SMBE 2013 abstracts

Some abstracts from the SMBE 2013 conference that will take place next week. 

Legacy of Early Migrants in Neolithic East Asian Hunter-Gatherer from Fukushima, Japan

K.K. Hideaki et al.   

Clarifying the genetic relationship between Neolithic East Asian Hunter-Gatherer, Jomon people, and modern human populations is one of the Keystones to understand the controversial history of modern East Asian populations. Jomon people inhabited in the Japanese archipelago from 16,000 years ago, and their origin and the relationship with modern humans have been debated for a long time. To solve these questions, we obtained 20 million base pairs of genomic DNA from a ~4,000-year-old Jomon male tooth, excavated in Sanganji shell mound, Fukushima, Japan. We compared his genetic components with the data of modern worldwide populations. Our major findings are: (1) Sanganji Jomon was very similar with modern East Asians when we compared the worldwide populations in the PCA plot; (2) when only East Asians were compared, Sanganji Jomon was distant from both modern Northeast and Southeast Asians, indicating that Sanganji Jomon people were already isolated from other continental populations for a long time; (3) the Sanganji Jomon male shared more SNP alleles with southern and northern minorities in China than geographically close Han Chinese, implying a complex history of people in China after the divergence between Jomon ancestors and Eurasian continent people; (4) Sanganji Jomon is genetically closer to modern mainland Japanese than continental populations, indicating that some of their components were transmitted to modern Japanese; (5) within Japanese archipelago, Ainu and Ryukyuan (the populations of northern and southern edges of the Japanese archipelago) have more Jomon components than mainland Japanese, indicating that the genetic effect of agricultural people who migrated from the Eurasian continent in and after the Yayoi period is stronger in Mainland Japanese than Ainu and Ryukyuan.

Extensive Gene Gain in Human Brain Evolution

Yong E. Zhang et al.
The genetic changes contributing to the evolution of the human brain have always attracted wide interest. A emerging consensus view is that while there have been no major patterns of genome-wide changes to the coding regions of brain-related genes, cis-regulatory changes of these genes have played a key role. Here, motivated by anecdotal studies of primate-specific genes implicated in brain function, we identified thousands of lineage-specific (primate-specific or rodent-specific) genes by mining syntenic vertebrate genomic alignments and examined the expression profile of these genes in both fetal and adult brains of human and mouse across different transcriptome profiling platforms. We found that an excess of lineage-specific genes are expressed in the early (fetal or infant) developing human brain compared with those in mouse brain. Expression data covering numerous subregions of the developing brain further demonstrate that these young genes are mainly transcribed in the neocortex. They originated in the evolutionary period during which the neocortex was expanding, suggesting the functional association of new genes with this newly evolving brain structure. Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination and also via evolution of regulatory networks, as hinted by the enrichment of primate-specific transcriptional regulators in our dataset. More than that, these ?ndings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach based on functional and evolutionary genomic methods to better annotate these non-conserved genes.

Recent Human Demography Impacts the Architecture of Genetic Disease in Populations but Not Individual Genetic Load

Yuval Simons et al.
Human populations have undergone dramatic changes in population sizes in the past 100,000 years, including a severe bottleneck of non-African populations and recent explosive population growth. There is currently great interest in how these demographic events may have affected the burden of deleterious mutations in individuals and the allele frequency spectrum of disease mutations in populations. Here we use population genetic models to show that--contrary to previous conjectures--recent human demography likely had very little impact on the average burden of deleterious mutations carried by individuals. This prediction is supported by exome sequence data showing that African American and European American individuals carry very similar burdens of damaging mutations. We next considered whether recent population growth has increased the importance of very rare mutations in disease. Our analysis predicts that, even given recent growth, it is unlikely that very rare mutations contribute a large fraction of disease heritability except for diseases that are largely due to strongly deleterious mutations. In summary, demographic history has dramatically impacted patterns of variation in different human populations, but these changes likely had little impact on either genetic load or on the importance of rare variants in most complex traits.

Functional and Population Genetic Analyses of a High-Coverage Neandertal Genome

Fernando Racimo et al.
We have sequenced the genome of a Neandertal from the Altai mountains in Siberia at 50-fold coverage. This Neandertal was located in the same cave as the Denisovan individual, but is phylogenetically closer to Neandertals from Western Eurasia. To avoid confusion, we call this individual the Altai Neandertal. Here we show an assessment of genome data quality and functional and population genetic comparisons with the Denisovan genome and a set of 25 high-coverage modern human genomes. We present an analysis of genes with recent changes in either the modern human lineage or the archaic human lineage (Neandertal+Denisova). We find enrichment for nonsynonymous changes in genes associated with melanosomes in the modern human lineage, and genes associated with particular muscoskeletal morphologies in the archaic human lineage. We utilize a compound deleteriousness scoring that allows us to combine a variety of conservation, regulatory and expression data to rank all modern and archaic-specific single-nucleotide changes and InDels across the genome, and predict which are those that could have been most disruptive in our evolutionary history. Furthermore, we overlap the modern-specific catalog with the top regions of a screen for selective sweeps exclusive to the modern human lineage, and observe enrichments for changes in genes related to ion channel activity, muscle contraction and membrane transport. Finally, we note an excess of ancestral alleles in the Denisovan individual relative to the Altai Neandertal individual, which is strongest at sites where modern humans are fixed derived. We develop an approximate Bayesian computation approach that allows us to test different models, and conclude that gene flow between the Denisovan individual and a more anciently diverged human lineage is most consistent with the patterns observed.

