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3: Evolutionary Mechanisms and the Diversity of Life - Biology

3: Evolutionary Mechanisms and the Diversity of Life - Biology


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3: Evolutionary Mechanisms and the Diversity of Life

Chemical Evolution and the Evolutionary Definition of Life

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of “just chemistry” and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

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Genetic Drift

Another way a population’s allele frequencies can change is genetic drift ([Figure 1]), which is simply the effect of chance. Genetic drift is most important in small populations. Drift would be completely absent in a population with infinite individuals, but, of course, no population is this large. Genetic drift occurs because the alleles in an offspring generation are a random sample of the alleles in the parent generation. Alleles may or may not make it into the next generation due to chance events including mortality of an individual, events affecting finding a mate, and even the events affecting which gametes end up in fertilizations. If one individual in a population of ten individuals happens to die before it leaves any offspring to the next generation, all of its genes—a tenth of the population’s gene pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the overall gene pool therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of even a relatively rare allele.

Imagine a population of ten individuals, half with allele A and half with allele a (the individuals are haploid). In a stable population, the next generation will also have ten individuals. Choose that generation randomly by flipping a coin ten times and let heads be A and tails be a. It is unlikely that the next generation will have exactly half of each allele. There might be six of one and four of the other, or some different set of frequencies. Thus, the allele frequencies have changed and evolution has occurred. A coin will no longer work to choose the next generation (because the odds are no longer one half for each allele). The frequency in each generation will drift up and down on what is known as a random walk until at one point either all A or all a are chosen and that allele is fixed from that point on. This could take a very long time for a large population. This simplification is not very biological, but it can be shown that real populations behave this way. The effect of drift on frequencies is greater the smaller a population is. Its effect is also greater on an allele with a frequency far from one half. Drift will influence every allele, even those that are being naturally selected.

Art Connection

Figure 1: Genetic drift in a population can lead to the elimination of an allele from a population by chance. In each generation, a random set of individuals reproduces to produce the next generation. The frequency of alleles in the next generation is equal to the frequency of alleles among the individuals reproducing.

Do you think genetic drift would happen more quickly on an island or on the mainland?

[reveal-answer q=�″]Show Answer[/reveal-answer]
[hidden-answer a=�″]Genetic drift is likely to occur more rapidly on an island, where smaller populations are expected to occur.[/hidden-answer]

Genetic drift can also be magnified by natural or human-caused events, such as a disaster that randomly kills a large portion of the population, which is known as the bottleneck effect that results in a large portion of the genome suddenly being wiped out ([Figure 2]). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population. The disaster must be one that kills for reasons unrelated to the organism’s traits, such as a hurricane or lava flow. A mass killing caused by unusually cold temperatures at night, is likely to affect individuals differently depending on the alleles they possess that confer cold hardiness.

Figure 2: A chance event or catastrophe can reduce the genetic variability within a population.

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location, or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population which results in the founder effect . The founder effect occurs when the genetic structure matches that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to a higher-than-normal proportion of the founding colonists, which were a small sample of the original population, carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause bone marrow and congenital abnormalities, and even cancer. 1

Visit this site to learn more about genetic drift and to run simulations of allele changes caused by drift.


3: Evolutionary Mechanisms and the Diversity of Life - Biology

Mechanisms: the processes of evolution

Evolution is the process by which modern organisms have descended from ancient ancestors. Evolution is responsible for both the remarkable similarities we see across all life and the amazing diversity of that life — but exactly how does it work?

Fundamental to the process is genetic variation upon which selective forces can act in order for evolution to occur. This section examines the mechanisms of evolution focusing on:

    and the genetic differences that are heritable and passed on to the next generation

Mutation, migration (gene flow), genetic drift, and natural selection as mechanisms of change

The random nature of genetic drift and the effects of a reduction in genetic variation

How variation, differential reproduction, and heredity result in evolution by natural selection and

How different species can affect each other's evolution through coevolution.


