June 24, 2012

SMBE 2012 abstracts (part I)

Some abstracts of interest from SMBE 2012. Part II will follow.

Reconstructing demographic histories from long tracts of DNA sequence identity 
Kelley Harris 1 , Rasmus Nielsen 1,2 1 UC Berkeley, Berkeley, CA, USA,  2 University of Copenhagen, Copenhagen, Denmark 
There has been recent excitement and debate about the details of human demographic history, involving gene flow that  has occurred between populations as well as the extent and timing of bottlenecks and periods of population growth.  Much of the debate concerns the timing of past admixture events; for example, whether Neanderthals exchanged  genetic material with the ancestors of non-Africans before before or after they left Africa. Here, we present a method for  using sequence data to jointly estimate the timing and magnitude of past genetic exchanges, along with population  divergence times and changes in effective population size. To achieve this, we look at the length distribution of regions  that are shared identical by state (IBS) and maximize an analytic composite likelihood that we derive from the  sequentially Markov coalescent (SMC). Recent gene flow between populations leaves behind long tracts of identity by  descent (IBD), and these tracts give our method its power by influencing the distribution of shared IBS tracts. However,  since IBS tracts are directly observable, we do not need to infer the precise locations of IBD tracts. In this way, we can  accurately estimate admixture times for relatively ancient events where admixture mapping is not possible, and in  simulated data we show excellent power to characterize admixture pulses that occurred 100 to several hundred  generations ago. When we study the IBS tracts shared between and within the populations sequenced by the 1000  Genomes consortium, we find evidence that there was no significant gene flow between Europeans and Asians within  the past few hundred generations. It also looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians  in a population-specific way, though there may have been admixture between Africans and an ancestral non-African  population. 

Which way did they go? Detecting directional migration from genetic data
Benjamin Peter, Montgomery Slatkin University of California, Berkeley, Berkeley, USA  
Range expansions and colonizations are ubiquitous in many species and are studied from many different perspectives in e.g. anthropology, biogeography and invasion biology. It has been well established that these colonization events lead to a loss of genetic diversity and that in many cases it is possible to infer the history of a species' range from present-day genetic data. Previous approaches were mainly based on within-population measures of diversity such as heterozygosity, which then have been compared between populations. However, it is also well established that these statistics are susceptible to confounding demographic factors such as unequal subpopulation sizes or population size changes. In this study, we propose a novel method using data from multiple populations to infer a population's history. Our approach is based on a statistic that detects asymmetries in the 2D-allele frequency spectrum that occur when one population consists mostly of offspring of another population, as we expect in an expanding population. We show that our statistic is able to detect the direction of an expansion using data from multiple populations. Using simulations, we further show that our statistic is generally more powerful than previous approaches and that it is robust to a wide array of confounding demographic factors. We further illustrate the use of our statistic on several data sets for humans, Drosophila and Neurospora and show that we are both able to detect global patterns of colonization and fine-scale population structure.

