Category: Evolution

The color of life as a coincidence

By Razib Khan | November 13, 2013 2:35 am

Credit: Eric Hunt

Credit: Eric Hunt

I do love me some sprouts! Greens, bitters, strong flavors of all sorts. I’ve always been like this. Some of this is surely environment. My family comes from a part of South Asia known for its love of bracing and bold sensation. But perhaps I was born this way? There’s a fair amount of evidence that taste has a substantial genetic component. This does not mean genes determine what one tastes, but it certainly opens the door for passive gene-environment correlations. If you do not find a flavor offensive, you are much more likely to explore it depths, and cultivate your palette.

220px-Durio_kutej_F_070203_ime

Dost thou dare?
Credit: W.A. Djatmiko

And of course I’m not the only one with a deep interest in such questions. With the marginal income available to us many Americans have become “foodies,” searching for flavor bursts and novelties which their ancestors might never have been able to comprehend. More deeply in a philosophical sense the question of qualia reemerges if there is a predictable degree of inter-subjectivity in taste perception (OK, qualia is always there, though scientific sorts tend to view it as intractable in a fundamental sense).

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Our forefathers were fierce & our foremothers were faithful

By Razib Khan | October 27, 2013 8:51 pm

Credit: Chineeb

Credit: Chineeb

One of the peculiarities of human historical genetics is that people can simultaneously accept the existence of aggressive polygynous males such as Genghis Khan, and promiscuous females who give rise to the idea that 1 out of 10 children have an incorrect assigned paternity. I’ve mentioned the cuckoldry myth before. It is a common evolutionary myth; I’ve heard many biologists quote the 1 out of 10 number, and have often made myself obnoxious by pointing to the contradictory literature in this area. This isn’t to say that cuckoldry doesn’t exist. There’s certainly an evolutionary reason so many males engage in “mate guarding.” But you don’t need a high frequency of a trait to allow it to be selectively constrained. If it’s deleterious, then it will be driven down in frequency rather quickly. Whenever you get outbreaks of males who are sanguine about providing resources for offspring who are not their biological issue, natural selection will kick in and guarantee that this generous spirit toward their cheating partners and the delinquent cads does not persist.

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Cuckoldry

If these bones could talk

By Razib Khan | October 19, 2013 1:34 pm
Credit: Thomas Roche

Credit: Thomas Roche

By now you have probably seen the articles about how a new skull has transformed our understanding of the human family tree. The original paper is at Science, A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo. More colorfully you might say that this publication burns down the “bushy” model of human origins, where you have a complex series of bifurcations and local regional diversity, and then rapid extinction with the rise of H. sapiens sapiens ~50,000 years ago. In general I’m more in agreement with those plant geneticists who are skeptical of excessive fixation on the concept of species, so this is not a shock to me. To me a species concept is not a thing, but an instrument to a thing (i.e., I’m in interested in population and phylogenetics). The reason these sorts of findings overturn the orthodoxy has more to do with human cognitive intuitions about why things are categorized, than the reality of how nature arranges itself.

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Evolution

Selection without adjective and bound

By Razib Khan | September 13, 2013 4:03 pm

A “space colony”

In my post below where I take a stand against the tired, but inevitable, assumption that a post demographic transition society necessarily entails a cessation of biology evolution, a reader brings up a trite but specious observation:

But you’re missing the point really. We’ve slowed (not stopped because it can’t be stopped) because we now control our environment. Evolution is moving from individual biological expression to cultural and technological evolution.

This isn’t novel or exceptional in its wrongheadedness. The same idea comes up when I engage in discussion with the types of intellectuals in sociology or anthropology unencumbered by the constraints of “Western linear thinking.” The presumption is that natural selection operates through exogenous environmental pressures, and as we attenuate those pressures we diminish the rate of evolutionary change. The stylized model being:

Rate of evolution ∝ natural selection ∝ 1/(control of environment)

As the magnitude of human control of the environment increases, the magnitude of natural selection decreases, and so does the rate of evolutionary change. This impression was already cursorily dispatched in my prior post. But as there hasn’t been strong selection in the human past for reading and comprehending something before commenting on it, this issue might require a little teasing out, as the stylized model above is so ubiquitous as to be a background assumption of many.