Mechanisms of Life History Evolution: The Genetics and Physiology of Life History Traits and Trade-Offs

Life history theory seeks to explain the evolution of the major features of life cycles by analysing the ecological factors that shape age-specific schedules of growth, reproduction, and survival and by investigating the trade-offs that constrain the evolution of these traits. While life history theory has made enormous progress in explaining the diversity of life history strategies among species, it traditionally ignores the underlying proximate mechanisms. In this book the editors and the authors argue that many fundamental problems in life history evolution, for example the nature of trade- . More

Life history theory seeks to explain the evolution of the major features of life cycles by analysing the ecological factors that shape age-specific schedules of growth, reproduction, and survival and by investigating the trade-offs that constrain the evolution of these traits. While life history theory has made enormous progress in explaining the diversity of life history strategies among species, it traditionally ignores the underlying proximate mechanisms. In this book the editors and the authors argue that many fundamental problems in life history evolution, for example the nature of trade-offs, can only be resolved if we begin to integrate information on developmental, physiological, and genetic mechanisms into the classical life history framework. The text is divided into seven parts that cover basic concepts (Part 1) the mechanisms which affect different parts of the life cycle (growth, development, and maturation reproduction and aging and somatic maintenance) (Parts 2–4) life history plasticity (Part 5) life history integration and trade-offs (Part 6) and concludes with synthesis chapter by a prominent leader in the field and postscript (Part 7).

Bibliographic Information

Print publication date: 2011 Print ISBN-13: 9780199568765
Published to Oxford Scholarship Online: December 2013 DOI:10.1093/acprof:oso/9780199568765.001.0001

Authors

Affiliations are at time of print publication.

Thomas Flatt, editor
Institute of Population Genetics, Vetmeduni Vienna, Austria

Andreas Heyland, editor
Department of Integrative Biology, University of Guelph, Canada


4. Social constructions

Human culture is a natural phenomenon, but a natural phenomenon that has the curious property which Searle [30], in his masterful analysis, labelled the characteristic of being able to induce a kind of ‘metaphysical giddiness’. The source of that giddiness lies in the capacity for this aspect of human culture to generate an endless array of cultural variants of seemingly insubstantial form whose very existence, like the existence of omnipotent beings, can be questioned. These are the social constructions of human culture, things that we construct within our minds, which we imagine, and then share with others, and in so doing generate diversity which is at once fragile and causally hugely powerful. Money and ideology are examples of social constructions that rule, and often destroy, the lives of almost all living humans. I rely almost entirely on Searle's analysis in the following pages.

Searle was not able to provide any kind of account of how the human mind evolved the properties that it currently has𠅊nd neither can anyone else. However, he assumes, rightly, that evolved it has, and the crucial capacity that underlies social constructions is conscious intentionality, which he defines as ‘the capacity of the mind to represent objects and states of affairs of the world other than itself’ [30, pp. 6𠄷]. Conscious intentionality is caused by the mechanisms of the human brain, and hence is a physical process. Thus, all that stems from intentionality does not in any way violate a materialist approach to human culture. It does, however, provide the basis for drawing a fundamental distinction between 𠆋rute’ facts, such as the presence of sand with minimal water content in a desert, and the ‘institutional’ or ‘social’ facts, like marriage or money, which are wholly dependent upon human intentionality. Deserts would exist had humans never evolved. Marriage and money are caused only by the existence of humans with specific neural and psychological mechanisms. Money does have a physical manifestation in coins, banknotes, cheques and the like, but the value of a banknote in terms of the paper on which it is printed (value itself is a social fact) is of little consequence to those who accept it in exchange for a loaf of bread or a flight to Edinburgh marriage is a contract (a form of social fact) written on a piece of paper, but entails a string of obligations regarding children and ownership of certain goods. Brute facts are intrinsic to nature social or institutional facts are wholly dependent upon human nature (which, of course, is itself a brute fact, if a special one). This distinction between brute facts and social facts is central to Searle's analysis. In the nineteenth century, Birmingham industries manufactured hundreds of different kinds of hammers [31], different from one another in terms of their shapes and the ways in which steel and wood were blended into a single object. The wood and metal were the brute facts of hammers—the hammers' intrinsic properties. That hammers are used to drive objects together is an epistemic addition to the wood and metal that is bestowed upon it by users and observers—humans with specific psychological processes and mechanisms. What Searle did was apply this basic distinction to human social interactions. He did this by arguing for three essential elements in the creation of social facts.

