Tag Archives: Human evolution

The Hofmeyr skull

For thoroughness sake I’m posting this piece on the Hofmeyr skull. Its the complete article, not just the abstract on the link.

Contrary to what I’ve seen in written a couple of sites, this isn’t a Caucasian skull. It’s got a mix of characteristics. Although Hofmeyr is similar in size to Eurasian UP crania, it differs from them in other respects (such as its broad nose and continuous supraorbital tori). that said, it does measure up closer to EUP crania than anything, as this twig diagram shows.

Late Pleistocene Human Skull from Hofmeyr, South Africa, and Modern Human Origins
F. E. Grine,1* R. M. Bailey,2 K. Harvati,3 R. P. Nathan,4 A. G. Morris,5 G. M. Henderson,6 I. Ribot,7 A. W. G. Pike8

The lack of Late Pleistocene human fossils from sub-Saharan Africa has limited paleontological testing of competing models of recent human evolution. We have dated a skull from Hofmeyr, South Africa, to 36.2 ± 3.3 thousand years ago through a combination of optically stimulated luminescence and uranium-series dating methods. The skull is morphologically modern overall but displays some archaic features. Its strongest morphometric affinities are with Upper Paleolithic (UP) Eurasians rather than recent, geographically proximate people. The Hofmeyr cranium is consistent with the hypothesis that UP Eurasians descended from a population that emigrated from sub- Saharan Africa in the Late Pleistocene.

I’m still having a think as to how this skull fits into the grand scheme of things. I’m going to take a look into sub Saharan DNA studies to see if there’s any indication of a migration from East Africa to South Africa at that time that could explain it’s presence.  From a little digging there may possibly have been a second movement out of Africa prior to 50k ago that might explain the similarities.

hofmeyr

 I should comment on the totally ridiculous date for the OOA exit (65k to 25k ago) since Aborigines seem to have arrived in Australia about 60,000 years ago, and the Eurasian M mt DNA clade is about 65,000 years old, as well as the remains in Israel being about 95k old. Its A failing in a lot of articles I see. They don’t seem to compare the dates of recent finds before typing up propsed exit dates.

The antiquity of M Mt DNA macrohaplogroup

Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages
Revathi Rajkumar,1 Jheelam Banerjee,1 Hima Bindu Gunturi,1 R Trivedi,1 and VK Kashyap1. Pub 2005

Background
Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.
Results
The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.
Conclusion
This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M major haplogroup.

They are going to have to redraw some of those migration pattern maps for the Mt DNA.

It seems that L3 was the OOA lineage, and both N and M arose in West Asia, about 63,500 and 65,000 years ago (although, personally I suspect the dates are a closer to the older edge of the possible range than the average, and are more like 80,000 years old for haplogroup M). This is the second study I’ve seen that places M as an Asian mutation.  I am uncertain as to the Gate of Tears (Red sea) as the exit route. I think the Nile still has a lot going for it as an exit point.

A serial founder effect model for human settlement out of Africa

A serial founder effect model for human settlement out of Africa

Omkar Deshpande, Serafim Batzoglou, Marcus W. Feldman, L. Luca Cavalli-Sforza

Abstract

The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50–60Kyr ago and archaeo–ethno–demographic information. In addition to a colonization rate of 0.09–0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.

I noticed this when nosing through Dienekes blog (once a week on average). This pretty much supports my ‘weak eden’ stance, although I’d certainly say huh? over the OOA date as being way to recent (Australoids were entering Oz and South America about 50k ago, and the Liujiang skull is at least 68k old). I’m not sure what kind of difference an older exit date would make to their study though. If I ever find the entirety of this paper I’ll post it.

The Dali crania, Shaanxi province China.

One of those awkward ‘doesn’t fit the OOA’ paradigm skulls, from China. It was found in 1978, and it’s age is very roughly 209,000 years old. It’s described as being morphologically halfway between modern humans and Homo Erectus, so it’s been placed in the ‘archaic’  Homo Sapiens category for now.

A more thorough discussion of the skull here.

ASPM and MCPH1 and intelligence not linked.

The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence.

Mekel-Bobrov N, Posthuma D, Gilbert SL, Lind P, Gosso MF, Luciano M, Harris SE, Bates TC, Polderman TJ, Whalley LJ, Fox H, Starr JM, Evans PD, Montgomery GW, Fernandes C, Heutink P, Martin NG, Boomsma DI, Deary IJ, Wright MJ, de Geus EJ, Lahn BT.

Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA.

