First evidence for cheese making at 8000 BP in northern Europe

http://www.nature.com.ezproxy.lib.utexas.edu/nature/journal/vaop/ncurrent/full/nature11698.html

Mmmmmmm.... cheeeese.

Just in case you don't know what cheese is:

http://www.sciencedirect.com.ezproxy.lib.utexas.edu/science/article/pii/S096098221200659

cultural skull modification

How did prehistoric man survive trepanation? Evidence of healed bone after trepanation fascinates us, since the first successful trepanation in history is from 1891. How did they do it?

I'm a bad student

Stries d'arret de croisance. Seulement visibles sur l'os spongieux.

Should be present on all long bones i.e. more or less symmetric lines on tibia and femur physial region

indicateur de stress, mais étiologies variées et mal connues

Mal de Pott = seul indicateur certain de TB vertebral

Tréponématose
=syphilis
=pian

TB
=typique
=LOMAT

Bone Tumors

métastases sont exceptionelles avant 40

ostéosarcome

Resnick, Diagnosis of Bone and Joint Disorders

Diagnose

• Age
• Localisation des lesions
• Nombre de lesions
• Aspect macroscopique et radiologique
• Est-ce un trama? infection?

périoste répare des fractures

pour mille métastases il y a un tumor malignant primaire

Bone fractures

How bone heals:

http://www.medscape.com/viewarticle/405699_6

trépanation

marqueurs osseux d'activité

enthèse

bursites

bourse séreuse empêche contact direct os et tendon

He sucks so bad at English. Half of the time I don't even realize he's using English words. He just said Bottom's Weaver.

Why do French people insist on saying anglo-saxon this anglo-saxon that. Wouldn't it be easier to just say 'anglais' ? I'm sure 90% of the time he's applying anglo-saxon to a word that was never used between 550 and 1066.

So it turns out that when analyzing bone pathologies due to various activities it is best to take into account the archeological context. Fascinating please tell me more.

Sometimes hard to tell whether or not the bone has changed because of repeated use or just the violence of a few events.

SNS spondylarthropathies
AS spondylarthrite ankylosante
PR polyarthrite rhumatoide

polyarthrite rhumatoide
-inflammation chronique
--articulations synoviales
--tissus de conjonction
-cause inconue
--autoimmune (hlr dr4 dw4
--liée à la présence d'IG anormale
--facteurs environnementaux
-maladie de femme (3/4 des cas)
-20-50ans
-1-2% de la pop

most common in hands, but can affect all joints

origine dans le nouveau monde?

HLA B27 associé a 50% RhPS à 95% pour SPA

spondylarthrite ankylosante
-homme jeune 15-30ans
connu depuis néolithique

basically the entire spinal column fuses and transverse condyles go batshit crazy. Nasty shit.

Ostéoporose

ostéoporose idiopathique

type 1 femme prost ménauposée
type 2 femme et homme

perte d'os trabéculaire et corticale

ossification des ligaments du rachis = "coulée de bougie"

hyperostose diffuses = ossification enthèses insertion ligamentaires "exubérant"

l. exuberare « abonder, déborder »

la cause est inconnue

Diffuse Idiopathic Skeletal Hyperostosis
(DISH or Forestier's Disease)

Diffuse idiopathic skeletal hyperostosis (DISH) is considered a form of degenerative arthritis or osteoarthritis. However, DISH is characterized by unique, flowing calcification along the sides of the contiguous vertebrae of the spine. And, very unlike typical degenerative arthritis, it's also commonly associated with inflammation (tendinitis) and calcification of tendons at their attachments points to bone. This can lead to the formation of bone spurs, such as heel spurs. In fact, heel spurs are common among individuals with DISH. DISH has also been called Forestier's disease.

os "coulée" est 'deux fois plus costaud' que l'os corticale normale. hypertose reste alors que le rachis est mangé