The first of these elements is the psychological property of assigning function, a specific aspect of human intentionality, though he allows the possibility for some rudimentary form of it in a small number of other species. We assign functions to natural objects, such as trees providing cooling shade, but we also construct objects that fulfil specific functions, like huts and houses that give shelter. Function is thus agentive and guided by specific purpose (this is a hammer and its purpose is to drive objects together) and non-agentive, by which we ascribe functions which do not serve our intentional goals (the function of the liver is to remove toxins). One crucial form of agentive function involves our understanding that one thing stands for another. ‘Standing for something’ is the function that they have, what their purpose is. A map, whether printed on a page, drawn with a pen or scratched out in sand is a representation of spatial relationships in which intentionality stands between the person drawing the map and the person being guided by it. Maps thus convey the function of meaning in which one thing stands for another. Language, whether spoken, written or signed, is the most important form of agentive function that we impose on the brute facts of sound, vocal tract movement or the movement of our hands.

The second of Searle's elements is what he refers to as 𠆌ollective intentionality’. The notion that individuals may be drawn into a collective identity based upon a common goal has been offered by other philosophers attempting to identify key aspects of human culture [32,33]. Collective intentionality is a shared intentional state, and may embrace any number of individuals, drawing them together into a loose unit of commonly held desires and plans. A football team, with its shared desires for victory, and agreed tactics and common understanding of their opponents' weaknesses, has the properties of collective intentionality as do the supporters of a football team. The defining feature of collective intentionality for Searle is that the collective intentionality exists and stands prior to individual intentionality, the former actually being a cause of the latter. What the individual wants and knows may be caused by the group of which they are a part. Collective intentionality is central to Searle's conception of social reality. It is not simply the sum of individual intentionalities making up a group and it is not reducible to them. It is the property of human social groups essential for the construction of social reality. ‘We intend’ is not simply the sum of ‘I intend’. It is a social force in its own right, and every social or institutional fact is in part caused by collective intentionality. It is the glue of human culture and the reason why humans gain pleasure from acting together, whether that acting together involves eating with others, gossiping in the office, or going to the cinema with a friend. It is, along with language, one of the things that makes us human.

The third essential element of social reality is what Searle refers to as constitutive rules, which create the conditions for specific social activities such as playing a game, being a shareholder in a company, or entering into religious beliefs and activity. Constitutive rules form the basis of institutional or social facts. When I buy shares in a company I hand over some money (itself a social fact) in order that I may participate in the profits and losses of that company (another social fact), but do not own the enterprise yet have some small part annually in determining how that company operates. As the citizen (a social fact) of a country (also a social fact), I have certain rights and obligations within that country, but not in other countries. Humans live in a world awash with social facts, the constitutive rules of which determine how we live our lives.

Constitutive rules, the assignment of functions and collective intentionality are all necessary ingredients of social reality, which is the collective imposition of functions within a social group. Searle argues that all social reality conforms to the structure of ‘X counts as Y in C’. A share certificate (X) counts as proof of being a shareholder (Y) in the UK (C). A marriage certificate (X) counts as proof of marital status (Y) within certain countries and religious organizations (C). X counts as Y in C is iterated repeatedly to form a complex, inter-related social reality. Being a citizen of the UK (X) allows me legal status to work in Poland (Y) because both countries are members of the European Union (C), but is a form of social reality that does not extend to the United States or Brazil.

‘The connecting terms between biology and culture’ Searle concludes 𠆊re, not surprisingly, consciousness and intentionality. What is special about culture is the manifestation of collective intentionality and, in particular, the collective assignment of functions to phenomena where the function cannot be performed solely in virtue of the sheer physical features of the phenomena. From dollar bills to cathedrals, and from football games to nation-states, we are constantly encountering new social facts, where the facts exceed the physical features of the underlying physical reality’ [30, pp. 227�].

