Tag Archives: Natural Selection

The Origin of Life and Life on Other Planets

The Origin of Life and Life on Other Planets

Several parallel discussions inspire me to write this post partly in the hope that you will chime in.

The chance of life elsewhere in the universe just went to near zero. Or did it?

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Pagel on Darwin

ResearchBlogging.orgMark Pagel, evolutionary theorist extraordinaire, has published an Insight piece in Nature on Natural selection 150 years on. Pagel, well known for myriad projects in natural selecition theory and adaptation, and for developing with Harvey the widely used statistical phylogenetic method (and for being a reader of my thesis) wishes Charles Darwin a happy 200th birthday, and assesses this question:

How has Darwin’s theory of Natural Selection fared over the last 150 years, and what needs to be done to bring this theoretical approach to bear as we increasingly examine complex systems, including human society?
Continue reading Pagel on Darwin

Elephants and Horses

In 1833, Darwin spent a fair amount of time on the East Coast of South America, including in the Pampas, where he had access to abundant fossil material. Here I’d like to examine his writings about some of the megafauna, including Toxodon, Mastodon, and horses, and his further considerations of biogeography and evolution.

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Rheas and the Birth of Evolutionary Theory

Everyone knows about Darwin’s Finches, of the Galapagos Islands. But of course, Darwin made observations of birds throughout his travels on The Beagle. Here, I present a number of passages from The Voyage that include some of these observations.

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Fossil Quadrupeds

Charles Darwin wrote a book called Geological Observations on South America. Since Fitzroy needed to carry out intensive and extensive coastal mapping in South America, and Darwin was, at heart, a geologist more than anything else (at least during the Beagle’s voyage), this meant that Darwin would become the world’s expert on South American geology. Much of The Voyage is about his expeditions and observations. Part of this, of course, was figuring out the paleontology of the region.
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The Origin of the Chicken

From whence the humble chicken? Gallus gallus is a domesticated chicken-like bird (thus, the name “chicken”) that originates in southeast Asia. Ever since Darwin we’ve known that the chicken originated in southeast Asia, although the exact details of which one or more of several possible jungle fowls is the primal form has been debated. The idea that more than one wild species contributed to the early chicken has been on the table for a long time, though perhaps not as long as the chickens themselves have been on the table

Notice the yellow legs on this chicken. If you pluck out the feathers, you’ll notice that the skin is yellow as well. But if you go find, say, a crow, and pluck its feathers, it will be grayish in color. Or maybe black, I don’t know, it’s been a while since I’ve defeathered a crow. The point is, that some birds are yellow, some are not.ResearchBlogging.orgThere is a gene that is expressed in certain tissues that produces an enzyme that cleaves the carotenoid molecules that provide the yellow color. If there is no functional copy of this gene (if the individual is homozygotic for the broken version) then this cleaving does not happen, and you get a yellow bird (depending on other factors we shall ignore).In short, new research confirms as previously thought that the red jungle fowl (Gallus gallus) is ancestral to the modern chicken, as Darwin suspected. But this research also suggests that another bird, the grey jungle fowl (Gallus sonneratii) also contributed to the chicken’s genome, providing the yellow color we see on this chicken’s legs.The research, reported in PLoS Genetics, gives us two results. One is the first characterization of the process of pigmentation mentioned above, and the second is a new family tree for this bird.

Many bird species possess yellow skin and legs whereas other species have white or black skin color. Yellow or white skin is due to the presence or absence of carotenoids. The genetic basis underlying this diversity is unknown. Domestic chickens with yellow skin are homozygous for a recessive allele, and white skinned chickens carry the dominant allele. As a result, chickens represent an ideal model for analyzing genetic mechanism responsible for skin color variation. In this study we demonstrate that yellow skin is caused by regulatory mutation(s) that inhibit expression of the beta-carotene dioxygenase 2 (BCDO2) enzyme in skin, but not in other tissues. Because BCDO2 cleaves colorful carotenoids into colorless apocarotenoids, a reduction in expression of this gene produces yellow skin. This study also provides the first conclusive evidence of a hybrid origin of the domestic chicken. It has been generally assumed that the red junglefowl is the sole ancestor of the domestic chicken. A phylogenetic analysis, however, demonstrates that though the white skin allele originates from the red junglefowl, the yellow skin allele originates from a different species, most likely the grey junglefowl. This result significantly advances our understanding of chicken domestication.

Here is the phylogenetic tree that the authors of this paper present:i-a782d8d10ab087febef2b5b4a719fe02-chicken_tree.jpgClick here for a much larger image (84kb)You will read in press reports that “Darwin got it wrong” when it comes to chickens. Let’s have a look at what he said and see how wrong he was. Darwin addressed the two major theories of his time. One is a multiregional theory, much like the now discredited version of human evolution, where each kind of chicken was domesticated from a different wild form. The other is that all descended from one ancestor, Gallus gallus bankiva, also known as Gallus bankiva.Darwin uses chickens in a big way in developing his ideas about evolution. Chickens were perhaps as important as pigeons for examining breed characteristics. Therefore, he wrote quite a bit about chickens. In the end, he favored the single origin hypothesis, but he also describes the primordial species of his choosing … the red jungle fowl … as much more diverse in character than it is generally characterized today…

