Articles

The Role of Predators in Evolution
By Branden Holmes on September 6, 2010

The evolutionary arms race between predator and prey is virtually universal. As such, it is vital to have a grasp of how predators can drive evolution in prey species. Of course, the arms race is run in evolutionary time rather than real time; adaptation and counter-adaptation, separated by a lag of several or many generations in genetic response. Adaptation is a long and steady process of replacement: maladapted individuals give way to adapted individuals, and adapted individuals give way to better adapted individuals. But the adaptations that are beneficial to an individual which lives free from predators are, as we shall see, diametrically opposed to those that individuals which experience the constant threat of being eaten, find to help aid survival.

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What is fitness?
By Branden Holmes on November 28, 2010

When evolutionary biologists speak of the "fitness" of an individual, what they usually mean these days is what is called reproductive success (RS): the extent to which some of their genes will still survive in the population x number of generations later. Because it is not enough just to only consider the contribution of offspring into the next generation. It is good that an individual may have many offspring, even twice as many as the average. But if none of those offspring are likewise endowed with fecundity, it doesn't matter how many offspring that individual has because they will not be disproportianally represented in terms of genes many generations later. How durable a species or gene is (the probability that that species or gene will still be extant after many generations) is what really counts in evolution. This is simply a temporal extension of reproductive success, where the period concerned is many, many generations later, and the entity concerned is the population as opposed to the individual, because individuals do not live for many generations. So, inheritability of fecundity is essential, otherwise the gene pool will simply be diluted and directional selection of fecundity will be impossible. But a number of other definitions for fitness are in wide use, somewhat confounding the problem of multiple definitions, which also partially overlap in meaning:

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Genetic drift as cause of evolutionary change
By Branden Holmes on November 22, 2010

There are two ways in which evolutionary change may occur. The first is of course natural selection, made famous by Darwin in the Origin (he coined the phrase). The second process is random sampling, better known by its popular name genetic drift. Natural selection deals with advantageous and disadvantageous mutations, whereas genetic drift governs how neutral and nearly neutral mutations will be inherited from one generation to the next. However, genetic drift is only an evolutionary force in small populations. This is because it is the random changing of the frequencies of different alleles at a given locus, or position where a gene resides upon a chromosome. For alleles to become fixated (where every individual in the population possesses that particular allele) by coincidence is much more probable given a small initial population because there are less individuals for the allele to spread to.

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The Myth of Darwin's Finches
By Branden Holmes on November 23, 2010

The finches of the Galapagos Islands, one of the modern "icons of evolution", and taking their name from the ornithologist David Lack's 1947 book Darwin's Finches (though Percy Lowe had called them that 11 years prior), in fact played little if any part in Darwin's initial thoughts about evolution. He had collected a large sample of them when he visited the islands in late 1835 (September), but he failed to annotate which islands which specimens came from. Thus, though John Gould later recognized more than twenty different species amongst the specimens he was given access to, Darwin was unaware of their significance, and was probably even unaware that some of them were finches (contemporary taxonomists only recognize 13, plus a fourteenth in the Cocos Islands). Instead he was more concerned with collecting as many specimens of plants and animals as possible.

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Natural Selection or Natural Process?
By Branden Holmes on November 25, 2010

When Darwin coined the phrase natural selection, he made it clear that it was roughly equivalent to Herbert Spencer's phrase "survival of the fittest". He called it natural selection to contrast with artificial selection, whereby humans consciously select for the traits (actually the trait values) that appeal to them. But nowadays natural selection is not considered to be a type of selection itself, but rather a label given to all of those non-random but unconscious types of selection: viability selection, fecundity selection, kin selection, sexual selection etc. Darwin considered sexual selection to be logically distinct from natural selection because the two could seemingly be at odds with each other when sexual selection produces traits which made the individual (generally male) susceptible to predation. Today we still recognize this friction between the two, but consider sexual selection to come under the banner of natural selection.

