Wednesday, December 26, 2012

Haven't we had this conversation before?

Update December 26th, 2012: The Mermaid's Tale also covers this story.

Isn't it supposed be Boxing Day?  I guess I'll always be a stranger in a strange land.

Joe Pickrell is tweeting that "researchers" at the University of Connecticut are going to sequence the genome of Adam Lanza to "discover" biological clues to extreme violence.  A journalist at the New York Times has actually written an article about it and it has been published in the "Science" section of yesterday's paper.


People have been studying psychopathy for years. For example, Robert Hare has devoted his life to its study.  Other researchers, too numerous to mention, have soldiered on, bravely looking at the interplay between drugs, illicit and otherwise, alcohol, stress and mental health.

I have been listening to the discussion, off and on, on NPR, to the public reaction to the Newtown gunman.  Once again, we discuss the cause:  the media, gun control, and mental health.

The mental health discussion caught my attention.  One women mentioned something to the effect that approximately one percent of the population struggles with schizophrenia, which is approximately the case.  She then made the statement that she had never met anyone with schizophrenia and proceeded to discuss schizophrenia in very simplistic terms, as if to say that if we could just round up all the people struggling with schizophrenia, put them in group homes, then we'd all be A-OK.  No need at all to do something about those assault weapons.  Finally, someone stepped in to say that many people who have schizophrenia have successful lives and are, in fact, heroic in their struggle with the disease.

Still, I found the conversation a reflection of our profound ignorance of mental health issues.

Moreover, the discussions about "gun control" are, in my opinion, ridiculous.  It will be very unAmerican of me to say so, but as far as I am concerned, there are a few reasons why you might want to have a rifle:  you need to get rid of the crows; maybe you're hiking in grizzly bear territory (outside of a national, state or provincial park); you're a hunter . . . but a .22 would probably do the job, maybe a little bear spray .  .  . if you wanted more, you could try a bow.

However, beyond an arms race, there is no place for automatic assault weapons in our cities.  Oh, right, the Second Amendment.  Been to any federal, state or city office lately?  They're defended to the teeth.  It's always nice to have to state your case to an official through bullet proof glass.  Makes for really cozy communication.

As to the "researchers" at the University of Connecticut, I am sympathetic to the plight of the many families.  I am sure they are desperate for answers.  However, the genome of the Newtown gunman will not provide any.  That is not to say that genomics will not eventually tell us something about schizophrenia, psychopathy and other diseases of the mind.

I am profoundly sad to say that we will likely be having this conversation again.

Saturday, December 22, 2012

Related Blogs sidebar moved up

I've moved the list of blogs I follow up near to the top of the right sidebar.  There's some great holiday reading there.  Thanks to all the bloggers for their terrific efforts ... makes me feel like all those years toiling away in communication semiconductor land were worth it.

Sunday, December 16, 2012

Seeing Ghosts

Six rainbows across Norway (link).  
While rainbows are often associated with magic and pots of gold, they are actually caused by refraction and reflection. An analogy occurs in population sampling, where diverged and remerged sub populations can cause the effect of seeing "ghosts", or images, in a sampled population.  This can cause several artefacts.  One possible artefact is the appearance of migration between nonadjacent populations. Another artefact can be that the apparent level of migration can be more than two orders of magnitude smaller than the actual level, depending on the number of waves of migration allowed by the model.

Seeing ghosts: the effect of unsampled populations on
migration rates estimated for sampled populations

Montgomery Slatkin
Department of Integrative Biology, University of California, Berkeley, CA 94720–3140, USA
29 September 2004

In 2004, the term ‘ghost population’ was introduced to summarize the effect of unsampled subpopulations that exchange migrants with other subpopulations that have been sampled.  Estimated long-term migration rates among populations sampled will be affected by ghost populations. Although it would be convenient to be able to define an apparent migration matrix among sampled populations that incorporate the exchange of migrants with ghost populations, no such matrix can be defined in a way that predicts all features of the coalescent process for the true migration matrix. This paper shows that if the underlying migration matrix is symmetric, it is possible to define an apparent migration matrix among sampled subpopulations that predicts the same within-population and between-population homozygosities among sampled populations as is predicted by the true migration matrix. Application of this method shows that there is no simple relationship between true and apparent migration rates, nor is there a way to place an upper bound on the effect of ghost populations.  In general, ghost populations can create the appearance of migration between subpopulations that do not actually exchange migrants. Comparison with published results from the application of the program, MIGRATE, shows that the apparent migration rates inferred with that program in a three subpopulation model differ from those based on pairwise homozygosities.  The apparent migration matrix determined by the method described in this paper probably represents the upper bound on the effect of ghost populations.migrate, shows that the apparent migration rates inferred with that program in a three- subpopulation model differ from those based on pairwise homozygosities.  The apparent migration matrix determined by the method described in this paper probably represents the upper bound on the effect of ghost populations.

Wednesday, December 12, 2012

Efficient moment-based inference of admixture parameters and sources of gene flow

Luis, you have to check out this new MixMapper paper.
The method employs a concept called scaffolding within a moment method.

There's an interesting discussion about the employment of f2 distances versus genetic drift D statistics, which I'm sure, you, Luis, will want to read. (See "Expressing branch lengths in drift units."). There's also a good discussion of ascertainment bias in the "Data Set" section.

Also, unsurprisingly, it appears that it is actually quite difficult to find populations that have little admixture: "Despite the focus of the HGDP on isolated populations, most of the 53 HGDP groups exhibit signs of admixture detectable by the 3-population test, as has been noted previously (Patterson et al., 2012)." And in the end, these researchers can find only 20 populations that are potentially unadmixed.

Regarding Europeans, there are virtually no unadmixed populations. But, on the bright side, Luis, apparently among Sardinians and Basques, there are 20-25% “ancient northern Eurasian” allele frequencies.

Other very interesting results are that the Daur, Hezhen, Oroqen, and Yakut—are likely descended from admixtures between native North Asian populations and East Asian populations related to Japanese.

Also interesting: "we found that Han Chinese have an optimal placement as an approximately equal mixture of two ancestral East Asian populations, one related to modern Dai (likely more southerly) and one related to modern Japanese (likely more northerly), corroborating a previous finding of admixture in Han populations between northern and southern clusters in a large-scale analysis of East Asia (HUGO Pan-Asian SNP Consortium, 2009)."

And corroborating various mtDNA, y-DNA, ADMIXTURE results: "Mozabite, Bedouin, Palestinian, and Druze, in decreasing order of African ancestry, are all optimally represented as a mixture between an admixed western Eurasian population (not necessarily European) related to Sardinian and an African population (Table 3)." 

I have a friend who is a Berber who is proud of her partly African ancestry . . . she told me so, not even knowing anything about these genetic studies.

Oh, and check this out: "Orcadian to an ancestor of Americans." Score one for the "Across Atlantic Ice" hypothesis. I'll have to add Dennis' book to my book list.

Way to go, MIT!

Here's the paper:

Efficient moment-based inference of admixture parameters and sources of gene flow
Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson, and Bonnie Berger

"[We] introduce MixMapper, a new computational tool that fits admixture trees by solving systems of moment equations involving the pairwise distance statistic f2 (Reich et al., 2009; Patterson et al., 2012), which is the average squared allele frequency difference between two populations. The theoretical expectation of f2 can be calculated in terms of branch lengths and mixture fractions of an admixture tree and then compared to empirical data. MixMapper can be thought of as a generalization of the qpgraph package (Patterson et al., 2012), which takes as input genotype data, along with a proposed arrangement of admixed and unadmixed populations, and returns branch lengths and mixture fractions that produce the best fit to allele frequency moment statistics measured on the data. MixMapper, by contrast, performs the fitting in two stages, first constructing an unadmixed scaffold tree via neighbor-joining and then automatically optimizing the placement of admixed populations onto this initial tree. Thus, no topological relationships among populations need to be specified in advance.

