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paleoanthropology, genetics and evolution

Anthropology 105

  • Modern human crania

    Mon, 2011-12-05 00:54 -- John Hawks
    Synopsis: 
    The skulls of modern humans are distinguished by several features from Neandertals and other ancient people.

    By the end of the Middle Pleistocene, people throughout the inhabited world had attained brain sizes in the range of living people. Technology had ad- vanced beyond the Acheulean in Africa and Europe, with more regional vari- ability and new tool types. But still, these ancient people were very different from living humans. They retained large faces and teeth, a sloping forehead, browridges, and other features that remain rare today. Even within the past 200,000 years, substantial evolutionary changes still were happening to an- cient people, transforming their bodies and brains.

    In comparison with most Middle Pleistocene fossils, living people usually have several features:

    • a more vertical forehead
    • a more rounded cranial vault profile
    • the reduction and loss of a browridge
    • the reduction in size of the face
    • and the presence of a chin

    These are sometimes called modern human features, because they are found in living populations and their immediate ancestors. These modern human features were not found equally in all regions during the Late Pleistocene. Most of them appeared first in Africans, particularly in the 190,000-year-old Omo I skull and the 165,000-year-old Herto crania. Somewhat later, these early modern humans ranged across Africa from the Mediterranean coast all the way to South Africa. By 100,000 years ago, a series of fossil individuals from present-day Israel shows the influence of these modern features.

    Only after 50,000 years ago did these modern human anatomies spread across South Asia, into Australasia and Australia, north into China, and northwest into Europe.

    Examine the crania at this station, which represent the earliest modern humans from present-day Israel (Skhul, around 100,000 years old), and from Europe. How are they different from the skulls of recent humans? How are they different from Neandertals?

    Study terms: 
  • Neandertal cranial anatomy

    Mon, 2011-12-05 00:43 -- John Hawks
    Synopsis: 
    A guide to features that distinguish the skulls of Neandertals

    The Neandertals were Late Pleistocene inhabitants of Europe, and their skeletal remains were among the first fossil humans that scientists recognized as representatives of an ancient human group. The name, “Neandertal” comes from the Neander valley in Germany, where a single partial skeleton was found in 1856. This name originally was spelled “Neanderthal” in written German of the late nineteenth century, and that spelling continues to be a correct alternative used in many scientific and popular publications. Lucky preservation and the great activity level of European archaeologists and pa- leontologists have left a substantial fossil record of the Neandertals, more so than in any other region of the world. The Neandertals persisted until after 30,000 years ago in Western Europe. Fossils with anatomical similarities to the European Neandertals have also been found in West and Central Asia, and are often called Neandertals themselves.

    It can be difficult or impossible to divide Neandertals from other people based on small fossil fragments. Instead of one single feature, usually a constellation of different features contribute to the identification of Neandertal fossils. Because there are so many Neandertal fossils, anthropologists have identified many different features that help to set them apart:

    At this station are some casts Neandertal skulls, in comparison with modern humans. Work at identifying the following features:

    • occipital bun
    • supraorbital torus
    • barrel-shaped vault
    • midfacial prognathism
    • high nasal angle
  • Piltdown

    Mon, 2011-12-05 00:15 -- John Hawks
    Synopsis: 
    The Piltdown specimen was a fake, which seemed to indicate a very different pattern of evolution than reality.

    Here you will find a cast of the Piltdown specimen. Both the skull and mandible were real bone; the problem is that the skull was human and the jaw orangutan. The remains were interred in a gravel bed where they were later unearthed and reconstructed. What you see here is the reconstruction. The darkened parts are the real bone, the lighter parts sculpted from plaster.

    The scientists who interpreted the Piltdown specimen believed it to be Early Pleistocene in age, making it possibly the earliest fossil human relative known at that time. They debated whether it could be linked to Pithecanthropus, now known as Homo erectus, and whether it was older or younger. Only later was it shown definitively that the specimen combined two different modern species, and that the scientists had been duped.