Multiple Episodes of Population Mixture in Southern African History

Joseph K. Pickrell et al.
The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved temporarily or permanently into the region. The influence of these interactions on the genetic structure of current populations remains unclear. Here, using patterns of linkage disequilibrium, we show that there are at least two admixture events in the genetic history of southern African hunter-gatherers and pastoralists: one involving populations related to Niger-Congo-speaking African populations, and one which introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We estimate that at least a few percent of ancestry in the Khoisan is derived from this latter admixture event, which occurred on average 1,200-1,800 years ago. We show that a similar signal of west Eurasian ancestry is present throughout eastern Africa; in particular, we also find evidence for two admixture events in the genetic history of several Kenyan, Tanzanian, and Somali populations, the earliest of which involved populations related to southern Europeans and which we date to approximately 2700 - 3300 years ago. We thus suggest that west Eurasian ancestry entered southern Africa indirectly through eastern Africa. These results demonstrate how large-scale genomic datasets can inform complex models of population movements, and highlight the genomic impact of largely uncharacterized back-to-Africa migrations in human history.

Mechanistic Models of Admixture and Approximate-Approximate-Bayesian Computation 

Noah Rosenberg et al.   

Investigations of the history of migrations that underlie admixed populations often use nonmechanistic admixture models rather than a modeling perspective that incorporates a population-genetic history of admixture built from first principles. We build a general model of admixture that mechanistically accounts for complex admixture processes, considering two source populations that contribute to the ancestry of a hybrid population, potentially with variable contributions across generations. For a random individual in the hybrid population at a given point in time, we study the fraction of admixture originating from a specific one of the source populations. Quite different admixture processes can produce identical mean admixture across individuals, but such processes typically produce different values for the variance of admixture. Interestingly, even without considering sex chromosomes, the variance of admixture for autosomes captures information about sex-specific migration in the contributions of the source populations to the admixed group. To perform inference under the model, we use approximate-approximate-Bayesian computation (AABC), a modification of approximateBayesian computation well-suited to estimation under complex mechanistic models that are computationally intensive to simulate. The model and inference method can contribute to an understanding of the theory and analysis of the history of admixed populations.

Inferring Human Population History and Migration Patterns from Multiple Genome Sequences

Stephan Schiffels, Richard Durbin
The availability of human genomes from populations across the world has given rise to new inference methods that exploit high-coverage sequence data. Among the most influential recent developments is the Pairwise Sequentially Markovian Coalescenct (PSMC) by Li and Durbin, 2011. While PSMC infers the demographic history for times between 20kya and 2mya with high resolution, neither the more recent evolutionary history nor migration patterns across populations can be adressed. Here we present a new method that overcomes both of these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) infers the recent evolutionary history within and across populations only a few thousand years ago and younger. MSMC models the pattern of mutations in multiple genome sequences under the coalescent with recombination. It fits local genealogical trees to the observed pattern, focussing on the first coalescence among any two individuals. We apply our method to the genome sequences from several family trios from the 1000 Genomes project with African, European, Asian and SouthAmerican ancestry. We infer population sizes and migration rates as a function of time with high resolution. In particular, our method resolves the more recent evolutionary history of non-African populations after the out-of-Africa event, such as the peopling of the Americas.

AAPA 2013 abstracts

The program of the 2013 meeting of the American Association of Physical Anthropologists is now online (pdf). As always, there is plenty of interest here, so I'll just highlight a few titles that caught my eye; feel free to add more in the comments.


Neolithic human mitochondrial haplogroup H genomes and the genetic origins of Europeans.

Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less prevalent amongst early Neolithic farmers (~19%) and virtually absent in Mesolithic hunter-gatherers. To investigate this haplogroup’s significance in the maternal population history of Europeans we employed novel techniques such as DNA immortalization and hybridization-enrichment to sequence 39 hg H mt genomes from ancient human remains across a transect through time in Neolithic Central Europe. The results of our population genetic analyses reveal that the current patterns of diversity and distribution of hg H were largely established during the Mid-Neolithic, but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers, which expanded out of Iberia in the Late Neolithic (~2800 BC). Using a strict diachronic approach allowed us to reconcile ‘real-time’ genetic data from the most common European mtDNA hg with cultural changes that took place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. This revealed the Late Neolithic (2800-2200 BC) as a dynamic period that profoundly shaped the genetic landscape of modern-day Europeans. Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.

Preliminary research on hereditary features of Yinxu Population.

... The 37 individuals sampled in this study have been discovered in middle to small size burials, and therefore constitute a representative sample to study Yinxu commoners’ society. Mitochondrial DNA analysis showed that the Yinxu population included the haplogroups D, G, A, C, Z, M10, M*, B, F and N9a. According to the analysis of molecular variance, the distribution frequency and the rare published data, the Yinxu population shows a closest genetic affinity with the populations of Dadianzi and Zhukaigou early Bronze Age sites (Inner Mongolia), but a more distant relation to the historical period populations. The Yinxu population is also very similar to the modern northern Han Chinese. ... 

Investigating lactase persistence in a Medieval German cemetery: A step towards understanding the rise of the European lactase persistence polymorphism (-3910C/T).

Previous ancient DNA-based studies on the Neolithic found that the incidence of LP falls below detection levels in most regions. Our research shows that between the Neolithic and Medieval periods, the frequency of LP rose from near 0% to over 50%. Also, given that the frequency of LP genotypes in modern-day Germany is estimated at 78.5%, our results indicate that rather than being stable by the Medieval period, the lactase persistent genotype has continued to increase in frequency over the last 1000 years. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistent trait and its global cultural implications.

 New Neanderthal remains from Kalamakia cave, Mani peninsula, Southern Greece.

Peeling back the layers: additional evidence for the date of the Petralona skull (Homo heidelbergensis), Greece.

,.. We conclude that there is no white sinter deposited directly on the skull and therefore the initial date of the skull given by Henning et al. and Grun’s revised date of ca. 200 ka are correct.

Analysis of archaic introgression in Ötzi the Tyrolean Iceman, a 5300 year-old prehistoric modern human.

... We carried out a series of comparisons to address these questions. By examining the Neandertal similarity of individuals from the 1000 Genomes Project, we have substantially expanded the sample of Neandertal-human comparisons. We also examined the genome of the Tyrolean Iceman, a European from approximately 5300 years ago. This is the first comparison of Neandertal genomes to the genome of a prehistoric modern human individual.

A quantitative approach for late Pleistocene hominin brain size.