"Our method is similar in spirit to the independently developed TreeMix method (Pickrell and Pritchard, 2012). Like MixMapper, TreeMix builds admixture trees from second moments of allele frequency divergences, although it does so via a composite likelihood maximization approach made tractable with a multivariate normal approximation. Procedurally, TreeMix is structured in a “top-down” fashion, whereby a full set of populations is initially fit as an unadmixed tree, and gene flow edges are added sequentially to account for the greatest errors in the fit (Pickrell and Pritchard, 2012). This format makes TreeMix well-suited to handling very large trees: the entire fitting process is automated and can include arbitrarily many admixture events simultaneously. In contrast, MixMapper is designed as an interactive tool to maximize flexibility and precision with a “bottom-up” approach, beginning with a carefully screened unadmixed scaffold tree to which admixed populations are added with best-fitting parameter solutions.

"We use MixMapper to model the ancestral relationships among 52 populations from the CEPH-Human Genome Diversity Cell Line Panel (HGDP) (Rosenberg et al., 2002; Li et al., 2008) using recently published data from a new, specially ascertained SNP array designed for population genetics applications (Keinan et al., 2007; Patterson et al., 2012). Previous studies of these populations have built simple phylogenetic trees (Li et al., 2008; Sir´en et al., 2011), identified a substantial number of admixed populations with likely ancestors (Patterson et al., 2012), and constructed a large-scale admixture tree (Pickrell and Pritchard, 2012). Here, we add an additional level of quantitative detail, obtaining best-fit admixture parameters and bootstrap error estimates for 30 HGDP populations, of which 20 are admixed. The results include, most notably, a significant admixture event in the history of all sampled European populations (Patterson et al., 2012), among them Sardinians and Basques."

Tuesday, December 11, 2012

First of His Tribe to this Fair Vale

                                            Loch Tay

'What aspect bore the man who roved or fled,
 First of his tribe to this fair vale -
 What hopes came with him?'
                                                            - Wordsworth -

Lindores Abbey and Its Burgh of Newburgh:  Their History and Annals
Alexander Laing, George Seton, Anthony Hamilton
Chapter 1:  Prehistoric, page 1.

It needs no evidence to prove that men who navigated our shores and rivers, in canoes hollowed out of single trees, had made but little progress in the constructive arts.  About sixty years ago two canoes, so made, were found in the bed of the Tay, opposite Lindores Abbey, the largest was twenty-eight feet long, and was quite entire. [1]

Another relic, telling of a condition and aspect of country widely different from the present, was discovered in the neighbourhood of Newburgh, in the end of the last century.  In draining what was called the Session Loch, at Mugdrum, the skull of a 'Great Ox,' Bos primigenius, or Urus, was found.  So huge was this skull, that even in that unscientific age the people flocked to see it.  Dr. Fleming, in his 'History of British Animals,' records that it was 27 1/2 inches in length. [2]  He says nothing of the kind of strata in which it was found, for geologists to build deductions on; but the cutting was carried through a great ridge of sand and river gravel, and the head was discovered at a considerable depth below the surface.  The Urus was little inferior to the elephant in size; one skull measured by Cuvier gave the proportions of the animal to be 12 feet in length and 6 1/2 in height.  Other skeletons have been found of much greater magnitude, affording indubitable evidence of the gigantic size of these wild denizens of the ancient Scottish forests.

The wild ox was a favourite object of the chase among our barbarian forefathers, and it was counted a great feat for a young man to bring home the horns of a Urus; they edged the finest of these horns with silver, and used them as drinking cups at great festive gatherings.[3]

[1]  These canoes were taken out of the Cruive bank opposite Lindores Abbey.  They were cut up and used for lintels in the erection of granaries at the west shore of Newburgh.  The largest canoe ever found in Scotland was 36 feet long and 4 feet wide - it was discovered at Carron - Wilson's Prehistoric Annals, Ed. 1851., p. 32.  Out of a list of about fifty ancient canoes, recorded as having been discovered in the west of Europe, only three are mentioned as larger than the largest found at Cruive bank.  There is one which was found in the Rhône, preserved in the museum at Lyons, 41 feet long. - Figuier's Primitive Man, p. 17.

[2]  Wilson's Prehistoric Annals, Ed. 1851., p. 23.

[3]  The representation of hunting scenes, on so many of the 'Sculptured Stones of Scotland', of which Mugdrum Cross is an instance, is enduring evidence of the importance of the chase among our forefathers.

Sunday, December 9, 2012

Sensor fusion in dynamical sytems

DREAM Seminar: Sensor fusion in dynamical systems - applications and research challenges
Seminar: DREAMS | December 11 | 4:10-5 p.m. | Soda Hall, Wozniak Lounge

Thomas Schön, Linköping University, Sweden
Electrical Engineering and Computer Sciences (EECS)

Abstract: Sensor fusion refers to the problem of computing state estimates using measurements from several different, often complementary, sensors. The strategy is explained and (perhaps more importantly) illustrated using four different industrial/research applications, very briefly introduced below. Guided partly by these applications we will highlight key directions for future research within the area of sensor fusion. Given that the number of available sensors is skyrocketing this technology is likely to become even more important in the future. The four applications are; 1. Real-time pose estimation and autonomous landing of the helicopter (using inertial sensors and a camera). 2. Pose estimation of a helicopter using an already existing map (a processed version of an aerial photograph of the operational area), inertial sensors and a camera. 3. Vehicle motion and road surface estimation (using inertial sensors, steering wheel sensor and an infrared camera). 4. Indoor pose estimation of a human body (using inertial sensors and ultra-wideband).

Bio: Thomas B. Schön is an Associate Professor with the Division of Automatic Control at Linköping University (Linköping, Sweden). He received the BSc degree in Business Administration and Economics in Jan. 2001, the MSc degree in Applied Physics and Electrical Engineering in Sep. 2001 and the PhD degree in Automatic Control in Feb. 2006, all from Linköping University. He has held visiting positions with the University of Cambridge (UK) and the University of Newcastle (Australia). He is a Senior member of the IEEE. He received the best teacher award at the Institute of Technology, Linköping University in 2009. Schön's main research interest is nonlinear inference problems, especially within the context of dynamical systems, solved using probabilistic methods. He is active within the fields of machine learning, signal processing and automatic control. He pursue both basic research and applied research, where the latter is typically carried out in collaboration with industry. More information about his research can be found from his home page:, 510-460-0280

Machine Understanding of Live Drum Performances

Dissertation Talk

Seminar: Departmental | December 10 | 11 a.m.-12 p.m. | 373 Soda Hall

Eric Battenberg
Electrical Engineering and Computer Sciences (EECS)

This talk will cover machine listening techniques for the automated real-time analysis of live drum performances. Onset detection, drum detection, beat tracking, and drum pattern analysis are combined into a system that provides rhythmic information useful in performance analysis, synchronization, and retrieval. The talk will focus on the drum detection and pattern analysis components of the the system.

For drum detection, a gamma mixture model is used to compute multiple spectral templates per drum onto which onset events can be decomposed using a technique based on non-negative matrix factorization. Unlike classification-based approaches to drum detection, this approach provides amplitude information which is invaluable in the analysis of rhythm.

The drum pattern analysis component uses a generatively pre-trained deep neural network in order to estimate high-level rhythmic information. The network is tested with beat alignment tasks, including downbeat detection, and significantly reduces alignment errors compared with a commonly used pattern correlation method.

Friday, December 7, 2012

Ghana, Shine Bright

Ghanaian President John Dramani Mahama addresses his nation on parliamentary elections today in Ghana.

". . . On such a historic occasion, it is worth reminding ourselves that whatever our political differences are, Ghana's stable institutions, democratic culture and the fortitude of its people have at each election, collectively risen to the occasion and made us proud as a nation."

"Fellow Ghanaians, an election is a contest between competing policy visions and must never set families, ethnic groups and religions against one another."

"Out of this contest of ideas shall emerge a President and leader whose character embodies and reflects our collective aspirations as a nation towards peace, unity and accelerated socio-economic development."

