Recherche : Paléoanthropologie

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[paleorecherche-blog]

I just got my free train card even though it's supposed to be only for the under-26 set.  This video properly represents the irrational exuberance I experienced after hoodwinking the SNCF.  I'm gonna ride the fuckin' train all day beeotch!!!

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New site.

So this site is done. Over.  No more. That was fast, huh? The new site is now at:

http://paleorecherche.blogspot.fr

I want to like tumblr, and I want to be liked by the cool kids here.  But the whole point of this site was for me to be able to easily search and re-find things I've found, and tumblr doesn't let you search the text of your posts.  You can only search for tags.  Ha.  Luckily, it turns out one thing that Google does well is search, and this extends to their blogging service.  So blogger it is. 

I was mildly teed since I had to repost everything, but mostly flabbergasted that a major New York big money start-up would neglect such a basic feature. Tumblr, get your shit together son.

[paleorecherche-blog]

Adam and Eve

Mme Degioanni made a good point today.  She asked us if there was an incompatibility with the fact that the mitochondrial ‘Eve’ is dated at around 200ky and that a similar study based on the Y-chromosome study (‘Adam’) cites a last common ancestor at around 90ky.  Eve never met Adam!  Nobody in the class could give an answer, but when she explained the reason it seemed so obvious. 

These studies are based on modern populations, so any haplotypes that went extinct are not represented. 

[paleorecherche-blog]

An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations

labuda - Neandertal haplotype in humans.pdf

An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations (2012)

doi:10.1093/molbev/msr024

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

http://news.discovery.com/human/genetics-neanderthal-110718.html

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Rarity, specialization and extinction in primates

Rarity, specialization and extinction in primates by A. H. Harcourt, S. A. Coppeto, S. A. Parks

2002

DOI: 10.1046/j.1365-2699.2002.00685.x

Main conclusions The most commonly demonstrated traits of susceptibility to extinction are those of high resource use, slow recovery rate, and specialization. Yet, while rarity is an inevitable precursor to extinction, specialization is the only trait found to correlate with rarity in this study. We cannot explain this apparent contradiction.

If nothing goes extinct without first being rare, why does rarity in primates correlate with only one of the sets of traits that have been shown to be associated with susceptibility to extinction in primates, not all of them, i.e. with only specialization, and not also with high resource requirements and slow population recovery rate? One of the most important issues an evolutionary biologist can address is, surely, the biology of extinction. If we are puzzled about a link between rarity and extinction, if we do not know what makes a taxon prone to extinction, we leave unexplained the course of evolution. We know what went extinct and when, but we do not know why. This analysis, with its huge amount of variation unexplained, and its surprising result, indicates that even for one of the better known mammalian orders, we are far from a complete understanding of the causes and consequences of rarity and extinction, and therefore of the processes of evolution.

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Meiotic drive in Drosophila melanogaster

nature - meiotic drive.pdf by Laurence D. Hurst and Andrew Pomiankowski

doi:10.1038/34526

Meiotic drive genes are one class of selfish gene. The best-described example is Segregation Distorter in the fruitfly Drosophila melanogaster. This is autosomal (that is, not on the X or Y chromosome) and acts in males. Males that have the driver on one chromosome but not the other have half of their sperm killed, the half that do not contain the drive gene. This, of course, is not 'good for the individual'. But it is 'good for the gene', and the drive gene spreads in the population because of the increased numbers of eggs that come to be fertilized by sperm containing it. Males in which both chromosomes have Segregation Distorter are sterile. As the driver spreads, this comes to be an increasingly common occurrence. In consequence, Segregation Distorter does not eliminate the original non-driving chromosome.

Although in no case is the mechanism of drive well understood, in all well-described instances the drive 'gene' is actually composed of two tightly linked types of gene. The simplest model proposes that one of these codes for a toxin. Even if only half of the sperm have this gene, all sperm are affected by its toxic product. — unless, that is, they contain the other gene, which codes for the antidote. Unlike the toxin, the antidote's activity is restricted to the sperm that contain the antidote gene.

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Grade vs. clade

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 19:

Any group of species may be classified according to the phylogenetic relationships of its members. A group that contains its most recent common ancestor and all its descendants is said to be monophyletic. If some, but not all, descendants are contained, it is a paraphyletic group. If the most recent common ancestor is not in the group, it is said to be polyphyletic. Traditionally, classification has been based on the concept of a grade, i.e. a grouping determined on the basis of overall morphological similarity. Such groupings often do not reflect the precise genetic relationships between the species, and are frequently paraphyletic or polyphyletic groups. The alternative is a clade-based classification, determined on the basis of common genetic origin, or monophyly. Because both morphological similarity and genetic relatedness between species are such primary concerns, both grades and clades remain important for taxonomy (Cronquist, 1987; Sokal, 1985). On the basis of the computer simulations mentioned in Section 1.3, Sepkoski and Kendrick (1993) found that, for incomplete data, polyphyletic groups may be just as useful ‘systematically’ as are clades (monophyletic groups). The species simulations in this book employ both techniques (see Section 3.1).