... The results of our study show that Neanderthals have smaller brains than the Pleistocene AMH despite the fact that the latter are smaller in body mass. However, the Holocene AMH (7 populations) have smaller brain sizes than those of Neanderthals. ...

Re-evaluating the functional and adaptive significance of Neandertal nasofacial anatomy.

... Among Middle and Late Pleistocene Homo, there is evidence that nasal morphology varies with climate, albeit within an archaic architectural nasofacial framework. Neandertal internal nasal dimensions are greater in both height and length than archaic humans from sub-Saharan Africa. Furthermore, while other aspects of the nose are relatively broad, superior internal breadth dimensions in Neandertals are narrowed relative to sub-Saharan archaics. These differences parallel those seen in modern humans, indicating that Neandertals had an increased capacity for nasal heat and moisture exchange over their African counterparts and thus exhibit clear evidence for cold-climate adaptation. 

Selection at FADS gene cluster in Africa

A couple of quick comments. First, from the paper:

Given 207 fixed differences between chimpanzee and human in this region, we estimate a TMRCA of 1.49 (SEM = 0.23) million years for the human haplotypes. Similarly, only considering the number of mutations within the haplotype group D1, the TMRCA was 85,000±84,000 years, thus suggesting that selection in Africa occurred approximately 85 kya. 

... 

Jointly, these two sets of data support the hypothesis that advantageous mutations within the FADS gene cluster occurred prior to human migration out of Africa (~85 kya), and swept to fixation within African but not European or Asian populations.

I don't know how 85+/-84 can be used to infer that this selection occurred prior to the human migration Out-of-Africa. It seems to me that 85+/-84 is compatible with a wide variety of events. On top of this, this date depends on human-chimp split (=6.5Ma), for which a recent estimate of 7-13Ma has been advanced recently, but also 3.7-6.6Ma. So, I would say that uncertainty about when this selection took place leaves little room for pronouncements that it took place either before, or after Out-of-Africa.

Look at the following frequency map:

I sometimes think that intellectual commitment to recent Out-of-Africa-and-never-back is so strong, that the obvious explanation is overlooked. When Africans are polymorphic and Eurasians are not, this is explained as the result of the OoA bottleneck. When Africans are monomorphic and Eurasians are not -as in this paper- this is explained as the result of selection-to-fixation in Africans.

Now, I don't doubt that there was selection in Africans at the FADS gene cluster. But, rather than imagine that African humans were "tethered to marine sources for LC-PUFAs in isolated geographic regions" throughout the ecologically diverse and geographically huge continent of Africa, I can simply imagine that there was a spread of the adaptive haplotype into Africa, followed by selection, as modern humans, who originated, perhaps, in North Africa, had to drastically shift their diet as they entered Sub-Saharan Africa. I am not convinced that this is what happened, but it is certainly worthy of consideration.

PLoS ONE 7(9): e44926. doi:10.1371/journal.pone.0044926

Adaptive Evolution of the FADS Gene Cluster within Africa

Rasika A. Mathias et al.

Long chain polyunsaturated fatty acids (LC-PUFAs) are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA) from plant-based medium chain (MC) PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS) gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ~85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60–80 kya.

Link

Our big human brains may depend on DUF1220 copy numbers

This is quite remarkable, notice how Neandertals who were bigger-brained than living humans had a higher DUF1220-domain copy number (as estimated from the Green et al. 2010 data).

Certainly wondering how many DUF1220-domain copies I have :) My running estimate using my own calculator is that I have 1,493gr worth of brain, which isn't Amud- or Turgenev-worthy, but quite respectable, and which ought to translate into plenty of DUF1220 copies; I guess I'll have to wait until full genome sequencing costs drop a little more before I can find out.

From the press release:

The human brain, with its unequaled cognitive capacity, evolved rapidly and dramatically. 

"We wanted to know why," says James Sikela, PhD, who headed the international research team that included researchers from the University of Colorado School of Medicine, Baylor College of Medicine and the National Institutes of Mental Health. "The size and cognitive capacity of the human brain sets us apart. But how did that happen?" 

"This research indicates that what drove the evolutionary expansion of the human brain may well be a specific unit within a protein – called a protein domain -- that is far more numerous in humans than other species." 

The protein domain at issue is DUF1220. Humans have more than 270 copies of DUF1220 encoded in the genome, far more than other species. The closer a species is to humans, the more copies of DUF1220 show up. Chimpanzees have the next highest number, 125. Gorillas have 99, marmosets 30 and mice just one. "The one over-riding theme that we saw repeatedly was that the more copies of DUF1220 in the genome, the bigger the brain. And this held true whether we looked at different species or within the human population."

From the paper:

Among primate lineages, there is a high correlation between DUF1220 copy number (the highest copy number, greater than 270, was found in Homo sapiens [human and Neanderthal]) and increased brain size ...  as well as an increased number of cortical neurons ... Taken together, these observations support the view that DUF1220-domain copy number, i.e., DUF1220-domain dosage, functions as a general effector of evolutionary, pathological, and normal variation in brain size. 

The American Journal of Human Genetics, 16 August 2012 doi:10.1016/j.ajhg.2012.07.016

DUF1220-Domain Copy Number Implicated in Human Brain-Size Pathology and Evolution

Laura J. Dumas

DUF1220 domains show the largest human-lineage-specific increase in copy number of any protein-coding region in the human genome and map primarily to 1q21, where deletions and reciprocal duplications have been associated with microcephaly and macrocephaly, respectively. Given these findings and the high correlation between DUF1220 copy number and brain size across primate lineages (R2 = 0.98; p = 1.8 × 10−6), DUF1220 sequences represent plausible candidates for underlying 1q21-associated brain-size pathologies. To investigate this possibility, we used specialized bioinformatics tools developed for scoring highly duplicated DUF1220 sequences to implement targeted 1q21 array comparative genomic hybridization on individuals (n = 42) with 1q21-associated microcephaly and macrocephaly. We show that of all the 1q21 genes examined (n = 53), DUF1220 copy number shows the strongest association with brain size among individuals with 1q21-associated microcephaly, particularly with respect to the three evolutionarily conserved DUF1220 clades CON1(p = 0.0079), CON2 (p = 0.0134), and CON3 (p = 0.0116). Interestingly, all 1q21 DUF1220-encoding genes belonging to the NBPF family show significant correlations with frontal-occipital-circumference Z scores in the deletion group. In a similar survey of a nondisease population, we show that DUF1220 copy number exhibits the strongest correlation with brain gray-matter volume (CON1, p = 0.0246; and CON2, p = 0.0334). Notably, only DUF1220 sequences are consistently significant in both disease and nondisease populations. Taken together, these data strongly implicate the loss of DUF1220 copy number in the etiology of 1q21-associated microcephaly and support the view that DUF1220 domains function as general effectors of evolutionary, pathological, and normal variation in brain size.