Recent studies have made great strides towards identifying putative genetic events underlying the evolution of the human brain and its emergent cognitive capacities. One of the most intriguing findings is the recurrent identification of adaptive evolution in genes associated with primary microcephaly, a developmental disorder characterized by severe reduction in brain size and intelligence, reminiscent of the early hominid condition. This has led to the hypothesis that the adaptive evolution of these genes has contributed to the emergence of modern human cognition. As with other candidate loci, however, this hypothesis remains speculative due to the current lack of methodologies for characterizing the evolutionary function of these genes in humans. Two primary microcephaly genes, ASPM and Microcephalin, have been implicated not only in the adaptive evolution of the lineage leading to humans, but in ongoing selective sweeps in modern humans as well. The presence of both the putatively adaptive and neutral alleles at these loci provides a unique opportunity for using normal trait variation within humans to test the hypothesis that the recent selective sweeps are driven by an advantage in cognitive abilities. Here, we report a large-scale association study between the adaptive alleles of these genes and normal variation in several measures of IQ. Five independent samples were used, totaling 2393 subjects, including both family-based and population-based datasets. Our overall findings do not support a detectable association between the recent adaptive evolution of either ASPM or Microcephalin and changes in IQ. As we enter the post-genomic era, with the number of candidate loci underlying human evolution growing rapidly, our findings highlight the importance of direct experimental validation in elucidating their evolutionary role in shaping the human phenotype.

Another brain function and DNA study

Recently-derived variants of brain-size genes ASPM, MCPH1, CDK5RAP and BRCA1 not associated with general cognition, reading or language

Timothy C. Batesa, b, , , Michelle Lucianoa, Penelope A. Lindb, Margaret J. Wrightb, Grant W. Montgomeryb and Nicholas G. Martinb aDepartment of Psychology, University of Edinburgh, UK bQueensland Institute of Medical Research, Australia

Received 11 September 2007;  revised 1 February 2008;  accepted 9 April 2008.  Available online 16 May 2008.

Abstract
Derived changes in genes associated with primary microcephaly (MCPH) have been suggested to be “currently sweeping to fixation” i.e., increasing in frequency in most populations, with the likely outcome that the derived allele will completely displace the ancestral allele over time. Possible causes for this sweep include effects on human reasoning and language. Here we test the hypothesis that these derived alleles are associated with current variation in spoken or written language and related traits. The association of derived alleles of the ASPM, MCPH1, CDK5RAP2 and BRCA1 genes was tested against well-validated measures of dyslexia, specific language impairment, working memory, IQ, and head-size in a family-based association study of over 1776 subjects from 789 families of twins. No evidence for association was found for any gene to any trait. The results strongly did not support the hypothesis that derived alleles in MCPH-related genes are related to the evolution of human language or cognition. Results were compatible with the alternate hypothesis, suggesting that adaptations in these genes associated with a dramatic increase in brain size have long since reached fixation and are now maintained by stabilizing selection.

Which kind of contradicts the last one at least a bit.

A common SNP of MCPH1 is associated with cranial volume variation in Chinese population

A common SNP of MCPH1 is associated with cranial volume variation in Chinese population

Jin-kai Wang1,2,4, Yi Li3 and Bing Su1,2,*
1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology 2 Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming, Yunnan, PR China 3 Department of Chemistry and Life Science, Qujing Normal University, Qujing, Yunnan, PR China 4 Graduate School of Chinese Academy of Sciences, Beijing, PR China

Received November 17, 2007; Revised December 23, 2007; Accepted January 16, 2008

Microcephaly (MCPH) genes are informative in understanding the genetics and evolution of human brain volume. MCPH1 and abnormal spindle-like MCPH associated (ASPM) are the two known MCPH causing genes that were suggested undergone recent positive selection in human populations. However, previous studies focusing only on the two tag single nucleotide polymorphisms(SNPs) of MCPH1 and ASPM failed to detect any correlation between gene polymorphisms and variations of brain volume and cognitive abilities. We conducted an association study on eight common SNPs of MCPH1 and ASPM in a Chinese population of 867 unrelated individuals. We demonstrate that a non-synonymous SNP (rs1057090, V761A in BRCA1 C-terminus (BRCT) domain) of MCPH1 other than the two known tag SNPs is significantly associated with cranial volume in Chinese males. The haplotype analysis confirmed the association of rs1057090 with cranial volume, and the homozygote males containing the derived alleles of rs1057090 have larger cranial volumes compared with those containing the ancestral alleles. No recent selection signal can be detected on this SNP, suggesting that the brain volume variation in human populations is likely neutral or under very weak selection in recent human history.

I don’t know if it makes the brain any bigger or better though. Although, I’ve seen a few studies that positively correlate brain size and IQ from MRI scans.

Analysis of multiple alleles reveals human family tree.