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Neanderthals: Man's Unfortunate Cousins
By Branden Holmes on November 26, 2010

The first Neanderthal remains discovered were a child’s skull in Engis Cave, Belgium, in 1830, and a woman’s skull from Forbes Quarry, Gibraltar, in 1848. But they weren’t recognized for what they were until decades later. Instead, the first Neanderthal remains uncovered and recognized as a new species of human were the third discovered, in 1856 in the Neander Valley (Feldhofer cave), Germany, from which Neanderthals derive their name. But the scientific description and classification, by Irish anatomist William King, came only in 1864, 8 years after their discovery. Neanderthals were morphologically distinct from ourselves, and on average only a few inches shorter than us (men were 5ft 6in; women were 5ft 3in), but much stockier with much thicker bones, owing to the colder climate in which they lived (we see the same sort of adaptations in modern Inuit’s). These much thicker bones meant that the attachment point where ligaments and tendons attached to the bone, were also proportionally larger. This means that even Neanderthal women would have been incredibly strong; almost as strong as any human male.

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Karyotypes and Karyotypic Evolution
By Branden Holmes on November 27, 2010

A karyotype is the number of, and the arrangement, of the chromosomes of an organism. Generally all individuals within a species (or sub-species) all have the same number of chromosomes. Thus we tend to speak of the karyotype of the species. However, within some species the number of chromosomes varies from individual to individual. The most familiar species which possesses this unusual characteristic is the red fox (Vulpes vulpes). Native to Britain, but introduced to many parts of the world where it has done considerable damage to the native fauna of those regions, their karyotypes vary from 34 to 38 chromosomes. The easiest way to understand this is to imagine that the “normal” karyotype of a red fox is 34 chromosomes. But some individuals have more chromosomes; what are called “satellite” chromosomes. These “extra” chromosomes contain genes which are not necessary to the development of the individual. Thus a red fox with only 34 chromosomes is no worse off fitness-wise than is an individual with 4 extra satellite chromosomes.

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The greatest book of all time
By Branden Holmes on November 27, 2010

On the 24th of November, 1859, Charles Darwin's magnum opus On the Origin of Species was published by John Murray of London. Remarkably, the whole print run of 1500 copies sold out that day. Even more remarkable however was the fact that the original agreement was for 500 copies to originally be offered. But Darwin's close friend, the geologist and famed author of The Principles of Geology, Charles Lyell, pressed John Murray to increase the print run three-fold; a very risky venture by the standards of the day. And as they say, the rest is history!

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Artificial Selection
By Branden Holmes on November 28, 2010

Charles Darwin preferred not to gather his information from theoreticians, but rather from people who had practical experience in their area of expertise. In the first chapter of Origin, “Variation Under Domestication”, Darwin sought to show a number of things. The most important of these was that: “Our oldest cultivated plants, such as wheat, still yield new varieties: our oldest domesticated animals are still capable of rapid improvement” (pg. 25). If that was not found to be the case, if variation had been shown to stop after artificial selection after only a few generations, it could never have continued for the millions of years that nature requires for such diversity as we see to have come from one or a few ancestors. That is probably the greatest hurdle to evolution, which Darwin showed to be fallacious all those years ago.

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Disease Resistance: Rabbits and Myxamatosis
By Branden Holmes on November 28, 2010

The first fleet to Australia (in 1788) brought with it rabbits to Sydney Cove as a staple. No doubt some of these would have escaped. But the wild population seems to have been kept in-check by the local carnivorous marsupials. However it was a different story on Tasmania. A newspaper article from 1827 states that there were “thousands” on some private properties. Tasmania clearly had an infestation, but it was isolated from the rest of the colonies. The infestation on the mainland is purported to have been caused by an English immigrant to Australia by the name of Thomas Austin. A keen rabbit hunter, he asked his nephew back in England to send him twenty four grey rabbits, five hares, seventy two partridges, and some sparrows. In October of 1859, he released them at his property Barwon Park in Victoria: “the introduction of a few rabbits could do little harm and might provide a touch of home, in addition to a spot of hunting.” But unfortunately the land is so vast that he was barely able to shoot any before their population exploded, helped no doubt by subsequent releases by other colonial settlers. Apart from Mr. Austin and probably a few other hunters the rabbits didn’t really have any predators, apart from birds of prey and the recently introduced dingo (Canis lupus dingo, around 3500-4000 years ago), and consequently they bred like their namesake.