Link

Orbital prefrontal cortex and social competence

Related article in Scientific American.

Neuropsychologia Volume 48, Issue 12, October 2010, Pages 3554–3562

Orbital prefrontal cortex volume correlates with social cognitive competence

Joanne L. Powell

Intentionality, or Theory of Mind, is the ability to explain and predict the behaviour of others by attributing to them intentions and mental states and is hypothesised to be one of several social cognitive mechanisms which have impacted upon brain size evolution. Though the brain activity associated with processing this type of information has been studied extensively, the neuroanatomical correlates of these abilities, e.g. whether subjects who perform better have greater volume of associated brain regions, remain to be investigated. Because social abilities of this type appear to have evolved relatively recently, and because the prefrontal cortex (PFC) was the last brain region to develop both phylogenetically and ontogenetically, we hypothesised a relationship between PFC volume and intentional competence. To test this, we estimated the volume of four regional prefrontal subfields in each cerebral hemisphere, in 40 healthy adult humans by applying stereological methods on T1-weighted magnetic resonance images. Our results reveal a significant linear relationship between intentionality score and volume of orbital PFC (p = 0.01). Since this region is known to be involved in the processing of social information our findings support the hypothesis that brain size evolution is, at least in part, the result of social cognitive mechanisms supporting social cohesion.

Link

Modern human vs. Neandertal brains

The long-term trend in human evolution has been towards larger brains. Neandertals, however, had somewhat larger brains than us. It turns out that modern humans surpassed Neandertals in the development of some areas of the brain.

Nature Communications 2, Article number: 588 doi:10.1038/ncomms1593

Evolution of the base of the brain in highly encephalized human species


Markus Bastir et al.


The increase of brain size relative to body size—encephalization—is intimately linked with human evolution. However, two genetically different evolutionary lineages, Neanderthals and modern humans, have produced similarly large-brained human species. Thus, understanding human brain evolution should include research into specific cerebral reorganization, possibly reflected by brain shape changes. Here we exploit developmental integration between the brain and its underlying skeletal base to test hypotheses about brain evolution in Homo. Three-dimensional geometric morphometric analyses of endobasicranial shape reveal previously undocumented details of evolutionary changes in Homo sapiens. Larger olfactory bulbs, relatively wider orbitofrontal cortex, relatively increased and forward projecting temporal lobe poles appear unique to modern humans. Such brain reorganization, beside physical consequences for overall skull shape, might have contributed to the evolution of H. sapiens' learning and social capacities, in which higher olfactory functions and its cognitive, neurological behavioral implications could have been hitherto underestimated factors.

Link

To survive: be fat or be smart

The bottom line is that it makes sense for an animal to combine the "fat" and "smart" strategies to survive. It makes sense: a very fat but very dumb animal has all the energy reserves it will ever need, but at the expense of locomotion efficiency, avoidance of predators, etc. A very smart but very lean animal has all the brain power needed to survive, but has very little "in the tank" if it finds itself in a bad spot and has to go without food for a long time.

The versatile strategy is best, and humans are the one species that seems to have gone the "brain power" way, without sacrificing completely other traits needed for survival.

Nature (2011) doi:10.1038/nature10629

Energetics and the evolution of human brain size

Ana Navarrete et al.

The human brain stands out among mammals by being unusually large. The expensive-tissue hypothesis1 explains its evolution by proposing a trade-off between the size of the brain and that of the digestive tract, which is smaller than expected for a primate of our body size. Although this hypothesis is widely accepted, empirical support so far has been equivocal. Here we test it in a sample of 100 mammalian species, including 23 primates, by analysing brain size and organ mass data. We found that, controlling for fat-free body mass, brain size is not negatively correlated with the mass of the digestive tract or any other expensive organ, thus refuting the expensive-tissue hypothesis. Nonetheless, consistent with the existence of energy trade-offs with brain size, we find that the size of brains and adipose depots are negatively correlated in mammals, indicating that encephalization and fat storage are compensatory strategies to buffer against starvation. However, these two strategies can be combined if fat storage does not unduly hamper locomotor efficiency. We propose that human encephalization was made possible by a combination of stabilization of energy inputs and a redirection of energy from locomotion, growth and reproduction.

Link

Interview about Morton skull collection @ Penn

This was the topic of a recent article which rehabilitated Morton and exposed Stephen Jay Gould's scientific misconduct.

Brain development in modern humans and Neandertals

From the paper:

We find that the modern human pattern of brain development is derived compared to Neanderthals. The pattern of endocranial shape changes between age groups 2 and 6 is similar among modern humans, Neanderthals and chimpanzees [7]. Neanderthals achieved endocranial volumes comparable to modern humans following this presumably ancestral pattern of development. Our results therefore provide an ontogenetic dimension to the findings of Bruner and colleagues [2]. This challenges the view that all morphological characteristics separating modern humans from Neanderthals are already established at the time of birth. However, our results are not incompatible with the findings reported by Ponce de León and colleagues [3,4,5]: when measurements of the face and neurocranium are analyzed together, the human and Neanderthal trajectories appear to be roughly parallel [3,4] because at the time of birth the face of a Neanderthal is already larger than that of a modern human (Figure 1A).

...