Populations genetics of the Neolithic transition
Joachim Burger 1 , Mark Thomas 2,3 1  
Johannes Gutenberg University, Institute of Anthropology, D-55128 Mainz, Germany,  2 Research Department of  Genetics, Evolution and Environment, University College London, Wolfson House, 4 Stephenson Way, London NW1  2HE, UK,  3 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE- 752 36 Uppsala, Sweden     
About 11,000 years ago, a change in human lifestyle took place in the territories of present-day western Iran, the Levant  region and south-east Anatolia, which is characterised particularly by four factors: the people founded permanent  settlements with buildings for various functions; plants such as Einkorn and beans were cultivated; goats, sheep, pigs  and cattle were domesticated; a new kind of culture evolved, that became conspicuous with the appearance of a new  material culture including ground stone tools and later, pottery products. The transition from the partly nomadic huntergatherer subsistence strategy to a settled lifestyle based on food production is also known as the “Neolithic Revolution”.  About 8,500 years ago, the Neolithic culture spread to the southeast of Europe and later expanded episodically across  central and northern Europe. The extent to which this movement of a farming culture was accompanied by a movement  of people, as opposed to just a spread of ideas and skills, has been a subject of considerable debate and dispute  over  the last 100 years. Population genetic computer simulations of genetic data from ancient human remains, based on  coalescent theory have shown that the early Neolithic farmers could not have been descended just from the later  hunter-gatherers of central Europe (Bramanti et al. 2009). As the hunter-gatherers had already been settled in Central  Europe since the retreat of the glaciers 20 kya, Neolithic famers must have migrated into this area.   
There is good evidence of cultural contact between hunter-gatherers and early farmers in central Europe. Whether the  exchange of hunting tools also led also to the exchange of men is still not clear, as Y-chromosomal DNA has not yet  been studied systematically in ancient human remains. Moreover, ancient DNA evidence is now emerging that other  regions don/t follow the patterns of population discontinuity observed in Central Europe. While the overall results  support a model of demic diffusion of farmers from southeastern Europe, or even further East, in to Central Europe, it is  very likely that modern populations in most parts of Europe were formed by varying degrees of admixture between  incoming farmers and indigenous hunter-gatherers. Analyses of the appropriate neutral and phenotypically informative  markers using next generation sequencing technologies will provide more information on this in the near future. 
Population genetic properties of time serial data with examples from ancient population-genomic data 
Mattias Jakobsson Uppsala University, Uppsala, Sweden  
Extracting genetic information from ancient material has for long been hampered by numerous difficulties since its first  steps some two decades ago, but in the last few years, many of these problems have been solved and the use of  ancient DNA (aDNA) is now beginning to show its full potential. We will likely see a wealth of genomic data from ancient  populations, but the statistical properties of time-structured genetic samples are considerably less explored than  population genetic patterns arising from spatial structure. Using simulations, we explore and highlight features of  temporal structure and spatial structure, such as an 'isolation-by-time' effect that is similar to isolation-by-distance.  Using model- and simulation-based approaches, we can now make novel inferences about demographic and  evolutionary questions from time serial data. We will discuss examples from the long standing debate about the  introduction of farming in Europe and question about archaic ancestry in East Asia using paleogenomic data.  
Inferences on dog domestication - genetic analysis of the most ancient dogs utilizing DNA capture arrays
Olaf Thalmann 1,2 , Daniel Greenfield 2 , Matthias Meyer 3 , Susanna Sawyer 3 , Pin Cui 3 , Mietje Germonpre 4 , Mikhail V.  Sablin 5 , Francesc Lopez-Giraldez 9 , Daniel LePont 1 , Brian Worthington 10 , Jeff P. Blick 6 , Jeniffer A. Leonard 7 , Richard E.  Green 8 , Robert K. Wayne 2 1 University of Turku, Turku, Finland,  2 University of California, Los Angeles, USA,  3 Max Planck Institute for Evolutionary  Anthropology, Leipzig, Germany,  4 Royal Belgian Institute of Natural Sciences, Brussels, Belgium,  5 Zoological Institute  RAS, Saint-Petersburg, Russia,  6 Georgia College & State University, Milledgeville, USA,  7 Estacion Biologica de  Donana- CSIC, Seville, Spain,  8 University of California, Santa Cruz, USA,  9 Yale University, New Haven, USA, 10 Southeastern Archaeological Research, Inc., Newberry, USA 
The geographical and temporal origin of the dog is controversial. Genetic data suggest a domestication event in Asia or  the Middle East about 15,000 - 30,000 years ago, whereas the oldest dog-like fossils are found in Europe dating to over  30 thousand years ago. We genetically analyzed the remains of 14 prehistoric wolves and dogs including some of the  oldest dog remains described from the New and Old World. Utilizing array based DNA capture techniques coupled with  Illumina double indexed sequencing, we targeted a total of ~750,000 nucleotides in each of the ancient canids and  additional 20 contemporary wolves from North America and Eurasia. The sequence information comprised the complete  mitochondrial genome, 3,000 SNPs previously identified as highly informative for differentiating dogs from wolves,  exonic sequences from 62 potential domestication genes and ~150,000 nucleotides of non-coding regions spread  throughout the genome.   Initial analyses reveal that we have successfully captured and sequenced the complete mitochondrial genome with high  coverage as wells as a substantial number of autosomal fragments from ten prehistoric canids and all contemporary  wolves. Phylogenetic analysis combining the complete mitochondrial genomes of the prehistoric canids with those of a  large collection of modern dogs and wolves result in a statistically well supported tree. While some haplotypes cluster  within modern dogs or wolves, others show a basal placement in the phylogeny. The latter finding might support a  previous notion that an aberrant lineage of dog-like canids might have existed throughout the northern hemisphere  during the late Pleistocene and became globally extinct during the last 20,000 years. We will test this hypothesis by  investigating the autosomal loci and employ sophisticated phylogenetic analyses, demographic modeling and selection  scans to better understand the influence of early human society and artificial selection on the canine genome.
Admixed human genomes reveal complex demographic patterns from early modern humans to the  contemporary era 
Simon Gravel 1 , Jeffrey M Kidd 2 , Jake K Byrnes 1 , Andres Moreno Estrada 1 , Fouad Zakharia 1 , Shaila Musharoff 1 ,  Francisco M De La Vega 1 , Carlos D Bustamante 1 1 Stanford University, Stanford, CA, USA,  2 University of Michigan, Ann Arbor, MI, USA     
A substantial proportion of humans are "admixed", in the sense that their recent ancestors belong to statistically distinct  groups. This needs to be accounted for if unbiased inference and associations are to be performed. We present a  diversity of methods for the analysis of whole-genome sequence data from admixed individuals, and apply them to 50  genomes sequenced by Complete Genomics, including 4 Mexican-Americans, 4 African-Americans and 2 individuals  from Puerto Rico, together with SNP genotype data from hundreds of additional samples.     
Many methods have been presented recently to infer the population of origin of specific loci along the genomes of  admixed individuals, leading to inferred mosaics of ancestry.  We first propose a simple Markov model that relates the  time-dependent migration history to the inferred patterns of local ancestry. We use this framework to infer the timing of  admixture and to differentiate between punctual and continuous models of migration: using demographic models that  are consistent with both historical records and genetic data, we find evidence for continuous migration patterns in both  Mexican and African-American populations.     
We also propose models to study the longer-term evolution of the ancestral populations, by considering the allele  frequency distribution, pairwise TMRCA's, and a simple extension of the recently introduced Pairwise Sequentially  Markovian Coalescent approach for demographic inference. The inferred source population demographic histories are  in broad agreement with previous results for European and West-African populations, and the inferred demography for  the Native source population closely follows the European one until about 20,000 years ago. Taken together, whole  genome sequencing and local ancestry assignment therefore permit inferences about long-term histories of unsampled  ancestral populations and highlights recent historical demographic processes that altered patterns of variation observed  in admixed populations. 
A genomewide map of Neandertal ancestry in modern humans
Sriram Sankararaman 1,2 , Nick Patterson 2 , Swapan Mallick 1,2 , Svante Paabo 3 , David Reich 1,2 1 Harvard Medical School, Boston, USA, 2 Broad Institute of Harvard and MIT, Cambridge, USA, 3 Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 
Analysis of the genomes of archaic hominins, such as Neandertals and Denisovans, has revealed that these groups have contributed to the genetic variation of modern human populations. Yet, we know little about how these ancient mixtures have shaped the genetic structure of human populations and even less about their impact on human evolution. To answer these questions systematically, we need a map of archaic ancestry i.e., a map that labels whether each region of an individual genome is descended from these archaics.