    What to do: Obviously, if Piltdown had not been a fake, it would predict a very different pattern of evolution from the one we now understand to explain the fossil record. Think about aspects of the present fossil record that are inconsistent with the Piltdown specimen. You can choose any part of the real fossil record for your examples, but be specific about the evolutionary changes that happened at the wrong time to be consistent with Piltdown.

    Hint: look at the browridge.

    Study terms: 
  • Understanding population differentiation

    Mon, 2011-11-28 00:48 -- John Hawks
    Synopsis: 
    Devising a story problem to illustrate Fst as a measure of population differentiation

    This lab has a take-home assignment, which is worth three points when you turn it in at next week's lab section.

    The genetic differentiation among populations is very important to understanding human diversity and its historical origins. The basic measurement of population differentiation is FST. You will be designing and providing the solution to a problem involving FST.

    1. Use the "Measuring population subdivision" exercise as an example to follow.
    2. You can also refer to the "Measuring differences between populations" text.
    3. Design a story problem with three populations.
    4. Your problem should involve a single gene locus, with two alleles. Each of the three populations should have a frequency for each allele (remember, the two will add to 100%).
    5. Show how FST should be calculated in your problem, with your allele frequencies.
    6. Use 1-2 sentences to explain what aspect of population differentiation your problem helps to illustrate. For example, does it show an example with one extremely different population? With very similar populations?

    Bring your story problem back to lab next week.

    Study terms: 
  • Measuring differences between populations

    Mon, 2011-11-28 00:28 -- John Hawks
    Synopsis: 
    Fst and its relationship to the number of migrants among populations

    When individuals mate locally, different populations tend to diverge from each other in the frequencies of their alleles. Genetic differences between populations are therefore differences in allele frequencies — and these differences in allele frequencies may have consequences in terms of phenotypic or adaptive differences. But every difference in allele frequencies is not equal. When populations encompass great genetic variation, large differences in allele frequencies still leave much overlap — the individuals in the different populations may not be very different from each other. In contrast, slight differences in allele frequencies might be very important between populations that are not variable, because individuals in these populations might vary extensively as a result.

    Geneticists measure the differences between populations by comparing the difference in allele frequencies to the amount of variation within the populations. When people mate with their neighbors, they tend to become more inbred — that is, they are more likely to mate with distant relatives. This means that people will tend to have greater genetic similarity than they would have if they mated equally with people who were born across the world.

    Increase in the level of inbreeding due to low gene flow is often used as a statistic, called FST, relating the increase in inbreeding in the subpopulation to that in the total population. When gene flow is high, FST is low, and vice versa. FST represents the proportion of differences between two individuals taken randomly from two subpopulations that are due to the differences in allele frequency between subpopulations alone. Other differences between the individuals are those that could be found between individuals taken randomly from the same subpopulation. FST therefore provides a comparison between the between-subpopulation and within-subpopulation components of genetic variation.

    The relationship of FST and migration between populations. When the forces causing genetic divergence between subpopulations are balanced by gene flow, the reduction of heterozygosity within subpopulations is a function of the number of people who move between subpopulations each generation, expressed by FST = 1 / (1 + 4Nm).

    Comparing human populations taken from different continents, FST is between 0.1 and 0.15, meaning that only between 10 and 15 percent of genetic differences between individuals are attributable to their geographic origins. This difference is relatively small compared to many other large mammal species spread among different continents, such as wolves or bears [1]. This level of similarity among human populations means that they have shared high levels of gene flow in the past. However, the meaning of these numbers depends on the relationship of gene flow and the other evolutionary forces.

    Because they are opposite in direction, gene flow and genetic drift will reach an equilibrium over time. At equilibrium, FST = 1 / (1 + 4Nm), where Nm is the number of migrants moving into each subpopulation. Neglecting the forces of selection and mutation, then, an FST of 0.1 for human continental populations means an average of 2 migrants have been entering each continent per generation for a long period of time. Many more people are moving from place to place today than two, so one prediction of this relationship is that the level of genetic differences among continents will in the future decrease. In the face of this gene flow, it is likely that most of the differences in allele frequencies that persist in humans are in fact affected by selection. Indeed many of the most obvious differences, related to physical appearances in different places, appear to bear this out.


