1. Human Evolution

2. Evolutionary Forces
Darwin's original theory of evolution was based on natural selection.
Natural Selection: the most fit individuals contribute more to the following generations so their genetic influence takes over the population.
"Fitness" is defined as
the ability to survive and reproduce
for the offspring to also survive and reproduce.

3. Neo-Darwinian Synthesis
The is a refinement of Darwin's theory using the knowledge of genetics gained from Mendel and his followers. (Darwin had only a crude and incorrect understanding of the mechanism of heredity).
In the neo-Darwinian model,
the frequencies of alleles in the population are examined.
Many genes have multiple alleles, and their frequencies are influenced by several factors, especially including natural selection.
The most important evolutionary event is speciation.

4. Speciation in the neo-Darwinian model
The creation of 2 distinct species from a single species.
This can occur when two groups within a species are physically isolated.
In this situation, allele frequencies change in different ways in response to different environmental pressures.
If the allele frequencies change enough, the two groups have become different species.

5. Sexual Selection
If, after speciation has occurred, the two new species are allowed to mate, their offspring will be less fit:
sterile,
weak,
unable to survive.
When this happens, there is a rapid period of sexual selection.
Sexual selection is where the two species evolve various mechanisms to prevent mating between the species:
behavioral,
anatomical,
biochemical.

6. Genetic Drift Genetic drift: random changes in allele frequencies
More recently, Kimura recognized that genetic drift can have a major influence on evolution.
Kimura’s theory is the neutral theory of evolution:
most alleles do not confer any selective advantage on the individual,
alleles frequencies change only in response to random events.

7. Current Belief
The current belief is that both selection and drift are important in evolution.
Genetic drift has the largest effects on small groups:
random events such as mate choices and environmental disasters can radically alter allele frequencies.
In large groups these random events tend to cancel each other out, making it hard to significantly alter allele frequencies.

8. Molecular clock
Mutations occur at random, but the rate of mutation is relatively constant.
Thus, on the average it is possible to gauge how long ago two lineages split apart.
This works best when synonymous mutations--mutations where the DNA is altered but the amino acid sequence remains the same-- are used. Such mutations are thought to be selectively neutral.
The molecular clock theory is the origin of the dates used for the genetic evidence described above.

9. Our History Starting at the beginning
Big Bang: all matter and energy in the Universe suddenly appear as a single point, extremely hot and dense.
Everything expands out form this point, a process continuing to this day.
This is the starting point of time also
We have no scientific evidence of anything before this point
There is strong evidence for this scenario, but I am in no way qualified to judge it.

10. More History Formation of the Earth: about 4.6 billion years ago.
as judged from uranium isotope dating of rocks from the Moon and meteorites: 4.6 billion years is as old as they get
Condensation of gases and dust out of a cloud: as particles get larger, their gravity attracts more particles. The big get bigger, etc.
Hadean era: 4.6 – 3.8 billion years ago. Many collisions between large objects periodically melt the Earth’s surface, making life impossible.
the Moon is thought to have formed when a very large object (the size of Mars) hit the Earth

11. Origin of Life
When: there are things that look like fossil bacteria and chemicals that may owe their origin to living organisms is rocks that are billion years old. Still controversial, but life seems to have started on Earth shortly after the surface solidified.
on Earth, the oldest known rocks are about 3.8 billion years old. They are metamorphic: sediments that have been processed by heat and pressure.
things that look like or seem to be derived from fossil bacteria: can they be generated by non-living processes?
stromatolites: finely layered mounds built by cyanobacteria living as a biofilm in the ocean and precipitating calcium carbonate around themselves. Seen in 3.5 billion year old rocks in Australia. They are found from all eras, and there are stromatolites living today (but they are rare).
However, the oldest ones remain controversial: possibly the product of abiotic processes.
Greenland rocks roughly 3.7 billion years old have microparticles of graphite that appear to be depleted in 13C relative to normal 12C. Living organisms do this routinely: enzymes slightly prefer the isotope because compounds containing it are lighter and move through the enzyme faster.
Molecular phylogenies of organisms living today seem to require several billion years back to the last universal common ancestor.

12. Origin of Life
How: still a mystery: how to get both genetics and metabolism going simultaneously.
RNA World idea
Fe-S crystals: metabolism first
Clay crystals
top-down approach: design a minimal prokaryote from sequenced genomes.