That social facts, money, legal obligations, the existence of the UK as a social fact which makes it other than a small island off the northwest coast of a northern continent, constitutes the fabric of our everyday lives, yet which is based only upon agreement, and continuing agreement, is what gives social constructions the property of ‘metaphysical giddiness’. In the recent global financial crisis, one possible solution to the UK's woes was what is called ‘quantitative easing’, which did not even entail the actual physical printing of money by the Royal mint, but merely changing the figures on the balances available to the major banks for lending to businesses. What, one is led to ask, is money but the collective agreement that it has value𠅋ut what is value? Several times in different parts of the world in the twentieth century, people stopped agreeing that money had value and traded instead in other commodities, often cigarettes. For decades, a specific ideology ruled the lives of hundreds of millions of people in Europe. The ideology, created by one person in the previous century, dictated where people could live and work, what they could earn, whether they lived free or in prison, and what they could read and, often enough, what they could say. Then in a brief period in the late 1980s, communism collapsed because people in sufficient numbers refused to agree that it was a social system of any value. About the same time, apartheid in South Africa was abandoned and the lives of non-white peoples in that part of the world changed radically. Scottish nationalists in the UK do not accept that they should be ruled by a parliament in London, just as the majority of the people of Ireland and India ceased in the twentieth century to subscribe to the belief that they were a part of Britain. Is the UK really United? Is there a European union? No one questions the existence of dry sand in the Sahara desert. But it is not difficult to look at a ꌠ note and wonder at its value. All social facts hinge upon the existence of some degree of agreement, of concerted and sustained agreement. The move from individual intentionality to collective intentionality may be, probably is, as important to the most recent evolutionary transition as the evolution of language itself.

Strange as social constructions might seem to be, there is no need to subscribe to a kind of Cartesian dualism in which this particular aspect of human culture is assigned some immaterial existence that floats ethereally between the individuals making up a culture. Social constructions are made up of the collective neural network states of individuals within social groups. There are, there must be, neurological and psychological mechanisms that give rise to social reality, and which place human social reality within the same causal framework as all other forms of human learning and knowledge. There are at least three identifiable psychological mechanisms whose neurological bases remain to be understood. The first is undeniably language, and there is no serious opposition to the Chomskian notion of language as an innate and evolved organ of mind [34,35]. Language alone, however, is unlikely to support modern human culture as it has evolved over the last 100 000 years or so. ‘Theory of mind’, the understanding that others have intentional mental states, has during the last few decades come increasingly to be understood as equal to linguistic communication in allowing us to comprehend the beliefs and knowledge of others [23,36,37], with the mirror neuron system of the brain implicated with increasing frequency as one of the mechanisms responsible for theory of mind [38�]. Mirror neurons have been observed in the brains of a number of different species of other primates, and may provide one of the bases for culture in other animals, though it should be emphasized that mirror neurons are very unlikely to be the lone causal sources of culture in any species.

There is widespread agreement on the importance of language and theory of mind in the evolution of human culture, as well as of HOKS. What is paid relatively little attention is what I have previously referred to as social force, though the notion of a conformity bias in the work of Boyd & Richerson [41] on gene𠄼ulture coevolution is a rare exception in placing social force at the centre of human culture. In the 1930s, the social psychologist Muzafer Sherif published the results of a series of studies [42] on how people within a small social group reach agreement about uncertain events. He used the visual illusion known as the autokinetic effect, where people were told to fixate their gaze on a stationary spot of light in a darkened room and after a short time the light appears to move. The subjects, not told that the apparent movement was an illusion, were asked to say how far the light had seemed to move. When tested in groups and requested to say aloud what they experienced, Sherif found that, in every case, people would rapidly home in upon an agreed amount of movement, which would eliminate the initial variation in the experienced and reported movement. People used the reported views of others to establish a frame of reference for their own judgements in short, Sherif was observing the establishment of group norms, a kind of constructive conformity which Sherif believed is a fundamental feature of human social interactions.

Sherif's work was extended by another social psychologist, Solomon Asch, in the 1950s [43], using a simple experiment that has subsequently been replicated and extended in a host of different cultures. Asch presented to a small group a vertical line on a card. He then presented to each subject another card with three lines on it and asked which of the three lines matched the length of the original. It was a simple task but only one of the group was a naive experimental subject, the rest being confederates, plants of the experimenter instructed to give in two out of three occasions the wrong answers. The situation was also rigged such that the single naive subject was always asked for their response after most of the stooges had deliberately given the wrong answers. Asch found that only one-quarter of the naive subjects stuck to their views and gave the correct answers the majority gave a clearly incorrect response that conformed with what most of the stooges had declared, or they wavered and gave answers that were uncertain and changeable. When asked why they had given what were clearly the incorrect answers, most people expressed anxiety at going against the majority view. The need to conform was greater than the evidence of their own visual experience and judgement. Subsequent studies of the Asch experiment in many different cultures have shown that while the strength of the bias to conform varies across cultures, the effect is always present. The need to conform is a universal human psychological trait.

