Variation phénotypique cours

Plasticité phénotypique

= babies born above 3000m are smaller. Have blood richer in red blood cells.

Too much sun and light skin:
Flavines carotenoids tocopherol folates sont sensible à la photodegradation

Folates - mineralisation osseuse et maturation neurocérébrale (Neural Tube Defects)

Also leads to male infertility

Vit D agit comme hormone et régule l'absorption du Ca. Not enough Vit D = Rickets

Map of skin pigmentation indicates the oldness of African habitation and the newness of American habitation. Ex: there wasn't enough time for amazonians to adapt to high UV levels as the Congolese have.

Mutated sperm

Men have far more replication of their germ line cells than women. Therefore as men age they have a higher chance of mutated sperm. Women's eggs were all created 'at once' so having a child at 20 or 40 changes nothing (at least in this respect).

Since we're having kids later and later, we're accumulating more and more mutations. More and more evolution! Fuck yeah!

Peuplement d'Amerique notes

Amerique (Amerigo Vespucci)

Etablir migration par données biologique:

1. Caracteres discrets morphometrie
2. Groupe sanguins
3. ADN

Stade 2 Last Glacial Maximum (LGM) - Baisse du niveau de la mer (120m)
Stade 1 Holocene (10kya)

18000ya Bering Strait is a plain. Vers 9000 l'etroit se forme.

à 18-20kya Il y a du gibier, il fait plus doux qu'aujourd'hui

Did they enter by the Ice Free Corridor or along the coast? Probably the easiest around 10ky.

Longevity. Cultural or Biological?

Is Human Longevity a Consequence of Cultural Change or Modern Biology?

By Caspari and Lee

DOI 10.1002/ajpa.20360

So they look at the OY ratio of human and neanderthals from Europe and western Asia at different time periods. Here's the sample:

They then cast some stats voodoo:

The approach of data-resampling provides a way to solve problems that lie outside the analytical boundaries of classical statistics (Efron and Tibshirani, 1993), e.g., using ratios as the statistic of interest, as in this study. Resampling also addresses the problem of interdependence of data within the death distribution, and the potential further dependence of later samples on earlier ones because of evolutionary change. As in our previous study, the null hypothesis that there is no difference in OY ratios among the different hominid groups can be stated as a question of probability: how likely is it to observe an OY ratio of a particular hominid group in another group of interest? When the test group’s OY ratio was smaller than that of the resampled group, we rejected the null hypothesis if a ratio the same as or lower than the observed OY ratio was found, on average, in 5% or less of the distribution generated from the comparative group. When the test group’s OY ratio was larger than that of the resampled group, we rejected the null hypothesis if, on average, 5% or less of the distribution was the same as or greater than the observed OY ratio.

So the OY ratio is different amongst Asian early moderns and Upper Paleolithic moderns and is different amongst Neanderthals from Europe and Asia. It is NOT different between Asian moderns and Neanderthals.

In sum, space and time make a difference, not phylogeny.

European Genetics Blog

http://eurogenes.blogspot.fr/2012/08/admixture-and-structure-tests-arent.html

This looks like a rich source of information on population genetics in general and european genetics in particular.

Admix.pas

List all alleles except one.

Input file is .dat

Remember to rename the output file between simulations, or else it will be overwritten.

Admix95

1st line : hybrid population name
2nd line : number of parental populations
3-5th line : parental population names (max. 8 characters)
6th line : number of loci
7-13th line : loci names (max. 8 characters) and number of alleles
14- line : the first number indicates the locus, the second the populations. You must follow the order that you have used in the lines above. Type all the allele frequencies in a line.

input file must be a .inp

Easy to use but no updates.

The Island Where People Forget to Die

By DAN BUETTNER

In 1943, a Greek war veteran named Stamatis Moraitis came to the United States for treatment of a combat-mangled arm. He’d survived a gunshot wound, escaped to Turkey and eventually talked his way onto the Queen Elizabeth, then serving as a troopship, to cross the Atlantic. Moraitis settled in Port Jefferson, N.Y., an enclave of countrymen from his native island, Ikaria. He quickly landed a job doing manual labor. Later, he moved to Boynton Beach, Fla. Along the way, Moraitis married a Greek-American woman, had three children and bought a three-bedroom house and a 1951 Chevrolet.

One day in 1976, Moraitis felt short of breath. Climbing stairs was a chore; he had to quit working midday. After X-rays, his doctor concluded that Moraitis had lung cancer. As he recalls, nine other doctors confirmed the diagnosis. They gave him nine months to live. He was in his mid-60s.

Neanderthal Thermoregulation and the Glacial Climate

Aiello - Wheeler 2003 Climate and Cold Adaptation.pdf

Main questions:

1. In terms of both energetic cost and survival, what quantitative advantage did the Neanderthal cold adapted body form provide at low environmental temperatures?
   
2. What were the actual environmental conditions that prevailed in Europe and European Russia at the time of Neanderthal occupation?