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Rate of Evolution

Man still evolves

By Razib Khan | September 12, 2013 8:02 pm

Still a great book!

Sir David Attenborough is the latest public intellectual who should know better than to opine that evolution has ended for human beings. Here are the quotes from The Telgraph: “Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection. We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

John Hawks does a good job hitting back the balls hanging just over the plate. There are still many parts of the world where 95-99 percent of babies being born do not reach adult. Second, there is still a great deal of variation in fertility. Some people choose not to have any children, while others are quite prolific. For adaptation by natural selection to occur what you need is heritable variation of some sort to correlate with this fertility variation. It seems highly plausible that indeed heritable variation does correlate with fertility variation. As John notes the advancement of genome sequencing over the population will probably answer these questions definitively within the next 10 years (e.g., I am willing to bet that siblings who score higher on impulsiveness and lower on IQ tests will be more reproductively fit than their less impulsive and more intelligent brothers and sisters).

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CATEGORIZED UNDER: Evolution, Genetics

The end of genomics, the beginning of analysis

By Razib Khan | September 11, 2013 12:26 am

A Tree of Life

Evolutionary processes which play out across the tree of life are subject to distinct dynamics which can shape and influence the structure and characteristics of individuals, populations, and whole ecosystems. For example, imagine the phylogeny and population genetic characteristics of organisms which are endemic to the islands of Hawaii. Because the Hawaiian islands are an isolated archipelago the expectation is that lineages native to the region are going to be less shaped by the parameter of migration, or gene flow between distinct populations, than might otherwise be the case. Additionally, presumably there was a “founding” event of these endemic Hawaiian lineages at some distant point in the past, so another expectation is that most of the populations would exhibit evidence of having gone through a genetic bottleneck, where the power of random drift was sharply increased for several generations. The various characteristics, or states, which we see in the present in an individual, population, or set of populations, are the outcome of a long historical process, a sequence of precise events. To understand evolution properly it behooves us to attempt to infer the nature and magnitude of these distinct dynamic parameters which have shaped the tree of life.

Credit: Verisimilus

For many the image of evolutionary processes brings to mind something on a macro scale. Perhaps that of the changing nature of protean life on earth writ large, depicted on a broad canvas such as in David Attenborough’s majestic documentaries over millions of years and across geological scales. But one can also reduce the phenomenon to a finer-grain on a concrete level, as in specific DNA molecules. Or, transform it into a more abstract rendering manipulable by algebra, such as trajectories of allele frequencies over generations. Both of these reductions emphasize the genetic aspect of natural history.

Credit: Johnuniq

Obviously evolutionary processes are not just fundamentally the flux of genetic elements, but genes are crucial to the phenomena in a biological sense. It therefore stands to reason that if we look at patterns of variation within the genome we will be able to infer in some deep fashion the manner in which life on earth has evolved, and conclude something more general about the nature of biological evolution. These are not trivial affairs; it is not surprising that philosophy-of-biology is often caricatured as philosophy-of-evolution. One might dispute the characterization, but it can not be denied that some would contend that evolutionary processes in some way allow us to understand the nature of Being, rather than just how we came into being (Creationists depict evolution  as a religion-like cult, which imparts the general flavor of some of the meta-science and philosophy which serves as intellectual subtext).

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Breeding a better companion cat

By Razib Khan | September 8, 2013 10:22 pm

John Bradshaw, author of Cat Sense: How the New Feline Science Can Make You a Better Friend to Your Pet, has an intriguing observation:

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Cats

Peeling back the palimpsest, and finding selection again

By Razib Khan | September 7, 2013 2:04 am

Layers and layers….