Jacobs & Campbell [44] described an interesting variation on Sherif's original experiment with the autokinetic illusion. They put together a group in which all but one of the so-called subjects was naive, the rest being plants who grossly overstated the amount of perceived movement and the naive subject delivered her or his judgement last. In line with Sherif's findings, the single naive subject gave an overstated judgement of perceived movement. Then, one by one, the stooges were withdrawn and replaced by naive subjects until eventually the entire group comprised naive subjects. Yet the 𠆌ultural tradition’ of overstating the perceived amount of movement was maintained even when the group was made up of individuals none of whom were stooges. Here was a case of conformity operating across ‘generations’ of individuals regarding a belief based upon an illusion.

But the most powerful demonstration of what social psychologists call conformity, obedience or group cohesiveness was reported in a series of papers in the 1960s, summarized by Milgram [45]. Using actors and stooges, Milgram repeatedly demonstrated how people without any history of cruelty or violence would, when ordered to do so by a figure of authority, inflict violent punishment upon others. Milgram's studies were merely a replication under controlled conditions of what we all know of from the Holocaust inflicted on the peoples of Europe by the Nazis, depicted by Hannah Arendt as the �nality of evil’ in which ordinary people living ordinary lives will commit unspeakable acts of evil against others when those acts are sanctioned by authority and interwoven into the ordinariness of everyday life. Subsequent events in Rwanda, the Balkans and the Middle East show how the death squads and death camps of the Nazis were an expression of a universal feature of human nature, social force that leads to obedience and conformity.

Exactly how the psychological mechanisms of language, theory of mind, and social force act in concert to generate human culture, is unknown. Understanding intentional mental states in others may be present in rudimentary form in chimpanzees [46], and the existence of something like social force in other species of apes has been consistently advocated by some primatologists [47]. It may be that culture in any primates which have been observed with certainty to share knowledge, is built upon similar psychological mechanisms. And it may be that the integrated functioning of communication by way of language, the ability to comprehend the intentional mental states of others, and the existence of social force of whatever kind, is a present-day, naive, assemblage of the mechanisms of human culture. We certainly have no knowledge whatever at present as to the causal structures that will one day be understood regarding the linkages between genes, neural and psychological mechanisms. But that such causal linkages do exist, and that human culture in whatever form is a product of evolutionary forces, is not to be doubted. That is the Lorenzian lesson.


Mechanisms of Evolution

Although the term “evolution” is often used synonymously with “natural selection,” they are actually referring to different concepts. Evolution is an observable phenomenon in which gene frequencies change over time, but it does not explain why a population is undergoing evolution. This is where natural selection—and other mechanisms—come into play. They explain “the why.”

There are four main mechanisms of evolution:

Let’s look at some examples of evolution and see if we can identify which evolutionary mechanism is at play.

Once you complete that, here is another game. This is a matching game using the images from the above quiz. As you match two images, recall which type of mechanism it is and why!

All of these mechanisms can cause changes in the frequencies of genes in populations, so all of them are mechanisms of evolutionary change. However, natural selection and genetic drift cannot operate unless there is genetic variation—that is, unless some individuals are genetically different from others. If the population of beetles was 100% green, selection and drift would not have any effect because their genetic make-up could not change.

Important Notes Regarding Mutations

Mutations are random

Mutations can be beneficial, neutral, or harmful for the organism, but mutations do not “try” to supply what the organism “needs.” In this respect, mutations are random—whether a particular mutation happens or not is unrelated to how useful that mutation would be.

Not all mutations matter to evolution

Because all cells in our body contain DNA, there are lots of places for mutations to occur however, not all mutations matter for evolution. Mutations that occur in non-reproductive cells won’t be passed onto offspring.

