Recent Foundation Publications

Blood or Bone?

The Latest Controversy in Human Evolution

Jane Hilton (2009)

Recent progress in understanding the evolution of modern humans has been largely due to the application of DNA techniques constructing gene trees. Now this achievement is confronted by new fossil evidence from China. Can we put blood before bone?

‘Out of Africa’ has been the catch cry since Cann, et al. showed mitochondrial DNA (mtDNA) analysis connected all modern humans to a root female genetic line or ‘Mitochondrial Eve’, originating in Africa around 200,000 years ago1. Subsequently an ‘Out-of-Africa Eve’ was identified, linking all modern humans who went on to populate the rest of the world.

News broke in October 2009 that a fragment of a human jawbone and teeth had been unearthed in Guangxi, southern China2. The discovery team classifies the fossil as primitive Homo sapiens. It is exceptional on the grounds it possesses a somewhat jutting chin (a chin being the mark of modern man) and is said to be about 110,00 years old, by uranium isotope dating. The locality has been a rich source of huge extinct apes and Ice Age species. The discovery may boost an alternative ‘Out of Asia’ view of man’s origins and place Chinese roots firmly on home ground.

The find has given fresh vigor to critics of the Out of Africa theory. They say it supports their wilting multi-regional hypothesis, which views modern humans as arising in situ from local Homo erectus populations dispersed around the globe. Racial differences are thus put down to isolated populations’ variation as they evolved convergently into a modern form from ancient H. erectus populations

China’s explanation for the moderately jutting jawbone is ‘continuity with hybridization’. This theory postulates the chin shape is due to interbreeding: immigrant H. sapiens from Africa making merry with local H. erectus. Naturally this presumes modern man left Africa before 110,000 years ago. Science journalist Richard Stone asks if the chin could have appeared through convergent evolution, such as if due to a single mutation, or if this proves interbreeding between species2.

The first sign of modern man outside Africa is fossil remains in the Levant (Israel and the Near East). This exodus was dated at around 125,000 years ago, which is close to a period of greening in the Sahara facilitating northward migration. Evidence for favourable conditions is found in marine sediment cores off the coast of West Africa, dated at 120,000 to 110,000 years ago3. DNA analysis, however, does not support an alternative Mitochondrial Eve surviving to modern times and it appears the first exodus failed to survive the subsequent Ice Age.

Remains in the Levant include both Neanderthal and H. sapiens. Kramer et al used non-metric traits over of a mixture of skulls to demonstrate an inability to reveal a separate

Neanderthal clade4 This argument supports an emerging human species interbreeding with resident hominins. Genetic evidence, so far, fails to support hybridization, and continues to lead back to a single south-easterly route out of Africa from which modern humans repopulate the world.

According to Svante Paabo, director of genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, analysis of the entire Neanderthal genome is imminent5. This will resolve the question of interbreeding between ‘us’ and ‘them’. He recently announced “I’m sure that they had sex, but did it give offspring that contributed to us? We will be able to answer quite rigorously with the new sequence.”

A PhD student from Leeds, Pedro Soares, recently devised a more reliable molecular clock that allows for natural selection’s removal of harmful gene mutations6. Molecular clocks depend on the accumulation over time of mutations you see in the family tree. For the first time his method uses data from the whole of the mtDNA molecule, producing more accurate and precise (narrower) date ranges. “This means that we can put a timescale on any part of the particular family tree, right back to humanity’s last common maternal ancestor...” he says. “Humanity’s ‘out of Africa’ migration was around 60-70,000 years ago—some 10-20,000 years earlier than previously thought.”

The Zhoukoudian caves of China— rich in Homo erectus remains.

This is still a whisker short of Oppenheimer’s exodus at 85,000 years—but what’s a few thousand between friends? In his book Out of Eden he sees an opportunity when an ice age lowered sea levels, combined with salinity of the Red Sea, to entice the early H. sapiens across the divide of The Gate of Grief between Africa and Arabia, towards India7. Fur- thermore, this fits with genetic and anthropological (tool) evidence of the Toba effect upon already dispersed populations in India and beyond. The eruption of Mt Toba in Sumatra left ash over much of India and a genetic divide can be found in the either side of the extinction zone between East and West Asian regions.