Arthrose

arthrose = pas de standards pour parler de la sévérité
détérioration/érosion du cartilage plutôt après 45 ans, 80% des cas après 70ans

primitive = idiopathique
secondaire = trauma activités infection inflammation

causes = age, genetique, surpoids, autres...

ostéophytose périarticulaire 'lipping'

= too much pressure on bad articulation = l'organisme essaie d'augmenter la surface de contacte pour reduire la pression sur la zone de contacte.

pitting = microporosités

éburnation = polissage ivory-like

sillons

remodelage de la surface articulaire

L'ankylose (du grec αγκυλος, tordu, de travers) est une fixation et une immobilité d'une articulation, ayant pour origine une blessure ou une maladie.

stade ultime de l'arthrose = fusion des os

Tattersall 2000

Harking back to Weidenreich 13 and his belief that each of today’s human “races” has roots deep in time (“Java Man” having given rise to modern aboriginal Australians, for example, and “Peking Man” to modern Chinese), multiregional continuity in its most recent incarnation claims that all evolutionary developments in the hominid line subsequent to Homo habilis (whatever that is) have taken place within the single species Homo sapiens.

p.4

Tattersall I. (2000). Paleoanthropology : the last half-century. Evolutionary Anthropology 9(1): 2-16.

The emboldened text is a weasley way to set up a straw-man. Nobody thinks that, as it implies that they evolved seperately.

Paléodemographie

"La restitution des structures par âges et par sexes à partir de l’étude anthropologique des cimetières." -Masset 1990

Intégration via profil paléodemographique
-Représentativité?

H. sapiens and H. neanderthalensis

Evolution in the Genus Homo
Annual Review of Ecology, Evolution, and Systematics
Vol. 42: 47-69 (Volume publication date December 2011)
First published online as a Review in Advance on August 11, 2011
DOI: 10.1146/annurev-ecolsys-102209-144653

There is a long-standing debate about whether H. sapiens arose in Africa and then migrated across the globe, replacing any and all premodern Homo populations, or whether these various migrations of modern humans engaged in significant levels (i.e., detectable genetically or morphologically) of interbreeding with the preexisting premodern Homo populations (e.g., Relethford 2001, Stringer 2002). The multiregional continuity hypothesis argues that once H. sapiens left Africa, significant gene flow took place between them and the hominins they encountered (Wolpoff et al. 2000) and that, moreover, this gene flow influenced the nature of regional variations in morphology seen among extant populations of H. sapiens. The strong version of the recent out-of-Africa model also posits that H. sapiens arose in Africa, but it suggests that no significant gene flow took place between them and the hominins they encountered beyond Africa. In the past two decades most of the genetic evidence has favored the recent out-of-Africa hypothesis. A seminal study from Allan Wilson's lab (Cann et al. 1987) suggested that the common ancestor of all (maternally inherited) modern mitochondrial DNA (mtDNA) lived in Africa approximately 200 ka, and studies investigating the evolutionary history of the paternally inherited Y chromosome suggested that the last common ancestor of modern humans lived well within the past 100 ka (Karafet et al. 2008, Thomson et al. 2000). Investigations of single nucleotide polymorphisms (SNPs) and autosomal microsatellites indicate that genetic diversity is highest in Africa and steadily decreases as the distance from the continent increases (Prugnolle et al. 2005, Ramachandran et al. 2005), and prior to 2010 research on mtDNA had not revealed any evidence of admixture (Briggs et al. 2009, Jakobsson et al. 2008, Krings et al. 1997, Serre et al. 2004, Tishkoff et al. 2009).