Thursday, December 6, 2012

UBC Green College: 2012/13 Seminars on the Evolution of Religion, Cooperation and Morality

University of British Columbia

The evolutionary and cognitive sciences have recently experienced an explosion of work on religion, cooperation, and morality, and in particular on their interrelationships. The emerging framework promises to re-energize these long-languishing topics by bringing a fully interdisciplinary approach to these topics that synthesizes the integrative rigor and precision of the evolutionary sciences with the depth of history and ethnography. The series will feature both leading researchers on these topics from Vancouver and experts from across the globe.

Wednesday, December 5, 2012

La majestueuse Méditerranée

Désert des Agriates, La Corse  (link)

de Un soir de veillee en Provence, par Jean-Michel Oprendek

"Et, à deux pas de là, intemporelle dans son bleu manteau d’écume, la majestueuse Méditerranée, la mare nostrum, ce berceau de peuples ardents, de cités, et de cultures, sculptait sans fin le sable, polissait les galets, au gré des vents du large qui, se mariant aux nôtres, portaient de mille rives tous les parfums de la vie, notre vie."

A Four Degree World is Catastrophic

Former Irish President Mary Robinson:
Climate Change the Biggest Human Rights Issue of Our Time


Amy Goodman of Democracy Now! interviews
Mary Robinson at the Climate Conference in DOHA

"Unfortunately, there is a lot of position taking.  It's almost like a trade negotiation, rather than an urgent meeting about staying below 2 degrees celsius, getting urgent commitments on emissions, on adaptation, on transfer of technologies and on finance.  It's really very frustrating for those who come hoping that the negotiators will take their responsibilities."

What are we waiting for, assembled in the forum?
      The barbarians are due here today.

Why isn’t anything going on in the senate?
Why are the senators sitting there without legislating?
      Because the barbarians are coming today.
      What’s the point of senators making laws now?
      Once the barbarians are here, they’ll do the legislating.

Why did our emperor get up so early,
and why is he sitting enthroned at the city’s main gate,
in state, wearing the crown?
      Because the barbarians are coming today
      and the emperor’s waiting to receive their leader.
      He’s even got a scroll to give him,
      loaded with titles, with imposing names.

Why have our two consuls and praetors come out today
wearing their embroidered, their scarlet togas?
Why have they put on bracelets with so many amethysts,
rings sparkling with magnificent emeralds?
Why are they carrying elegant canes
beautifully worked in silver and gold?
      Because the barbarians are coming today
      and things like that dazzle the barbarians.

Why don’t our distinguished orators turn up as usual
to make their speeches, say what they have to say?
      Because the barbarians are coming today
      and they’re bored by rhetoric and public speaking.

Why this sudden bewilderment, this confusion?
(How serious people’s faces have become.)
Why are the streets and squares emptying so rapidly,
everyone going home lost in thought?
      Because night has fallen and the barbarians haven't come.
      And some of our men just in from the border say
      there are no barbarians any longer.

Now what’s going to happen to us without barbarians?
Those people were a kind of solution.

Waiting for the Barbarians, C.P. Cavafy: Collected Poems
Translated by Edmund Keeley and Philip Sherrard
Translation Copyright © 1975, 1992 by Edmund Keeley and Philip Sherrard
Reproduced with permission of Princeton University Press

Monday, December 3, 2012

The Adaptive Landscape in Evolutionary Biology


"The 'Adaptive Landscape' has been a central concept in population genetics and evolutionary biology since this powerful metaphor was first formulated by Sewall Wright in 1932. Eighty years later, it has become a central framework in evolutionary quantitative genetics, selection studies in natural populations, and in studies of ecological speciation and adaptive radiations. Recently, the simple concept of adaptive landscapes in two dimensions (genes or traits) has been criticized and several new and more sophisticated versions of the original adaptive landscape evolutionary model have been developed in response. No published volume has yet critically discussed the past, present state, and future prospect of the adaptive landscape in evolutionary biology. This volume brings together prominent historians of science, philosophers, ecologists, and evolutionary biologists, with the aim of discussing the state of the art of the Adaptive Landscape from several different perspectives."

Amazon (link)

Wednesday, November 28, 2012

Understanding the Red Sea response to sea level

Fig. 1. Map of Red Sea bathymetry and surrounding topography. Note the small surface area of the Red Sea rainfall catchment marked by the bold dashed line.

This paper describes a novel method to study the sea level record over the last 20 thousand years using Red Sea oxygen isotope records.  The larger scope of the work is described at the University of Southampton Red Sea Project site.

Mark Siddall, David A. Smeed, Christoph Hemleben, Eelco J. Rohling, Ina Schmelzer, William R. Peltier, David A. Smeed, Christoph Hemleben, Eelco J. Rohling, Ina Schmelzer, William R. Peltier
Earth and Planetary Science Letters 225 (2004) 421– 434

Abstract:  "Here we outline a new, pragmatic methodology to derive relative sea-level estimates from central Red Sea oxygen isotope records based on a previously published model. In this paper, the methodology is described in detail, and it is shown that sealevel change is the dominant factor responsible for the recorded variability in Red Sea delta-O-18 (PDB) for sea level changes greater than 12 m. Variables such as temperature or net evaporation are shown to have relatively small effects on the oxygen isotope record. The modelled delta-O-18 (PDB) to sea level relationship is given in terms of a fifth order polynomial which may be used to describe relative sea level from central Red Sea oxygen isotope records. We show how established sea level records from fossil reef terraces for the last 20 kyr are successfully simulated from central Red Sea oxygen isotope records. We also examine the spatial variability of delta-O-18 (PDB) in the basin over the last 13 kyr."

Wednesday, November 21, 2012

Homo Spiritualis

Traditional people, and I think, the people of the paleolithic, had very probably two concepts which changed our vision of the world.  They are the concept of fluidity and the concept of permeability.  Fluidity means that the contiguities that we have:  man, woman, horse, tree, etc., can shift: a tree may speak, a man can get transformed into an animal and the other way around, given certain circumstances.  The concept of permeability is that there are no barriers, so to speak, between the world where we are and the world of the spirits . . . Humans have been described in many ways, right? and for a while, it was homo sapiens, and it's still homo sapiens:  the man who knows.  I don't think it's good definition at all . . . I would think homo spiritualis.   [From the film Cave of Forgotten Dreams.]

The Elephant in Pre-Colonial Ghana: Cultural and Economic Use Values
Kwame Osei Kwarteng
Journal of Philosophy and Culture, Vol. 3, No. 2 June 2006

Rites Associated with Elephant Hunting Among the Akan

". . . McCaskie notes that ‘the elephant was both unpredictably dangerous–spiritually as well as physically–and the largest single source of animal food in Asante forest.’[36] This made elephant hunting a perilous venture. The Akan of Ghana have the intrinsic belief that just like mankind, some animals, including the elephant, have spirits which survived the death of the animal. Rattray,[37] Nketia,[38] and Sekyi–Baidoo[39] state that hunters classified wild animals into two: those with spirit (sasammoa) and those without (mmoa). The former were deemed to have malevolent spirits which lived on after the animal had been killed by a hunter, and which could haunt its killer and cause calamity to befall him during subsequent hunting expeditions. Sasamoa include bongo, elephant, roan, waterbuck, duyker, black duyker, yellow–black duyker and antelope. Sekyi–Baidoo points out that, uniquely among these animals, the killing of the elephant reportedly brought honour to the hunter; for this reason, and in spite of the inherent risks, some hunters targeted the elephant, while others avoided it.[40] Clearly, the elephant enjoyed special status among animals with spirit (sasammoa), because it was considered as the king of the jungle. This is illustrated by Akan proverbs such as ‘Ǥsono akyiri nni aboa’ ( there is no wild animal besides elephant), ‘wodi Ǥsono akyiri a hasuo nka wo’ (if you follow the trail of elephant you would not be drenched by dew’etc.)