Kleiber equation (1961):

BMR(W) = 3.4 × mass(kg)^0.75

The values predicted by this equation show good agreement with those of living humans and other primates (Aiello & Wheeler 1995).

Based on the inferred body mass and stature data presented in Table 9.1 and the assumptions outlined above, the three hominin body forms show very little difference in the ambient temperature at which thermoregulatory thermogenesis must be initiated or in the minimum sustainable ambient temperature at which a heat production equivalent to 3 times BMR is reached (Table 9.2; Fig. 9.1). Neanderthals with a BMR predicted by the Kleiber equation would need to initiate additional heat production at 27.3°C (81.2°F) 1 , Homo erectus at 28.5°C (83.3°F) and Homo sapiens at 28.2°C (82.7°F). The minimum sustainable ambient temperature for Neanderthals would be 8.0°C (46.5°F), for Homo erectus 11.6°C (52.8°F) and for Homo sapiens 10.5°C (50.9°F).

olol tumblr

Oh man, tumblr hasn't worked all day. Glad I got out when I did since I really needed to access my shit today. They say they're sorry. They don't explain anything though. Dildos.

Mélange = Admixture

Quatrefages: le mélange est une source de progrès et le moteur de l'Humanité

Cavalli-Sforza 1997

LD
New mixtures, new hybrids have higher levels of linkage disequilibrium.

Sex Biased Mixture, Sex-Specific Admixture
Ex: Colonial explorers were mostly men.

Cohen Y-Chromo...

If you want a bourse, work on Basque genetics!

Logiciels
Adimix95
Adimix.pas
Admix 2.0
Mitsura

NB Principle Components Analysis Patterns

Luigi Luca Cavalli-Sforza's work in population genetics has been fundamental to the field, and we have the utmost respect for his many pioneering contributions. It is with some regret, then, that we must disagree with some of his comments on our 2008 paper in the interview published in the June 2010 issue of Human Biology. Here we attempt to clarify some particular points of contention that arose during the interview, referring the reader to the original paper (Novembre and Stephens 2008) and related recent work (e.g., Francois et al. 2010; McVean 2009) for a fuller treatment.

First, we emphasize that our paper was not intended to condemn the use of principal components analysis. Indeed, principal components analysis has proved itself an incredibly useful and powerful technique across a wide range of disciplines, including population genetics. Instead, our paper aimed to draw attention to results that affect how the results of a principal components analysis should be interpreted. In particular, we noted how principal components analysis tends to produce sinusoidal patterns, such as gradients and waves, when applied to data that exhibit a spatial dependence structure. These patterns occur quite generally and have a fundamental mathematical basis related to Fourier series. Indeed, the phenomenon has been noted previously in several different scientific fields [see citations in Novembre and Stephens (2008)], and our primary goal was to draw these results to the attention of the population genetics community. We agree with Cavalli-Sforza that many of our simulations were simple--indeed, they were deliberately designed this way to emphasize that wavelike patterns arise under extremely simplistic scenarios as a result of intrinsic mathematical properties of spatial data. This does not mean that we believe human demographic history to be simple or that human populations have not engaged in expansions and large-scale migrations at various points in history. However, it does mean that a gradient or wave in a principal components analysis should not be regarded as a footprint specific to such events.

In our experience, much of the controversy regarding inferences of population expansions centers around the inference of a Neolithic expansion in Europe. It seems worth emphasizing, then, that our work does not imply that no Neolithic expansion took place. A thorough examination of this issue requires, as Cavalli-Sforza strongly championed, a synthesis of different types of data from multiple sources. One major interest of ours in writing the paper, and an ongoing interest, is how spatial patterns in genetic variation can best serve as one such source of historical insight.

On a personal note, we regret that our response to Cavalli-Sforza's review of our paper was not shared with him [by the editors of Nature Genetics--Editor] and that he did not appreciate the various changes and improvements to our paper that took place in response to his review.

Literature Cited

Francois, O., M. Currat, N. Ray et al. 2010. Principal component analysis under population genetic models of range expansions and admixture. Mol. Biol. Evol. 27:1257-1268; doi:10.1093/ molbev/msq010.

McVean, G. 2009. A genealogical interpretation of principal components analysis. PLoS Genet. 5(10):e1000686; doi:10.1371/journal.pgen.1000686.

Novembre, J., and M. Stephens. 2008. Interpreting principal components analyses of spatial population genetic variation. Nat. Genet. 40:646-649.

NYT: If Smart Is the Norm, Stupidity Gets More Interesting

DAVID DOBBS

Few of us are as smart as we’d like to be. You’re sharper than Jim (maybe) but dull next to Jane. Human intelligence varies. And this matters, because smarter people generally earn more money, enjoy better health, raise smarter children, feel happier and, just to rub it in, live longer as well.

But where does intelligence come from? How is it built? Researchers have tried hard to find the answer in our genes. With the rise of inexpensive genome sequencing, they’ve analyzed the genomes of thousands of people, looking for gene variants that clearly affect intelligence, and have found a grand total of two.