This perspective was challenged in 2010 with the publication of the draft sequence of the nuclear genome reconstructed from DNA recovered from three H. neanderthalensis fossils from Vindija Cave in Croatia (Green et al. 2010). This study also found that all of the H. sapiens DNA samples tested (with the notable exception of those from Africa) contained between 1% and 4% of the distinctive DNA sequence recovered from Neanderthal fossils. By identifying and analyzing SNPs between the two groups of genomes, the researchers discovered that Neanderthal DNA is significantly closer to non-African modern human DNA than it is to African DNA, and statistical analysis of the gene flow led the researchers to argue that the gene flow was from Neanderthals to the ancestors of non-African modern humans. This evidence suggests that once early anatomically modern humans left Africa, some interbreeding did occur with the indigenous groups of Neanderthals they encountered, conceivably in the Middle East before modern humans moved into Eurasia and prior to the divergence of the European, East Asian, and Papuan groups. These new data are consistent with the assimilation hypothesis espoused by Fred Smith (Smith 1985; Smith et al. 1989, 2005; Trinkaus & Smith 1985). As new evidence accumulates, the theory of modern human origins will most likely move away from a simple recent out-of-Africa explanation to a more intricate and sophisticated account in which several different groups of ancestors lived in pockets around the globe.

The last Homo heidelbergensis and their descendants the Neandertals: Orgnac 3, Lazaret and Zafarraya dating

http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.crpv.2011.06.002

This article presents the dating results recently obtained on three archaeological sites in Europe. At Orgnac 3 (Ardèche, France) from where the last Homo heidelbergensis fossils are associated with the first evidence of levallois technique, two speleothem formations from the 5b–6–7^th layers were U-Th dated with MC-ICPMS, giving an age range of 319–255 ka (2σ) (MIS 8–9), while the volcanic ash-bearing second layer was dated by ⁴⁰Ar/³⁹Ar, obtaining a preliminary date of 308.2 ± 6.8 ka (2σ). The combined ESR/U-Th dating of red deer enamel teeth from Lazaret cave (Alpes-Maritimes, France) attributed ages of 120–190 ka to the Acheulean and pre-Mousterian layers (MIS 6), which is in agreement with previous TIMS U-Th dates between 108 and 44 ka on calcite samples from the overlying TRA trench (MIS 5, 4, 3). At Zafarraya (Andalousie, Espagne), a number of ¹⁴C measurements on charcoal samples as well as combined ESR/U-Th dates on Capra and Equus dental enamels assigned the Mousterian artefacts and neandertalian fossils-bearing deposits an age interval between 42 and 34 ka (MIS 3).

Dating Homo heidelbergensis at Mauer, Germany

Mauer – the type site of Homo heidelbergensis: palaeoenvironment and age

http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.quascirev.2010.01.013

The mandible of Homo heidelbergensis was found 1907 in the sand pit Grafenrain at Mauer in coarse fluvial sands 24 m below the surface, deposited in a former course of the Neckar River. These ‘Mauer sands’ are overlain by a series of glacial-climate loess deposits with intercalated interglacial palaeosols, which can be correlated with Quaternary climate history, thus indicating an early Middle Pleistocene age for H. heidelbergensis. The ‘Mauer sands’ are famous for their rather rich mammal fauna, which clearly indicates interglacial climate conditions. The faunal evidence – in particular the micromammals – place the ‘Mauer sands’ into MIS 15 or MIS 13 although most stratigraphic arguments favour correlation to MIS 15 and therefore to an age of ca 600 ka.

Radiometric dating of the type-site for Homo heidelbergensis at Mauer, Germany

doi:  10.1073/pnas.1012722107

Here we show that two independent techniques, the combined electron spin resonance/U-series method used with mammal teeth and infrared radiofluorescence applied to sand grains, date the type-site of Homo heidelbergensis at Mauer to 609 ± 40 ka. This result demonstrates that the mandible is the oldest hominin fossil reported to date from central and northern Europe and raises questions concerning the phyletic relationship of Homo heidelbergensis to more ancient populations documented from southern Europe and in Africa.