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Biological species vs. Phylogenetic species

Biological species concept: a group of organisms is a species if it consists of actually or potentially interbreeding individuals, and is reproductively isolated from other such groups (Mayr, 1969).

Phylogenetic species concept: a group of organisms is a species if it is the least inclusive monophyletic group definable by at least one autapomorphy (i.e. a derived character state exclusive to a particular taxon) (Mishler and Donoghue, 1982). Closely related to this is the diagnostic species concept (Cracraft, 1983), where the classification is based on character states that are fixed and not necessarily autapomorphic.

In practical terms, these two definitions are not as different as they at first seem. Both of them attempt to define a species essentially as an evolutionarily independent unit; in genetic terms, the biological species concept implies that gene flow can occur, whereas the phylogenetic species concept implies that gene flow has occurred.

However, both concepts have limitations. The biological species concept is unable to classify asexual species, and neither can it be applied to fossil species; it tends to be overly lumpy and results in groups larger than perhaps are desired; and it can also be argued that, because the ability to interbreed is a primitive trait, the biological species concept may result in grouping of species that are not actually closest genetic relatives. The phylogenetic species concept is limited in ways that are in many respects the flip-side of the above problems. It tends to be overly splitting, resulting in groups smaller than desirable; organisms may be grouped on characteristics of unclear biological relevance; and different species (according to this definition) may interbreed, leading to interspecies gene flow.

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Sarich and Wilson, 1967

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 3:

Sarich and Wilson employed an immunological technique, measuring the cross-reaction of antigens and antibodies from different hominoid species, as a method of comparing amino acid sequences, the degree of cross-reaction being a measure of similarity. The immune system is obviously highly important in natural selection, and therefore the results obtained by using this method are strongly correlated with the evolution of the species being studied. Results from this new research revealed the fact that humans, chimpanzees and gorillas are in fact more closely related to each other than any of them is to orangutans, so a more accurate phylogeny groups humans, gorillas and chimpanzees (the African apes) together, with orangutans as a sister taxon (see Figure 1.1). The ground-breaking aspect of this work was the imposition of a time scale, leading to an estimate of the time of the human–chimpanzee common ancestor of around 5 million years ago, far more recent than was being indicated by other work at the time.

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Coalescent theory in a nutshell

From Coalescing into the 21st century: An overview and prospects of coalescent theory. Theor. Popul. Biol. 56, 1–10. By Fu and Li (1999)

To infer the past from a sample taken from a present population, a new approach is required. Coalescent theory arose from this necessity. The essence of coalescent theory is to start with a sample, and trace backward in time to identify events that occurred in the past since the most recent common ancestor of the sample. Since the seminal work of Kingman (1982a, b), coalescent theory has been the most active topic in theoretical population genetics, and it is now widely recognized as the cornerstone for various statistical analyses of molecular population samples. The usefulness of the theory comes mainly from three features. First, it is a sample-based theory. Since the study of a population usually relies on a sample of individuals from that population, a theory that describes the properties of a sample is more relevant than the classical population genetics theory that describes the properties of the entire population. Second, it is a highly efficient approach. An important by-product of coalescent theory is the development of highly efficient algorithms for simulating population samples under various population genetics models, allowing various aspects of a model to be examined numerically. Third, coalescent theory is particularly suitable for molecular data, such as DNA sequence samples, which contain rich information about the ancestral relationships among the individuals sampled.

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Coalescent theory is a probabilistic framework

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) pp 13:

The study of a population is generally retrospective in nature, starting with a sample from an existing population and then attempting to describe the observed features in terms of the population’s prior evolution. Results are then generalised from the sample to the entire population. Coalescent theory (Kingman, 1982b; Hudson, 1990) provides a probabilistic framework perfectly suited to this approach, and has therefore become an extremely important tool in population genetics over the past 20 years. In brief, coalescent theory describes the merging of lineages from a sample of a population as one goes backwards in time, to the point where only a single lineage remains, i.e. the common ancestor. It is particularly well suited to molecular data, and although the usual formulation is based on the neutral model (Kimura, 1968) and a single, randomly mating population of constant size, extensions to cover recombination (Hudson, 1983), population growth (Kuhner et al., 1998), population subdivision (Hudson, 1990; Donnelly and Tavaré, 1995) and selection (Neuhauser and Krone, 1997) are well developed and are the subject of much ongoing research. A good review may be found in Fu and Li (1999).