13. General Principles of Phylogeny
Phylogeneticists theses days attempt to put organisms into monophyletic groups: groups that contain the last common ancestor and all of its descendents. A monophyletic group is also called a clade.
Paraphyletic groups : the group contains its most recent common ancestor but not all descendants of the last common ancestor are included.
Reptiles are a good example: since birds are descended from reptiles, the last common ancestor of all reptiles has birds as well as reptiles among its descendants. Thus, reptiles are a paraphyletic group.
Phylogeneticists argue about the value of paraphyletic groups
Polyphyletic: the group does not contain its last common ancestor
for example, “warm-blooded animals”, which would include birds and mammals but not reptiles.
Discerning and separating polyphyletic groups is a principle goal in phylogeny

14. A Tour through Phylogeny
First stop: 3 domains of life: Archaea, Eubacteria, and Eukarya.
Based on extensive sequencing of 16S ribosomal RNA genes (18S in eukaryotes).
largely confirmed by sequencing other genes
but: prokaryotes do a lot of lateral gene transfer, moving genes between species.
Eukaryotes are closer Archaea than to Bacteria. Divergence time 3.6 billion years or so.
Green plants, along with red and green algae branch off.
Fungi branch off later: we are more similar to fungi than to plants
Animals (=metazoans) are sister taxa to choanoflagellates, a group of protists that resemble the collar cells of sponges and have long been speculated to be closely related to sponges.

15. Metazoan Phylogeny
Sponges are the most primitive animals, with no nervous system or muscles, no axis of symmetry, and no real germ layers. Sponge development reaches teh blastula stage but does not undergo gastrulation.
Cnidarians (jellyfish) are diploblasts: only 2 embryonic germ layers (ectoderm and endoderm)
All other animals have three germ layers, including the mesoderm = triploblasts
Bilaterans all have bilateral symmetry at some point in their life
echinoderms (starfish for example) are bilaterally symmetric as larvae
bilaterans and triploblasts are (at least roughly) the same organisms.
Another major split roughly 1 billion years ago: protostomes vs. deuterostomes.
based on whether the mouth or anus develops first in embryonic life
protostomes (mouth first): mollusks, annelids, arthropods, nematodes, flatworms
deuterostomes (anus first): echinoderms and chordates
Chordates have a notochord, a rod of cartilage in their back, at some point during development.
in vertebrates the notochord is eventually replaced by the vertebrae
Craniates have a skull enclosing the brain, eyes, nose, and ears
Vertebrates have vertebrae: skeletal elements flanking the spinal nervous system

16. Vertebrate Phylogeny Various kinds of fish
as opposed to terrestrial vertebrates: amphibians, reptiles, birds, and mammals
Amphibians: tetrapods (4 limbs): started with lobe-finned fish.
Reptiles: the amniote egg, which is resistant to dessication, allowed animals to lay eggs on dry land and thus escape dependence on bodies of water.
Birds branched off from the reptiles
Mammals
Placental mammals (as opposed to monotremes which lay eggs and marsupials which raise their young in a pouch after a very early birth).
Primates: lemurs, tarsiers, monkeys (old World and New World), apes
Great apes: orangutans, gorillas, chimpanzees (2 species), humans

17. Human Evolution
The broad outlines of the story seem clear, but the details are very hazy.
In reality, we have only a few bones from ancient times to examine.
Anthropologists tend to create new species names for almost every new find.

18. The Great Apes The primates can be divided into
the New World Monkeys,
the Old World Monkeys,
the Great Apes (including humans).
These days. the family Hominidae (the hominids) are considered to include all of the Great Apes. past and present, including all human ancestors.
in former times, the Great Apes were classified as Pongidae. Since humans share a common ancestor with the Pongidae but were put into the family Hominidae, the pongids were a paraphyletic group.
About millions years ago there as an “adaptive radiation” of Great Ape species in Africa: many species appeared rather suddenly.
Most of them have long since died out
Great apes of today:
chimpanzees
bonobos (pygmy chimps),
gorillas,
orangutans, and
humans

19. Hominin Species
Hominin = a subfamily, species whose living descendants are humans only and not other apes.
At some point maybe 4 million years ago one of these species evolved into Australopithecus, the first hominin species.

