Evolutionary Biology Lecture Notes PDF

+Lesson 1: The Rise of Evolutionary Thoughts **Scientific revolution-** period of drastic change that took place during 16^th^ and 17^th^ centuries. It replaced the Greek view of nature that had dominated science for almost 2, 000 years **Darwinian revolution-** scientific revolution that overturn...

+Lesson 1: The Rise of Evolutionary Thoughts **Scientific revolution-** period of drastic change that took place during 16^th^ and 17^th^ centuries. It replaced the Greek view of nature that had dominated science for almost 2, 000 years **Darwinian revolution-** scientific revolution that overturned an existing idea about how nature works Models of Diversity of Life- used only five living species, for simplicity 1. **Plato- Typological Thinking** -Theory of special creation where every organism is believed to be an example of a perfect essence or a type created by God and these types were **unchanging.** \- Plato's typological thinking is defined as a way of looking at things that classifies only in terms of the types to which they belong, and **ignores variations among animals** **-"perfect organisms"** created by God 2. **Aristotle-**presents order of organisms in a **hierarchy of simple to complex forms or linear scale** - The **Scala naturae (**scale of nature/ladder of life) was a continuous hierarchy of all beings arranged in order of "perfection" - Started with minerals that originate in nonliving matter 3. **Jean-Baptiste Lamarck-** theories were largely ignored \- **Theory of use and disuse** proposed that organism that used one part of their **body repeatedly would increase their ability.** Conversely**, disuse would weaken** an organ until it disappeared For example: **Yolk sac and appendix** as a vestigial structure But later, it was clarified that appendix has shown functions such as maintaining the homeostasis and for immune function as a lymphoid organ, assisting with the maturation of B lymphocytes and production of A antibodies \- Organisms **are not static,** hence he was remembered for his concept of the inheritance of traits where **variation is acquired.** (ex. giraffe's neck hypothetically acquired from environment). -opposed by Darwin's theory of **"variation is inherited"** stating that some individuals are born happen to have longer necks, and longer necks are more successful hence produces successful individuals that have longer necks and they are usually the ones that thrives longer, that's why giraffe's species as of the present are those offspring of longer neck ancestors **4. George-Louis Leclerc, Comte de Buffon** -rejected the idea that species would evolve into another species Agnatha-jawless fish Chondrichthyes-cartilage fish Osteichthyes-bony fish **Sarcopterygii**-**lobe-finned fish** **Actinopterygii- ray-finned fish** **5. George Cuvier-introduced fossils in the study of biology** **-theory of catastrophism (fossils show that animal and plant species are destroyed time and again by deluges and other natural cataclysms, and that new species evolve only after that) example are the mass extinction of dinosaurs due to meteorite impacts** **6. Charles Darwin** **- Theory of evolution by natural selection become the foundation of modern evolutionary studies** **- formulated his theory in private after returning from a voyage around the world abound HMS Beagle, not until 2 decades later that he finally gave it full public expression on the Origin of species.** **-observations gathered include Saddle-back tortoise (have a shell that is easier to lift their heads high to eat tree cactus and to resolve disputed over limited food resources by raising their heads as high as possible during social interactions) and Dome-shaped tortoise (live on islands where there is an abundance of vegetation close to the ground, making it less necessary for them to raise their heads to feed).** **-Darwin's Finches Speciation** **-Speciation in the Galapagos finches occurred by:** **a.) founding of new species** **b.) geographic isolations** **c.) gene pool changes- happens as a result of the birds adapting to their local environment**  d.) reproductive isolation- if some birds from island B fly back to island A, they may have changed enough that they can no longer interbreed e.) ecological competition **7. Alfred Russel Wallace-**Published "Darwinism" and studied butterfly \- Most outstanding legacy is his formulation of theory of evolution by natural selection which predated Charles Darwin's published contributions -according to him every species has come into existence coincident both in space and time with a pre-existing closely allied species Lesson 2: Evidence of Evolution in living species **Pattern of Evolution** Evidence of change through time ❑Evidence from living species ❑Evidence from the fossil record ❑Evidence of descent with modification Evidence of common ancestry ❑ Phylogenetic tree/ evolutionary tree ❑ Ring species ❑ Homology **Special Creation** (perfect) **-**species do not change **-**each species separately created **-**Earth and Life are young **Descent with modification** (evolution) **-**species change over time **-**species derive from common ancestors **-**Earth and life are old **Evidences of theory of evolution** 1. **Soapberry Bugs** *(Jadera haematoloma)* **-**long beaks in balloon vine fruit **-**short beaks on flat podded golden rain tree **-**soapberry bugs in Florida lived exclusively on their native host, the round capsuled balloon vine **-**gardeners in central Florida began planting as an ornamental flora, the golden rain tree **-** Balloon vine was introduced in Australia and has been spreading as an invasive weed for some 80 years. The bugs evolved significantly longer beaks than their ancestors 2. **Vestigial Organs-**useless or rudimentary version of a body part that has an important function in other, closely applied species Examples: ***Apteryxx mantelli*-**flightless bird --vestigial wings but relatively tinier ***Charina bottae** (*rubber boa)**-**has tiny remnant hind limb ***Haasiophis terrasanctus*** (comes from holy ***L*** land) fossilized snake with fully formed hind limbs **Human Coccyx** (tiny tail bone) --suggesting that ancestors may have a tail **Arrector Pilli-** erect hair - \- for predator in animals and goosebumps for humans - ❑Humans have one DNA sequence that looks like a gene for CMAH in Chromosome 6 but mutation by a 92-base-pair deletion disables it. - ❑ Most mammals, including primates, make CMAH in abundance, but humans cannot. - ❑ This CMAH deficiency has a number of proposed effects on humans, including increased brain growth and improved self-recognition by the human immune system. - -**We are descendant with modification of ancestors with CMAH enzymes** **Vestigial Traits tested through experimentation** **-*Gasterosteus aculeatus*** (threespine stickleback) -- a small fish that lives in coastal waters throughout the Northern Hemisphere and readily invades freshwater **Marine sticklebacks-** heavily armored and dominant **Freshwater sticklebacks-** slightly armored and recessive; modified descendants of armored fishes Cresco et al., 2004 suggested that freshwater sticklebacks were descended from marine ancestors that had invaded lakes left by melting glaciers at the end of the last ice age Bell and colleagues hypothesized that marine populations invading freshwater might evolve toward the freshwater form Loberg Lake (Alaska) was poisoned in 1982 so that it could be restocked with trout and salmon for recreational fishing In 1988, the lake has been invaded by marine sticklebacks from nearby Cook Inlet. Monitoring of population from 1990-2001 showed that population changed from over 95% fully plated fish to over 75% lightly plated Lesson 3: Evidence of Evolution from fossil records Geologic Time Scale- a record of the geologic events and the evolution of life forms as shown in the fossil record **Fossil-**trace of any organism that lived in the past/pieces of evidence **Radiometric dating-** The decay rate such as some unstable isotopes **Relative age dating-**comparison of fossils **Specific absolute dating-** actual age of fossil **Carbon dating-** cannot be used for evolutionary events **Ediacaran epoch (**Proterozoic Eon) - presence of the **Aspidella** or one of the most common fossils of the Ediacara biota. They are one of the Earth's **oldest eukaryotic organism** dating for about 570 million years ago and very **fist multicellular** organism that was ever discovered. Found in every continent except in Antarctica. Paleozoic Era **Cambrian period-**marked with dramatic increase in the diversity of life "Cambrian explosion" **-**diversifying of multicellular forms **-**several continental plates have come together to form **southern land mass "Gondwana"** **Ordovician period-**marked with proliferation of **marine filter feeders s** such as sponges from Porifera and chordate. Appearance of small plants such as bryophytes. **-**Massive glaciers and ice cups caused the majority of plants and animals extinction during this period **Silurian period-**witness the aggregation of northern continents, continents are beginning to form Gondwana cluster moving up. -**Evolution of swimming marine animals** such as jellyfish -First appearance of the arthropods and vascular plants **Devonian period-** all nature groups of fishes already evolved. There is cartilaginous fish and bony fish **-**On land, the first insects and amphibians **-**forests is filled with clubmosses and ferns **-mass extinction of 3 quarters of marine species** due to collision of large meteorites with earth **Carboniferous period-**Coal **-**fossilized remains are tree ferns, and now called coal **-**saw the appearance of first reptiles, evolved from amphibian's ancestors **-**winged insects **Permian period-**marked with the formation of **super continent Pangaea** **-**as