The development of cognitive abilities during individual growth is linked to the maturation of the underlying neural circuitry: in humans, major internal brain reorganization has been documented until adolescence, and even subtle alterations of pre- and perinatal brain development have been linked to changes of the neural wiring pattern that affect behavior and cognition [9]. The uniquely modern human pattern of early brain development is particularly interesting in the light of the recent breakthroughs in the Neanderthal genome project [10], which identified genes relevant to cognition that are derived in living humans. We speculate that a shift away from the ancestral pattern of brain development occurring in early Homo sapiens underlies brain reorganization and that the associated cognitive differences made this growth pattern a target for positive selection in modern humans.

Related: Anatomically modern humans

Current Biology, Volume 20, Issue 21, R921-R922, 9 November 2010 doi:10.1016/j.cub.2010.10.018

Brain development after birth differs between Neanderthals and modern humans

Philipp Gunz et al.

Neanderthals had brain sizes comparable to modern humans, but their brain cases were elongated and not globular as in Homo sapiens[1,2]. It has, therefore, been suggested that modern humans and Neanderthals reached large brain sizes along different evolutionary pathways [2]. Here, we assess when during development these adult differences emerge. This is critical for understanding whether differences in the pattern of brain development might underlie potential cognitive differences between these two closely related groups. Previous comparisons of Neanderthal and modern human cranial development have shown that many morphological characteristics separating these two groups are already established at the time of birth [3,4,5], and that the subsequent developmental patterns of the face are similar, though not identical [6]. Here, we show that a globularization phase seen in the neurocranial development of modern humans after birth is absent from Neanderthals.

Link

Brains to Hand-axes

Stone Age Humans Needed More Brain Power to Make Big Leap in Tool Design

Stone Age humans were only able to develop relatively advanced tools after their brains evolved a greater capacity for complex thought, according to a new study that investigates why it took early humans almost two million years to move from razor-sharp stones to a hand-held stone axe.

Wikipedia on Acheulean, and Oldowan.

PLoS ONE 5(11): e13718. doi:10.1371/journal.pone.0013718

The Manipulative Complexity of Lower Paleolithic Stone Toolmaking

Aldo Faisal et al.

Background
Early stone tools provide direct evidence of human cognitive and behavioral evolution that is otherwise unavailable. Proper interpretation of these data requires a robust interpretive framework linking archaeological evidence to specific behavioral and cognitive actions.

Methodology/Principal Findings
Here we employ a data glove to record manual joint angles in a modern experimental toolmaker (the 4th author) replicating ancient tool forms in order to characterize and compare the manipulative complexity of two major Lower Paleolithic technologies (Oldowan and Acheulean). To this end we used a principled and general measure of behavioral complexity based on the statistics of joint movements.

Conclusions/Significance
This allowed us to confirm that previously observed differences in brain activation associated with Oldowan versus Acheulean technologies reflect higher-level behavior organization rather than lower-level differences in manipulative complexity. This conclusion is consistent with a scenario in which the earliest stages of human technological evolution depended on novel perceptual-motor capacities (such as the control of joint stiffness) whereas later developments increasingly relied on enhanced mechanisms for cognitive control. This further suggests possible links between toolmaking and language evolution.

Link

Parasites and Intelligence (Eppig et al. 2010)

This is as good an explanation for global differences in IQ as I have ever seen. It proposes that IQ differences between human groups are created during ontogeny due to an energetic trade-off between brain development and immune response to infectious disease. In regions of the world with a high parasite burden, there is an elevated amount of energy used up to fight disease, at the expense of brain development.

Notice that this is not an explanation requiring genetic adaptation. Parasite burden inhibits cognitive function development. Indeed, if one were to make an adaptive argument (and I will not!), it would be in the direction of greater brain development genetic potential in parasite-heavy locales to counteract the effects of disease, i.e., the selection of individuals that may withstand the rigors of fighting off infectious disease without compromising cognitive function.

The authors write:

Multiple regression shows that, of infectious disease, temperature, evolutionary novelty and AVED, infectious disease is the best predictor of intelligence by a large margin.

...

If the general pathway we propose is correct, there are two plausible mechanisms by which a trade-off in allocation of energy to immune function versus brain development and maintenance may occur. First, parasitic infection may intermittently cause the redirection of energy away from brain development. In this case, during periods of infection, the brain receives fewer energetic resources, but this allocation to brain function will return to pre-infection levels during healthy periods. During periods of infection, whatever aspects of the brain that are growing and developing will suffer reduced phenotypic quality. Second, exposure to infectious agents may cause a developmental pathway that permanently invests more energy into immune function at the expense of brain growth. In this scenario, large amounts of energy would be allocated into immune function during periods of health, as opposed to only redirecting energy during periods of infection. This could operate through a variety of mechanisms. A plausible mechanism is that higher investment in immune system is triggered by individual exposure to infectious disease at some point during ontogeny. This may include triggering from exposure to maternal antibodies while in utero.

...

Our findings suggest that the heritable variation in intelligence may come from two sources: brain structure and immune system quality. Thus, two individuals may possess identical genes for brain structure, but have different IQ owing to differences in immune system quality reflecting their personal allocation of energy into brain development versus immunity.

...

Our findings are consistent with a number of other findings in the literature. In particular, the Flynn effect (Flynn 1987) demands that any hypothesis regarding the worldwide variation and distribution of intelligence must be able to account for some factor that allows for large IQ gains over time spans seemingly too short to be attributed to evolution by natural selection. The parasite-stress hypothesis allows for such a factor in the form of reduced parasitic infection. As societies become modernized, decreased parasite stress may occur through multiple pathways. As national wealth increases, medicine, vaccinations and potable water can be purchased by both the government and by individuals. Moreover, there is cross-national evidence that, as democratization increases, there are corresponding increases in public health legislation and infrastructure. Democratization also increases levels of education, better allowing individuals to seek out and understand information that reduces parasitic infection (Thornhill et al. 2009). This source of endogeneity is not a flaw, but a prediction of our hypothesis.

Related:

• Pathogens and Collectivism
• Religious Diversity and pathogens

Proceedings of the Royal Society B doi:10.1098/rspb.2010.0973

Parasite prevalence and the worldwide distribution of cognitive ability

Christopher Eppig et al.

