john hawks weblog

paleoanthropology, genetics and evolution

explainer

  • Laboratory inquiry 3: Forensic case

    Sun, 2013-04-21 20:40 -- John Hawks
    Synopsis: 
    Identifying the possible remains of a long-lost aviator
    Amelia Earhart and Fred Noonan

    Amelia Earhart was a famous aviator and pioneer in flight during the 1920s and 1930s. In 1932 she became the first woman to fly solo nonstop across the Atlantic Ocean, and she set an altitude record for flight in an autogyro in 1931. She was well known for her efforts to increase the role of women pilots and publicize the growing importance of airplanes.

    Earhart attempted an around-the-world flight in 1937, taking a tropical route. One of the final legs of this flight was planned from Lae, New Guinea to Howland Island in the South Pacific Ocean, a total distance of 2550 miles. On July 2, 1937, Earhart took off with her navigator, Fred Noonan, to make this flight. Earhart was known to have reached the vicinity of Howland because of her radio transmissions; the U.S. Navy vessel USS Itasca was tasked with communicating with Earhart and helping guide her to her destination. Her final transmission, at 8:43 am, came after more than an hour of searching for Howland on very low remaining fuel.

    After a 17-day search effort across more than 100,000 square miles of ocean, Earhart was given up for dead. However, many people operating shortwave radio sets across the U.S. claimed to have heard faint transmissions from Earhart during this time. Stories about her possible survival have persisted since that time, and archaeologists and aviation enthusiasts continue to investigate her disappearance.

    One of the most striking stories about Earhart's disappearance is that she may have survived the crash of her plane on another island. The most common island mentioned is the uninhabited Nikumaroro island in present-day Kiribati. A skeleton was recovered on this island by British colonial officials in 1940 and sent to Fiji, from where the remains later disappeared.

    The skeletal remains in this lab were recovered from a private residence on Fiji. One or more of them may have been part of the collection curated by the British government on the island, which were sent away for safekeeping during the Second World War.

    Your task is to determine whether these remains may have belonged to Earhart or Noonan. Earhart was 39 years old at the time of her disappearance and stood approximately 5 feet 8 inches (173 cm) tall. Noonan was 44 and stood approximately five feet 11 inches (180 cm) tall.

    Assess the sex, race, stature and age of these skeletal remains, to the extent possible. Can they be the remains of Earhart or Noonan?

  • Group life in primates

    Mon, 2013-02-04 00:48 -- John Hawks
    Synopsis: 
    A discussion of some factors affecting group size and dynamics in primates

    Primates form different kinds of groups. While there is variation within every species, each species has its own typical range of group sizes. Primate groups also vary in their structures. The structure of a group involves details about what kinds of individuals live in a group together. The group structure includes the number of adult males compared to females, called the sex ratio. It also includes the pattern of interactions among individuals, such as whether the entire group spends all its time together, or whether different individuals break into smaller parties for substantial amounts of time. The size and structure of groups have an adaptive role --- some kinds of groups are better suited to certain ecological or social contexts than others.

    Group size and structure are products of adaptation.

    The size and structure of groups in a species is a product of selection on individuals. Individuals always have choices: they can stay in a group, or they can leave; they can permit others to join their group or they can confront newcomers aggressively; they can join together to form a new group, or they can go it alone. Some choices will be more adaptive than others, and individuals who make the right choices about what kind of group to live in will tend to survive or reproduce more. This is how group sizes and structures evolve.

    In an evolutionary context, the kinds of groups found in different primate species are products of their ecology and social interactions. Typical group sizes can vary greatly among even closely related species or primates. The typical social group in orangutans, for example, consists of a single mother and her offspring. In contrast, chimpanzees --- who are relatively close in body size and diet to orangutans --- live in complex communities averaging over fifty individuals. The differences between these species' social groups must be explained by differences in their habitat, movement, mating system, and history. By studying primate groups, primatologists attempt to understand how these factors result in certain kinds of groups but not others.

    Predation

    Most primates are small to medium-sized mammals, and they are vulnerable to many kinds of predators. Carnivores, including leopards and hyenas in the Old World, and jaguars in the Americas pose a serious threat, even to large primates. Other natural predators include hawks and eagles, snakes, humans and other primates. Indeed, other primates are the most significant predators of some species. For example, chimpanzees are the most common predator of red colobus monkeys, as described below.

    Small primates who live in exposed habitat are most vulnerable to predation.

    Most monkeys suffer high rates of predation by carnivores and other predators, but these rates are highest for those species that live in relatively open, exposed habitats. In vervet monkeys, which live in relatively open savanna, predators account for up to 70 percent of deaths (Cheney and Wrangham 1986). Baboons are much larger primates than vervet monkeys, but the rate of predation on savanna baboons is very high as well. At these levels, predation exerts a strong selective force on these populations.