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One Perspective: Directional, Stabilizing and Disruptive Selection
By Branden Holmes on November 28, 2010

One way to look at the whole natural selection mechanism is to separate natural selection into directional selection, stabilizing selection, and disruptive selection. Imagine a trait for a particular species. It doesn't matter what the trait is; all that matters is that the value of the trait varies between individuals to a large extent. Some individuals will possess a below average value for that trait, others the average, and others again above average. The "value" of a trait simply means the physical size of that trait.

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Sexual Recombination
By Branden Holmes on November 28, 2010

“In one sense, we are all equally old, about four billion years, that is, as old as life itself. The difference between an individual who is sixty years old and one who is twenty is how far back into the past their unique genotypes extend. The genes inside a twenty-year-old have survived just as long as those in a sixty-year-old. It is just that in the twenty-year-old the genes were united just 21 years ago, from two separate individuals, each conjoined with other genes. In short, they have undergone recombination more recently than have the genes of the sixty-year-old.” (Robert Trivers, Natural Selection and Social Theory, pg. 241) Even without considering mutations, there is much variation that can created through sexual recombination: the shuffling of genes from two parents into one child’s DNA. Of course, this takes a large number of heterozygous genes (numerically not proportionally) as an assumption. But because genes only code for proteins and not traits directly, different combinations of proteins will produce slightly different phenotypes, while still retaining a general and recognizable phenotype unique to that species (excepting cryptic species). For this reason, we are not averages of our parents.

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Exaptation
By Branden Holmes on November 28, 2010

Given the fact that plants and animals have evolved so much since the first replicating strands of DNA, different traits have changed roles many times during the course of the history of life on Earth. This is one of the fundamental aspects of evolution. Because natural selection has only the pre-existing body plan to work with, any subsequent change in form must modify the existing format in some way; even the origination of traits from scratch requires an initial duplication of contemporary genes. This change in the role of different traits has been named exaptation by Stephen Jay Gould and Elisabeth Vrba, who introduced the term in a now famous paper entitled, Exaptation-a missing term in the science of form (1982).

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Biogeography
By Branden Holmes on November 28, 2010

The very specific distribution of plants and animals across the face of the globe is arguably the best evidence for evolution. As with many things pertaining to evolution, Darwin inaugurated the field in 1859. He started off chapter XII (Geographical Distribution) with these words: “In considering the distribution of organic beings over the face of the globe, the first great fact which strikes us is, that neither the similarity nor the dissimilarity of the inhabitants of various regions can be wholly accounted for by climatal and other physical conditions.” (Charles Darwin, On the Origin of Species, pg. 482) In a typically brilliant experiment he floated 87 different species of seeds in sea-water for 28 days before sowing them. He noted that 64 of the species thus germinated. He then performed a similar experiment but this time used branches with ripe fruit on them. This time he obtained results of 18 out of 94 kinds. He thus reasoned that the seeds and/or fruits of 14/100 species from any country in the world could survive a 28-day ocean crossing. Averaging figures of the speeds of various of the Atlantic currents he returned a figure of 33 miles per day, and thus reasoned that a seed would on average travel 924 miles in that time-span (if they had not encountered land during that time). He additionally noted that several of the species could survive immersion for a much greater period (at least 137 days in the case of some of the seeds) and could thus colonize islands much more distant from the original dispersal point.

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Carolus Linnaeus: The Father of Modern Taxonomy
By Branden Holmes on November 28, 2010

Carl Linnaeus (commonly called Carolus Linnaeus) was born on the 23rd of May, 1707, in Rashult, Smaland, Sweden. He was the first of five children born to Nils Ingemarsson Linnaeus and Christina Linnaeus (nee Brodersonius). His interest in flowers was apparently innate; so much so that he would calm down when upset after being given a flower as a child. He attended a grammar school for seven years, not doing terribly well owing to his infatuation with plants. But his teacher in his final year, who also happened to be the headmaster of the grammar school, Daniel Lannerus, had already noticed the young Linnaeus’ passion for plants. He gave Linnaeus both control of his garden, and introduced him to the state doctor, Dr Johan Rothman, who was also a teacher at Vaxjo Gymnasium. He was transferred to Vaxjo Gymnasium in 1724. His father Nils visited the Gymnasium in Carolus’ last year there, where his father was told by nearly all of the professors that he would not fulfil his father’s hope and become a priest. But Dr Rothman offered to take the young man under his wing, give him a home, and teach him both botany and medicine, which Carolus’ father gratefully accepted.