Building such a map is technically challenging because of the antiquity of these gene flow events. We have identified signatures based on patterns of variation at single SNPs as well as haplotypes that are informative of ancient gene flow.

We propose a principled method based on the statistical framework of Conditional Random Fields (CRFs) that integrates these patterns leading to highly accurate predictions. We applied our method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genomewide map of Neandertal ancestry. Analysis of this map reveals several findings:

1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow.

3. Several of the Neandertal-derived alleles identified in 1) above are found in the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. These Neandertal derived variants are found to be risk variants associated with obesity and protective variants against breast cancer.

4. We also investigate the possibility of using this map to reconstruct the genome of the introgressing Neandertal. Using the ancestries in Europe and East Asia, we can reconstruct about 600 Mb which we expect to increase with larger samples and additional populations.
Origins and evolution of the Etruscans’ DNA
Silvia Ghirotto 1 , Francesca Tassi 1 , Erica Fumagalli 2,1 , Vincenza Colonna 3,1 , Anna Sandionigi 4 , Martina Lari 4 , Stefania Vai 4 , Emmanuele Petiti 4 , Giorgio Corti 5 , Ermanno Rizzi 5 , Gianluca De Bellis 5 , David Caramelli 4 , Guido Barbujani 1 1 Department of Biology and Evolution, University of Ferrara, Ferrara, Italy, 2 Department of Biotechnologies and BiosciencesUniversity of Milano-Bicocca, Milano, Italy, 3 Institute of Genetics e Biophysics "Adriano Buzzati-Traverso", National Research Council, Napoli, Italy, 4 Department of Evolutionary Biology, University of Firenze, Firenze, Italy, 5 Institute for Biomedical Technologies (ITB), National Research Council (CNR), Milano, Italy

