Evidence of Evolution by Natural Selection 2007-2008 Dodo bird

Evidence supporting evolution Fossil record transition species Anatomical record homologous & vestigial structures embryology & development Molecular record protein & DNA sequence Artificial selection human-caused evolution

Fossil record Layers of sedimentary rock contain fossils new layers cover older ones, creating a record over time fossils within layers show that a succession of organisms have populated Earth throughout a long period of time

Fossil Record

Fossil record A record showing us that today’s organisms descended from ancestral species

Evolutionary change in horses 550 500 450 Equus 400 350 Body size (kg) 300 250 Merychippus increase in size, loss of toes, increase in size of molars 20-25 mya grasslands became widespread in Norh America molars = easer to eat grass hoof = faster locomotion on grassland 200 Mesohippus 150 Hyracotherium 100 50 Nannippus 60 55 50 45 40 35 30 25 20 15 10 5 Millions of years ago

Evolution of birds Archaeopteryx lived about 150 mya links reptiles & birds The avian nature of the brain and inner ear of Archaeopteryx (Alonso et al. 2004) - Archaeopteryx, the earliest known flying bird from the Late Jurassic period, exhibits many shared primitive characters with more basal coelurosaurian dinosaurs (the clade including all theropods more bird-like than Allosaurus), such as teeth, a long bony tail and pinnate feathers. However, Archaeopteryx possessed asymmetrical flight feathers on its wings and tail, together with a wing feather arrangement shared with modern birds. This suggests some degree of powered flight capability but, until now, little was understood about the extent to which its brain and special senses were adapted for flight. Alonso et al. (2004) investigated this problem by computed tomography scanning and three-dimensional reconstruction of the braincase of the London specimen of Archaeopteryx. A reconstruction of the braincase and endocasts of the brain and inner ear suggest that Archaeopteryx closely resembled modern birds in the dominance of the sense of vision and in the possession of expanded auditory and spatial sensory perception in the ear. Alonso et al. (2004) concluded that Archaeopteryx had acquired the derived neurological and structural adaptations necessary for flight. An enlarged forebrain suggests that it had also developed enhanced somatosensory integration with these special senses demanded by a lifestyle involving flying ability. Smithsonian Museum, Washington, DC

Where are the transitional fossils? Land Mammal ? Where are the transitional fossils? There are innumerable intermediate & transitional forms Whales as land creatures returning to the water…. Where are the intermediate forms of whale ancestors? Cartoon making fun of this idea. The cartoons disappeared 10-12 years ago when this fossil was found. Ambilocetic natans = “Walking whale who likes to swim” 4-5 intermediate forms all found in last 2 decades Indus River valley in between India & Pakistan.

2006 Fossil Discovery of Early Tetrapod Tiktaalik “missing link” from sea to land animals

Study of Paleontology ( Three scientists) Older sediments are below younger sediments. Georges Cuvier (1769-1832) 2005-2006

Gradualism James Hutton (1726-1797) 2005-2006 Earth’s geologic features — profound change formed as product of slow but continuous & cumulative processes 2005-2006

Uniformitarianism Charles Lyell (1797-1875) geologic processes have not changed throughout Earth’s history Conclusion: Earth must be much older than 6,000 years 2005-2006

II. Anatomical record Looking at morphological divergence and morphological convergence

morphological divergence Proof in Homologous structures Have similarities in characteristics resulting from common ancestry BUT Diverge into separate species

Homologous structures Similar structure Similar development Different functions Evidence of close evolutionary relationship recent common ancestor

Homologous structures spines leaves succulent leaves tendrils needles colored leaves

Example of Morphological divergence (text) All modern vertebrates share a ‘stem reptile’ who crouched low to the ground (common ancestor) Descendents of this stem reptile diversified in new habitats and became bird, reptiles, mammals Its 5-toed limbs became many things

Stem reptile: walked crouching on the land

Morphological convergence: Proof: Analogous structures Separate evolution of structures Look alike in different lineages But… different internal structure & development different origin no evolutionary relationship Don’t be fooled by their looks! Solving a similar problem with a similar solution

Example of…Convergent evolution Flight evolved in 3 separate animal groups evolved similar “solution” to similar “problems” Have analogous structures Does this mean they have a recent common ancestor?