"Nketia has documented the necessary ritual preparations which fortified elephant hunters spiritually before they embarked on hunting expeditions. This process of fortification involved undergoing a ritual bath.[41]

"In the case of hunters celebrating their first elephant kill, a second ritual called abǤfuo,[42] ‘elephant funeral’, was performed to appease the spirit of the animal.[43] For experienced hunters, abǤfuo was not performed after every kill, since it was assumed that they possessed sufficient spiritual endowment to render them immune to any threat or danger posed by elephant spirits.[44]"

". . . Nketia states that a hunter who killed an elephant plucked a leaf and put it in his mouth and then went home to report the killing, after which he would undergo the necessary ritual bath, which made him acquire physical and spiritual power over animals.[47]

"He suggests that the rationale behind the elaborate ritual was that a hunter was assumed to have died and been resurrected after killing a dangerous animal like an elephant. The occasion was thus both joyous and sobering. The king of all animals, which was thought to have a spirit like a human being, had been killed and this was equated to homicide. Thus while celebrating the elephant kill, cleansing rites needed to be performed to prevent the spirit of the elephant from haunting the hunters.[48] In Kunso, these ‘elephant funeral’ rites commenced at 8.00 pm, and entailed the pouring of libation by the chief hunter to invoke the spirit of dead hunters for their permission and protection against any unforeseen events, which was followed by the singing of hunting songs, drumming and dancing.[49] Failure to appease the spirit of the dead elephant could result in one or another of the following disasters striking the hunter: ‘he would never again be able to kill an elephant; he would grow immensely fat and die; he would always want to sleep; he would eat all day and never be satisfied.’ Rattray explains that these disasters would be caused by the sasa, the spirit of the elephant.[50]"

"While elephant hunting was undoubtedly a hazardous venture, the importance of the elephant and its products in the performance of important social, cultural and economic functions in society meant that hunters risked their lives to hunt the pachyderm."


36. R.S. Rattray, Religion and Art in Ashanti, Oxford University press, Oxford, 1927, p183–184.
37. Nketia, Abofodwom, Ghana Publishing Corp, Accra, 1973, pp7–9.
38. Sekyi–Baidoo, A Study of the Cosmological and Aesthetic Freatures of the Akan Hunters' Song Amoung the People of Kunso, M.Phil Thesis Submitted to the Institute of African Studies, University of Ghana, Legon, 1994, p41.
39. Ibid.
40. Nketia, Abofodwom, op cit, p8.
41. Ibid.
42. Rattray, Religion and Art in Ashanti, , op cit, p184–185, See also Ross, Doran H, ‘More than Meets the Eye: Elephant Memories Among the Akan’ in Elephant : The Animal and Its Ivory in African Culture , Edited Doran H. Ross Hong Kong, Pear River Printing Company, 1992, p 140.
43. Nketia, Abofodwom, op. cit, p8. 44. Sekyi–Baidoo, op cit, p42.
47. Nketia, Abofodwom, op cit, pp8-9.
48. Sekyi–Baidoo, op cit, pp79–100. For full details on the elephant funeral rites read the above pages.
49. Rattray, Religion and Art in Ashanti, op. cit, p184.
50. Nketia, Abofodwom, op. cit, pp8–9.

Tuesday, November 20, 2012

Hidden Markov Model Tutorial on Youtube

Part I

Part II

The Hidden Markov Model Tutorial

A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition
Lawrence R. Rabiner

Extension to Hidden Markov Models

"So far we have considered Markov models in which each state corresponded to an observable (physical) event.  This model is too restrictive to be applicable to many problems of interest.  In this section we extend the concept of Markov models to include the case where the observable is a probabilistic function of the state - i.e., the resulting model (which is called a hidden Markov model) is a doubly embedded stochastic process that is not observable (it is hidden), but can only be observed through another set of stochastic processes that produce the sequence of observations."

Natural Selection through the eyes of Information Theory

I'm going to be covering different sections of this fundamental paper piece by piece over the next month or so.  Thanks to the Haldane's Sieve blog for putting it up.  Especially, thanks to the author Steven A. Frank.  I've been stumbling around for almost two years now, knowing the underlying connection between population genetics and communication theory was entropy, but lacking the mathematical formalism to describe the connection.  Interestingly, Frank is at UC Urvine, home of the Henry Samueli School of Engineering.  Here's the intro to the paper:

Natural selection. V. How to read the fundamental equations of evolutionary change in terms of information theory

Steven A. Frank
Journal of Evolutionary Biology
Article first published online: 16 NOV 2012


   "I show that natural selection can be described by the same measure of information that provides the conceptual foundations of physics, statistics and communication. Briefly, the argument runs as follows. The classical models of selection express evolutionary rates in proportion to the variance in fitness. The variance in fitness is equivalent to a symmetric form of the Kullback-Leibler information that the population acquires about the environment through the changes in gene frequency caused by selection.

   "Kullback-Leibler information is closely related to Fisher information, likelihood, and Bayesian updating from statistics, as well as Shannon information and the measures of entropy that arise as the fundamental quantities of communication theory and physics. Thus, the common variances and covariances of evolutionary models are equivalent to the fundamental measures of information that arise in many different fields of study.

   "In Fisher's fundamental theorem of natural selection, the rate of increase in fitness caused by natural selection is equal to the genetic variance in fitness. Equivalently, the rate of increase in fitness is proportional to the amount of information that the population acquires about the environment [2].

   "In my view, information is a primary quantity with intuitive meaning in the study of selection, whereas the genetic variance just happens to be an algebraic equivalence for the measure of information. The history of evolutionary theory has it backwards, using statistical expressions of variances and covariances in place of the equivalent and more meaningful expressions of information. To read the fundamental equations of evolutionary change, one must learn to interpret the standard expressions of variances and covariances as expressions of information."

Monday, November 19, 2012

Woolly Mammoth, Woolly Rhinoceros and Reindeer Lived On Iberian Peninsula 150,000 Years Ago

Spanish researchers found the fossil remains of fauna of glacial climate in 72 Iberian sites,
mostly in the north of the peninsula. (Credit: Peter Novák)

ScienceDaily (Sep. 9, 2010) (Link) — A team made up of members of the University of Oviedo (UO) and the Complutense University of Madrid (UCM) have gathered together all findings of the woolly mammoth, the woolly rhinoceros and the reindeer in the Iberian Peninsula to show that, although in small numbers, these big mammals -- prehistoric indicators of cold climates -- already lived in this territory some 150,000 years ago.

The presence of the woolly mammoth (Mammuthus primigenius), the woolly rhinoceros (Coelodonta antiquitatis), the reindeer (Rangifer tarandus), and to a lesser extent the wolverine (Gulo gulo), the arctic fox (Alopex lagopus), the musk-ox (Ovibos moschatus) and the Saiga antelope (Saiga tatarica), has been linked to the paleoclimatic scale created on the basis of the isotopic composition of oxygen in the ice of Greenland.

"The findings of cold climate fauna in the Iberian Peninsula coincide with the periods of greatest global cooling recorded in the ice of Greenland," Diego Álvarez-Lao, main author of the work and researcher in the Palaeontology Department of the UO explains.

The study, which has been published in the journal Quaternary International, reveals that the oldest remains of mammals adapted to cold climates found in the Iberian Peninsula belong to great prehistoric mammals which lived isolated in Spain 150,000 years ago.

The "glacial fauna" entered the Peninsula at that time because "the environmental conditions in central and northern Europe were so extreme that the animals were obliged to migrate to the south, where the climate was less severe," Álvarez-Lao explains.

Thursday, November 15, 2012


Multipath signalling in a communication system is a propagation phenomenon where a signal propagates by multiple paths from sender to receiver.  As the signal travels through the media in each path, it experiences destructive and constructive interference and phase shifting.

Successfully communicated multipath signals at the receiver are usually redundant.  If not, they would likely not survive negative impacts of multipath such as fading and could not be reconstructed into a comprehensible format at the receiver.