Neanderthals versus Modern Humans: Evidence for Resource Competition from Isotopic Modelling

doi:10.4061/2011/689315

Virginie Fabre, Silvana Condemi, Anna Degioanni and Estelle Herrscher

During later MOIS3, in Europe two populations were present, autochthonous Neanderthals and modern humans. Ecological competition between these two populations has often been evoked but never demonstrated. Our aim is to establish whether resource competition occurred. In this paper, in order to examine the possibility of ecological competition between these two populations, 599 isotopic data were subjected to rigorous statistical treatment and analysis through mixing models. The aim of this paper was to compare dietary strategies of Neanderthals and modern humans over time. Our conclusions suggest that Neanderthals and modern humans shared dietary habits in the particular environmental context of MOIS3 characterised in Europe by climatic deterioration. In this environmental context, the resource competition between Neanderthals and modern humans may have accelerated the disappearance of the Neanderthal population.

Décrire un squelette

1. diagnostic du site - est-ce que ça vaut le coût
2. sondage de 7-10%
3. fouille
4. etude - rapport finale d'operation (RFO)
5. publication

dépot = terme neutre pour des restes
sépulture = geste funéraire

adduction = membre contre
abduction = membre éloigné

extension/flexion

mains

• supination = radius et ulna parallèles
• pronation = radius et ulna croisés

connexion

• stricte
• lâche - légère déconnexion
• déplacée - déconnexion totale

espace colmaté = os restent en place, legères déconnexions
espace vide = plus de déconnexions; colmatage differé souvent
espace mixte = who cares

contraintes transversales/longitudinales
=vêtements, ficelle, cercueil trop étroit/court

effet de paroi = how a wall changed the placement of bones

linceuls=enveloppes textiles enroulées cousues ou épinglées = "shroud"
bas moyen âge
= pieds en extension ou "en danseuse"
=contraintes transversales

vêtements= un peu comme linceuls mais l'effet est plus localisé
=conservation du volume costal
=micro espaces vides où colmatés

1. décrire
2. analyser
3. interpréter

"de haut en bas" = commence pas par les pieds

"Effective" population size

Bocquet-Appel-Recent_Advances_in_Palaeodemography-9781402064234

Chapter 1 by J Hawks.

In the absence of selection, allele frequencies vary as a stochastic process. The parameters influencing this process are themselves demographic: population size and mating pattern. Ultimately, the rate of evolution of a population must be constrained by these parameters. This means that the observable genetic characteristics of populations are to some extent natural estimators of demographic characteristics. The relationship between the demographic parameters of a population and its genetic characteristics may in some cases be approximated by a single parameter: the “effective population size.” Effective population size refers the demographic complexity of some real population to the simplicity of some ideal population — in other words, it is a measure of the extent to which a natural population corresponds to some theoretical population model.

...

The model-dependence of effective population size is rarely considered in analyses of molecular data. Ewens (2004) gives a good account of the problem:

Except in simple cases, the concept [of effective population size] is not directly related to the actual size of the population. For example, a population might have an actual size of 200 but, because of a distorted sex ratio, have an effective population size of only 25. This implies that some characteristic of the model describing this population, for example a leading eigenvalue, has the same numerical value as that of a Wright- Fisher model with a population size of 25. It would be more indicative of the concept if the adjective “effective” were replaced by “in some given respect Wright-Fisher model equivalent.” Misinterpretations of effective population size calculations frequently follow from a misunderstanding of this fact (Ewens, 2004, 37–38).

...

The utility of effective population size comes from the fact that it concatenates many separate stochastic phenomena into a single parameter. As an example, a gene frequency is a single value, with a single degree of freedom. It is therefore sufficient to estimate only a single parameter. This approach obviously runs into trouble when more than one stochastic factor varies in the population.