Shen and colleagues, from Nanjing Normal University in China, have applied a relatively new dating method on layers surrounding fossils2. Based on isotopes of aluminium and beryllium in quartz grains, they have revised dates to about 200,000 years older than first thought.

A more precise time-line for early Homo erectus now reads as leaving Africa approximately 2 million years ago, dispersing from Dmanisi, Georgia by 1.75 MYA and reaching South-East Asia by 1.6 MYA. It survived successive warm and cold periods in northern Asia, and persisted until about 30,000 to 50,000 YA, before being supplanted by modern humans derived from Africa.

Whether or not H. erectus reached Europe is still disputed, with identity of specimens, such as Spanish fossils, uncertain

With the discovery of Homo floresiensis (The Hobbit) in Flores it appears more than one early hominid dispersed from Dmanisi into far reaches of the globe. Debbie Argue’s team used cladistic analysis— based upon 60 skull and skeletal features—comparing two H. floresiensis skulls with other hominins and great apes8. Results suggested two equally probable scenarios: Homo floresiensis beginning in Africa at 1.66 million years ago, or later at 1.9 million years ago and branching after Homo habilis. Thanks to the isolation of Flores, a second human species survived up to modern times.

So will blood, or will bone, resolve puzzles of human evolution? DNA evidence builds at the same time as perplexing new fossils are exposed. In the usual way of science—more answers bring more questions!

REFERENCES

1. Cann, R.L. et al. (1987) Mitochondrial DNA and human evolution. Nature 325:31-36.

2. Stone R., (2009) Signs of Early Homo sapiens in China? Science 30:Vol. 326. no. 5953, p. 655

3. Castañeda, Isla S. et al. (2009) Wet phases in the Sahara/Sahel region and human migration patterns in North Africa. Proceedings of the National Academy of Sciences USA (PNAS)46.

4. Andrew Kramer et al (2001) Out of Africa and into the Levant: replacement or admixture in Western Asia? Quaternary International 75 Issue 1., Pages 51-63.

5. http://www.timesonline.co.uk/
tol/news/science/biology_evolution
/article6888874. ece

6. Soares, P. et al. (2009) Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. The American Journal of Human Genetics. 84, Issue 6, Pages 740- 759.

7. Oppenheimer, S. (2003) Out of Eden, The peopling of the world. Constable & Robinson Ltd

8. Debbie, A. et al (2009) Homo floresiensis: A Cladistic Analysis. Journal of Human Evolution. (in press).

9. Stringer, CB. & Andrews, P. (1988) Genetic and fossil evidence for the origin of modern humans. Science 239 (4845): 1263–8.

The History of Cattle

Adapted from an original PowerPoint presentation by J Pfistershammer

Ancient fossils show the existence of bovidae some 20 Million years ago.

There are alternative spatial and chronological models for the origin and spread of domesticated cattle.

Domestication started in southwest Asia and tamed cattle came into Europe via migrating pastoralists.

Selected, not-so-wild, Bos primigenius females were either accepted or their tractability may have been reinforced by Neolithic breeders.

Mitochondrial DNA (mtDNA) shows taurine and zebu cattle diverged before Holocene. Domestication occurred independently

Ancient DNA suggests that the Northern European Aurochsen contributed little toward domestic cattle, with the exception of some native Scandinavian and Russian and ancient Japanese breeds. The Southern European Aurochsen albeit had a significant input.

Archaeological data suggest that the major center of domestication for European Bos taurus breeds was the Fertile Crescent because a mtDNA sequence from a Syrian specimen dated from 8 - 9,000 years ago shows a typical European haplotype found both in modern breeds and the Italian Aurochsen.

Evolutionary diversification in Africa and Eurasia and subsequent remingling

Figure 1. From the Bovidae to the Bovinae and on to the present Bovine, it has taken some

20 Million years of relentless evolution

Figure 2. Phylogenetics among bison, Indian, African, European, and Japanese cattle Populations

Mannen, H. et al. Genetics 1998;150:1169-1175

Some historical facts

Hunted by man throughout the Stone Age, aurochs were immortalized by cave artists as early as 30,000 B.C.