20. Australopithecines
The first well-known Australopithecus species is Australopithecus afarensis.
A afarensis walked on 2 legs, as seen by a set of 3.4 million year old footprints.
The Australopithecines evolved into 2 branches:
the robust Australopithecines, which had enormous jaws and small brains. Also called Paranthropus
the gracile (lightly-built) Australopithecines, which had large brains.
The robust Australopithecines (several species: robustus, boisei, aethiopicus ) eventually died out.
The gracile Austraopithecines (afarensis, garhi, amanensis, and perhaps africanus) evolved into genus Homo.
A. africanus is well known in the fossil record, but its position in the lineage is unclear: ancestral t paranthropus? ancestral to Homo? Neither? Both?

21. Homo species
Several species described, and it’s not clear which are actually our ancestors, or even which are actually separate species. e.g. ergaster, antecessor, rudolfensis, heidelbergensis
H. habilis
The best known early Homo species.
Lived 2-4 million years ago in Africa.
made crude stone tools. Possibly the first species to do this.
H. erectus
Started about 2 million years ago.
Homo erectus left Africa and colonized the entire Old World (Europe, Asia, Africa).
Various forms evolved out of H. erectus,
including H. sapiens, our species, which evolved in Africa about 100, ,000 years ago.
Other species, including the Neanderthals, also arose from H. erectus.
possibly survived until recently: the “hobbit people” H. floresiensis lived on a small island near Java until 15,000 years ago.

22. Neanderthals
Originally found in 1864 in a limestone quarry in the Neander Valley in Germany. The first non-H. sapiens skeleton recognized.
Many other bones found in Europe and the Middle East.
Lived in Europe between 200,000 years ago and 30,000 years ago
Modern humans also lived in Europe for the last 5000 years of this period.
Physical description: short, stocky, heavy build, large head, protruding brow ridges and a large nose. Their brain was as large or larger than ours. The oldest known was 40 years old when he died, and nearly all Neanderthal skeletons show signs of injury: healed bones.

23. What did Neanderthals Look Like?

24. Alternate Views

25. Neanderthal Behavior
Could they talk? It’s a little late for a conversation! An argument has been made that the structure of the base of the skull would not have allowed the larynx (voicebox) to produce the range of sounds that modern humans have. Another contribution to this controversy: in one skeleton, the hyoid bone in the throat (connects the tongue to the lower jaw) has been found. It is shaped like a modern human hyoid, and not like the hyoid bone in gorillas and chimps.
Evidence for human-like behavior. Neanderthal bones are sometimes found in what look like funeral burials, arranged in a comfortable position. Some evidence that flowers were used to cover one of them. This evidence is controversial, however. In one case, Shanidar (named after the site), the person had had severe injuries, including destruction of an eye socket. These wounds were healed, and they were severe enough so that he wouldn’t have survived without assistance.
A fragment of a flute has been found from Neanderthal times ( years ago) It is bone, with holes spaced in a way that allows several modern-style notes on it.
They definitely made stone tools and used fire.

26. What happened to the Neanderthals?
About 35,000 years ago, modern humans came into their territory in western Europe. The modern humans are sometimes called “Cro-magnon”, based on the first archeological site they were found at. Although there is no obvious evidence of conflict, after several thousand years of co-existence, the Neanderthals apparently died out.
Two competing theories. 1. The Neanderthals were the same species as modern humans, and the distinctive Neanderthal type disappeared by interbreeding. This implies that people of today carry Neanderthal genes. 2. Alternatively, the Neanderthals may have been an entirely different species, unable to produce fertile hybrids with modern humans. This implies that people today carry no Neanderthal genes.
Theories are tied up in a larger context. The older theory , called the “Multi-regional hypothesis”, says that all of the human-like creatures that lived in the past two million years or more (including Homo erectus, generally considered to be our ancestral species) are part of the same species, Homo sapiens, and that they evolved worldwide from the primitive forms into the forms we see today. The mechanism for the spread of new genes was a slow process of interbreeding between neighboring groups. This theory suggests that many of today’s populations have lived in the same area of the world for a very long time: the Chinese evolved in China, the Africans evolved in Africa, etc.
The newer theory, called “Out of Africa” says that there have been many different species of human-like creatures, with Neanderthals just one of these species. Modern humans evolved in Africa about 100,000 years ago, then spread out from there. All other human species were eliminated.