Example of Convergent evolution Fish: aquatic vertebrates Dolphins: aquatic mammals similar adaptations to life in the sea not closely related Those fins & tails & sleek bodies are analogous structures!

Parallel Evolution Convergent evolution in common niches marsupial filling similar ecological roles in similar environments, so similar adaptations were selected but are not closely related marsupial mammals placental mammals

Parallel types across continents Niche Placental Mammals Australian Marsupials Burrower Mole Anteater Mouse Lemur Flying squirrel Ocelot Wolf Tasmanian “wolf” Tasmanian cat Sugar glider Spotted cuscus Numbat Marsupial mole Marsupial mouse Nocturnal insectivore Climber Glider Stalking predator Chasing

This is not LaMarck’s loss from “disuse”! Vestigial organs Modern animals may have structures that serve little or no function remnants of structures that were functional in ancestral species deleterious mutations accumulate in genes for non-critical structures without reducing fitness snakes & whales — remains of pelvis & leg bones of walking ancestors eyes on blind cave fish human tail bone This is not LaMarck’s loss from “disuse”!

Vestigial organs Hind leg bones on whale fossils Why would whales have pelvis & leg bones if they were always sea creatures?

III. Comparative embryology Similar embryological development in closely related species all vertebrate embryos have similar structures at different stages of development gill pouch in fish, frog, snake, birds, human, etc.

Similarity due to: Master Genes (Homeotic genes) A set of genes that determine development in the embryo Failure of one of these genes most often leads to devastating results in body plan These genes are highly ‘conserved’ meaning that they have not changed over evolutionary time.

Embryos of many vertebrate species develop in similar ways Example: All vertebrates go through a stage with four limb buds and a tail

Ex. Master Genes and Appendages DLx gene expression leads to appendages

So, what controls where appendages grow on the body? HOX master gene When present, it suppresses the activity of Dlx Example: embryonic pythons – Hox is expressed along the length of snake’s body – no appendages. Read about this on page 306

Why compare these genes? Molecular record Comparing DNA & protein structure universal genetic code! DNA & RNA compare common genes cytochrome C and b (respiration) hemoglobin (gas exchange) Why compare these genes? 25 50 75 100 125 Millions of years ago Horse/ donkey Sheep/ goat Goat/cow Llama/ cow Pig/ Rabbit/ rodent Horse/cow Human/rodent Dog/ Human/ Human/kangaroo Nucleotide substitutions Closely related species have sequences that are more similar than distantly related species DNA & proteins are a molecular record of evolutionary relationships

Comparative hemoglobin structure Human Macaque Dog Bird Frog Lamprey Why does comparing amino acid sequence measure evolutionary relationships? 8 32 45 67 125 10 20 30 40 50 60 70 80 90 100 110 120 Number of amino acid differences between hemoglobin (146 aa) of vertebrate species and that of humans

DNA and amino acid sequence differences... ...are greatest among lineages that diverged long ago, ...and less among recently diverged lineages

Comparing Cytochrome b Sequences 10 different species compared to the Honeycreeper (bird) Differences shown in red They tend to be neutral mutations and do not affect the overall sequence for the cytochrome b protein (found in cellular respiration)

Building “family” trees Closely related species (branches) share same line of descent until their divergence from a common ancestor

What data from whole genome sequencing can tell us about evolution of humans

Example: the Evolutionary Hypothesis of Common Ancestry Chromosome Numbers in the great apes: human (Homo) 46 chimpanzee (Pan) 48 gorilla (Gorilla) 48 orangutan (Pogo) 48 Testable prediction: If these organisms share a common ancestor, that ancestor had either 48 chromosomes (24 pairs) or 46 (23 pairs).