A possible analogy in population genetics can be drawn when a population splits into two or more separated, isolated populations.  Over time, these separated populations undergo positive and negative selection as well as diffusion.  When the separated populations encounter each other again, and are measured, it is possible to misinterpret the underlying structure of the reconstructed population if the measurement system cannot model multipath effects.

Another analogy can be drawn with respect to redundancy.  The genome seems to have high redundancy.  Recent examples of this are the finding of the development of lactase persistence in Europeans and East Africans and the development of high altitude adaptation in Tibetans and Ethiopians on different loci.

(Update November 19th:  It occured to me that some might take this communication system analogy as an argument for intelligent design.  The analogy is not meant as an argument for Intelligent Design. Rather, it is meant to suggest that some ideas from formal communication theory may be illustrative in population genetics.  I mentioned the seminal communication theory paper by Claude Shannon in the last post, MULTIMIX.  Here's the link again:  A Mathematical Theory of Communication, Claude Shannon, The Bell System Technical Journal, 1948.)

Related papers:

The genetic architecture of adaptations to high altitude in Ethiopia
Alkorta-Aranburu et al.

The Origins of Lactase Persistence in Europe
Yuval Itan et al.
PLoS Comput Biol 5(8): e1000491. doi:10.1371/journal.pcbi.1000491

Genetic Evidence for High-Altitude Adaptation in Tibet
Tatum S. Simonson et al.
Science Vol. 329. no. 5987, pp. 75 - 78
DOI: 10.1126/science.1190371

Convergent adaptation of lactase persistence in Africa and Europe
Tishkoff et al.
Nature Genetics 39, 31 - 40 (2007)
Published online: 10 December 2006 | doi:10.1038/ng1946

Wednesday, November 14, 2012

On "[ ] is a complex disease"

Anne Buchanan writes a super post about reality in genetic and genomic research.  (link)

Thank you.



MULTIMIX is a program that fits a statistical model to linked genome-wide SNP data from admixed individuals to learn about their ancestral origins. It is applied to a dense set of biallelic SNPs and will estimate the ancestral population of origin at each SNP - the local ancestry.

To infer the population of origin at each locus along the admixed chromosome MULTIMIX uses panels of either phased haplotypes or unphased genotypes sampled from each of the candidate ancestral population. The MULTIMIX model is applicable to any number of ancestral source populations, as well as any combination of phased or unphased admixed samples and source panel data.

The user has a choice of three statistical methods with which to implement the model : MCMC sampling, the EM algorithm or the Classification-EM (CEM) algorithm. Each of these methods makes inference on the local ancestry at windows of SNPs meaning that the sites of switches in ancestry are restricted to occur only at the boundaries between these windows. To refine the estimate on the location of switches, an additional step to resolve the boundaries between chunks of differing ancestry can be implemented.

The paper:

Claire Churchhouse, Jonathan Marchini
Genetic Epidemiology
7 Nov 2012
DOI: 10.1002/gepi.21692

Abstract:  "We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model—Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported."

Related paper:

A Mathematical Theory of Communication
Claude Shannon
The Bell System Technical Journal
Vol. XXVII, No. 3, July 1948


This is an excerpt of some field recordings which were recorded by Nana Kimati Dinizulu in the Northern Region of Ghana, West Africa. [The Dagomba people inhabit the northern savannah of Ghana.] The music featured in this segment is performed by Fusani Tia on Jenjeli, which is a one string instrument of the Dagomba people and his son Muhammad Kusani who plays Denkenkelen, an idiophone made of iron. This is an ancient form of music that is now played by few musicians.

Hunting Elephants: From the Earliest Times . . .

The Elephant in Pre-Colonial Ghana: Cultural and Economic Use Values
Kwame Osei Kwarteng Journal of Philosophy and Culture, Vol. 3, No. 2
June 2006

"From the Earliest Times"

". . . according to Nketia, before the advent of the cash crop economy, not only was hunting the most important profession in Ghana, it also required bravery and a thorough knowledge of the forest. Nketia categorises hunters into assistant hunters and master hunters. The distinction between the two was based on the type of animal hunted. Assistant hunters killed only small animals, while master hunters killed dangerous animals like elephants and buffaloes. Master hunters were also ranked according to their exploits, chiefly the number of elephants that they killed during their career. Accordingly, there were three distinct ranks of master hunter: the lowest on the rung were hunters who had killed only one elephant; occupying an intermediate rank were those who had killed two elephants; while those who killed three or more elephants in their career as hunters were ranked highest. [1]"

"What were the likely origins of hunting in Ghana? Evidence gleaned from archaeology, and corroborated by oral tradition, provides some answers. According to Anquandah, recent archaeological studies carried out in the woodland savannah and forest belts of Ghana have revealed that from about 10,000 B.C. onward, Late Stone Age hunter–gatherers who fashioned microlithic and flake industries occupied the savannah and forest, and set up intensive food gathering, fishing and hunting economies [2] . . ."

"The archaeological evidence suggests further that Early and Later Stone Age populations were culturally adapted to their specific ecological zones. For example, a microlithic population represented at Gao lagoon in the Accra plains combined hunting with exploitation of shellfish and other fish resources in the local lagoon and river environment. On the other hand, the populations of the savannah zone of Ghana had a strong microlithic tradition which exploited the animal resources of that ecological belt. However, in the forest zone, opportunities for hunting were minimal, with people specialising in grubbing up wild tubers and roots using stone picks and hoes[3] . . ."

"What were the hunting methods employed by the ancient hunters? This may be inferred by examining the various hunting methods known to have been employed in various African cultures which were contemporaneous with the period we are considering. Van Couvering identifies some hunting tactics employed by modern African hunters which were also used by ancient hunters as mob attacks with spears; pitfalls; burning of game–rich bush; and hamstringing.[4]"

"It is reasonable to suppose that of these techniques, the ancient elephant hunters in Ghana during the Late Stone Age used either bush burning or hamstringing, although Van Couvering admits that the latter ‘entailed a high risk on the part of a hunter equipped only with a stone axe or knife’[5]"

"During the Iron Age both the Akan in the forest belt adn savannah groups like the Gonja and Mole-Dagbani used bows and arrows, spears and javelins as traditional weapons for war as well as for hunting purposes. However, from the 1650s, European trading companies introduced firearms into the Gold Coast with the result that arms proliferated in the coastal and forest regions and were used for military and hunting purposes. The adoption of muzzle–loading guns to hunt elephant and other game led to the emergence of two distinct elephant hunting methods in the country. Coastal groups, along with the Akan who lived in the forest belt (Asante, Assin, Denkyira, Kwahu, Akwamu, Akyem, etc), where European goods circulated freely, bought these guns and used them, both for defensive and offensive purposes, and for hunting elephants and other animals. At the same time, savannah inhabitants continued to use their traditional bows, arrows and spears for elephant hunting. Arhin indicates that arms and ammunition became available in the northern markets after 1874, when Asante authority over her hinterland was undermined by the British invasion of Kumasi. It appears that long after Asante had stopped restricting movement of arms and ammunition to the north, savannah elephant hunters continued to use bows, arrows and spears. This is borne out by Cardinall, a former District Commissioner of Northern Territories and Western Ashanti who notes in In Ashanti and Beyond that the north had practically no guns in the early twentieth century, and thatelephants were killed with bows, arrows and spears.[6]"

"There is reason to believe, too, that both the Ntereso and Kintampo areas have a long tradition of hunting and history of large elephant populations. Indeed elephant hunting here, which started in pre–historic times, appears to have persisted into the twentieth century. In the case of Kintampo, hunting traditions recorded by Sekyi–Baidoo indicate that local towns and villages, and adjacent districts in the northern part of Brong Ahafo Region, particularly towns like Kunso, Dromankese, Krabonso, Tanoboase, Tuobodom, Nchiraa and Droboso, were noted for elephant hunting until the disappearance of elephants from these areas.[7] Traditions related by Nana Kwabena Bofuo, a renowned elephant hunter and the Chief Hunter of Kunso and Nana Kwame Ntem, a hunter and Atufuohene of Abease traditional area, confirm the abundance of elephants in the the Nkoranza, Kintampo and adjoining districts up to the Afram plains . . ."