    References

    1. Templeton AR. Human races: a genetic and evolutionary perspective. American Anthropologist. 1998;100:632–650.
    Study questions: 
    1. If the present FST among human continental groups is consistent with two migrants among populations each generation, what do you predict will happen to human FST in the future?
    2. It is remarkable that genetic drift and migration balance each other at a given number of actual individuals migrating, so that large and small populations are held in equilibrium by the same number of migrants. Are there any differences between large and small populations?
  • Measuring population subdivision

    Sun, 2011-11-27 22:58 -- John Hawks
    Synopsis: 
    The statistical measurement of differentiation among populations is Fst

    The basic measure of genetic difference between two populations is the statistic, FST. In genetics, the term F generally stands for ``inbreeding'', which tends to reduce genetic variation in the population. Genetic variation can be measured by heterozygosity, and so F generally expresses a reduction in the heterozygosity in the population. FST is the reduction in heterozygosity in subpopulations compared to the total population of which they are part.

    To estimate FST, take the following steps:

    1. Find the allele frequencies for each subpopulation.
    2. Find the average allele frequencies for the total population.
    3. Calculate the heterozygosity (2pq) for each subpopulation.
    4. Calculate the average of these subpopulation heterozygosities. This is HS.
    5. Calculate the heterozygosity based on the total population allele frequencies. This is HT.
    6. Finally, calculate FST=(HT-HS)/HT.

    Don't forget that the HS term is the average across all subpopulations.

    Example: The gene SLC24A5 is a key part of the melanin expression pathway, which contributes to skin and hair pigmentation. A SNP that is strongly associated with lighter skin pigment in Europe is rs1426654. The SNP has two alleles, A and G, with G being associated with light skin, at a frequency of 100% in Utah European-Americans. The SNP varies in frequency in populations in the Americas with mixed African and American Indian ancestry. A sample in Mexico had 38% A and 62% G; in Puerto Rico the frequencies were 59% A and 41% G, and a sample of African-Americans from Charleston had 19% A with 81% G. What is the FST in this example?

  • Cranial features and race

    Sun, 2011-11-27 21:51 -- John Hawks
    Synopsis: 
    A primer on assigning forensic race to crania based on their morphology

    Individuals whose ancestry derives mostly from different parts of the world sometimes have different cranial features. Forensic anthropologists have studied these differences for many years, finding some that are especially useful for distinguishing ancestry. In American legal contexts, ancestry is usually at issue as a way of determining the racial affinity of unidentified skeletal remains. Hence, the forensic anthropologist usually tries to make a determination as to whether a skull has features that indicate African, European, Asian or Native American ancestry.

    Cranial features are not perfect indicators of ancestry: Forensic anthropologists using multiple features claim at best 85% accuracy in their assessment of racial ancestry. When we know less about the context of a skull, we will be less and less accurate.

    Here are some traits that vary between skulls with different race backgrounds. Most of them are on the face or palate.

    • Shape of the eye orbits, viewed from the front. Africans tend to a more rectangular shape, East Asians more circular, Europeans tend to have an ``aviator glasses'' shape.
    • Nasal sill: Europeans tend to have a pronounced angulation dividing the nasal floor from the anterior surface of the maxilla; Africans tend to lack a sharp angulation, Asians tend to be intermediate.
    • Nasal bridge: Africans tend to have an arching, ``Quonset hut'' shape, Europeans tend to have high nasal bones with a peaked angle, Asians tend to have low nasal bones with a slight angulation.
    • Nasal aperture: Africans tend to have wide nasal apertures, Europeans narrow.
    • Subnasal prognathism: Africans tend to have maxillae that project more anteriorly (prognathic) below the nose, Europeans tend to be less projecting.
    • Zygomatic form: Asians tend to have anteriorly projecting cheekbones. The border of the frontal process (lateral to the orbit) faces forward. In Europeans and Africans, these face more laterally and the zygomatic recedes more posteriorly.