Climate and the demise of the Neandertals

From "Time for the Middle to Upper Paleolithic transition in Europe"

by Wil Roebroeks; Faculty of Archaeology, Leiden University, P.O. Box 9515, 2300RA Leiden, The Netherlands

http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.jhevol.2008.08.008

Ice core studies have taught us that the time span of Middle and Upper Paleolithic was punctuated by rapid climatic transitions on timescales of centuries or even decades (Adams et al., 1999). Vegetation responses to such rapid fluctuations must have varied on small scales among sites and regions, according to the differences in initial environmental conditions, local and regional species pool, and the climate events concerned, and the same applies to faunal elements, including Neandertals and modern humans. Various authors have suggested that such climatic fluctuations were instrumental in the disappearance of the Neandertals, one of the latest climatic hypotheses having been presented by Mellars (2006) who suggests that their final demise may have coincided with the sudden onset of the much colder and drier conditions of the Heinrich Event 4. However, extremes of temperatures reached during this period were not exceptional, and had been experienced in earlier glacial-interglacial cycles survived by Neandertals, where the extremes of OIS 4 and 6 led to abandonment of the northern parts of Europe, as did the most extreme parts of OIS 2, for modern humans (e.g., Roebroeks et al., 1992). Recently Tzedakis et al. (2007) have also made the point that climate change was probably not the key factor here, as before 28 ka ¹⁴C BP (i.e., according to most of the papers in this volume long after their demise) Neandertals would have faced a pattern of climatic fluctuations that they had been surviving for at least 100,000 years already.

The consequences of Middle Paleolithic diets on pregnant Neanderthal women

http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.quaint.2011.07.002

The authors critique various assumptions made by others about Neanderthal lifeways by showing that Neanderthal births would be impossible under these conditions.

3. Lessons learned
There are a large number of potential lessons to be learned here. Principle among them is that researchers should consider the possibility that previous models have, to one degree or another:

1. Under-appreciated the Neanderthals’ abilities to regulate body temperature;
2. Under-appreciated the Neanderthals’ abilities to efficiently hunt terrestrial animals;
3. Under-appreciated the degree of sexual division of labor within Neanderthal groups generally, and for pregnant and lactating women, specifically;
4. Under-appreciated the amount of non-mammal foods eaten by Neanderthals, such as fish, shellfish, insects, birds and eggs;
5. Under-appreciated the amount of plant foods eaten by Neanderthals;
6. Under-appreciated the differences in metabolic processing of essential nutrients such as protein between Neanderthals and modern humans;
7. Under-appreciated the role of micronutrient deficiencies to Neanderthal extinction;
8. Exaggerated the degree of mobility in the average Neanderthal group compared to modern hunting-gathering societies; and
9. Exaggerated the degree of close-encounter, dangerous hunting techniques that Neanderthal women participated in.

Taille minimale de la population néanderthalienne: modélisation de son extinction

Néandertal

• histoire de la population
• hypothèses sur son extinction
• caractéristiques démographiques
• son environnement (climats)

Démographie

   Paramètres démographiques : données connues et effet sur le devenir de la population

• chez les chasseur cueilleurs actuels
• chez les premiers sapiens
• chez Néandertal  

  taille

  génération time

  sex-ratio

  Nombre d’enfants moyen par femme (à la naissance, qui atteignent l’âge adulte)

  Mono/polygamie

  Endo/exo mariages

parametres sont des intervales pris dans la litterature

Extinction

 Causes de l’extinction des espèces animales 

 (sans intervention de l’homme = sans valeur marchande) :

• changement climatiques
• changements ressources
• … épidémies ???
• fractionnement de la population, …

Modélisation exciton

 Bases de matlab

Transitions or turnovers?

http://dx.doi.org.ezproxy.lib.utexas.edu/10.1016/j.quascirev.2008.08.015

John J. Shea (2008)