There is the fact of evolution. And then there is the long-standing debate of how it proceeds. The former is a settled question with little intellectual juice left. The latter is the focus of evolutionary genetics, and evolutionary biology more broadly. The debate is an old one, and goes as far back as the 19th century, where you had arch-selectionists such as Alfred Russel Wallace (see A Reason For Everything) square off against pretty much the whole of the scholarly world (e.g., Thomas Henry Huxely, “Darwin’s Bulldog,” was less than convinced of the power of natural selection as the driving force of evolutionary change). This old disagreement planted the seeds for much more vociferous disputations in the wake of the fusion of evolutionary biology and genetics in the early 20th century. They range from the Wright-Fisher controversies of the early years of evolutionary genetics, to the neutralist vs. selectionist debate of the 1970s (which left bad feelings in some cases). A cartoon-view of the implication of the debates in regards to the power of selection as opposed to stochastic contingency can be found in the works of Stephen Jay Gould (see The Structure of Evolutionary Theory) and Richard Dawkins (see The Ancestor’s Tale): does evolution result in an infinitely creative assortment due to chance events, or does it drive toward a finite set of idealized forms which populate the possible parameter space?*

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Who needs sex when you have gene conversion?

By Razib Khan | July 22, 2013 4:49 am

Credit: Gross, Liza. “Who Needs Sex (or Males) Anyway?.” PLoS Biology 5.4 (2007): e99.

Bdelloid rotifiers get a fair amount of attention because they seem to be a lineage of obligate asexual metazoans (Richard Dawkins discusses them extensively in The Ancestor’s Tale). The fact that they don’t have sex isn’t that big of a deal. Bacteria do not have sex, and they’re quite successful. Rather, the issue is that they don’t have sex, they are complex, and, they are successful as a lineage. These do not usually go together. One of the posited explanations is that complex organisms are subject to phenomena such as Muller’s Ratchet, where they begin accumulating a load of deleterious alleles. Sex, with genetic recombination, is a way to evade this process, by mixing and matching alleles. By producing offspring with more than the expected payload of deleterious alleles the lineage can slough off unfavorable mutations which might otherwise fix. Without the ability to offload bad mutations over time they build up, and eventually one presumes the lineage would be unviable. This is just one of the myriad reasons biologists give for the long term lack of success of parthenogenetic metazoan lineages. Sex is ubiquitous among metazoans despite its two-fold cost. That is an overwhelming fact against which stands the example of the bdelloids.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics
MORE ABOUT: Evolution

An illusion of neutrality and synonymous sites

By Razib Khan | July 11, 2013 7:42 am
Central Dogma

Central Dogma

One of the elementary aspects of understanding genetics on a biophysical scale is to characterize the set of processes which span the chasm between the raw sequence information of base pairs (e.g. AGCGGTCGCAAG….) and the assorted macromolecules which are woven together to create the collection of tissues, and enable the physiological processes, which result in the organism. This suite of phenomena are encapsulated most succinctly in the often maligned Central Dogma of Molecular Biology. In short, the information of the DNA sequence is transcribed and translated into proteins. Though for greater accuracy and precision one must always add the caveats of phenomena such as splicing. The baroque character of the range of processes is such an extent that molecular genetics has become a massive enterprise, to a great extent superseding classical Mendelian genetics.

One critical structural detail from an evolutionary perspective is that the amino acids which are the building blocks of proteins are generally encoded by multiple nucleotide triplets, or codons. For example the amino acid Glyceine is “four-fold degenerate,” GGA, GGG, GGC, GGU (for RNA Uracil, U, substitutes for Thymine in DNA, T), all encode it. Notice that the change is fixed upon the third position in the codon. Altering the first or second position would transform the amino acid end product, and possibly perturb the function of the final protein (or perhaps disrupt transcription altogether in some case). These are synonymous substitutions because they don’t change the functional import of the sequence, as opposed to the nonsynonymous positions (which may abolish or change function). In an evolutionary context one may presume that these synonymous substitutions are “silent.” Because natural selection operates upon heritable variation of a phenotype, and synonymous substitutions presumably do not change phenotype, it is often assumed that evolutionary change on these bases is selectively neutral. In contrast, nonsynonymous changes may be deleterious or beneficial (far more likely the former than the latter because breaking contingent complexity is easier than creating new contingent complexity). Therefore the ratio of gentic change on nonsynonymous and synonymous bases across lineages has been a common measure of possible selection on a gene.