Abstract

In this study, we hypothesize that the worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks. Using three measures of average national intelligence quotient (IQ), we found that the zero-order correlation between average IQ and parasite stress ranges from r = −0.76 to r = −0.82 (p less than 0.0001). These correlations are robust worldwide, as well as within five of six world regions. Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic product per capita and several measures of education are controlled for. These findings suggest that the Flynn effect may be caused in part by the decrease in the intensity of infectious diseases as nations develop.

Link

Brain structure and Personality Big Five

From the paper:

The associations of personality traits with volume in predicted brain regions were generally consistent with the hypothesis that larger brain tissue volume is associated with increased function (with the exception of the negative association of Agreeableness with volume in superior temporal sulcus). For example, Neuroticism was positively associated with volume in a region of the cingulate linked to the detection of error and response to pain, both of which increase with Neuroticism. Also, Neuroticism was negatively associated with volume in a region of PFC associated with emotional regulation, which decreases with Neuroticism. However, our findings do not provide definitive evidence to allow generalizations about the relation of volume to function, and further research should target this question directly.

Psychological Science doi:10.1177/0956797610370159

Testing Predictions From Personality Neuroscience
Brain Structure and the Big Five

Colin G. DeYoung et al.

Abstract

We used a new theory of the biological basis of the Big Five personality traits to generate hypotheses about the association of each trait with the volume of different brain regions. Controlling for age, sex, and whole-brain volume, results from structural magnetic resonance imaging of 116 healthy adults supported our hypotheses for four of the five traits: Extraversion, Neuroticism, Agreeableness, and Conscientiousness. Extraversion covaried with volume of medial orbitofrontal cortex, a brain region involved in processing reward information. Neuroticism covaried with volume of brain regions associated with threat, punishment, and negative affect. Agreeableness covaried with volume in regions that process information about the intentions and mental states of other individuals. Conscientiousness covaried with volume in lateral prefrontal cortex, a region involved in planning and the voluntary control of behavior. These findings support our biologically based, explanatory model of the Big Five and demonstrate the potential of personality neuroscience (i.e., the systematic study of individual differences in personality using neuroscience methods) as a discipline.

Link (pdf)

Empathy for one's own race neurally distinct from empathy from mankind

From the related public release:

In a rare neuroscience look at racial minorities, the study shows that African-Americans showed greater empathy for African-Americans facing adversity – in this case for victims of Hurricane Katrina – than Caucasians demonstrated for Caucasian-Americans in pain.

"We found that everybody reported empathy toward the Hurricane Katrina victims," said Joan Y. Chiao, assistant professor of psychology and author of the study. "But African-Americans additionally showed greater empathic response to other African-Americans in emotional pain."

The more African-Americans identified as African-American the more likely they were to show greater empathic preference for African-Americans, the study showed.

NeuroImage doi:10.1016/j.neuroimage.2010.03.025

Neural basis of extraordinary empathy and altruistic motivation

Vani A. Mathur et al.

Abstract

A central evolutionary challenge for social groups is uniting a heterogeneous set of individuals towards common goals. One means by which social groups form and endure is by endowing group members with extraordinary prosocial proclivities, such as ingroup love, towards other group members. Here we examined the neural basis of extraordinary empathy and altruistic motivation in African-American and Caucasian-American individuals using functional magnetic resonance imaging. Our results indicate that empathy for ingroup members is neurally distinct from empathy for humankind, more generally. People showed greater response within anterior cingulate cortex and bilateral insula when observing the suffering of others, but African-American individuals additionally recruit medial prefrontal cortex when observing the suffering of members of their own social group. Moreover, neural activity within medial prefrontal cortex in response to pain expressed by ingroup relative to outgroup members predicted greater empathy and altruistic motivation for one's ingroup, suggesting that neurocognitive processes associated with self identity underlie extraordinary empathy and altruistic motivation for members of one's own social group. Taken together, our findings reveal distinct neural mechanisms of empathy and altruistic motivation in an intergroup context and may serve as a foundation for future research investigating the neural bases of intergroup prosociality, more broadly construed.

Link

Human brain recognizes race

From the public release:

Typically, when people observe others perform a simple task, their motor cortex region fires similarly to when they are performing the task themselves. However, the UofT research team, led by PhD student Jennifer Gutsell and Assistant Professor Dr. Michael Inzlicht, found that participants' motor cortex was significantly less likely to fire when they watched the visible minority men perform the simple task. In some cases when participants watched the non-white men performing the task, their brains actually registered as little activity as when they watched a blank screen.

From the paper:

A deficit in the spontaneous ‘‘catching” of outgroup members’ actions and intentions can have serious consequences for intergroup interactions. Perception–action-coupling, and the sharing of somatic, autonomic, and emotional states, facilitate social understanding and foster helping, morality, altruism, and justice
(Batson et al., 1997; Cialdini, Brown, Lewis, Luce, & Neuberg, 1997). Thus, people might not be as responsive to outgroup member’s needs and feelings and be less likely to understand their intentions; they might also be less likely to help and effectively communicate with them.

This sounds like a good example of what I called friction in a recent post.

Also from the paper:

When we breakdown the omnibus outgroup correlation into the specific racial outgroups, we find results that are consistent with a Canadian context: the correlation was strongest for South-Asians, r (28) = .56, p less than .01, and followed by Blacks, r (28) = .36, p = .05; the correlation for East Asians, however, fell below traditional levels of significance, r (28) = .30, p = .11. Since mu activity is inversely related to motor cortex activity, these findings suggest that the more participants are prejudiced, the less their motor cortex fires in response to the passive viewing of outgroup members’ actions—an effect that is magnified for disliked outgroups (South-Asians, then Blacks, followed by East Asians).

The order of the outgroups suggests that genetic-phenotypic similarity is not the end-all, as South Asians are closer to whites but perhaps less familiar to them, due to a shorter period of their presence in Western societies.