For instance, if a skin cell has a mutation that causes uncontrollable cell division (i.e., cancer), that mutation is not passed to the next generation.

See the “Protein Structure and Function” chapter in this textbook for more information.


Where Do Cellular Innovations Map onto the Tree of Life?

A first step in nearly all studies in evolutionary biology is the elucidation of phylogenetic patterns of variation. Although a purely historical perspective cannot reveal the mechanisms by which evolution proceeds, it does clarify what needs to be explained. Traditional cell biology is largely devoid of comprehensive comparative analyses, but recent studies demonstrate the power of such approaches, as illustrated by the following three examples.

The first example addresses the evolutionary origins of the network of organelles and underlying molecular features by which membrane trafficking emerged in eukaryotes. The sorting of proteins and lipids among the intracellular compartments of eukaryotic cells is mediated in part by a family of protein complexes called adaptins. Although it had been accepted for over a decade that there are only four adaptin complexes in eukaryotes, comparative genomics suggested the presence of a fifth highly divergent adaptin-like complex across eukaryotes (53). Subsequent characterization of the protein in human cells identified its cellular location and function, thereby fundamentally altering our basic understanding of vesicle-transport systems and the likely order of evolutionary events leading to their diversification. An even more recent phylogenetic analysis suggests the existence of a sixth form of adaptor complex (54), raising the possibility that still more remain to be discovered, perhaps with some complexes being restricted to a subset of taxa.

A second striking example of the power of comparative analysis to inform our basic understanding of cell biology involves the discovery of an evolutionary relationship between what were considered two very different kinds of membrane-deformation proteins. Cargo transport in eukaryotic cells involves the use of diverse pathways initiating with membrane-coated vesicles supported by clathrin, and the cage forming proteins of cytoplasmic coat protein complexes I and II (COPI and COPII). Although these proteins are lacking in amino acid sequence similarity, comparative structural analysis suggests a common molecular architecture that is also related to the membrane-curving proteins involved in both the nuclear-pore complex (NPC) (55) and the adaptins discussed above. The structural and functional insights emerging from these observations guided the development of a mechanistic understanding of the NPC (56) and yielded a novel evolutionary proposal—the “protocoatomer” hypothesis, which postulates that many vesicle-coating complexes and the NPC arose by descent with modification (55). Among other things, this concept has provided a potential explanation for how the diverse body plans of eukaryotic cells could have arisen from a simpler prokaryote-like ancestor.

In a third example, an integration of molecular and morphological phylogenetic analysis has led to the identification of novel components of centrioles and cilia, as well as to evolutionary hypotheses for how their coordinated biogenesis and functions in different cellular contexts have been achieved through duplication and divergence of an ancestral gene set (57, 58).

This small set of examples illustrates the considerable potential for more elaborate comparative analyses to elucidate the evolutionary foundations of the most basic eukaryotic cellular features. Of course, ascertainment of where cell-biological innovations map onto the Tree of Life and inference of phylogenetic points of gain and loss of various modifications will require a substantial increase in taxonomic sampling of cellular diversity. Of the estimated 5–100 million extant species, only ∼1.5 million have been described at even a rudimentary level, and most of these taxa are heavily biased toward plants, animals, fungi, and microbes with direct human impact (59) (Fig. 1). Future studies of biodiversity are likely to continue to extend to the discovery of novel phyla for quite some time (e.g., refs. 60 ⇓ –62). These issues, together with the fact that typically about a third of predicted protein-coding genes per sequenced genome are undefined and/or restricted to narrow taxonomic groupings, make clear that we are still missing immense swaths of information on cellular diversity. This “missing phylogeny” is likely of high value to applied research efforts in medicine, agriculture, and environmental science.