    What to do: This station includes several casts representing skulls of different ancestries, along with one ``mystery skull''. Examine the features that vary by ancestry in this skull, comparing it with the others. Can you assess the racial origin of the mystery skull?

  • Why do people differ in skin color?

    Wed, 2011-11-16 08:43 -- John Hawks
    Synopsis: 
    Pigmentation in humans reflects UV radiation and its effects on biology and health in recent human evolution.

    The color of human skin is determined by the amount of two pigments, eumelanin and pheomelanin. These pigments are the basic ones underlying all kinds of coloration in animals — even blue colors like those in the irises of blue eyes result from light reflecting above a layer of dark brown-black eumelanin. The darkest human skin and hair tones contain an abundance of eumelanin, while brown and reddish hair and freckles of the skin contain a large proportion of pheomelanin.

    Genes can influence skin and hair pigmentation in many ways. The overall color of the skin results from both the number of pigment-making cells (called melanocytes) and their level of activity. Most skin is capable of tanning, which means that exposure to UV radiation induces greater melanin production. Today, more than 20 genes are known to influence skin pigmentation in humans. Genetic changes can alter the development and migration of melanocytes, the regulation and expression of genes that generate melanin, or the chemical steps in the synthesis of the pigments themselves. As a result of such genetic changes, two people who live in the same environment may have very different shades or patterns of skin coloration.

    Some of the genes that influence skin pigmentation also cause variation in hair color or eye color. For example, variation in the gene OCA2 explains most of the variation in eye color in Europeans. People with blue eyes are mostly homozygotes for an allele of this gene; these people also tend to have slightly lighter skin due to this allele. Likewise, the variation in the gene MC1R explains some of the variation in skin color in Europe, but also explains a large proportion of variation in hair color. Red and blond hair each result from some of the distinctive alleles of MC1R.

    Dark skin evolved in ancient humans

    Relatively light-skinned populations include the native inhabitants of Europe, West Asia, East Asia, the Arctic, and the Americas. The lightest skin tones are found in Europe, while the darkest are in tropical Africa, southern India, Indonesia and Melanesia, and Australia. The level of skin pigmentation shows a close correspondence with latitude — people living near the equator tend to have dark skin, while light-skinned people live nearer the poles.

    Selection on skin color depends on the level of UV radiation.

    Cline of skin color in global human populations

    Skin pigmentation correlates with latitude because it serves as a defense against UV radiation. Like all solar radiation, UV is more intense at lower latitudes, where the sun is more often directly overhead. High-energy UV light damages and destroys the molecules that skin is made of. In sufficient amounts, this UV radiation can cause severe burns, that are painful and leave the skin unable to maintain its normal protective and cooling functions. UV radiation also can cause long-term damage to the DNA of skin cells, resulting in dangerous skin cancers.

    Dark-skinned people have a lower incidence of skin cancers in most countries compared to people with less pigmentation. The highest skin cancer rates in the world are suffered by people of European origin who currently live in equatorial places; Australia is presently the highest. Still, skin cancer may be a relatively weak cause of natural selection, because deaths from skin cancer tend to occur later than the mid-30s, relatively late in most peoples' reproductive lifespan.

    Dark skin reduces the incidence of skin cancer and sunburn.

    Possibly more important was the incidence of heat stroke in severely sunburned people. Today, relatively few people in Western societies succumb to heat exhaustion and heat stroke today, but this was potentially a great danger in the past and remains so in some places today. This danger of sunburn especially influences children, whose smaller masses allow less room for error in water loss and overheating.