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Humans as the aquaphilic ape

By Razib Khan | July 4, 2013 6:58 pm

Credit: Nature (2013) doi:10.1038/nature12228

Every now and then I’m asked about the ‘aquatic ape hypothesis’. My standard response is that there’s nothing to see, and everyone should just move on. But reading a new (open access) paper in Nature, Great ape genetic diversity and population history, it crossed my mind again. The reason is this section of the legend of figure 1, “The Sanaga River forms a natural boundary between Nigeria–Cameroon and central chimpanzee populations whereas the Congo River separates the bonobo population from the central and eastern chimpanzees.” I knew of the latter division. The former was novel to me. In fact I’d never even heard of the Sanaga river prior to this paper. Though the Congo seems clearly a significant geological and hydrological entity, I’m not quite so sure of the Sanaga. The division between the chimpanzees of Nigeria-Cameroon and those of the western Congo region may be one with an overdetermined number of causes. Nevertheless, taking these riverine features as a given parameters in generating allopatric speciation and subspecies level differences, I am struck by the contrast between ourselves and our cousins. In particular, the phylogeny above seems to imply that bonobos and common chimpanzees diverged on the order of ~2 million years ago, while the Nigeria-Cameroon population separated from the western Congo population ~500,000 years before the present (depending on the method of inference you rely on, though the qualitative insight here is preserved even if you switch them around). Though it took H. sapiens sapiens to break out of the world island of Afro-Eurasia, even our erectine cousins pushed on toward the southeastern extremities of Eurasia over 1 million years ago. It seems then that our savanna ape lineage is characterized by the behavior of wander lust and lack of fear of water.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

The Y chromosome shall not die

By Razib Khan | July 4, 2013 2:09 am

Credit: Dan Reeves

The Y chromosome is strange. It’s gene poor and loaded with repeats. That’s one reason mtDNA phylogenetic and phylogeographic analysis preceded the Y chromosome by about 10-15 years (the other major reason in the pre-PCR age is that mtDNA is very copious). While the hypervariable region of mtDNA is an excellent molecular clock because of its high mutation rate (though at a deep enough time depth this causes problems, as bases start to turnover), in the pre-next generation sequencing era hunting around the Y chromosomes for SNPs was tedious (a significant portion of Spencer Wells’ Journey of Man focused on the nitty gritty of extraction and preparation).

Despite all this one of the weirder stories over the past decade in relation to the Y chromosome is the peculiar theory promoted by Oxford geneticist Bryan Sykes, and outlined in his book Adam’s Curse: A Future without Men. As I observed above the Y chromosome has a tendency to be filled up with genetic garbage (since it does not recombine deleterious mutations tend to accumulate). There are a few important functional regions (e.g., SRY), but there’s also a reason that sex-linked diseases occur: in most cases males have to rely on the X chromosome to pick up the slack for the Y. Extrapolating this genetic decay Sykes posited that human males would disappear within ~10 million years due to this process working its inevitable logic. Needless to say most scientists were skeptical. Extrapolating without seeing if the projections pass the sniff test is a fool’s errand. And in any case there’s no Law of Nature that sex determination has to be via the Y chromosome. Birds and reptiles have males despite a somewhat different sex determination system.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

Molecules as more than markers

By Razib Khan | July 3, 2013 12:40 am

Genetics has numerous uses. There are some biologists for whom genetics implies very specific chemical and physical properties of a particular flavor of DNA molecule. Consider a scientist focused on the biophysical properties of zinc finger proteins and the ZYF gene. Then there are biologists for whom genetics is a more abstract and evolutionary enterprise. David Haig and the late W. D. Hamilton fall into this class of thinkers. This is a way of looking at genetics as the scaffold or currency of evolutionary process. Finally, there are those for whom genes are simply discrete convenient markers to trace out historical and spatial patterns. The field of molecular ecology describes this attitude, though the application of phylogenetic techniques from the life sciences in linguistics illustrates the generality of these methodologies.