    For these primates, large groups tend to minimize predation risk. A large group of primates has more eyes, and is therefore more likely to notice the approach of a predator. Another strategy to resist predators is for individuals to raise a cry or alarm when they see a predator approach. Alarm calls can be a benefit to such groups, but an individual raising an alarm also raises its own risk --- predators will notice its noisy alarm. But in larger groups, a sudden scatter of alarmed primates competes for attention with the alarm call itself. In large groups, individuals can spend less time scanning for predators, meaning that they can devote more time to foraging. Likewise, the collective action of some individuals may deter predators from attacking. The mere presence of a collection of large male baboons may deter a not-so-hungry jackal, when a lone female and infant would be more likely to suffer attack.

    Movement and food patches

    Some kinds of habitat are much harder to move through than others. Terrestrial primates can move very quickly on the ground. But if they are on the ground far from a tree, they can be highly exposed to terrestrial and aerial predators. Small primates may be highly mobile through dense forest, because they can move quickly from tree to tree. Large primates must move more deliberately through trees, since not every branch can easily support their weight.

    Primates who cannot move easily or quickly may be limited in group size.

    Size and difficulty of movement may partially underlie the differences in group size between chimpanzees and orangutans. Chimpanzees can move effectively across the forest floor, and this terrestrial movement is their major way of traveling from place to place. In this way, they can maintain relatively large groups, as sets of individuals can forage or patrol over relatively long distances and still return regularly to other group members. In contrast, much of the forest habitat of orangutans has a swampy or closed forest floor through which it is very difficult to move. In some parts of the orangutan range, tigers add to the danger of the forest floor. As a result, orangutans spend the overwhelming majority of their time in the forest canopy, where movement is slow but safer (Knott 2001).

    Another element of ecology interacts with movement costs to affect group size: the distribution of food. Foraging for food is one of the major activities that primates conduct every day. Whether a group of primates is large or small, every individual must eat. For a group of primates that finds a huge tree with ripe fruit, life is relatively easy --- they can stay there and eat as long as they are not driven off by competitors or predators. If such large patches of food are common enough, the primates can stay in a large group and move from one patch to another. But nature does not only consist of large patches of ripe fruit and other primate foods. Sometimes fruits ripen a few at a time, so any tree can only feed a few primates. The availability of food can also vary from season to season, so that sometimes there may be plenty of food to eat, but at other times there is little.

    The availability of food limits group size. If patches of food are small, then individuals within a large group may compete intensely for each bite. Being in a large group is a serious cost when resources are slim. This kind of limit to group size also affects orangutans. Orangutans eat a large amount of ripe fruit, but once they find a patch the amount of ripe fruit is usually relatively small for such a large-bodied primate (Terborgh and van Schaik 1987). Larger groups are generally impossible to maintain --- the orangutans would just go hungry unless they could find their own food sources, and it is too costly to move quickly between small patches of fruit. Indeed, in some forests where food is more plentiful, orangutans do tend to spend more time in groups of multiple individuals (Delgado and van Schaik 2000).

  • Human and ape feet

    Mon, 2012-01-23 09:01 -- John Hawks
    Synopsis: 
    Laboratory exercise on the anatomical differences between human and ape toes

    At this station, you'll find some articulated human feet. "Articulated" means that the bones are assembled together at their joints -- two bones that articulate with each other are connected at a joint.

    You will also find some feet from two living species of great apes, gorillas and orangutans. These feet are obviously different from human feet in several respects. Most obviously, ape feet have an opposable first toe. The first toe in humans is often called the "big toe" or "great toe", but in these apes it is quite a bit shorter than the other toes. In anatomical terms, the first toe is called the hallux, and it is on the medial side of the foot, the one closest to the midline of the body.

    The other toes, which are lateral to the hallux, are substantially longer in apes than in humans. Each of these toes consists of three bones, which are called phalanges. The closest to the rest of the foot is the proximal phalanx, the furthest is the distal phalanx. The one in the middle of the toe is called the intermediate phalanx.

    Take a look at the intermediate phalanges in the human and ape feet. What do you notice about them? This is a substantial difference in the anatomy of human and ape feet, as human toes have greatly reduced all the phalanges but particularly the intermediate ones.

    Think of a hypothesis to account for the shorter toes in humans. Why would it make a difference how long the lateral toes are?

  • Neandertal postcrania

    Mon, 2011-12-05 01:00 -- John Hawks
    Synopsis: 
    A quick explainer on the distinctive characters of Neandertal long bones

    Neandertals were very robustly built. This means that they had relatively thick bones, with thick layers of cortical bone. It also means they had relatively extensive and rugose muscle attachments.

    In comparison with most living humans, Neandertal long bones were distinctive in being strongly curved along their shafts. In addition to this curvature, they had very large joint surfaces.

    What to do: Compare the Neandertal femur at this station to the sample of modern humans. What makes it different? Explain the mechanical reasons for these features.

    Study terms: 
  • 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?

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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.