    Some evidence suggests that dark skin pigmentation first appeared in humans within the last 500,000 years. African apes are polymorphic in skin coloration. Chimpanzees in particular are variable — some chimpanzees have quite light skin, and others have very dark skin; skin color tends to darken with age in these primates. But humans who live in equatorial Africa today show very little variation in skin color. Dark skin has been strongly selected in that population. One gene that contributes to skin pigmentation phenotypes, MC1R, shows evidence for positive selection in Africans sometime between 200,000 and 1 million years ago [1]. This date is interesting — humans first appeared nearly 2 million years ago, and our divergence from chimpanzees was far earlier, at over 6 million years ago. So the evolution of dark skin pigmentation was continuing at a relatively recent date. One suggestion is that people lost their body fur sometime during the last million years. With fur, there was no survival benefit to dark skin, but exposed skin creates the susceptibilities that select for darker pigmentation.

    Light skin pigmentation evolved recently

    Light skin pigmentation is a more difficult problem than dark pigmentation. The advantages of dark skin are clear, and genetic evidence shows that dark skin has been around for a long time. But light skin evolved relatively recently.

    The variation among light-skinned populations helps to illuminate the problem. Europeans and Asians today are broadly similar in their range of pigmentation. Northern Europeans average a bit lighter in skin color than north Asians, but the ranges of variation in pigmentation greatly overlap. Still, there are regional differences. For example, both hair and eye coloration are more polymorphic in Europeans than in living Asians. These phenotypes suggest that different alleles may affect pigmentation in these populations.

    Recently, geneticists have identified more than a dozen different genes influencing skin coloration in Europeans and Asians. The variation in pigmentation associated with these genes is mostly explained by new alleles under recent positive selection. For example, northern Europeans carry a new allele from a gene called SLC24A5 at a frequency near 100 percent. This allele has spread as far west as Spain, and as far east as Pakistan; it is also common in North Africa. Yet, the new mutation originated very recently, approximately 6000 years ago. Likewise, a gene called DCT has a new allele common in China, which appears to have originated less than 10,000 years ago. Both Europeans and Asians have 10 or more alleles influencing their light skin pigmentation, but these alleles are only rarely shared between these populations. Variation in eye color in Europeans is mostly explained by a recnet mutation in the gene OCA2. This same gene has another allele under recent selection in China, which does not strongly influence eye color. European hair color variation is mostly explained by variation in MC1R; this gene has many new alleles in Europe, but does not greatly influence hair color in East Asia. In every case, the new mutations occurred recently and have not yet had time to spread and proliferate from one end of Eurasia to the other.

    The recent evolution of light skin can only be explained by a strong pattern of selection favoring it. Scientists have focused on ways that dark skin may create disadvantages for people in places with lower natural UV radiation. One way that UV radiation is necessary is in the metabolism of vitamin D. Humans synthesize vitamin D in the skin, where exposure to UV radiation allows the transformation of precursor molecules into the necessary vitamin. Vitamin D is necessary for normal bone development, and people who suffer from a deficiency of vitamin D get a disorder known as rickets, characterized by deformation of the bones. Such abnormalities in bone growth can be potent causes of selection, either by decreasing mating attractiveness or by impeding normal activities. Such problems can extend to reproduction itself, as a pelvis deformed by rickets can make it impossible for a woman to give birth normally.

    There is some evidence that dark skin is less capable of maintaining vitamin D metabolism. Most notably, people with darker skin living at higher latitudes in historic times, such as in London, apparently have suffered a higher incidence of rickets. However, today people acquire vitamin D primarily through dietary supplements, including dairy foods enriched with the vitamin, so that dietary differences between peoples of different skin tones in Western nations may partially account for differences in rickets incidence. Nevertheless, vitamin D metabolism remains the most prominent hypothesis to account for the distribution of light skin in the northern parts of the world.

    Even so, some differences in skin color are probably explained by other factors. For example, northern Europeans are markedly lighter in skin color than people who live at the same latitude in East Asia. Many Europeans also have less melanin in their hair, which ranges in tone from blond to brown and red, while most high-latitude Asians have black hair.