The Etruscan culture is documented in Etruria, Central Italy, from the 7 th to the 1 st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals. Comparing ancient and modern diversity with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the modern inhabitants of two communities, Casentino and Volterra, but not to most contemporary populations dwelling in the former Etruscan homeland. We also estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, without a significant contribution of recent Anatolian immigrants.
Human population genomics in time and space: paleogenomics of populations in Bulgaria
Meredith L. Carpenter 1 , Hannes Schroeder 2 , Nikola Theodossiev 3 , M. Thomas P. Gilbert 2 , Carlos D. Bustamante 1 1 Department of Genetics, Stanford University, Stanford, CA, USA, 2 Centre for Geogenetics, University of Copenhagen, Copenhagen, Denmark, 3 Department of Archaeology, Sofia University, Sofia, Bulgaria

With a few exceptions, most ancient human DNA studies to date have restricted their analysis to the mitochondrial DNA (mtDNA) and Y chromosome. These approaches have led to some interesting theories regarding the spread of human populations; however, they are inherently limited by their use of these two non-recombining markers, which are subject to forces such as genetic drift and natural selection and also represent only the histories of the female and male lines, respectively, from which they descend. Recently, the whole genomes of several ancient individuals have been sequenced. These genomes yielded much more information about the individuals’ ancestry than their mtDNA alone; nevertheless, a single ancient individual is not sufficient for population genetic analyses. Thus, the goal of our study is to sequence the genomes of multiple ancient individuals from the same population. This type of study has the potential to dramatically improve our ability to address demographic questions about ancient human populations. We have begun the low-coverage sequencing of genomic DNA from the teeth of 16 individuals from different time periods (1500 BC-400 BC) in Bulgaria, and we plan to ultimately extend the study to at least 50 ancient Bulgarian individuals from the Neolithic to the Iron Age (6300 BC-400 BC). The results of these initial experiments will be presented, including the identification of mtDNA haplogroups and initial population genetic analyses. Ultimately, we plan to analyze whole-genome sequence variation in these individuals and to compare it to variation present in modern populations. This will be the first systematic population-level study of ancient human genomes and therefore will allow us address demographic questions that have previously been restricted to the realm of theoretical modeling using extant populations.
Horse domestication: a computer simulation approach
Michela Leonardi 1 , Christine Weber 1 , Norbert Benecke 2 , Mark G. Thomas 3,4 , Joachim Burger 1 1 AG Palaeogenetik, Institute of Anthropology, SBII, Johannes Gutenberg University, Colonel Kleinmann-Weg 2, 55128, Mainz, Germany, 2 German Archaeological Institute, Im Dol 4-6, 14165, Berlin, Germany, 3 Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK, 4 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Uppsala, Sweden

The domestication of horse played a key role in human history. It seems to have happened far both in time and space from the domestication of other ungulates such as cattle, pig, sheep and goat. Archaeological studies, nevertheless, failed in determining exactly the region and modality for horse domestication: several centers have been proposed (at least one in Europe and one in Central Asia) and the relationship between wild and early domestic populations are not clear. From a genetic point of view a phylogenetic approach on modern mitochondrial diversity could not find any structure related with geography or breeds. In the last decade ancient DNA became an important tool to reconstruct past demography. We obtained more than 100 HVR I sequences from pre domestic and domestic specimens found in Europe and Central Asia. After collecting all the previously published ancient and modern comparable sequences from the sub mentioned regions, computer simulations with a Bayesian approach were performed in order to test demographic models related with single or multiple domestications with or without gene flow. A single domestication appears to be unrealistic on the basis of mitochondrial data, while possible model of multiple domestications will be discussed.
The complete mitochondrial genome of a third individual from Denisova Cave
Susanna Sawyer 1 , Bence Viola 1 , Marie-Theres Gansauge 1 , Michael Shunkov 2 , Anatoly Derevianko 2 , Svante Paabo 1 1 Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 2 Paleolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia

A draft genome sequence was determined in 2010 from a small finger bone found in Denisova Cave in southern Siberia and was recently completed to 30-fold coverage. Its analysis reveals that it derived from an individual that belonged to a population related to, but distinct from, Neandertals. A large molar has also been described from Denisova Cave and shown to carry an mtDNA genome closely related to that of the finger bone. A second molar was found in Denisova Cave in 2010. We have captured and sequenced the complete mitochondrial genome of this tooth. While the mtDNAs of the finger bone and the first molar differ at only two nucleotide positions, they carry 86 and 84 differences, respectively, to the second molar. Thus, the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available. Interestingly, the mtDNA of the second molar has a shorter branch than the other two Denisovan mtDNAs, suggesting that it may be older than the others.