Taxonomic distribution of research articles and sequenced genomes. Modern taxonomy identifies five major eukaryotic supergroups: the Excavates (turquoise), Chromalveolates (orange), Archaeplastida (green), Amoebozoa (purple), and Opisthokonts (red). Although the total number of species on earth remains unknown, it is clear that there are far more unicellular eukaryotes than the combined total of all animals (Metazoa, an Opisthokont lineage), fungi (also Opisthokonts), and plants (Archaeplastida). However, research activity displays considerable taxonomic bias. As of January 2014, the National Center for Biotechnology Information taxonomy browser (www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi) lists 338 Archaeal genomes (dark gray), 20,709 Eubacteria (light gray), 769 Metazoa, 1,201 Fungi, 251 green plants/algae, and 336 genomes from all other eukaryotic taxa (13% of eukaryotic genomes). The taxonomic distribution of PubMed citations is as follows: Archaea, 19,000 Eubacteria, 397,000 Metazoa, 576,000 Fungi, 135,000 green plants/algae, 168,000 and all other eukaryotes combined, 97,000 (<9% of publications on Eukaryotes).

Unfortunately, parts lists inferred from genome information alone can take us only so far. Although results from transcriptomics, metabolomics, etc. can provide additional information, such work must ultimately be coupled to detailed studies of individual gene products in diverse taxa. To this end, we envision the need for a new grand challenge in biology, such as the proposed Atlas of the Biology of Cells (www.nsf.gov/publications/pub_summ.jsp?ods_key=bio12009). The fundamental idea here is to develop a database for cellular/subcellular features for a judiciously chosen, phylogenetically broad set of organisms, with the goal of sampling the functional diversity of metabolic and cellular morphological traits in the fullest possible sense. To be maximally productive, such an enterprise will require the further development of automated, generalizable, and high-throughput cell-biological methods. Significant support for appropriate phylogenetic sampling, development of reliable culture methods, and standardized measurement methodology will also be necessary. Most importantly, the latter will require the establishment of not only controlled vocabularies and ontologies to provide a conceptual framework for data comparison, but also quantitative metrics for defining, comparing, and predicting cell-biological structures and processes.

The payoffs of such an organized research program are likely to be substantial. As an analogy to where evolutionary cell biology is and where it might lead, consider that whole-genome sequencing was barely a dream 25 y ago but, in the past decade, has revolutionized virtually every aspect of biology, vastly increasing our understanding of human-genetic disorders, methods for disease control, energy production, and ecosystem function. Such advances continue to inspire the development of new ’omics technologies with enormous increases in accuracy and efficiency, as well as the emergence of novel computational technologies for storage, integration, and analysis that facilitate the rapid transformation of data into knowledge.


11.2 Mechanisms of Evolution

The Hardy-Weinberg equilibrium principle says that allele frequencies in a population will remain constant in the absence of the four factors that could change them. Those factors are natural selection, mutation, genetic drift, and migration (gene flow). In fact, we know they are probably always affecting populations.

Natural Selection

Natural selection has already been discussed. Alleles are expressed in a phenotype. Depending on the environmental conditions, the phenotype confers an advantage or disadvantage to the individual with the phenotype relative to the other phenotypes in the population. If it is an advantage, then that individual will likely have more offspring than individuals with the other phenotypes, and this will mean that the allele behind the phenotype will have greater representation in the next generation. If conditions remain the same, those offspring, which are carrying the same allele, will also benefit. Over time, the allele will increase in frequency in the population.

Mutation

Mutation is a source of new alleles in a population. Mutation is a change in the DNA sequence of the gene. A mutation can change one allele into another, but the net effect is a change in frequency. The change in frequency resulting from mutation is small, so its effect on evolution is small unless it interacts with one of the other factors, such as selection. A mutation may produce an allele that is selected against, selected for, or selectively neutral. Harmful mutations are removed from the population by selection and will generally only be found in very low frequencies equal to the mutation rate. Beneficial mutations will spread through the population through selection, although that initial spread is slow. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. It should be noted that mutation is the ultimate source of genetic variation in all populations—new alleles, and, therefore, new genetic variations arise through mutation.

Genetic Drift

Another way a population’s allele frequencies can change is genetic drift (Figure 11.7), which is simply the effect of chance. Genetic drift is most important in small populations. Drift would be completely absent in a population with infinite individuals, but, of course, no population is this large. Genetic drift occurs because the alleles in an offspring generation are a random sample of the alleles in the parent generation. Alleles may or may not make it into the next generation due to chance events including mortality of an individual, events affecting finding a mate, and even the events affecting which gametes end up in fertilizations. If one individual in a population of ten individuals happens to die before it leaves any offspring to the next generation, all of its genes—a tenth of the population’s gene pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the overall gene pool therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of even a relatively rare allele.