In view of early humans' dependence on cattle for sustenance and - long before the horse - transportation, it isn't surprising that bulls and cows figured prominently in ancient religious beliefs and myths.

In most bull cults the bull was a more sacrificial victim than other gods. In ancient Crete, birthplace of the legendary half-man, half-bull Minotaur, the Minoans paid particularly savage homage to the bull.

Bull sacrifice was practiced by the Greeks, Romans, and Druids. Bovines often fared better in Egypt, where it was believed that the sacred bull-god Apis was mysteriously born and reborn in a series of black bull calves.

In England, bull baiting, in which dogs attacked shackled cattle, was a popular sport from 1570 to 1835, when it was mercifully outlawed. Even today, the cult of bull sacrifice endures in the bullfighting rings of Spain, where there's, in the end, always one sure loser - the bull.

Christopher Columbus carried long-horned cattle from Spain to the West Indies on his second voyage to the New World in 1493; and the Pilgrim Fathers imported cattle to New England in 1624.

By the early 1970s, there were more than 1,118 million cattle in the world; of those, about 112 million were in the U.S. India has more cattle (over 300 million) than any other country, but because of its religious taboos the lowest consumption of beef.

The purpose of domestication

Historically cattle were dual-purpose animals

Neolithic man domesticated beasts to provide a more reliable source of protein in the form of milk and meat for his group. Later on, due to the need for moving armies around their empire, the Romans preferred large cattle breeds that also gave some milk for the soldiers. In the early days of farming, before the horse became the main power source, cattle provided draught power in addition to meat and milk. In Africa some cattle are even kept for their blood. So cattle can in fact be triple-, or multipurpose.

Modern dual-purpose

These are breeds, such as the Simmental, the Fleckvieh, the Gelbvieh, the Maine- Anjou, etc. that provide both meat and milk.

Loss of popularity

British farmers especially wanted more specialised breeds. They got fed up with females that went to beef and beef animals that went to milk! The breeding objectives could easily get confused - it was easier to specialise and progress towards a preferred type was faster.

Specialization

Dairy farmers wanted litres, fat and protein - and not beef. Genetic improvement programmes and AB brought about great increases in dairy characteristics. They did not want this complicated by beef traits. Beef farmers do not need nor want the excessive milk that modern dairy cows are able to produce. The fact that the Shorthorn, for example, was split into a Dairy Shorthorn and a Beef Shorthorn shows the frustration breeders found with the original dual-purpose Shorthorn breed.

Ideal beef through the last few centuries

In Britain the ideal beast initially was extremely fat since most beef was either cooked on the spit or either smoke or salt cured. Fat yielded a much sought after energy source for soldiers and workers alike. Only late in the last century have dieticians forced a much leaner type of meat onto the market.

In conjunction with an economic desire for greater growth efficiency and the requirement to avoid poly-unsaturated fats the beef industry ended up with high-yielding carcasses covered in tasteless muscle.

It seems with the discovery of Wagyu beef that this excessive trend is in regression. A sensible amount of fat, as long as it in the form of white marbling and of a predominantly mono-unsaturated type, is once again a sought after component of beef. Also, a reasonable fat cover is desirable to protect the carcass during chilling and freezing.

The case for a Jersey origin as a probable source of Wagyu marbling

The history of the Jersey breed can be traced back to 6000BC to the middle east. Dutch emigrants took Jersey cows with them to provide milk whilst on board and wherever they settled. In the 16th and 17th century there were European (e.g. Portuguese & Spanish missions) trading settlements in the West of Japan where beef consumption was common way before it became fashionable in the rest of the country (Lane Earns, University of Wisconsin, Oshkosh).

Today Jerseys are well known for their high fat content milk production capacity (i.e. lactations of over 10,000L). The Wagyu, on the other hand, is a rather poor milk producer (lactations of a mere 1,000L are the norm), like the Jersey used to be.