Chromosome Numbers in the great apes (Hominidae): Testable prediction: Common ancestor had 48 chromosomes (24 pairs) and humans carry a fused chromosome; or ancestor had 23 pairs, and apes carry a split chromosome. Ancestral Chromosomes Fusion Homo sapiens Inactivated centromere Telomere sequences Chromosome Numbers in the great apes (Hominidae): human (Homo) 46 chimpanzee (Pan) 48 gorilla (Gorilla) 48 orangutan (Pogo) 48 Centromere share a common ancestor with apes? This has the potential of contradicting evolution There are genetic similarities between humans & apes But humans have 2 fewer chromosomes (24 pairs vs. 24 pairs) Where’s the missing chromosome? can’t lose it = lethal Must have been a fusing. So should be able to look at our genome & find the fusing. If we don’t find it then evolution is wrong. Nifty little markers = centromeres & telomeres. Fusing would put telomeres in the middle of a chromosomes. If we don’t find this then evolution is wrong. Chr #2 was formed by head to head fusion of 2 primate chromosomes The centromere that has been inactivated corresponds to chimp chromosome #13 Telomere

Inactivated centromere Human Chromosome #2 shows the exact point at which this fusion took place “Chromosome 2 is unique to the human lineage of evolution, having emerged as a result of head-to-head fusion of two acrocentric chromosomes that remained separate in other primates. The precise fusion site has been located in 2q13–2q14.1 (ref. 2; hg 16:114455823 – 114455838), where our analysis confirmed the presence of multiple subtelomeric duplications to chromosomes 1, 5, 8, 9, 10, 12, 19, 21 and 22 (Fig. 3; Supplementary Fig. 3a, region A). During the formation of human chromosome 2, one of the two centromeres became inactivated (2q21, which corresponds to the centromere from chimp chromosome 13) and the centromeric structure quickly deterioriated (42).” Homo sapiens Inactivated centromere Telomere sequences share a common ancestor with apes? This has the potential of contradicting evolution There are genetic similarities between humans & apes But humans have 2 fewer chromosomes (24 pairs vs. 24 pairs) Where’s the missing chromosome? can’t lose it = lethal Must have been a fusing. So should be able to look at our genome & find the fusing. If we don’t find it then evolution is wrong. Nifty little markers = centromeres & telomeres. Fusing would put telomeres in the middle of a chromosomes. If we don’t find this then evolution is wrong. Chr #2 was formed by head to head fusion of 2 primate chromosomes The centromere that has been inactivated corresponds to chimp chromosome #13 Chr 2 Hillier et al (2005) “Generation and Annotation of the DNA sequences of human chromosomes 2 and 4,” Nature 434: 724 – 731.

IV. Artificial selection Artificial breeding can use variations in populations to create vastly different “breeds” & “varieties” “descendants” of wild mustard “descendants” of the wolf

Natural selection in action Insecticide & drug resistance insecticide didn’t kill all individuals resistant survivors reproduce resistance is inherited insecticide becomes less & less effective The evolution of resistance to insecticides in hundreds of insect species is a classic example of natural selection in action. The results of application of new insecticide are typically encouraging, killing 99% of the insects. However, the effectiveness of the insecticide becomes less effective in subsequent applications. The few survivors from the early applications of the insecticide are those insects with genes that enable them to resist the chemical attack. Only these resistant individuals reproduce, passing on their resistance to their offspring. In each generation the % of insecticide-resistant individuals increases.

Evolution is "so overwhelmingly established that it has become irrational to call it a theory." Born in 1904 in Germany, Mayr trained as a medical student but realized he had a greater passion for studying birds and biology. Emigrating to the United States, he became a curator at the American Museum of Natural History, working on bird classification while formulating his key ideas about evolution. In 1942 he published his most important work, Systematics and the Origin of Species. Mayr moved to Harvard University in 1953 and served as director of the school's Museum of Comparative Zoology from 1961 to 1970. Since then, he has published a number of books and chapters and received the prestigious Japan Prize for Biology in 1983. In his landmark 1942 book, Mayr proposed that Darwin's theory of natural selection could explain all of evolution, including why genes evolve at the molecular level. On the stubborn question of how species originate, Mayr proposed that when a population of organisms becomes separated from the main group by time or geography, they eventually evolve different traits and can no longer interbreed. It's this isolation or separation that creates new species, said Mayr. The traits that evolve during the period of isolation are called "isolating mechanisms," and they discourage the two populations from interbreeding. Moreover, Mayr declared that the development of many new species is what leads to evolutionary progress. "Without speciation, there would be no diversification of the organic world, no adaptive radiation, and very little evolutionary progress. The species, then, is the keystone of evolution." -- Ernst Mayr What Evolution Is 2001 Professor Emeritus, Evolutionary Biology Harvard University (1904-2005) 2007-2008

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