    It is possible that some of these differences may be the result of sexual selection, as different populations create different long-term patterns in sexual attractiveness and mating. Scientists have also applied sexual selection to explain differences in hair form among populations, from short and kinky to long and straight, and differences in hair color among equatorial populations. In all such cases, there is no ready environmental explanation for the differences. Even so, human cultures are very flexible and change rapidly, especially when compared to biological evolution, so that a stable sexual preference for such a characteristic as skin color or hair color, expressed over many hundreds of generations, would appear to conflict with the rapid cultural changes that affect mating preferences.


    References

    Study questions: 
    1. Pigmentation varies among other species of primates, with different coat colors and color patterns. Do you think the same explanations work for these primates as for humans?
    2. Some humans in the distant past lived at high latitudes, like the Neandertals. What would you expect about their pigmentation?
  • Sex and the mandibles of early hominins

    Tue, 2011-11-15 08:44 -- John Hawks
    Synopsis: 
    Early hominins have a different pattern of sexual dimorphism of the mandible compared to humans and other primates.

    Determining sex from human mandibles (as you will do in another part of this lab) depends on a series of characteristics that tend to differ between male and female humans. But those same features do not necessarily vary in the same way in every population of people living today. The pattern of sexual dimorphism in the human mandible has evolved over time, and therefore varies.

    When we look at the mandibles of earlier hominins, we see that they vary in a different pattern compared to recent humans. With a fossil mandible, it can be very difficult to determine whether it represents a male or female. Any determination must depend on the variation known to exist within the ancient population.

    We can compare early hominins to other primates, and we find that again, the pattern of sexual dimorphism is somewhat different. Chimpanzees, bonobos, gorillas and orangutans have a clear pattern of canine size dimorphism. Males have larger canines, females smaller. The lower third premolar also is somewhat dimorphic in shape, and even more so in size and wear pattern due to the presence of the large upper canine. With substantial body size dimorphism in gorillas and orangutans, the male mandibles are noticeably larger than female mandibles. All of these primates have a bar on the posterior side of the mandibular symphysis, called a simian shelf. The size and robusticity of this feature and other parts of the mandible reflect sex.

    Early hominins do not have the same extent of canine size dimorphism as other hominoids, but the males do tend to have larger canines than females. In early hominins like A. afarensis, this dimorphism is marked in both projection and diameter of the canines, and the lower third premolars also vary in shape and orientation between males and females. In later hominins, who accentuate the large chewing teeth, the canines still have some size dimorphism in their diameters, but this loses its utility in the robust australopithecines.

  • Meet Homo heidelbergensis

    Tue, 2011-11-15 08:28 -- John Hawks
    Synopsis: 
    The Mauer mandible is the type specimen of Homo heidelbergensis

    The Mauer mandible comes from just southeast of Heidelberg, Germany, and was found in ancient sands deposited just more than 600,000 years ago. Upon its description, the mandible was attributed to a new species, Homo heidelbergensis.

    Through the years, anthropologists considered H. heidelbergensis to be a more primitive species than Neandertals, very different from recent humans. Many anthropologists attribute other remains from the European Middle Pleistocene to this species. Probably the most important sample would be the Sima de los Huesos remains from Spain, but other crania and skeletal elements from sites across Europe have been put into the species. A few anthropologists would also include specimens from other parts of the world.

    Other anthropologists disagree. They believe that Mauer is an early member of the same population that includes Neandertals. Others would go further, noting the evidence that Neandertals are part of the ancestry of modern humans, and put Mauer into our species, Homo sapiens.

    This station has several mandibles for you to compare with Mauer, including some Neandertals, modern humans, and Homo erectus individuals.

    What to do: Compare the morphology of the Neandertal and Mauer mandibles to the modern humans. What features differ?

    Consider what you know about earlier hominid mandibles (or compare one at the station). Do you think Mauer is a possible ancestor of Neandertals? What about an ancestor of modern humans? Does it have mostly primitive dental features, or does it share derived features with one or the other?

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.