27. Neanderthal-H. sap interbreeding
Multi-regionalists think that Neanderthals extensively interbred with modern humans, that they were essentially one species.
evidence from “intermediate” fossil bones
including apparent recognition of “Chinese” features in H. erectus skeletons found in China and dated to 300,000 years ago
Out of Africa types have believed that Neanderthals and modern humans were two separate species who never interbred
Mitochondrial DNA evidence from about 10 different Neanderthals shows that the lineages diverged roughly 300,000 years ago, well before the appearance of modern humans.
There is currently a project to sequence the entire Neanderthal genome.

28. Microcephalin
Recent work (Evans et al., 2006) on genes involved with brain development has found a gene that has several alleles, microcephalin. Patterns of variation among alleles at this gene have been examined in light of the molecular clock theory.
There are two rather different groups of alleles of this gene, called D and non-D.
The variations among the D group alleles are very slight, implying a common ancestor about 37,000 years ago. D alleles are found in about 70% of humans today, implying a very rapid spread through the population caused by a significant selective advantage.
The non-D alleles are much more variable.
The differences between D alleles and non-D alleles imply a separation of about 1.1 million years.
The origin of D alleles is not certain, but the times suggest Neanderthals.
There may be other genes that fit this pattern—ongoing research
Does not imply a thorough mixing of modern humans and Neanderthals, but rather a rare or unique event, compatible with the two being different species.

29. Current Human Speciation Theory
Current thought on speciation: usually occurs in a small isolated group as a result of genetic drift and natural selection.
This event can be thought of as
a "bottleneck"
the population of a species is reduced to a small number and then builds up
"founder effect“
where a new species starts out with just a few members.
In both cases,
the allele frequencies are quite different from the original population,
many alleles are fixed--only one allele in the population for a given gene.
Much genetic evidence points to a bottleneck in the human species between 100,000 and 300,000 years ago.
we are very different in appearance from the other Great Apes
our genes, both nuclear and mitochondrial, have relatively few neutral alleles compared to other Great Apes.
This period probably represents the origin of Homo sapiens.
An amusing theory about the cause: the Toba supervolcano in Indonesia erupted about 70,000 years ago with a force about 3000 times greater than Mt. St. Helens. This was enough to lower the Earth’s temperature by 3-4oC and possibly trigger an ice age, which killed most of the humans alive at that time.

30. mtDNA Evidence for the Out of Africa theory
recall that mitochondrial DNA is inherited through the mother only
thus mtDNA can be considered as a single haplotype
when mitochondrial haplotypes are compared, the people with the largest amount of variation, and the most distantly related variants are sub-Saharan Africans. This implies an African origin for modern humans.
Molecular clock theory implies a common ancestor for mtDNA about ,000 years ago.
“mitochondrial Eve”
there were other humans alive at that time, but their mtDNA lineages didn’t make it into the current population.
Similar results for the Y chromosome (which also doesn’t recombine):” Y chromosome Adam”
largest amount of variation among Africans
most distantly related lineages among Africans

31. Beginning of civilization
About 30,000 years ago, is as good a point as any to mark the beginning of civilization
a great flowering of art and culture
perhaps associated with the development of language? A big mystery, really.
maybe that microcephalin gene
seen most vividly in the cave paintings in France.

32. Human Migrations Started in Africa Spread to Asia and Australia
getting to Australia requires boats, 40-60,000 years ago
much later spread to Americas
a bit of controversy: very clear archeological sites dating to about 12,000 years ago. But possibly some older ones? Population must have been very sparse.
started at Bering Strait which was dry land then, and spread over both continents in less than 2000 years
last settlements:
Iceland settled around 800
Pacific islands weren’t completely populated until 1500
Madagascar was settled from Asia around 600 from Asia as part of teh same migration that populated the Pacific islands
Azores Islands in the Atlantic weren’t discovered until 1432

33. Race
What is the genetic basis for distinct sub-groups in the human species?
Studies of allele frequencies among different ethnic groups shows that about 85% of all variation is seen between groups, and
only about 10% is limited to a single group.
these numbers vary a bit because of difficulty objectively defining different ethnic groups,
Thus, most human traits are shared among all groups, and the idea of a strong racial identity is not supported by genetics.
trying to establish groups based solely on DNA variation generates 5 major groups: sub-Saharan Africa, Europe+Middle East+South Asia+North Africa, East Asia, American Indians, and Pacific Islanders.