Reconstruction of Human Evolutionary Tree Using Polymorphic Autosomal Microsatellites

ABSTRACT Allelic frequencies of 182 tri- and tetraautosomal microsatellites were used to examine phylogenetic relationships among 19 extant human populations. In particular, because the languages of the Basques and Hunza Burusho have been suggested to have an ancient relationship, this study sought to explore the genetic relationship between these two major language isolate populations and to compare them with other human populations. The work presented here shows that the microsatellite allelic diversity and the number of unique alleles were highest in sub-Saharan Africans. Neighbor joining trees based on genetic distances and principal component analyses separated populations from different continents, and are consistent with an African origin for modern humans. For the first time, with biparentally transmitted markers, the microsatellite tree also shows that the San are the first branch of the human tree before
the branch leading to all other Africans. In contrast to an earlier study, these results provided no evidence of a genetic relationship among the two language isolate groups. Genetic relationships, as ascertained by these microsatellites, are dictated primarily by geographic proximity rather than by remote linguistic origin.

Fig. 3. Principal components (PC) analyses based on allele frequencies of 182 microsatellite markers in 19 worldwide human populations. A: Two-dimensional plot of PC1 vs. PC2, including chimpanzee samples. Bidimensional plots of PC1 vs. PC2 (B), PC1 vs. PC3 (C), and PC2 vs. PC3 (D), excluding chimpanzee samples.

You’ll need to enlarge this one to read it.

As can be seen from this analysis of multiple loci (182 to be precise) Greeks are neatly placed in with the rest of Europe, effectively contradicting the dumbass ‘study’ by a Macedonian from a few years ago that tried to claim they were all originally from Ethiopia and not closely related to other Europeans.

This paper supports the out of Africa theory, and I have a quibble with it. The number of unique alleles in Africa is 125, but in the rest of the world is 268, showing more unique DNA ‘out of Africa’ than in it. This would seem to contradict the OOA theory somewhat. I mean, Europe has had a much smaller human occupation period than Africa, and smaller population, but the ‘unique allele’ number is only about half of Africa’s (125 v 59). Bearing in mind that humans have been in Africa in the the longest and probably had the largest modern human population for most of our evolution, …  there should be a lot more difference between the two. A lot of ‘unique alleles’ seem to appear in too short a time in the non-African population.

Population expansions and the acceleration of human divergence since the Neolithic.

I was reading (can’t remember where) that the speed of human population differentiation really seems to have speeded up since the introduction of agriculture, for multiple reasons. Essentailly, the main reason is that due to our revolutionary changes in lifestyle (diet, sedentism) we’ve been put through more selective sweeps in the past ten thousand years than you’d have seen in the past tfifty thousand.

 I’ve decided to list a few of the causes, and some of the effects. Anybody who spots anything I’ve missed let me know.

Diet:

Hunter gatherers eat a diet that is primarily made of animal flesh, fat and protein. Farmers eat mainly carbohydrate. There are several changes needed to adapt to this new diet, and variations of it.

  • Lower insulin resistance… insulin resistance plus a high carb diet equals diabetes, infertility and obesity. This is seen very clearly in recently integrated hunter gatherer peoples like the Aborigines. There is also the suggestion that many degenerative diseases are attributable to high carbohydrate diet and it’s lower levels of antioxidants (vitamins and uric acid).
  • Lighter skin (cooler climes)….grain based diets are much lower in vitamin D. Only a minor issue if you are a hunter gatherer with access to plenty of fresh offal, but critical if you eating a subsistence grain based diet.
  • Omega three oils… plentiful in a hunter gatherers diet, but rare and only of poor quality in vegetable sources. This is going to encourage the development of people with brain development less sensitive to low levels of O3 oils (mental health and behavioural issues are made worse/introduced on a low O3 diet).
  • Lactose tolerance… The lactase persistence trait in Europeans is approaching fixation in Northern Europe, but it’s only about 8,000 years old.
  • Gluten tolerance.. crucial if you are eating a wheat based diet. Gluten intolerance will make you quite sick, and appears to have been rapidly selected out of Europeans, with places like Ireland and Finland showing just a couple of percent of the population being gluten intolerant now.
  • Alcohol tolerance.. Living in a sedentary fashion gives rise to dense populations and contaminated water. In Europe, the standard method of sterilising the water was to add alcohol to it. In the far East the method of sterilising it was to boil it and make tea. This seems to have made Europeans a little better at processing the toxic by-products of alcohol.

Diseases;

Living in much greater population densities than hunter gatherers ever could, farmers are exposed to more pathogens because;

  • More people to harbour a new virulent disease mutation (twice the population, twice the risk of a nasty new disease).
  • More people to act as host and carrier to new and old diseases.
  • Lack of mobility. Mobile people can much more easily quarantine a sick individual by moving on.
  • Contaminated water, not such an issue for lower population densities, or mobile people.
  • Continuous contact with livestock introducing new pathogens (bird flu, poxes, etc) and parasites.