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From Simulating Human Origins and Evolution by Ken Wessen (2005)

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Hypothesis and explanation in human evolution

hypothesis+explainationHumanEvol.pdf

Hypothesis and explanation in human evolution by Donald L. McEachron in J. Social Biol. Struct. (1984)

Abstract:

Many attempts to reconstruct the evolutionary history of Homo sapiens have been hampered by a failure to incorporate evolutionary limitations and adhere to proper scientific methodology. Models of human evolution should be strictly derived from general evolutionary hypotheses which have been tested and to some extent verified with living forms. To preserve the testability of such models, researchers should begin by determining the environmental parameters faced by the hominids in the past and then design alternative evolutionary pathways in an attempt to retrodict the characteristics of modern humans. Differences between retrodictions would then provide tests of alternative explanations. Traits of modern humans should not be used, other than determining taxonomic relationships with fossil species, in creating a model, since the model would then become a tautological explanation and not a scientific hypothesis.

...

Models of evolutionary processes are limited only by the rules of logic and the researcher's imagination. Biological evolution itself, however, is subject to numerous constraints, including but not limited to :

(1) the amount, structure, and variability of the available genetic material;

(2) the chronology of the factors mentioned under (1), i.e. what genetic material was available at what times in relation to the selection pressures exerted at those times;

(3) stochastic effects, such as mutation and genetic drift;

(4) the amount and directions of the selection pressures;

(5) the timing of these pressures-when and for how long they operated;

(6) the rate of reproduction.

...

The following steps should be taken when attempting to reconstruct the phylogenetic history of a species with living descendants. First, use fossils to establish the taxonomic status, physical characteristics and limitations in the ancestral species. This provides the range of conceivable models, both by comparison with existant members of related species, and by delimiting the kinds of behavior which would have been possible physically. Next, establish the ecological conditions prevailing at the time and locations in question. Finally, incorporate these parameters in designing several different evolutionary models using the most general (i.e. most widely applicable to modem species) models possible. One should be careful that these pathways be logical and consistent derivations from the general models.

...

Modern species must be used to establish the taxonomic relationships with probable ancestors, but this must be the limit to which they are used to begin construction of an evolutionary model. There are several reasons for this. First, and most importantly, by using the attributes of the modern species to create the evolutionary model, the ability to test the model is lost. The adaptations which should have been predicted by the hypothesis are the very ones used to create it. At that point, the model ceases to be a scientific hypothesis and becomes a tautological explanation. Second, there is a tendency for researchers to develop a single explanation for the evolution of numerous traits which may or may not have evolved simultaneously, thus ignoring the possibility of mosaic evolution. Finally, extrapolating present adaptations onto past species indicates a failure to recognize evolution as a process of change from the ancestral to the modern forms. If the ancestral species had possessed behavioral and morphological characteristics identical to those of the living forms, there would have been no change between then and now (and thus, no evolution).

...

As a further example, consider how these researchers examine the question of the early hominids' mating system. Morris (1967), Wilson (1978), and Lovejoy (1981) apparently consider modern humans to be monogamous-an assumption, for that matter, which itself is highly debatable (Bermant & Davidson, 1974; Martin & May, 1981). In fact, polygyny is quite common in human societies (Davenport, 1976), and in a survey of one hundred and eighty-five human societies, one hundred and fifty-four were found to be basically polygynous (Ford & Beach, 1951). Even if modern Homo sapiens were monogamous, however, that is not sufficient reason for assuming that the early hominids practiced monogamy; nor does that assumption establish the exact time when monogamy developed, since the pre-hominids may or may not have been monogamous themselves. By deciding that the hominids were monogamous before creating their evolutionary models, Morris, Wilson, and Lovejoy are forced to design their models with the following question in mind: 'Why were the hominids monogamous, and in what way did human characteristics contribute to this mating system'? Posing the question in this manner severely limits the kind of models that can be offered as answers - all must be based on monogamy. The question should be stated: 'Given the ecological constraints, habitat, and the modern primates' range of genetic and social variation, what mating systems could the early hominids have had'? Posed in this way, no possibilities are excluded a priori and various hypotheses can be tested against each other.