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The ants nest as extended phenotype of the queen
By Branden Holmes on November 28, 2010

The Hymenoptera, or social insects (ants, bees and wasps), have a very unusual family structure. In many species there is only a single female, the queen, which produces all other members of the nest. She controls the production of sterile female workers and males; this special system is called haplodiploidy. The colony as a whole functions as one superorganism with a specific division of labour amongst the various castes, or types, of social insect within a given nest. As only the queen reproduces, and the rest of the colony are all sterile, it is the genetic ability of the queen to create a highly organized colony which is being selected. Any colony which breaks out into mutiny will not produce a new queen to fly off and found a new colony. Thus only those females which successfully propagate a new generation of queens, pass on their genes.

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The Cambrian "explosion"
By Branden Holmes on November 28, 2010

“If modern zoology admits of anything approaching a full-blown origin myth, it is the Cambrian Explosion. The Cambrian is the first period of the Phanerozoic Eon, the last 545 million years, during which animal and plant life as we know it suddenly became manifest in fossils. Before the Cambrian, fossils were either tiny traces or enigmatic mysteries. From the Cambrian onwards, there has been a clamorous menagerie of multicultural life, more or less plausibly presaging our own. It is the suddenness with which multicultural fossils appear at the base of the Cambrian that prompts the metaphor of explosion.” (Richard Dawkins, The Ancestor’s Tale, pg.449) There were three great flourishings of life. The first was the origin of life itself. The second was the evolution of the eukaryotic cell. The third, the one for which we have palaeontological evidence, was the “Cambrian Explosion”. Within a geologically short period of 15 or 20 million years most of the current Phyla appear abruptly. Nobody knows exactly why this is, though of course many have taken guesses; some more educated than others. If you read the fossil record literally then it was in every sense an explosion. With no identified ancestors, the Cambrian fauna seems in every sense to have been an explosion of life forms.

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Deception and Mimicry
By Branden Holmes on November 28, 2010

Deception in both the animal and plant kingdoms is one of the most amazing phenomena. Yet the phenomenon is quite easily explained, which betrays the seeming complexity that they present to us: “In the deserts of southern Africa, pebble plants¾also known as ‘living stones’¾blend so perfectly with their stony background that they can be spotted only during their brief flowering season. It is their way of coping with the threat of passing browsers…They are so skilled as mimics that each species is tied to a particular rock formation, imitating its form, colour or texture. Some even reproduce the shine of quartz grains.” (Nature’s Masterpieces, Readers Digest, pg. 90)

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Speciation
By Branden Holmes on November 28, 2010

The mechanism by which new species arise is called speciation. There are three basic ways in which this may happen. Firstly, a previously reproductively-connected population may become geographically separated into two or more sub-populations because of a geographical barrier which arises. Interbreeding between these sub-populations then becomes physically impossible. And if they stay geographically isolated for a long enough period of time, different selection pressures combined with genetic drift will cause them to diverge genetically. This is called allopatric speciation and is believed to be the main way in which new species arise.

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The Agricultural Revolution
By Branden Holmes on November 28, 2010

About 8,000 BC a major turning point occured in the Near East, the so-called "Fertile Crescent". People there started to grow their own food; they began to give up their hunter-gatherer lifestyles in favour of something much more permanent. As is often the case, this probably happened independently in at least five areas around the world: the Fertile Crescent, China, India, the New Guinean highlands, the New World, the Ethiopian highlands, the Sahel, and West Africa (Richard Dawkins, The Ancestor's Tale, 2005, pp. 27; new genetic evidence confirms that the farmers of Europe were actually from the Middle-east; a people who brought their farming practices all the way to Europe). Several earlier domestications occurred, including the dog 12-18,000 years ago, but virtually all domestications around the world occurred between 8,000 BC and 1500 BC.

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