Imagine a population of ten individuals, half with allele A and half with allele a (the individuals are haploid). In a stable population, the next generation will also have ten individuals. Choose that generation randomly by flipping a coin ten times and let heads be A and tails be a. It is unlikely that the next generation will have exactly half of each allele. There might be six of one and four of the other, or some different set of frequencies. Thus, the allele frequencies have changed and evolution has occurred. A coin will no longer work to choose the next generation (because the odds are no longer one half for each allele). The frequency in each generation will drift up and down on what is known as a random walk until at one point either all A or all a are chosen and that allele is fixed from that point on. This could take a very long time for a large population. This simplification is not very biological, but it can be shown that real populations behave this way. The effect of drift on frequencies is greater the smaller a population is. Its effect is also greater on an allele with a frequency far from one half. Drift will influence every allele, even those that are being naturally selected.

Visual Connection

Do you think genetic drift would happen more quickly on an island or on the mainland?

Genetic drift can also be magnified by natural or human-caused events, such as a disaster that randomly kills a large portion of the population, which is known as the bottleneck effect that results in a large portion of the genome suddenly being wiped out (Figure 11.8). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population. The disaster must be one that kills for reasons unrelated to the organism’s traits, such as a hurricane or lava flow. A mass killing caused by unusually cold temperatures at night, is likely to affect individuals differently depending on the alleles they possess that confer cold hardiness.

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location, or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population which results in the founder effect . The founder effect occurs when the genetic structure matches that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to a higher-than-normal proportion of the founding colonists, which were a small sample of the original population, carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause bone marrow and congenital abnormalities, and even cancer. 4

Concepts in Action

Visit this site to learn more about genetic drift and to run simulations of allele changes caused by drift.

Gene Flow

Another important evolutionary force is gene flow , or the flow of alleles in and out of a population resulting from the migration of individuals or gametes (Figure 11.9). While some populations are fairly stable, others experience more flux. Many plants, for example, send their seeds far and wide, by wind or in the guts of animals these seeds may introduce alleles common in the source population to a new population in which they are rare.


Cogs and Wheels

To save every cog and wheel is the first precaution of intelligent tinkering.

—Aldo Leopold, Round River: from the Journals of Aldo Leopold, 1953

Leopold—often considered the father of modern ecology—would have likely found the term biodiversity an appropriate description of his “cogs and wheels,” even though idea did not become a vital component of biology until nearly 40 years after his death in 1948.

Literally, the word biodiversity means the many different kinds (diversity) of life (bio-), or the number of species in a particular area.

Biologists, however, are always alert to levels of organization, and have identified three unique measures of life’s variation:

  • The most precise and specific measure of biodiversity is genetic diversity or genetic variation within a species. This measure of diversity looks at differences among individuals within a population, or at difference across different populations of the same species.
  • The level just broader is species diversity, which best fits the literal translation of biodiversity: the number of different species in a particular ecosystem or on Earth. This type of diversity simply looks at an area and reports what can be found there.
  • At the broadest most encompassing level, we have ecosystem diversity. As Leopold clearly understood, the “cogs and wheels” include not only life but also the land, sea, and air that support life. In ecosystem diversity, biologists look at the many types of functional units formed by living communities interacting with their environments.

Although all three levels of diversity are important, the term biodiversity usually refers to species diversity!

Video Review

Watch this discussion about biodiversity:

Biodiversity provides us with all of our food. It also provides for many medicines and industrial products, and it has great potential for developing new and improved products for the future. Perhaps most importantly, biological diversity provides and maintains a wide array of ecological “services.” These include provision of clean air and water, soil, food and shelter. The quality—and the continuation— of our life and our economy is dependent on these “services.”

Australia’s Biological Diversity

Figure 2. The short-beaked echidna is endemic to Australia. This animal—along with the platypus and three other species of echidnas—is one of the five surviving species of egg-laying mammals.

The long isolation of Australia over much of the last 50 million years and its northward movement have led to the evolution of a distinct biota. Significant features of Australia’s biological diversity include:


Watch the video: Genetic Drift (February 2023).