"With respect to Ntereso in northern Ghana, there is evidence which suggests that the area’s long tradition and history of elephant hunting was due to the area’s rich elephant resources which might date to antiquity. Daaku writes, for instance, that Gonja and Dagomba in northern Ghana were major sources of Asante ivory supplies in pre–colonial times, notably when the two areas were under the hegemony of Asante. Also, during the colonial era, elephant hunting was prevalent in the north, particularly in Gonja district. For instance, in 1924 the Chief Commissioner of the Northern Territory in a report referred to the invasion of then Bole District by Asante hunters, providing confirmation that elephant hunting was still taking place in the first half of the twentieth century in Ntereso."


[1] James Anquandah, Rediscovering Ghana's Past, Longman, Essex, p. 53.

[2] Rattray, Ashanti Law and Constitution,op cit, p. 218, the exact time Rattray is referring to is not known, but probably he is referring to the period before the introduction of guns into the country in the 17th Century.

[3] Ibid, p. 54.

[4] John A. Van Couvering, ‘Proboscineans, Hominids, and Prehistory’ in Elephant: The Animal and Its Ivory in African Culture, Ed. Doran H. Ross, Pear River, Hong Kong, 1992, p75.

[5] A.W. Cardinall, In Ashanti and Beyond, Johnson Print Corporation, London, 1971, p167.

[6] Sekyi–Baidoo, A Study of The Cosmological and Aesthetic Features of the Akan Hunters’ Song Among the People of Kunso, M.Phil Thesis Submitted to Institute of African Studies, University of Ghana, Legon, 1994, p. 30.

[7] Interview with Nana Kwabena Bofuo, Chief Elephant Hunter, 80 years old Kunso, 24/01/06.

Tuesday, November 13, 2012

The Transitional Humans

A nice introduction to early transitional humansHomo erectus, Neandertals and Glacial Cycles has been put up by Dr. Dennis O'Neil, a behavioral scientist at Palomar College, San Marcos, California. (link)

Dynamics of genetic and morphological variability within Neandertals

John Hawks
Journal of Anthropological Sciences Vol. 90 (2012), pp. 1-17

I got around to reading John Hawks' paper which I thought would be a summary paper of current work on Neandertals.  While it is a summary paper, I found it to be the most riveting description of Neandertal behavior I have ever read.  You probably want to read the entire paper.  I started excerpting the paper but ended up copying about a third of it here.  The paper is highly relevant to the model of a refugia and range shift model for human origins.

Neandertal variation and "varieties"

"Southwest Asian Neandertals"

"This group included the entire known fossil record of the Levant to the Zagros, including Skhul, Tabun, Zuttiyeh, and Qafzeh (all in the Levant) and Shanidar, Iraq.  Howell [1957] noted the divergent opinions of anthropologists about the evolutionary scenario that generated this sample.  He offered the opinion that the Tabun had affinities with Early Neandertal people, and that the region had undergone a trend of "sapiensization" explaining the Skhul sample."

"Howell identified these varieties of Neandertals to clarify his position on the Neandertal ancestry of recent humans.  In his view, several previous authors had been too categorical in their insistence that Neandertals could not have been ancestors of modern peoples.  He allowed that the classic Neandertals may have been too specialized to have given rise to later populations within Europe.  But the early Neandertals were less anatomically specialized and may have been ancestral to modern humans in some other, non-European, region.  Moreover, the Southwest Asian Neandertals appeared to provide evidence of an evolutionary trend toward modern humans."

Emerging problems with Neandertal varieties

"Several workers after Howell added the concept of a north-south axis of Neandertal diversification within Europe.  Rosas and colleagues (2006) noted that southern Neandertals tend to have increased heights of the lower face and broader faces than the northern sample of Neandertals within Europe."

"Mitochondrial DNA"

"The pattern of mtDNA evolution within Neandertals suggests that repeated turnover of the population of European Neandertals did happen.  When considering the entire sample of mtDNA, the amount of variation within the Neandertal sample is approximately equal to the variation within living people across the same geographic range, from Spain to Central Asia (Caramelli et al., 2008, Krause et al., 2007).  The common ancestor of all Neandertal mtDNA sequences lived approximately 200,000 years ago, around the same time as the modern human mtDNA last common ancestor (Dalen et al., 2012).   Taken by themselves, these comparisons are consistent with the hypothesis that Neandertals had approximately the same population structure and demographic history as modern Eurasians.  However, when we compare earlier and later Neandertals, the picture is more complex.  The sample of Neandertal mtDNA taken from European specimens after 50,000 years ago is depauperate in variation compared to the full sample (Lalueza-Fox et al. 2008).  The lack of variation in later European Neandertals is not consistent with these being a sample drawn from a small geographic area of a large distribution, without demographic turnover (Dalen et al., 2012.)  Instead, it appears that the western part of the Neandertal range underwent at least one episode of large-scale migration and partial population replacement.  A tightly related clade of sequences includes the specimens from Vindija, El Sidron and Feldhofer, seven specimens in all.  These are among the latest Neandertals in the west.  The Central Asian or eastern European portion of the Neandertal range retained greater mtDNA variation in this later time period, possibly indicating that this area was a source for later Neandertals in Western Europe . . ."

"Fabre and colleagues (2009) also emphasized a biogeographic division of mtDNA into easter and western groups.  They used a different methodology, focused upon whether the geographic range of Neandertals could be divided into replicable subsamples.  In addition to the division into Central Asian and European groups, the study also suggested that the Italian and Croatian specimens might belong to a "southern" group.  This study did not consider the times represented by different sites, and adding the dynamic reflected by time would likely change the groupings.  By testing a priori models, the study avoided some of the problems attendant upon the tree-based approaches described above."

"Nuclear DNA"

"Three Neandertals from Vindija have been represented by substantial sequencing of the nuclear genome, averaging nearly 1x coverage for each of them.  Much smaller fractions of the nuclear genome have been recovered from Neanderthal specimens from Feldhofer Cave, El Sidron, and Mezmaiskaya (Green et al., 2010).  All of these except for Mezmaiskaya are among the group of later Western European Neandertals discussed above, all of which fall intoa single mtDNA clade.  This is therefore a highly constrained set of Neandertals in space and time.   The full set of mtDNA extends includes an eastern range with greater diversity and much earlier specimens in Western Europe."

"The most celebrated result from the nuclear DNA evidence is the finding that non-Africa populations today derive a proportion of their ancestry from Neandertals (Green et al., 2010).  The fraction of ancestry represented by such introgression form Neandertals is between 1 and 4 percent of the genealogical ancestry of individuals with European, Asian or other non-African origins.  Some of the similarity of non-Africans to Neandertals may be attributable to the ancient Middle Pleistocene structure of African populations (Eriksson & Manica, 2012), but this effect alone cannot explain the pattern of similarities, which therefore require substantial introgression (Yang et al., 2012).  It is possible that some similarities of living people and Neandertals resulted from gene flow between Neandertals and African contemporaries before the Late Pleistocene dispersal of modern populations . . ."

Reconciling paleogenomics and morphology

". . . Two avenues of evidence will provide more insights about Neandertal population dynamics.  Obviously, uncovering more nuclear genomes from Neandertals or early Upper Paleolithic humans would advance our knowledge greatly.  Tempering this expectation is that the later western Neandertals, with lower genetic diversity, are the ones most likely to provide more genetic data.  Earlier Neandertals, and the Neandertals from central Asia, would be most useful to uncover new knowledge about the population dynamics of this ancient group. A second source of evidence may come from the introgression of Neandertal genes into later human populations.  As we begin to uncover the genes of living people that came from Neandertals, we face the possibility that these genes may represent different ancient Neandertal groups to greater or lesser degrees.  The initial work on Neandertal genetics suggested that most of the population mixture with Neandertals may have happened in west Asia (Green et al., 2010).  That would suggest that European Neandertals are themselves somewhat genetically distinct from the population that gave rise to most Neandertal genes in recent populations.  Comparing different Neandertals with each other will help us uncover the structure of the population that gave rise to Neandertal ancestry in living people . . ."