Reproductive strategies;

Female hunter gatherers tend to space out pregnancies to every three or three and a half years, usually by prolonged breastfeeding. It’s impractical to have two babies that need carrying, so the elder child needs to be walking well before the new baby comes.

However, agricultural communities don’t have to abide by this. Babies can be weaned early onto goat or cows milk, fed soft soaked grains at an earler date than pre-chewed meat, and they don’t need to be able to keep up with the grown ups before the next baby is born. This makes the spacing for the births closer together. Slightly detracting from this higher fertility rate is the higher mortality rate from poor nutrition and disease, but the farmers will still have an increasing population.

Also, male reproductive strategies are different. Land can be owned, wealth accumulated and more than one wife can be supported by a succesful man. Also, a new wife later in life is possible, as a landowner doesn’t have to personally do the labour, and lives longer and can provide for children even at a later age (not an option for an ageing hunter). This will reduce the amount of males that reproduce.

All this recent selective pressure, probably starting around 15,000 years ago in several locations, might explain the recent rapid changes in the areas that have farming. The dentition has certainly changed; Europeans and Asians generally have much smaller teeth than their ancient ancestors, and less developed jaws as food has become more processed.

One of the effects this kind of selection would also lead to is the success of groups that have some kind of genetic adaption to it’s new lifestyle. Like the development of a resistance to malaria in the Bantu people. If an adaptation is a trait to survive in a new environment is due to multiple genes, the new population will have a massive advantage. A ‘single gene’ trait like lactose tolerance will spread very rapidly under it’s own selective pressure, probably outrunning the spread of the original population that it arose in. However, if a trait (like a disease resistance) requires multiple genes to be effective, the original population will expand massively, partially absorbing but most replacing the people there before. This would drastically alter the appearance of the people living in an area.

This might explain the fast, massive expansions of the Mongoloid east Asians and the Bantu Africans. Each appears to have expanded very rapidly from a relatively small core population, effectively replacing the people who were there before. Also, this could explain the colonisation pattern of the Americas, where Australoid people seem to have been the first settlers. The Jomon-like Asians appear to have moved in later in North America, as well as the European Solutreans at a similar date. Then the Mongoloid Americans (place of origin uncertain) arose and expanded over the entire continent.

There also appears to have been a population expansion originating from Southern Turkey about 10,000 years ago, which spread across North Africa, Southern Asia, Western China and Southern Europe. This appears to have been the expansion of the Neolithic revolution, oddly in two languages, Afro-Asiatic and Indo-European. This is probably why Southern Europeans don’t look a lot like the earlier inhabitants from 15,000 years ago, they were overwhelmed by colonists from Turkey. Northern Europeans do still seem to bear a strong resemblance to ‘Cro Magnon’ people, generally just being slightly smaller in proportion, so it seems that expansion stalled in Southern Europe.

The Liujiang skull.

So this is the skull that’s causing all the fuss, the Liujiang skull. it was found in Tongtianyan in the Guangxi Zhuang Autonomous Region (South Easternmost China) in 1958 by people collecting fertilizer.

There’s a bit of uncertainty over its age; a uranium series gave a date of 67,000 years +/-5,000; but the flora and fauna in the cave seem to indicate an older date. There are also some modern human teeth found in the same area with a very old date of 94,000 BP. So really the only date you could give it is ‘inconveniently old for the recently out of Africa theory’.

The skulls don’t really bear more than a passing resemblance to modern mongoloid Asians, there being some significant differences in the teeth at least. The eye orbits are more rectangular as well. This also agrees with other data showing that modern mongoloids area a rather recent arrival in Asia, who have become massively successful in a very short space of time- the oldest Mongoloid shaped skull in Asia being about 7,000 years old.

  

 

U-Series dating of Liujiang hominid site in Guangxi, Southern China

21 July 2002;  accepted 9 September 2002.

It has been established that modern humans were living in the Levant and Africa ca. 100 ka ago. Hitherto, this has contrasted with the situation in China where no unequivocal specimens of this species have been securely dated to more than 30 ka. Here we present the results of stratigraphic studies and U-series dating of the Tongtianyan Cave, the discovery site of the Liujiang hominid, which represents one of the few well-preserved fossils of modern Homo sapiens in China. The human fossils are inferred to come from either a refilling breccia or a primarily deposited gravel-bearing sandy clay layer. In the former case, which is better supported, the fossils would date to at least 68 ka, but more likely to 111–139 ka. Alternatively, they would be older than 153 ka. Both scenarios would make the Liujiang hominid one of the earliest modern humans in East Asia, possibly contemporaneous with the earliest known representatives from the Levant and Africa. Parallel studies on other Chinese localities have provided supporting evidence for the redating of Liujiang, which may have important implications for the origin of modern humans.