As with the Wagyu, one of the most outstanding characteristics of beef from Jersey cattle is the high level of intramuscular fat. Even under pasture feeding conditions alone, the genetic potential of the breed to deposit intramuscular fat implies that a high level of marbling can be obtained at low carcass weights.

Beef from Jersey cattle has the lowest values of Warner-Bratzler shear force, which is an objective mechanical measurement of tenderness. Taste panels have consistently rated meat from Jersey cattle as being more acceptable due to its greater tenderness, juiciness, flavour and overall acceptability.

Jersey cross cattle have mono-unsaturated fat concentrations that are significantly higher than other breeds. The interest in mono-unsaturated fat level arises from the ‘Beef Production from Jersey Cattle, Massey University, 2001 fact’ that these fatty acids, once seen as cholesterol “neutral”, are today considered cholesterol “lowering” or “healthy” and are preferable to high levels of poly-unsaturated fats.

Sadly, beef from Jersey cattle does contain more yellow fat compared to larger dairy and most beef breeds. Consumers prefer white or creamy white fat in beef as yellow fat is typically associated with old cattle. However, the differences in fat colour at slaughter between the breed groups are often not evident after a careful consideration of carotin-free feed components and chilling of the carcass for at least 48h.

The latest trend in beef production

Derived from the Jersey, Wagyu (i.e. “Japanese cattle/beef ”) has a softer fat, which improves the meat flavour and taste. The improvement is due to the higher ratio of mono-unsaturated fatty acids (MUFA) to saturated fatty acids. The IMF (intermuscular fat) of Wagyu cattle is twice as high in mono-unsaturated fats as traditional breeds. This results in a ’healthier’’product.

Research that first identified this higher level of mono-unsaturated fat in Wagyu cattle has also considered that this is the explanation for the characteristic superior flavour. Marbling is the most reliable indicator of meat taste and tenderness. Wagyu are most renowned for their inherent marbling ability or intramuscular fat (IMF). They have recorded 17% more IMF by chemical extraction than Angus with the same marbling score.

To its credit, Australia has the best accumulation of Wagyu (Japanese Black Cow as against Japanese Brown Cow and Japanese Polled Cow) genetics outside of Japan. We are a country free of those diseases, which restrict exports from other countries. Luckily Australia is a clean, green supplier of Wagyu for the world, and the Australian Wagyu Association keeps it that way with mandatory DNA parentage verification of all seed stock submitted for registration. Sadly, though, the pure Wagyu is unsuited for Australian managements.

Conclusion

It can be said that the Wagyu, as we know it now is a fixed cross between the native Japanese and the Jersey, with the Angus breed a later addition. In the late 19th and the early 20th century, during the so called “Meiji Restoration”, European cattle (inter alia Angus) were for the first time allowed back into Imperial Japan.

The official records have it that the Japanese Black Poll, which is the least numerous of the 3 Wagyu strains, is actually derived from Angus. The latter having been crossed with the then still unimproved Japanese cattle. The Japanese Brown is the 2nd least numerous and probably stems from crossings with Fleckvieh or Gelbvieh.

Since each Prefecture (e.g. Kobe) cultivated its own closely guarded crossbred cattle it is entirely feasible that for the sake of a small increase in meat production the relatively small and at that time still largely unimproved Angus was wittingly introduced as the 3rd breed to create the Japanese Black, the most numerous.

Japanese farm holdings are quite small and the animals needed to be tethered. Horn growth did not matter. In fact, the latter was sought after since a polled animal makes a poor worker when pulling a plough or cart.

Anyhow, the fact is that there now exists a unique animal that yields healthy, tasty and tender beef!

Evolution

Professor Roger L. Dawkins

A recent critique of Charles Darwin explores the origin of the ideas as distinct from the evidence presented in ‘The Origin of Species’ (1959). Melvyn Bragg (2008) quotes Darwin who wrote that Robert Chambers (1844) displayed “little accurate knowledge” but thanked him for “preparing the ground for the reception of analogous views”. Darwin acknowledged that W C Wells (1818) recognised the principle of natural selection. Even earlier, Lamarck (1809) had understood the issues but, according to Bragg, distorted the facts because he believed that men had been created recently to wit at 0900 on October 23rd, 4004 BC.