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CATEGORIZED UNDER: Evolution, Phylogenetics

The beloved brontosaurus and other tales

By Razib Khan | June 23, 2013 4:31 pm


Classic 1897 painting of Diplodocus


Contemporary depiction of Diplodocus
Credit: Nobu Tamura

A few weeks ago I happened to listen to a fascinating interview on NPR with Brian Switek, the blogger behind Laelaps, and author of Written in Stone: Evolution, the Fossil Record, and Our Place in Nature. Switek was discussing his newest book, My Beloved Brontosaurus: On the Road with Old Bones, New Science, and Our Favorite Dinosaurs. To be frank I was captivated by the discussion, and immediately purchased a copy of the book. The reason is simple: despite our current divergent interests Brian Switek began at the same place I did, with dinosaurs. Though after reading My Beloved Brontosaurus I can’t assert that my dinomania matched Switek’s, it was of the same quality. The difference is that while Switek remained true to dinosaurs, my own interests wandered into other domains. Today I am focused more upon evolutionary forces operating on the scale of thousands of years within a species, rather than geological scale transmogrifications. But every now and then I wonder about dinosaurs, and whatever happened to them over the past 20 years after my “dinosaurs years” faded into the distance.

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CATEGORIZED UNDER: Evolution, Paleontology

Sexual selection: ignore the blonde?

By Razib Khan | June 23, 2013 2:56 pm

Frank analytic clarity?

Sexual selection is a big deal. A few years ago Geoffrey Miller wrote The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, which seemed to herald a renaissance of the public awareness of this evolutionary phenomenon, triggered in part by debates over Amotz Zahavi’s Handicap Principle in the 1970s. Of course Charles Darwin discussed the process in the 19th century, and it has always been part of the arsenal of the evolutionary biologist (I first encountered it in Jared Diamond’s The Third Chimpanzee, where he lent some credence to Darwin’s supposition that human racial differences may be a consequence of sexual selection). But this bump in recognition for sexual selection seems to be accompanied by its co-option as a deus ex machina for all sorts of unexplained events. And yet as they say, that which explains everything explains nothing.

To get a better sense of the current scientific  literature I consulted A Guide to Sexual Selection Theory in the Annual Review of Ecology, Evolution, and Systematics. The image above is from an actual box in this review! Normally technical boxes illuminate with an air of superior authority (e.g. “it therefore follows from eq. 1…/”), but it seems to me that the admission that a parameter can be represented by the verbal assertion that it’s complicated tells us something about the state of sexual selection theory. In short: its formal basis is baroque because the dynamic itself is not amenable to easy decomposition.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

What is a population?

By Razib Khan | June 10, 2013 11:12 pm

Anyone who reads the genomic posts with any interest on his weblog must read Daniel Lawson’s fine review of the topic which he has posted on arXiv, Populations in statistical genetic modelling and inference (via Haldane’s Sieve). Even if you don’t have a population genetic and genomic background the gist is entirely accessible. If you do have a population genetic and genomic background and haven’t used various packages such as STRUCTURE or EIGENSOFT yourself, I would recommend reading Lawson’s characterizations, as they are all spot on.

Also, if you have not, I recommend Lawson’s website for ChromoPainter and fineSTRUCTURE. The utility of these methods is outlined in the paper Inference of Population Structure using Dense Haplotype Data.