Population dynamics

" . . . The attention to "early" Neandertals as a group dating to the last interglacial brought with it the understanding that Neandertals had persisted through at least one entire glacial cycle.  Howell (1952) proposed that glacial cycles provided the isolation that enabled classic Neandertals to evolve their specialized anatomy.  Weckler (1954) argued that isolation was one consequence of glaciations, but that long-distance migrations and recolonizations of formerly periglacial habitat was an important cause of population change in Neandertals and the modern humans who encountered them."

"Today, our knowledge of the geographic range of Neandertals confirms their existence across a broad range of climate regimes.  From the Altai to Spain, the known geographic range of Neandertals covered more than 7000 kilometers east to west.  On the longitudinal range is little doubt, because of the mtDNA evidence European Neandertal specimens to Okladnikov Cave (Krause et al., 2007).  Okladnikov is at present the easternmost site to produce skeletal remains attributable to Neandertals, although other sites with similar archaeology are found in the Altai.  The Neandertals also covered a substantial range in latitude.  The northernmost Neandertal site may be Byzovaya, which does not present skeletal remains but does include a Late Mousterian assemblage with some technical links to central European Neandertal sites (Slimak et al., 2011) . . . Although the European climatic conditions oscillated considerably during the Late Pleistocene, the Neandertals seem likely to have been capable of adapting to change conditions, either by tracking ecotones as climate shifted or by changing their subsistence strategies to meet new requirements.  In other words, the archaeological record by itself is sufficient to show us that Neandertal populations were highly dynamic in areas where habitation was possible only during intermittent climatic periods."

"Archaeological evidence along gives us some indications that Neandertals rapidly colonized new regions when they became suitable for habitation.  The possible excursion of Late Mousterian people north of the Arctic Circle to Byzyvaya and Mamontovaya Kurya are strong indicators of such potential, if these sites truly represent Neandertal activity.  Bar-Yosef (1992) suggested that later Neandertal sites in the Levant, including Amud and Kebara, may represent the recolonization of this area from Europe as cold conditions intensified during the Wurm glaciation.  Shea (2008) considered the record of modern and Neandertal activity in the Levant to represent multiple cases of population turnover, as climate shifts caused successive populations of Paleolithic humans to abandon the area or become locally extinct."

"Across northwestern Europe, from Britain to Poland, an area of more than a million square kilometers was abandoned by Neandertals during the early stages of the last glaciation and not reinhabited until after approximately 60,000 years ago.  The intermittent occupation of these parts of Europe was likely not a function of "habitat tracking" by Neandertals, but instead a record of regional expansions and partial extinctions when climatic conditions deteriorated (Hublin & Roebroeks, 2009).  White & Pettitt (2011) suggested a very small Neandertal population size in northwestern Europe during the late Middle Paleolithic, and considered the possibility that the occupation of Britain was maintained as seasonal hunting camps rather than permanent settlements.  This kind of occupation would put movements of several hundred kilometers into the ordinary behavior pattern of individual Neandertals.  At an extreme, the survival of Neandertals on the northwestern tier of Europe may have been precarious (White, 2006).  From the perspective of population dynamics, this does not suggest a dense, stable population, but instead one of great mobility and repeated ability to colonize and exploit new opportunities . . ."

Sunday, November 11, 2012

"Refugia and Range Shifts Model" and the Origin of Modern Humans

I've added a side bar on the right for the posts on this blog that together construct a picture of the "Refugia and Range Shifts Model" for the origin of modern humans as an interaction between Eurasian and African refuges due to climate change induced by glacial cycles during the Quaternary.

Thursday, November 8, 2012

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

Rosaria Scozzari, Andrea Massaia, Eugenia D’Atanasio, Natalie M. Myres, Ugo A. Perego, Beniamino Trombetta, Fulvio Cruciani
PLOS ONE, November 2012
(Open Access link)

Published today is a new paper on an updated y-chromosome phylogeny.  Dienekes has kindly put the phylogeny and abstract online, so I won't recopy them here. 

The most significant finding of the paper is the connection of four A1b y-chromosomes, the deepest phylogeny in the tree, to two men from Ghana, one man in Cameroon and one in Algeria: "Two A1b chromosomes from a previous work (one from Algeria and one from Cameroon) [16] were included in this study together with two newly identified A1b chromosomes, whose geographic origin can be traced back to west-central Africa (Ghana) on the basis of the microsatellite profile (data not shown). It is worth noting that three additional A1b chromosomes have been recently found in Caribbean populations, which exhibit substantial Y-STR haplotype sharing with Y chromosomes from Gabon [35], [36]. Taken together, all these data reinforce the hypothesis of an origin in the north-western quadrant of the African continent for the A1b haplogroup [16], and, together with recent findings of ancient Y-lineages in central-western Africa [19], provide new evidence regarding the geographical origin of human MSY diversity."

A second finding is the identification of "a chromosome from southern Europe as a new deep branch within haplogroup C (C-V20 or C7, Figure S1). Previously, only a few examples of C chromosomes (only defined by the marker RPS4Y711) had been found in southern Europe [32], [33]. To improve our knowledge regarding the distribution of haplogroup C in Europe, we surveyed 1965 European subjects for the mutation RPS4Y711 and identified one additional haplogroup C chromosome from southern Europe, which has also been classified as C7 (data not shown). Further studies are needed to establish whether C7 chromosomes are the relics of an ancient European gene pool or the signal of a recent geographical spread from Asia." 

The paper also includes better definition of other aspects of the A and B y-chromosomes as well as some important additions to the basal F y-chromosome.

It's great to see more in depth attention paid to the genetics of West Africa and also nice to see Italy considered both as a refuge and as a potential path for Out of Africa expansions.


News Flash:  Developments with Y Haplogroup A (link)

For those of you new to this blog, in the right hand side bar under "WEST AFRICA", there is a list of the posts covering culture, language, geography and genetics of West Africa.

Wednesday, November 7, 2012

The Date of Interbreeding between Neandertals and Modern Humans

Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, David Reich
PLOS Genetics, October 2012

This paper evaluates various models of divergence between Africans, Europeans and Neandertals.  Hybrid model (e) of the paper, shown in Figure 2, below, is most closely akin to the human version of the "refugia and range shifts model" of the Marbled White butterfly.  In one possible scenario of this model, the first branch occurs when Africans diverge from Neandertals during the Holstein interglacial (Timeline of glaciation).  Then early Scladina-like Neandertals admix back with Africans, possibly in Iberia or Morocco, 150 kya when the sea level is low enough to make it more likely.  As the sea level rises, the Scladina Neandertal-Africans on the European side are cut off in an increasingly icy domain.  The Scladina Neandertal-Africans in Morocco thrive.  Their descendants marry Africans who have little or no Scladina ancestry.  At about 50 kya, the Scladina Neandertals who are cutoff in Western Europe are replaced by the Vindija like Neandertals. Shortly thereafter, Africans with perhaps a remnant of Scladina Neandertal admixture arrive once again in Europe. Occasionally, they have children with the Vindija Neandertals.  All of the Neandertals, Vindija in Europe and Scladina in Africa, are eventually absorbed into the dominant population of homo sapiens from Africa . . .
Figure 2.  Classes of demographic models relating Africans (Y), Europeans (E), and Neandertals (N).  a) Recent gene flow but no ancient structure. RGF I has no bottleneck in E. RGF II has a bottleneck in E after gene flow while RGF VI has a bottleneck in E before the gene flow. RGF IV and V have constant population sizes of Ne = 5000 and Ne = 50000 respectively. b) Ancient structure but no recent gene flow. AS I has a constant population size while AS II has a recent bottleneck in E. c) Neither ancient structure nor recent gene flow. NGF I has a constant population size while NGF II has a recent bottleneck in E. d),e) Ancient structure+Recent gene flow. HM IV consists of continuous migration in the Y-E ancestor and the Y-E-N ancestor while HM I consists of continuous migration only in the Y-E ancestor. HM II consist of a single admixture event in the ancestor of E while HM III also models a small population size in one of the admixing populations.

