sequences would be more similar. Similarly for the rabbits. Being able to make such quantitative tests turns evolution into normal quantitative science.

Speciation and Extinction

"In the modern world the antithesis of a species that is becoming extinct is one whose population size (and usually its geographical range) is increasing. Since virtually all species are thought to begin as relatively small, localized populations, the interval between speciation and extinction can be likened to a developmental cycle in which a series of phases can be recognized. This taxon cycle has been most extensively documented on islands where historical records can be used to trace the dates of species’ arrival at or disappearance from specific geographical points. By constructing historical maps of species’ geographical distributions the classical taxon cycle stages of expanding (stage I), differentiating (stage II), fragmenting (stage III) and endemic (stage IV) distributions can be recognized. (Note that while these taxon cycle maps are particularly easy to construct for island biotas, the concept is generalizable to continental and even marine settings.) The ecological forces that drive the cycle appear to be primarily competitive" (McLeod 2002).

Origin of New Information

A major problem for classical evolutionary theory was how genetic information increased with time. This was called, by Darwin, the ‘oyster to an Alderman’ problem, and more recently, by Karl Popper, the ‘amoeba to an Einstein’ problem. Molecular evolution studies (again initially in the decade of the 1960s) have provided a mechanism.

Some of the earliest proteins sequenced were haemoglobins a and b (from blood) as well as myoglobin (from muscle). These three proteins are highly similar both as sequences and in three-dimensional structure – whether there were the four protein chains (2a and 2b) of typical adult haemoglobins, or the single protein chain of myoglobin. The simplest hypothesis is one original globin gene for a single chain protein which eventually duplicated, one copy being expressed in muscle (myoglobin) and one in blood (haemoglobin). Repeating the duplication of the haemoglobin gene, and divergence of the two copies, gives the a and b proteins (Figure 1). In practice, the process has been repeated several times for haemoglobins, to give an a cluster and a b cluster of haemoglobins that are expressed sequentially during development.

This is Darwin’s model of ‘descent with modification’ – but for genes, not species – and allows an increase in genetic information over time. Subsequently many gene families have been identified, lending further support to the proposed mechanism; that is, gene duplication and divergence accounted for a wide range of phenomena – it is always pleasing in science when a mechanism explains a large number of events.

Other mechanisms can lead to in increase in genetic information. Duplication of a part of a gene and recombination between genes can lead to novel and/or improved proteins. The first mechanism is illustrated by the fibrous protein collagen where a 3-amino acid motif has apparently been duplicated many times to give this family of animal proteins. And although it resulted in a globular protein, a similar mechanism has been suggested for the origin of the ubiquitous electron carrier, ferredoxin. The best known examples for rearrangement between existing genes include the protein factors involved in the cascade leading to cleavage of fibrinogen and blood clotting. Other examples are the serine protease inhibitors (serpins). In both examples the proteins are strings of domains encoded by exons already recognized in other proteins. Duplication of entire genomes (polyploidy) is common in plants, and has also been suggested in early vertebrate evolution.

References

Arthur, Wallace 1997: The Origins of Animal Bodyplans. Cambridge University Press, London.

MacLeod, Norman (2002, in press): Extinction. In Encyclopedia of Life Sciences. Nature Publishing Group, Macmillan.

Ridley, Matt 1999: Genome. Fourth Estate. 344 pp.