9 comments:

princenuadha said...

"We identify around 35,000 Neandertal-derived alleles in Europeans"

Wow, this might mean that there has been some genetic continuity in Europe since 35kya.

But, we still don't know where that mixing took place.

Annie Mouse said...

My main problem with this is that the main "Neanderthal" genome they tend to use for these studies was IMO potentially half-neanderthal/half-sapiens. So are these sequences related to the Neanderthal half or the archaic sapiens half. It makes a very big difference. These sequences may not be neanderthal at all (and I am a supporter of the idea we inter-bred neanderthals).

terryt said...

"The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians".

I suppose there will still be some who claim we see no higher level of Neanderthal genes in Europeans than in any other region. Interesting that 'Neanderthal' genes are found in East Asia though. What about in South Asia? None?

"Wow, this might mean that there has been some genetic continuity in Europe since 35kya".

I'd actually be more surprised if there wasn't.

"So are these sequences related to the Neanderthal half or the archaic sapiens half. It makes a very big difference. These sequences may not be neanderthal at all"

It's true that they may not be 'Neanderthal' but they do not seem to be African. Any 'archaic sapiens' genes that had survived in Europeans would disappear in the analysis. They would most likely be much the same as 'African'.

eurologist said...

the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available

While we need to be a bit cautious about these results, they do agree with the idea that (older than Neanderthal) heidelbergensis-like people were the main source of Denisovans. Of course, the next step is to clarify whether there was input from yet much older (by a factor of ~three) Asian erectus.

shenandoah said...

http://www.sciencemag.org/content/316/5822/222/F1.expansion.html
"If you needed a blood transfusion, you could get it from these Neanderthals," says Carles Lalueza-Fox, a geneticist at Pompeu Fabra University in Barcelona, Spain, who led the study.

That's not to say all Neanderthals were type O – [negative] others may have also boasted genes for the A and B blood types..."

http://www.scienceforums.net/topic/53486-does-rh-neg-blood-link-back-to-the-neanderthals/
"... only O negative is a [']universal donor[']."

http://www.sciencemag.org/content/316/5822/222.full
"Critical progress in biomedicine attributed to macaques includes the identification of the “rhesus factor”..."

Contrary to popular belief, the rhesus factor (D) is a dominant gene which expresses the antigen or blood protein AGAINST Rhesus monkey blood. Rhesus negative blood doesn't agglutinate in the Anti-D (aka "Anti-Human") testing reagent. Which means Rh-, Rhesus macaque, and evidently Neanderthal blood chemistry is all compatible at that level.

I repeat my theory again, that the Neanderthal creatures were Human x Rhesus monkey HYBRIDS, not a separate species but a sub-species of Homo Sapiens or Cro Magnon.

Denosivan is probably another type of Hybrid, as are some of the other smaller-brained and more primitive, extinct hominids.

Both Neanderthal and Denisovan mtDNA (from their maternal lineages) are essentially and practically Human, which means their uniquely unHuman genetic markers must have originally been inherited mainly from their ~male progenitors.

Which in my opinion, were apes. We didn't evolve from them, but most or many of us are ~descended from some of them (to varying degrees).

I know it's hard to accept (it wasn't easy for me, either).

terryt said...

"Both Neanderthal and Denisovan mtDNA (from their maternal lineages) are essentially and practically Human, which means their uniquely unHuman genetic markers must have originally been inherited mainly from their ~male progenitors".

That's avery strange idea, and difficult to support in any way.

Justin said...

^please don't post here again. you wasted 30 sec. of my life and then another for typing this.

eurologist said...

That's a very strange idea, and difficult to support in any way.


Terry, I think it has something to do with compressing human evolution into a 6,000-year framework, and being able to vividly imagine Paris Hilton going naughty with her pet monkey without your head exploding. It takes special people...

shenandoah said...

http://www.newscientist.com/article/dn16386-neanderthals-might-have-made-good-blood-donors.html

(This is the correct link for the first quote in my comment.)