Further comments (November 8th):  In reality, there is very strong evidence based on Y-chromosome and mtDNA, that for many if not most populations, Hybrid model (e) is incomplete.  There are subsequent events, such as the migration of the carriers of the E y-chromosome into Europe, some time since the last ice age and before the Holocene Climatic Optimum.  Carriers of the R-V88 y-chromosome and H1 mitochondrial DNA make their appearance in North Africa over the same time frame.  Therefore, a hybrid model for the interaction of populations between Europe and Africa up to the Holocene Climatic Optimum demands allowance for at least four major admixing events: (1) Scladina-like Neandertals with Africans approximately 150kya, (2) Vindija-like Neandertals with Europeans in the window suggested in the above paper, (3) Europeans with North Africans during the last ice age, and (4) North Africans with Europeans during the last ice age. Further complicating the picture are the layers due to recent demographic events of the Holocene Climatic Optimum and the last several thousand years.  This already complex model doesn't even begin to touch upon the migrations to Asia, Southwest Asia and the Americas.  Drift, diffusion, isolation, migration and selection are always at work.  It is therefore not surprising that finding the genetic signature to prove this complex model is very difficult.

Mousterian at Jebel Irhoud: Wherefore Art Thou?

O Romeo, Romeo! wherefore art thou Romeo?
Deny thy father and refuse thy name;
Or, if thou wilt not, be but sworn my love,
And I'll no longer be a Capulet.

So then, what is the timing of our Neandertal and Homo sapien Romeos and Juliets?  How many times and when do they meet in North Africa?  In Europe?  I've put together all the quotes, diagrams, and references I believe are contributing to my current thinking on this topic.  I hope that all the children of the Montagues and Capulets can learn to get along on this fragile planet.

Neanderthal extinction as part of the faunal change in Europe during Oxygen Isotope Stage 3
John R. Stewart
Acta Zoologica Cracoviensa - Series A: Vertebrata, Vol. 50, Numbers 1-2, May 2007, pp. 93-124(32)

"The cold-adapted mammals as a whole, such as the extinct mammoth and extant species like the reindeer and arctic fox, did not retreat from the north as the climate cooled like the Neanderthals."

"... Neaderthals were presumably a warmer-continental adapted species, based on their geographical distribution through time.  Neanderthals seem to have been better-suited to the Mediterranean during the Late Pleistocene than to the more northern parts of Europe."

Partial Genetic Turnover in Neanderthals:  Continuity in the East and Population Replacement in the West
Dalen et al
Molecular Biology and Evolution (2012) 29 (8): 1893-1897

"Our analyses indicate that recent western European neandertals (<48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (>48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region."

The Neanderthal Genome
Science Online Magazine

Figure from the Neanderthal Genome article:  "At home in Eurasia"

Marnie'e note:  With regard to the southern extent of the Neandertal range, this map may need a little refinement.


Related Posts on this blog:

The Who and When of the Neanderthal Survivors (link)

Ancient Crossings (link)

Related Posts on John Hawks' blog:

Taking the mtDNA pulse of Neandertal populations (link)

Which population in the 1000 Genomes Project samples has the most Neandertal similarity? (link)

Related Media, Ethnomusicology and Archaeological Research:

Grotte Scladina:  Un patrimoine archéologique exceptionnel à découvrir absolument (link)

Cave of Forgotten Dreams [Werner Herzog film about the archaeological research at the Chauvet Cave] (link)

Fliegel Jezerniczky EXPEDITIONS [Rock Art Expeditions and rock art archaeological research] (link)

Vintage Palmwine
Daniel Amponsah[Koo Nimo], Thomas Osai Ampoumah [T. O. Jazz], Kwaa Mensah
Highlife recorded in Ghana in the Bokoor Studios, Ghana
John Collins Recording
2003 Otrabanda Records & Music Distributor (link)
From Amazon (link)

Additional Related Papers and References:

North African genetics through the prism of ADMIXTURE
Luis Aldamiz
Dec, 2011

The Archaeology of Africa:  Food, Metals and Towns (One World Archaeology)
Bassey Andah (Editor), Alex Okpoko (Editor), Thurstan Shaw (Editor) and Paul Sinclair (Editor)

A Coperican Reassessment of the Human Mitochondrial DNA Tree from its Root
Behar et al
The American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012

The Identity and Timing of the Aterian in Morocco
A. Bouzouggar and R. N. E. Barton
in Modern Origins:  A North African Perspective, Chapter 7
Jean-Jacques Hublin and Shannon P. McPherron, Editors
Springer, 2012

Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia:  New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12
Cruciani et al
Mol Biol Evol24 (6): 1300-1311. doi: 10.1093/molbev/msm049

Ancient watercourses and biogeography of the Sahara explain the peopling of the desert
Drake et al
PNAS 2010

The Civilizations of Africa:  A History to 1800
Christopher Ehret
University of Virginia Press

mtDNA Diversity of Ghana:  a forensic and phylogeographic view
Liane Fendt, Alexander Roeck, Bettina Zimmerman, Martin Bodner, Thorsten Thye, Frank Tschentscher, Ellis Owusu-Dabo, Tanya M. K. Goebel, Peter M Schneider, Walther Parson
Forensic Science International: Genetics

Y-Chromosomal Variation in Sub-Saharan Africa:  Insights Into the History of Niger-Congo Groups
de Filippo et al.
Oxford Journals

Refining the eustatic sea-level curve since the Last Glacial Maximum using far- and intermediate-field sites
Fleming et al
Earth and Planetary Science Letters 163 (1998) 327-342

Fliegel Jezerniczky EXPEDITIONS
(Rock Art Expeditions and Web Site)

The Messak Project and Natural Preservation and Sustainable Tourism (south-western Libya)
Gallinaro et al
Antiquity  Volume 086 Issue 331 March 2012

Modern Human Desert Adaptations:  A Libyan Perspective on the Aterian Complex
E. A. A. Garcea
in Modern Origins:  A North African Perspective, Chapter 9
Jean-Jacques Hublin and Shannon P. McPherron, Editors
Springer, 2012

A Draft Sequence of the Neandertal Genome
Green et al
Science 7 May 2010:
Vol. 328 no. 5979 pp. 710-722
DOI: 10.1126/science.1188021

From Africa to Europe and back:  refugia and range shifts cause high genetic differentiation in the Marbled White butterfly Melanargia galathea
Jan C Habel, Luc Lens, Dennis Roedder and Thomas Schmitt
BMC Evolutionary Biology 2011, 11:215

Comparative phylogeography of African savannah ungulates
E. D. Lorenzen, R. Heller, H. R. Siegismund
Molecular Ecology, Volume 21, Issue 15, pages 3656-3670, August 2012

Hunter-Gatherer Foraging Strategies in Tropical Grasslands:  Model Building and Testing in the East African Middle and Later Stone Age
Curtis W. Marean
Journal of Anthropological Archaeology 16, 189-225 (1997)

The genetic prehistory of southern Africa
Pickrell et al

A propos de quelques gravures rupestres de l'Ajal
Jean-Loïc Le Quellec
Persée, Bulletin de la Société préhistorique française, 1993, vol. 90, issue 5, pp. 368-376.

North African Populations Carry the Signature of Admixture with Neanderthals
Sánchez-Quinto et al
PLOS ONE, 2012

Spatial and Temporal Variation in the Nature of Pleistocene Pluvial Phase Environments Across North Africa
J. R. Smith
in Modern Origins:  A North African Perspective, Chapter 3
Jean-Jacques Hublin and Shannon P. McPherron, Editors
Springer, 2012

The genetic structure and history of Africans and African Americans
Tishkoff et al
Science, 2009