Journal of Experimental Social Psychology doi:10.1016/j.jesp.2010.03.011

Empathy constrained: Prejudice predicts reduced mental simulation of actions during observation of outgroups

Jennifer N. Gutsell, and Michael Inzlicht

Abstract

Perception–action-coupling refers to the vicarious activation of the neural system for action during perception of action, and is considered important for forms of interpersonal sensitivity, including empathy. We hypothesize that perception–action-coupling is limited to the ingroup: neural motor networks will fire upon the perception of action, but only when the object–person belongs to the ingroup; if the object–person belongs to an outgroup these motor neurons will not fire. Using electroencephalographic oscillations as an index of perception–action-coupling, we found exactly this: participants displayed activity over motor cortex when acting and when observing ingroups act, but not when observing outgroups – an effect magnified by prejudice and for disliked groups (South-Asians, then Blacks, followed by East Asians). These findings provide evidence from brain activity for yet another detrimental aspect of prejudice: a spontaneous and implicit simulation of others’ action states may be limited to close others and, without active effort, may not be available for outgroups.

Link

People who eat a Mediterranean-like diet less likely to have brain infarcts

Mediterranean diet may lower risk of brain damage that causes thinking problems

ST. PAUL, Minn. – A Mediterranean diet may help people avoid the small areas of brain damage that can lead to problems with thinking and memory, according to a study released today that will be presented at the American Academy of Neurology's 62nd Annual Meeting in Toronto April 10 to April 17, 2010.

The study found that people who ate a Mediterranean-like diet were less likely to have brain infarcts, or small areas of dead tissue linked to thinking problems.

The Mediterranean diet includes high intake of vegetables, legumes, fruits, cereals, fish and monounsaturated fatty acids such as olive oil; low intake of saturated fatty acids, dairy products, meat and poultry; and mild to moderate amounts of alcohol.

For the study, researchers assessed the diets of 712 people in New York and divided them into three groups based on how closely they were following the Mediterranean diet. Then they conducted MRI brain scans of the people an average of six years later. A total of 238 people had at least one area of brain damage.

Those who were most closely following a Mediterranean-like diet were 36 percent less likely to have areas of brain damage than those who were least following the diet. Those moderately following the diet were 21 percent less likely to have brain damage than the lowest group.

"The relationship between this type of brain damage and the Mediterranean diet was comparable with that of high blood pressure," said study author Nikolaos Scarmeas, MD, MSc, of Columbia University Medical Center in New York and a member of the American Academy of Neurology. "In this study, not eating a Mediterranean-like diet had about the same effect on the brain as having high blood pressure."

Previous research by Scarmeas and his colleagues showed that a Mediterranean-like diet may be associated with a lower risk of Alzheimer's disease and may lengthen survival in people with Alzheimer's disease. According to the present study, these associations may be partially explained by fewer brain infarcts.

Genetic Covariation Between Brain Volumes and IQ, Reading Performance, and Processing Speed (Betjemann et al. 2010)

Related:

• Big-brained people are smarter
• Expanding Heads and Shrinking Faces
• Neuroanatomical correlates of intelligence
• Intelligence predicted by brain structure and function
• Brain volume and IQ in children

Behav Genet. 2010 Jan 14. [Epub ahead of print]

Genetic Covariation Between Brain Volumes and IQ, Reading Performance, and Processing Speed.

Betjemann RS, Johnson EP, Barnard H, Boada R, Filley CM, Filipek PA, Willcutt EG, Defries JC, Pennington BF.

Although there has been much interest in the relation between brain size and cognition, few studies have investigated this relation within a genetic framework and fewer still in non-adult samples. We analyzed the genetic and environmental covariance between structural MRI data from four brain regions (total brain volume, neocortex, white matter, and prefrontal cortex), and four cognitive measures (verbal IQ (VIQ), performance IQ (PIQ), reading ability, and processing speed), in a sample of 41 MZ twin pairs and 30 same-sex DZ twin pairs (mean age at cognitive test = 11.4 years; mean age at scan = 15.4 years). Multivariate Cholesky decompositions were performed with each brain volume measure entered first, followed by the four cognitive measures. Consistent with previous research, each brain and cognitive measure was found to be significantly heritable. The novel finding was the significant genetic but not environmental covariance between brain volumes and cognitive measures. Specifically, PIQ shared significant common genetic variance with all four measures of brain volume (r (g) = .58-.82). In contrast, VIQ shared significant genetic influence with neocortex volume only (r (g) = .58). Processing speed was significant with total brain volume (r (g) = .79), neocortex (r (g) = .64), and white matter (r (g) = .89), but not prefrontal cortex. The only brain measure to share genetic influence with reading was total brain volume (r (g) = .32), which also shared genetic influences with processing speed.

Link

Brain structure and IQ

PLoS Comput Biol doi:10.1371/journal.pcbi.1000395

Brain Anatomical Network and Intelligence

Yonghui Li et al.

Abstract

Intuitively, higher intelligence might be assumed to correspond to more efficient information transfer in the brain, but no direct evidence has been reported from the perspective of brain networks. In this study, we performed extensive analyses to test the hypothesis that individual differences in intelligence are associated with brain structural organization, and in particular that higher scores on intelligence tests are related to greater global efficiency of the brain anatomical network. We constructed binary and weighted brain anatomical networks in each of 79 healthy young adults utilizing diffusion tensor tractography and calculated topological properties of the networks using a graph theoretical method. Based on their IQ test scores, all subjects were divided into general and high intelligence groups and significantly higher global efficiencies were found in the networks of the latter group. Moreover, we showed significant correlations between IQ scores and network properties across all subjects while controlling for age and gender. Specifically, higher intelligence scores corresponded to a shorter characteristic path length and a higher global efficiency of the networks, indicating a more efficient parallel information transfer in the brain. The results were consistently observed not only in the binary but also in the weighted networks, which together provide convergent evidence for our hypothesis. Our findings suggest that the efficiency of brain structural organization may be an important biological basis for intelligence.

