Tag Archives: Genetics

Gene Genie #24

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Welcome to Gene Genie #24: with a heavy emphasis on Personal Genetics

The previous Gene Genie was hosted at DNAdirect Talk and it is still fresh, so go have a look if you have not already. The next Gene Genie will be hosted at My Biotech Life. By the way, the Gene Genie logo was created by Ricardo at My Biotech Life — see the other award winning artwork here.

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And, now, on with the show:

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Geographic Patterns of Genome Admixture in Latin American Mestizos

ResearchBlogging.orgSignificant cultural and physical differences … the stuff of race and ethnicity … are prominent when people move across continents or between them. Eventually, the ponderous events of history, which involve occasional foldings in the continuum of human variation, causing apparent patchiness, are offset by the frequent events of human activities, resulting in genetic and cultural admixtures. What colonialism, invasion, and migration do is undone.A new study out in PLoS Genetics examines this phenomenon for Latin America, with a study of genetic admixture. Continue reading Geographic Patterns of Genome Admixture in Latin American Mestizos

Genetics of Behavior: Fire Ants

ResearchBlogging.orgA common presumption is that behavior is part of phenotype, and since phenotype arises from genotype (plus/minus Reaction Norm), that there can be a study of “behavioral genetics.” This is certainly an overstatement (or oversimplification) for organisms with extensive and/or complex neural systems, such as humans and mice. Neural systems probably evolved (not initially, but eventually) to disassociate behavior with the kind of pre-determined micro-management of behavior that a simple gene-behavior link requires. However, in organisms with neural systems the size of the period at the end of this sentence, we often do see cases of allelic variations causing behavioral variation in the whole organism. The study discussed here is an example of this. Continue reading Genetics of Behavior: Fire Ants

Why the Hobbits of Flores Were Probably Not Broken People

There is a new paper out suggesting that the Flores hominids, known as Hobbits, were “human endemic cretins.”From the abstract of this paper:

… We hypothesize that these individuals are myxoedematous endemic (ME) cretins, part of an inland population of (mostly unaffected) Homo sapiens. ME cretins are born without a functioning thyroid; their congenital hypothyroidism leads to severe dwarfism and reduced brain size, but less severe mental retardation and motor disability than neurological endemic cretins. We show that the fossils display many signs of congenital hypothyroidism, including enlarged pituitary fossa, and that distinctive primitive features of LB1 such as the double rooted lower premolar and the primitive wrist morphology are consistent with the hypothesis. We find that the null hypothesis (that LB1 is not a cretin) is rejected by the pituitary fossa size of LB1, and by multivariate analyses of cranial measures. We show that critical environmental factors were potentially present on Flores, how remains of cretins but not of unaffected individuals could be preserved in caves, and that extant oral traditions may provide a record of cretinism.

Continue reading Why the Hobbits of Flores Were Probably Not Broken People

Evolution of the Flu Virus

i-96914fa457dda10e92990f0d4ed3fc49-flu_pandemic.jpgThe flu is caused by the influenza virus, of which there are several types. H1N1 is known as the “Spanish Flu,” H2N2 as the “Asian Flu” and so on. These funny letters and numbers refer to specific genotypes. The H1N1 is the version of the flu that caused the Great Influenza Pandemic of 1918 and 1919, which was responsible for the death of between 50 and 100 million people.Considering that the difference between a bird or pig flu that may be hanging around in the background and a human pandemic causing flu can be a few dozen changes in the genome, understanding the evolutionary patterns for Influenza A viruses seems important. Continue reading Evolution of the Flu Virus

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

What did the immediate ancestor of chimps and humans look like?

Comparing living chimpanzees to living humans, in reference to the species that gave rise to these two closely related species, is one way to frame questions about the evolution of each species. Continue reading What did the immediate ancestor of chimps and humans look like?