… Gallus bankiva, has a much wider geographical range than the three previous species; … This species varies considerably in the wild state. Mr. Blyth informs me that the specimens, both male and female, brought from near the Himalaya, are rather paler coloured than those from other parts of India; whilst those from the Malay peninsula and Java are brighter coloured than the Indian birds. I have seen specimens from these countries, and the difference of tint in the hackles was conspicuous. The Malayan hens were a shade redder on the breast and neck than the Indian hens. The Malayan males generally had a red ear-lappet, instead of a white one as in India; but Mr. Blyth has seen one Indian specimen without the white ear-lappet. The legs are leaden blue in the Indian, whereas they show some tendency to be yellowish in the Malayan and Javan specimens. In the former Mr. Blyth finds the tarsus remarkably variable in length. According to Temminck20 the Timor specimens differ as a local race from that of Java. These several wild varieties have not as yet been ranked as distinct species; if they should, as is not unlikely, be hereafter thus ranked, the circumstance would be quite immaterial as far as the parentage and differences of our domestic breeds are concerned. The wild G. bankiva agrees most closely with the blackbreasted red Game-breed, in colouring and in all other respects, except in being smaller, and in the tail being carried more horizontally. But the manner in which the tail is carried is highly variable in many of our breeds,…(Darwin 1868:233)

What we see here (my emphasis added) is evidence that skin color varied across different populations of this species.The study at hand asserts:

On the basis of observed character differences and cross-breeding experiments, Darwin concluded that domestic chickens were derived solely from the red junglefowl, though this was later challenged by Hutt [1], who stated that as many as four different species of junglefowls may have contributed to chicken domestication. Molecular studies of mtDNA and retroviral insertions have supported Darwin’s view. A study that analyzed both repeat nuclear elements and mitochondrial sequences found evidence that grey and Ceylon junglefowls may hybridize with domestic chickens, but did not provide evidence that these two species have contributed to chicken domestication. To date, no studies have compared gene sequences associated with a specific phenotype found in domestic chickens across numerous wild junglefowls and domestic breeds….We searched for the causal mutation … This analysis revealed a surprisingly high sequence diversity between the two groups (0.81%), well above the genome average for chicken (~0.5%) [15] and approaching the sequence divergence between chimpanzee and human (1.2%). We therefore included three other species of junglefowls in the sequence comparison: grey (G. sonneratii), Ceylon (G. lafayetii), and green (G. varius) junglefowls. This step was also motivated by the fact that grey and Ceylon junglefowls have red or yellowish legs which implies deposition of carotenoids and a Y/Y genotype…In contrast, mtDNA sequences from the same samples showed the expected pattern in which domestic chickens cluster with red junglefowl within a clade well separated from other junglefowls

The grey and red jungle fowl have, at present, disjunct ranges, but that may be a product of recent ecological changes, including human alterations of habitats. Also, in the early days of chicken domestication, there is no reason to suspect that a single origin would be followed by immediate isolation from wild forms, and in fact, all the available evidence including that reported here suggests the contrary.I think the truth of the matter is that Darwin did not really get the origin of the chicken wrong … he had it substantially right. Rather, Darwin had a better idea of variation in the wild forms than we may appreciate today, and he leaned a bit more towards a simpler history at the start than we tend to today. That’s not bad considering that all of the modern theory about origins of domesticated forms post dates, and often derives from, Darwin.In other words, Newton understood gravity, so today we can design an airplane. But if Newton designed and airplane that did not fly, would that mean that he got gravity wrong?I think not.


(More on Darwin here)Darwin, C. R. 1868. The variation of animals and plants under domestication. London: John Murray. First edition, first issue. Volume 1.Eriksson, J., Larson, G., Gunnarsson, U., Bed’hom, B., Tixier-Boichard, M., StrÃ?¶mstedt, L., Wright, D., Jungerius, A., Vereijken, A., Randi, E., Jensen, P., Andersson, L., Georges, M. (2008). Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genetics, 4(2), e1000010. DOI: 10.1371/journal.pgen.1000010

The Modes of Natural Selection

There many ways of dividing up and categorizing Natural Selection. For example, there are the Natural Selection, Sexual Selection and Artificial Selection, and then there is the Modes of Selection (Stabilizing, Directional, and Disruptive) trichotomy.

We sense that these are good because they are “threes” and “three” is a magic number. Here, I’m focusing on the Mode Trichotomy, and asking that we consider that there are not three, but four modes of Natural Selection. This will cause tremors throughout the Evolutionary Theory community because Four is not a magic number, but so be it.

In Stabilizing Selection the extremes of a trait are selected against and the mean value of the trait remains the same. Mutations constantly introduced into the population tht produce traits out at the extremes are selected against. In Directional Selection the values of a trait at one end of the distribution are selected against and/or values at the other end are selected for, so that the distribution of values, and it’s mean, move in one direction. In Disruptive Selection the average values are selected against so that the distribution of the trait becomes bimodal.

That was pretty simple, but Continue reading The Modes of Natural Selection

The Three Necessary and Sufficient Conditions of Natural Selection

Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition.

In this post, we will do the following:

  • Discuss historical and contextual aspects of the term “Natural Selection” in order to make clear exactly what it might mean (and not mean).
  • Provide what I feel is the best exact set of terms to use for these “three conditions,” because the words one uses are very important (there are probably some wrong ways to do it one would like to avoid).
  • Discuss why the terms should be put in a certain order (for pedagogical reasons, mainly) and how they relate and don’t related to each other.

When you are done reading this post you should be able to:

  • Make erudite and opaque comments to creationists that will get you points with your web friends.
  • Write really tricky Multiple Choice Exam Questions if you are a teacher.
  • Evolve more efficiently towards your ultimate goal because you will be more in control of the Random Evolutionary Process (only kidding on this third one…)

Continue reading The Three Necessary and Sufficient Conditions of Natural Selection