Abstract

The East Mediterranean Levant is a focal point for debate about evolutionary continuity among Late Pleistocene hominin populations. Changes in the Levantine Middle and Upper Palaeolithic archaeological records are almost invariably described in terms of adaptive shifts and behavioural transitions, rather than as changes in hominin populations. This paper examines evidence for hominin evolutionary continuity in the Levant between 130 and 25 ka. Two inflection points, one within the Middle Palaeolithic ca 75 ka and the other between the Middle and Upper Palaeolithic ca 45 ka, are examined in light of recently-discovered evidence for rapid climate change and environmental deterioration. It is proposed that both periods mark regional extinctions and turnovers of hominin populations. The first of these occurred among early Homo sapiens, the second among Neanderthals. Each event was followed by dispersal of hominin populations into the Levant from adjacent regions. Differences in Middle vs. Upper Palaeolithic Homo sapiens’ long-term success in the Levant may reflect recently-evolved strategies for coping with rapid climate change and with colder arid habitats.

Classic demographic models

The classic population growth model from Malthus (1798):

The carrying capacity model by Verhulst (1838):

r for rate, K for Karrying Kapacity?

Neander Homo transition citation

Processus démographique et culturel, la « transition » désigne globalement la période allant de l'arrivée des Homo sapiens en Europe à la disparition des Néandertaliens. Elle regroupe donc deux volets, d'une part la disparition des Néandertaliens et les processus qui y ont mené; d'autre part l'apparition des Hommes modernes en Europe et avec eux une culture et une industrie qui leur sont propres. Dès lors, deux conceptions s'opposent a transition a-t-elle été un simple remplacement sans contact d'une espace par une autre (Mellars 1992; Stringer 1988, 1989, 2011; Stringer et Gamble 1994; Stringer et Andrews 1988; Stringer et McKie 1998; Stringer, Barton, et Finlayson 2000) ou bien une période d'échanges (Hawks et Wolpoff 2001; Thorne et Wolpoff 1981; Wolpoff 1992, 1994; Wolpoff et Caspari 2011; Wolpoff et al. 2001) comme le supposent plusieurs auteurs sur la base (i) de certains fossiles (Dobos 2010; Frayer 1992; Smith 1991; Smith, Falsetti, et Donnelly 1989; Thorne et Wolpoff 1981; Trinkaus 2011a; Trinkaus et al. 2003; Wolpoff et al. 1994; Zilhão et Trinkaus 2002), (ii) de certaines études génétiques (Abi-Rached et al. 2011; Green, Krause, et al. 2010 ; Plagnol et Wall 2006; Wall et al. 2009), (iii) de certaines interstratifications (Bordes 2003; Gravina, Mellars, et de l'étude 17 Ramsey 2005 ; Mellars, Gravina, et Bronk Ramsey 2007; Zilhão et al. 2007) ou encore (iiii) de certaines industries lithiques (d'Errico, Zilhão, et al Hublin, Spoor, et al. 1996; White 2001)? Cette question semble fondamentale pour comprendre les pressions exercées par l'arrivée des Homo sapiens en Europe mais elle est cependant très soumise aux datations proposées concernant les derniers Néandertaliens comme les premiers Homo sapiens (Jöris et Street 2008; Jöris et al. 2011).

-Virginie Fabre, Thèse p 16-17

keep the model simple

...trop complexifier un modèle revient à l'orienter. En effet, un modèle très complexe a de grandes chances de conclure par ce qu'on a voulu lui faire dire ; on ne sait alors pas si cela est dû à la construction du modèle lui-même ou aux valeurs attribuées aux différents paramètres. Au contraire, si avec un modèle simple on obtient une représentation cohérente avec l'hypothèse de dэpart, on pourra alors attribuer cette conclusion aux valeurs de paramètres qu'on aura choisies.

-Virginie Fabre, Thèse p 14

Inferring ethnic origin by means of an STR profile

By Lowe et al.

http://dx.doi.org/10.1016/S0379-0738(00)00387-X

They seem to be saying that putting people in arbitrary categories and then trying to guess which category they fit in based on their DNA does not work very well.

LOL Middle Eastern. That's what you get for being at the crossroads of humanity.

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

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 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.