All commentators acknowledge that Alfred Russell Wallace collected independent evidence to arrive at the same conclusions as Darwin.

Bragg invites the conclusion that Darwin’s extraordinary pre-eminence and increasing fame are largely based on his careful management of what might now be denigrated as media spin. Nevertheless, it is clear that he owes a debt to his extraordinary and influential friends and to a society which permitted wealth and leisurely study. Increasingly, there must be many potential Darwins, Wallaces and Lamarcks who need long-term friends and patient support. The Village hopes to identify such potential.

2008/2009 Genetic Activity Summary

John Millman

Haplospecific Markers.

The understanding of the underlying principles driving successful prediction of heritable polymorphisms via Entwinement has progressed dramatically. Entwinement identifies sequence structures which are not polymorphic but rather are very stable in genomes. These identifiable structures are bounded by sequence which is relatively highly polymorphic and useful for haplotype identification. This class of structures tend not to be geometric in the sense associated with Haplospecific Geometric Elements (HGEs) and hence are not detectable using more traditional methodologies (e.g. dotplots or Blast)

Workshops have been run to empower CYO staff to utilise the technology and time will tell if there is significant usage made of the ENTWINEMENT invocation of the technology. The MRip cattle marker was developed using the embedded mathematical approach when all other technologies had been unsuccessful. Markers have been developed in the TRPM1 region of the horse genome to define genetic identifiers for the APALOOSSA phenotype. This is an ongoing project which has had mixed but undefinable success to date. Much has been learnt and we are now in a very good position to carry this work forward.

Significant Single Nucleotide Polymorphisms (SNPs)

Predicting where to look for significant SNPs has been progressing using the hypothesis that SNPs which dramatically change the secondary and tertiary structures within either single stranded DNA or RNA will change either the protein expressed or regulate the expression of the associated molecule. We can, and have, been able to identify significant SNPs in a number of tests.

ENTWINEMENT – Human Chromosome 1 – The RCA region

Building a meaningful story to make publication of Entwinement worthwhile has meant choosing a project with high public and scientific interest but relatively small progress. Availability of appropriately well categorised DNA with known phenotypic information and defined providence as well as age matched controls was a major consideration. Defining relationships between the Autoimmune system (Complement) and Autism Spectrum Disorders was chosen as the vehicle for demonstrating the utility of Entwinement as a method for exploring previously unknown genetic order. Markers in the RCA block on chromosome 1 have been developed for C4BPa and C4BPb. (C4 is a major component of the immune cascade. C4 Binding Protein (C4BP) is the major regulator of C4 and acts by binding with C4 and hence down-regulating the amount of systemically available C4. C4BP consists of two proteins – encoded by C4BPa and C4BPb.) Preliminary data suggests previously undiscovered multiple copies of C4BPb in some individuals. An interesting fringe benefit of the work has been the discovery of an association between the number of copies and particular alleles of C4BPb and Sjogren’s’ Disease (P < 0.03). DNA extraction, purification and quantification from approximately 90 ASD and 100 age matched controls has been completed. (A positive diagnosis of ASD demands onset of symptoms before age three hence the need for age matching.)

Pulsed Magnetic Field Separation (PFMS) of large molecules and DNA fragments.

A significant problem has been identified as part of the Apaloossa project being headed by Dr Charlie Stewart. There is strong evidence to infer that different arrangements of the area of the specific chromosome differs between animals. We would like to have the ability to define structure other than by sequencing ~15Mbase fragments. A similar problem has been identified as part of the previously mentioned project where we would like to be able to view the structure of the RCA block by magnetic separation, antibody provocation and staining.

The preliminary design work and working drawings have been produced for this project. The materials for the construction of the magnetic field creation and control have been purchased and sized. The drawings for the carrier devices and separating membranes have been completed and given to a local TAFE for fabrication via CNC machining. There is growing support for this project given that it has the potential to be able to separate and identify haplotypes of DNA segments as a side effect. This project also has the potential to act as an excellent joint venture between TAFE and CYO and will be useful in making young people aware of the existence and work of the CYO ERADE Village.