Link

Brain volume and IQ in children

Intelligence doi:10.1016/j.intell.2008.10.005

A genetic analysis of brain volumes and IQ in children

Marieke van Leeuwen et al.

Abstract

In a population-based sample of 112 nine-year old twin pairs, we investigated the association among total brain volume, gray matter and white matter volume, intelligence as assessed by the Raven IQ test, verbal comprehension, perceptual organization and perceptual speed as assessed by the Wechsler Intelligence Scale for Children-III. Phenotypic correlations between the brain volumes and intelligence traits ranged between .20 and .33. Processing speed and brain volume did not correlate. The relation between brain volume and intelligence was entirely explained by a common set of genes influencing both sets of phenotypes.

Link

Intelligence predicted by brain structure and function

J Neurosci. 2008 Oct 8;28(41):10323-9.

Multiple bases of human intelligence revealed by cortical thickness and neural activation.

Choi YY, Shamosh NA, Cho SH, DeYoung CG, Lee MJ, Lee JM, Kim SI, Cho ZH, Kim K, Gray JR, Lee KH.

We hypothesized that individual differences in intelligence (Spearman's g) are supported by multiple brain regions, and in particular that fluid (gF) and crystallized (gC) components of intelligence are related to brain function and structure with a distinct profile of association across brain regions. In 225 healthy young adults scanned with structural and functional magnetic resonance imaging sequences, regions of interest (ROIs) were defined on the basis of a correlation between g and either brain structure or brain function. In these ROIs, gC was more strongly related to structure (cortical thickness) than function, whereas gF was more strongly related to function (blood oxygenation level-dependent signal during reasoning) than structure. We further validated this finding by generating a neurometric prediction model of intelligence quotient (IQ) that explained 50% of variance in IQ in an independent sample. The data compel a nuanced view of the neurobiology of intelligence, providing the most persuasive evidence to date for theories emphasizing multiple distributed brain regions differing in function.

Link

Carl Zimmer article on Intelligence (and some thoughts on nature/nurture and IQ)

Carl Zimmer blogs about his Scientific American article on Intelligence. From the article:

It was with great delight that Plomin got his hands on microarrays that could detect 500,000 genetic markers--hundreds of times more than he had previously used. He and his colleagues got cheek swabs from 7,000 children, isolated their DNA, and ran it through the microarrays. And once more the results were disappointing.

“I’m not willing to say that we have found genes for intelligence,” Plomin declares, “because there have been so many false positives. They’re such small effects that you’re going to have to replicate them in many studies to feel very confident about them.”

I had blogged about this study when it came out. I repeat my comments from 2006 which are still valid today:

It appears that the hunt for genes affecting intelligence is not going well. I can't say that I'm surprised, because I have always maintained that intelligence is an emergent property of a set of co-operating genes during development in a particular environment and I don't anticipate that the geno-centric approach will take us closer to understanding it.

Intelligence, and -I believe- other complex traits are like complex dishes with many ingredients. The ingredients themselves (e.g., salt, lettuce, or chicken) are themselves unremarkable, but it is the way that they are put together and turned on and off by internal and external stimuli (the pot, the temperature, time, etc.) that makes a good dish.

I have expressed the same view in the recent entry on genome-wide association studies:

This Lego-block paradigm is based on the notion that most of our alleles are commodity "building blocks"; if they are brought together harmoneously, they produce positive results. The occasional allele may have a large effect, and some alleles fit better together than others. Yet, most of the success or failure of a construction depends on how the components fit together, and not what they are.

From the Carl Zimmer article:

Researchers have made images of their developing brains once a year, and Shaw has focused much of his attention on what the pictures reveal about the growth of the cortex, the outer rind of the brain where the most sophisticated information processing takes place.

...

In all children the cortex gets thicker as new neurons grow and produce new branches. Then the cortex thins out as branches are pruned. But in some parts of the cortex, Shaw found, development took a different course in children with different levels of intelligence. “The superclever kids started off very thin,” Shaw says. “They got really relatively thicker, but in adolescence they got thinner again very quickly.”

I had blogged about this study in 2006; check out that blog entry to see the thickness curves of cortex in development.

At the dawn of the genetics era, physical anthropologists' ideas that intelligence was correlated with the brain's observable properties were often ridiculed. And, yet neuronatomical correlates are pretty much the only game in town when it comes to giving a prediction (admittedly a very coarse one) of a person's IQ

That doesn't mean that genes don't play a role in intelligence; they do, and it's a sizeable one. But that role is hidden in a gene-gene and gene-environment interaction web of thousands of factors, where the individual components aren't really important, but the way they are put together are.

This realization also leads one to question genetic fetishists' conclusions about environmental influences on IQ.

It is true that scientists have looked at a lot of possible environmental influences on IQ and have come up short on significant environmental factors that can boost a person's IQ. There is simply very limited evidence that any particular environment can achieve this --sort of really bad influences such as malnutrition or some infectious diseases in childhood. And, yet we know that part of the variation of IQ is due to environmental influences. What gives?

What scientists have looked at are recognizable, "obvious", environmental influences (parenting style, schooling, etc.), which are analogous to the "common variants" in genetics.

Just as a microarray-based genome-wide association study has no clue about the rare family-level gene complexes and disease factors, so studies of environmental influences have no clue about the rare family/school/peer group micro-environments affecting a person's development.

Thus, the failure to find strong environmental influences on IQ doesn't strengthen the nature side of the nature-nurture divide, just as the failure to find strong genetic influences on IQ doesn't strengthen the nurture side.

The truth is, that Intelligence is an emergent property of a complex web of genetic and non-genetic interactions.

A human being is like a black box with zillions of inputs, some of them genetic, others environmental. We know that the box's output, e.g. its IQ score on a test is related to its inputs; but the relationship isn't linear and tidy: you can try different inputs from here to eternity, but you won't be able to figure out what the output is.

As I wrote in my post on height and body mass index, real progress will come about only when we finally look into the box:

Real progress will only come about with more developmental and functional studies, i.e. studies that actually look at what genes do in the body.

Figuring out how humans "work" is easier said than done. But, I believe, there is no shortcut.