CATEGORIZED UNDER: Evolution, Genomics
MORE ABOUT: Evolution, Genomics

The dog days of evolutionary genomics

By Razib Khan | June 9, 2013 1:44 am

Credit: PartnerHund

It’s an exciting time for those interested in the evolutionary genomics of the dog. In 2010 a big SNP-array paper came out, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Today we’re going whole genome, which is important because many of the SNP-arrays are ascertained on domestic dogs (i.e., they are designed to pick up dog variation, and so may distort our perception of the variation in wolves). Recently I talked about an analysis of the evolutionary genomics of the dog, The genomics of selection in dogs and the parallel evolution between dogs and humans. The main interesting result of that group was to push the divergence of the dog and wolf lineages further back in time, ~30,000 years, in line with some archaeological and mtDNA finds. I did not find their arguments for the origin of the dog in East Asian convincing. Now a new preprint on arXiv, Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs, pushes this even further.

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Pumapard, leopard-puma hybrids?

By Razib Khan | May 30, 2013 2:11 am

Pumapard, 1904

You are probably aware of Panthera hybrids from Napoleon Dynamite. Specifically, Ligers, the largest of all the big cats. But the hybridization of the Panthera species shouldn’t be so shocking. They have diversified only within the last 2 to 4 million years. The lone New World variant (or at least surviving New World variant, recall the extinct American lion), the jaguar, arrived a few million years ago across Beringia. This is not too surprising, as many iconic “American” animals, such as the American bison, made the same journey (Camels went the other direction). But there were already “big cats” in the New World. The puma or cougar. These are not Panthera, and I only recently realized that jaguars were not closely related to this species. Rather, the puma is the ironically largest of the “small cats”.

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CATEGORIZED UNDER: Evolution

Dog and man: a 30,000 year friendship

By Razib Khan | May 21, 2013 8:16 pm

Cite: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.

To the left is a figure which illustrates the phylogenetic inferences from a new paper in Nature Communications, The genomics of selection in dogs and the parallel evolution between dogs and humans (see Carl Zimmer’s coverage in The New York Times). Why is this paper important? The first thing that jumped out at me is that because they’re using whole genomes (~10X coverage) of a selection of dogs and wolves the results aren’t as subject to the bias of using “chips” of polymorphisms discovered in dogs on wolves (see: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication). The second aspect is that the coalescence of the dog vs. wolf lineage is pushed further back in time than earlier genetic work, by a factor of three. A standard model for the origin of dogs is that they arose in the Middle East ~10,000-15,000 years ago , possibly as part of the broad shift of lifestyles which culminated in the Neolithic Revolution.

This model is now in serious question. Though there have always been claims of fossils of older domestic canids (adduced as such in terms of morphology) than the ones discovered in the Middle East ~15,000 years ago, this year there has been publication of ancient mtDNA results from ~30,000 years before the present which imply the separation of putative domestic and wolf lineages at least to that date. Over the past few years I have wondered about the specific nature of the emergence of both modern humans and modern dogs, and their co-evolutionary trajectory, over the Pleistocene and into the Holocene, in light of these results.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics

Human mutation unveiled

By Razib Khan | May 21, 2013 11:38 am

Credit: Campbell, Catarina D., and Evan E. Eichler. “Properties and rates of germline mutations in humans.” Trends in Genetics (2013).

What a great age we live in. Until recently critical parameters in population genetics such as mutation rates had to be inferred and assumed, even though they served as bases for much more complex inferences. Now with humans (and humans are only the beginning!) much of what was inferred is being assessed in a more direct fashion. Caterina Campbell and Even Eichler have a review in Trends in Genetics which surveys the field as it stands now, Properties and rates of germline mutations in humans. Notice that there’s a rough convergence using pedigree analysis of a mutation rate in the low 10-8 range. Additionally, it does seem that a disproportionate number of novel mutations come through the paternal lineage via sperm. This should increase our moderate worry about older fathers (something reiterated in the piece, with caveats). Finally, the authors suggest these results are a floor for the mutational rate, in part due to the long term conflict with the inferred ‘evolutionary rates,’ which are higher. This matters because to infer the last common ancestors between lineages the value of the mutation rate is obviously critical.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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