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History of Simulating Evolution

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 12:

Raup et al. (1973) studied the generation of species lineages by modelling speciation as an equilibrium process of random lineage branching. All lineages stem from a common ancestor, and may continue in time, become extinct, or produce a new lineage by branching, with a probability based on the difference between the existing diversity and a predetermined equilibrium value. An algorithm for the automatic identification of clades was included, allowing study of the taxonomy of the resulting phylogeny. The simulations produced quite a variety of clade shapes, which were then compared with actual clades for the Reptilia. An important fact demonstrated by this work is that differences in evolutionary pattern do not necessarily imply an inherent difference in the associated taxonomic groups: simulated groups evolving under identical constraints can behave very differently. Sepkoski and Kendrick (1993) used a similar model to simulate phylogenies. Employing exponential, logistic and mass-extinction diversification profiles, the resulting phylogenies were degraded in various ways (to model the effects of fossilisation, for example) and the information content remaining was analysed with respect to the ‘true’ phylogeny. Both these models can be generalised to allow the study of higher taxa, e.g. genus, family, etc. Nee et al. (1994) also used a similar approach to study the reconstruction of phylogenies, looking particularly at the role of lineages that become extinct.

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Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) p 9:

It must be remembered that a species tree is actually a combination of several individual gene trees, and the overall picture may only be recoverable through the study of several of these individual genes (Moore, 1995). The three species shown in Figure 1.2 contain a gene whose form in species C is older than the form in species A and B (the B–C species ancestor being polymorphic). Sampling this particular gene would incorrectly imply a closer relationship between species A and B than between B and C. (Analogously, in a morphological study, many independent morphological characters may be needed for accurate resolution of a species tree.)

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Molecular Clock Problems

Wessen-Simulating-human-origin-evo.pdf

Simulating Human Origins and Evolution by Ken Wessen (2005) pp 9-11:

As is apparent from the above discussion of the work by Cann et al. (1987), molecular methods rely on knowledge of the mutation rate of DNA across time and between species. The molecular clock hypothesis is a consequence of the neutral theory of evolution (Kimura, 1968) and implies an approximately constant rate of mutation, so long as the DNA sequence retains its original function. If this is the case, then the degree of difference between sequences being compared is simply proportional to the time since the sequences diverged. By incorporating fossil evidence, the clock can be calibrated, and thus divergence times can be attached to a molecular phylogeny.

In fact, particular DNA sequences and proteins can mutate at vastly different rates at different times and in different lineages, and although there may be some local validity of the molecular clock hypothesis, in general there is global failure (Avise, 2000; Gibbons, 1998; Ruvolo, 1996; Strauss, 1999; Wills, 1995). The fast-mutating microsatellite loci, i.e. short repetitive sections of DNA that lie between genes, have been used to construct an alternative method for timing lineages that does not rely on external calibration of the rate of molecular evolution (Goldstein et al., 1995). However, because of mutational saturation, nuclear microsatellites are only useful for timing relatively recent events. In particular, the deepest split in the human phylogeny can be recovered with such a method, but saturation will occur in less time than the five million years or more back to the human–chimpanzee common ancestor (Jorde et al., 1998).

This situation also affects substantially the common ancestor calculations described above. For example, Wills (1995) includes a variable mutation rate across mtDNA sites and obtains a range of 436 000 to 800 000 years ago for the mitochondrial common ancestor, depending on the date used for the human–chimpanzee common ancestor.

In general, the molecular data seem to support the replacement hypothesis, but when all the aforementioned caveats are considered, it remains far from conclusive. The dates vary widely, depending on the method and assumptions employed. Furthermore, a recent African origin has difficulty with the observed continuity of regional morphological traits, especially outside of Europe, whereas the multiregional hypothesis has difficulty with the amount of gene flow required for its support, as well as with a number of aspects of the molecular data. Perhaps the only thing that is truly clear is that population size, breeding patterns, local geographic events, migrations and reproductive barriers present a severe challenge when it comes to interpreting these results (Lahr and Foley, 1998). So long as positions at both extremes in this debate consider themselves equally well supported by the same data, be it fossil or molecular, substantial further study into the basis of all these methods is obviously of great importance.

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Forward

Have you ever learned a bunch of stuff, and then later forgotten where all that stuff you learned came from?  Ever desperately needed to cite aforementioned stuff and spent fruitless hours tracking it down again? Have you ever said to yourself, "Fuck it, I'll just become a stripper" and drowned your sorrows in mass-produced artificially-carbonated alcoholic beverages?

This blog is a way for me to catalog and tag snippets of things I think I might need to easily access for my masters research.  I'm keeping it public just in case somebody else finds it interesting. 

Also FYI: since a lot of my 'snippets' come from pdfs I downloaded, I use this line break remover to allow me to easily ctrl-c ctrl-v all day long.

Alright.  Let's do this thing.