One determines the risk of Alzheimer’s and affects I.Q. only late in life; the other seems to build a bigger brain, but on average it raises I.Q. by all of 1.29 points.

Interview with Cavalli-Sforza

Selon Luca Cavalli-Sforza, généticien et, surtout, auteur de célèbres études sur la diffusion des langues et des techniques, l'évolution culturelle ne s'explique pas autrement que celle des organisme vivants. Mutation, dérive et sélection : telles sont les nouvelles clés de l'aventure des cultures humaines.

Dans l'introduction de votre livre, prenant le contre-pied des traditions scientifiques qui considèrent que l'évolution biologique et l'histoire culturelle sont indépendantes, vous avancez que la « théorie de l'évolution biologique peut être étendue à la culture ». Que voulez-vous dire par là ?
La théorie génétique de l'évolution biologique reconnaît quatre facteurs d'évolution biologique : la mutation, qui est la source de toutes les diversités entre individus et espèces et se transmet par hérédité ; la sélection naturelle, découverte simultanée de Charles Darwin et de Alfred Wallace, qui trie les mutations en fonction de leur succès reproductif ; la dérive génétique, ou hasard généralisé, qui est la conséquence de deux faits : d'abord, les mutations sont rares et apparaissent au hasard ; ensuite, le nombre d'enfants engendrés par chaque parent est très variable en raison d'une multitude de facteurs qui ne sont pas sous notre contrôle et ne peuvent être abordés que par des méthodes statistiques. Tout cela nous autorise à dire qu'une partie du changement évolutif est le produit du hasard. Enfin, le quatrième facteur est la migration des individus et des populations, qui opère des mélanges génétiques.

Ces phénomènes sont tous liés à une propriété centrale du vivant : les organismes sont capables de reproduire des individus extrêmement semblables à eux-mêmes, et c'est ce qu'on appelle aussi la capacité d'autoreproduction. Naturellement, tout cela est possible seulement dans un environnement qui offre tous les matériaux et les conditions physiques nécessaires pour la reproduction des êtres vivants.

What is agriculture?

1. Sédentarisme 
2. Domestication des animaux et des plantes 
3. Preparation du sol 
4. Croisements sélectifs 
5. Propagation 
6. Protection des céréales 
7. Récolte 
8. Stockage 
9. Esclavage
10. Malnutrition, diète monotone
11. Zoonoses
12. Maladies infectieuses

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 today's modern populations, so any haplotypes that went extinct are not represented.  Had they used a sample from say 100 or 1000 years ago, the picture could be quite different, potentially pushing the LCA estimate back. 

That's the nature of the beast with classic mtDNA analyses. This is why recent breakthroughs in using fossil DNA is so exciting. Seeing snapshots in the past will help correct the bias inherent in using a sample from today's existing haplotypes.

Mungo Man

What is this H. sapiens doing in Australia so early (68-40ky), and why isn't his mtDNA human?  MYSTERIOUS.

Test Tajima (Tajima's D)

Test de neutralité sélective basé sur la diversité moléculaire des échantillons.  Si marqueurs sont neutres, la difference est 0.  Si D ≠ 0, there is selection.  

D < 0, excès de variant rares

D > 0, déficit de variant rares

Bamshad et al.

Why are humans so homogenous?

Origine récente?
Haut niveau d'échanges génétiques entre populations? (Gene flow)

Mais pourquoi certains marqueurs montrent des fréquences différentes?  Ils étaient selectionnés?
Quel est l'effet de la sélection?
Quelle est la valeur Fst attendue si les marqueurs sont neutre?

Π = average number of pairwise differences between two individuals.

STRUCTURE software

Pritchard et al 2000

• On assume qu'un certain nombre K de groupes sont présents. 
• On assume que chaque groupe est caractérisé par un groupe de fréquences d'alleles à chaque locus.

Degioanni is very skeptical of this software that is very à la mode these days. Results are too dependant on a researchers choice of groups.

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.

An unintuitive truth

Human genetic diversity is always more pronounced within a given group than between given groups.

References:
Lewontin 1972
Barbujani et al. 1997
Jorde et al. 2000
Tomualdi et al. 2002

Species Tree vs. Gene Tree

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.)

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.

Qu'est-ce que c'est qu'une population ?

"C'est un joker." - Mme Degioanni
On parle souvent de:

• Proximité géographique 
• Même langue 
• Partage réligion, culture, ethnie (moins de probabilité de mariages intergroupe)

2011, year of 1000 genomes

Exciting stuff. http://www.1000genomes.org/

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.

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).

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.

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.

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.

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).

Francis Galton

This cousin of Darwin looks like a fascinating guy. Should look at his life.

 http://en.wikipedia.org/wiki/Francis_Galton#Heredity_and_eugenics

 Probably should find something better that wikipedia...

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.

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.

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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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 for now but I may want to keep it private once things get 'serious'.  If you know me and want to make sure you have access send me an email.  perrine dot ad at gmail dot com.

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.