the climate became cooler, reptiles become the dominant land vertebrates **-**lineage of retiles where mammals evolve became distinct **-**most extensive of all mass extinction is brought by Permian period due to warming of the earth's climate, changes in the ocean (acid rain) **-**Volcanic activity on a massive scale which marked the end of Paleozoic era Mesozoic Era-middle, Pangaea slowly separates **Triassic period-** C plants and Conifers dominance in terrestrial vegetation **-**reptiles were still the dominant on land -there is an occurrence of mass extinction after Triassic period caused by huge spread of volcanic eruption and an increase in the atmospheric carbon dioxide **(Triassic extinction)** **-**Killed 67% or ¾ of the marine and terrestrial species of earth **Jurassic period-** radiation of dinosaurs **-**from quadruplet to bi-pedal dinosaurs and even flying dinosaurs **-**First appearance of mammals were record **-**bony fish in marine and freshwater dominance **Cretaceous period-**marked by complete separation of southern and northern continents **-**First flowering plants (angiosperms), evolved from gymnosperms **-**diversification and dominance of dinosaurs but this is the last age, due to collision of large meteorites with earth causing the extinction of dinosaurs Cenozoic Era- modern groups of plants animals evolve during this era **-Tertiary-** continents have drifted towards their present position, climate become cooler and drier **-** Extensive grassland formation **-**Mammals radiated extensively **-**extinction of dinosaurs gave way to evolution of mammals and formation of other vertebrates **-**humans spread geographically **-**many species of birds especially the large ones and large mammals also became extinct **-Neogene period -** Pliocene epoch -- Miocene epoch **-Paleogene period--** Oligocene epoch --Eocene epoch --Paleocene epoch **-Quaternary period** **-** Holocene epoch --Pleistocene epoch **OBSERVATIONS OF FOSSIL RECORD THAT HELPED EVOLUTIONARY BIOLOGISTS TO REALIZE THAT FOSSILS ARE PIECES OF EVIDENCE OF VOLUTION** **GEORGE CUVIER-**published a 23 extinct species **-**provide proof of extinction, that extinction is real **-**among the extinct species includes giant salamanders, reptiles and elephants **-**the deeper the depth of fossil, the unique and different it is compared to the living species that we see in the present **-**the shallow the depth of the fossil, the closer it is when compared to the present organisms **-Fossils of Mammoths** is a proof of common ancestry, a proof of descent with modification and a proof of extinction **-Fossil of Irish elk** have been found throughout the northern Europe, and analysis of Cuvier prove that this Irish elk is not a moose, not also a rain deer, or belongs to any other living species **Charles Darwin argue on the concept of Plato's special creation:** extinct species are relative of living species. He pointed out that the fact of extinction is an evidence of plants and animals have changed through time. **Law of Succession --**same as the concept of Alfred Russel Wallace on species from comes from pre-existing species. **William Clift-** proposed that "fossil and living organism in the same geographic region are related to each other and are distinctly different from organisms in other areas" **-**examples are the marsupials and glyptodonts and armadillo. **-descendent with modification with ancestors on the same region** **Transitional Forms-**according to Charles Darwin, species descendent with modification from earlier forms and that fossils represent past populations **-**fossil record should capture evidences of transformation in progress, showing mixed features of organisms that includes typical of ancestral combination and novel traits seen on the descendants -Fossil record formation changes of animals/organism from one group to another **Archaeopteryx fossil-** 150 million years ago found in Germany **-** had feathers and wings **-**evolutionary biologist **identifies it as a bird but resembles reptilian skeleton**, with beak, 3 claw hands and long bony tails; segments of caudatal vertebrate ***Sinosauropteryx prima***- First Chinese dragon feather; first dinosaur found with feather ***Caudipteryx zoui***- tail feathered ***Microraptor gui***- a four-winged dinosaur; most abundant non-avian dinosaur; first ever fossil found with assymetrical feathers on its back legs This transitional forms supports the claims the birds evolve from dinosaurs ***Balaena mysticetus*** (bowhead or Greenland right whale) as a transitional form of elephants due to its vestigial femur and pelvis suggesting that the ancestors of whale also lived on land or formerly land dwelling animals ***Basilosaurus isis***- fossil with tiny and fully formed hindlimbs ***Ambulocetus natans***- aquatic animal that is an excellent swimmer that uses its limbs -intermediate between limb ancestors and limbless descendants Lesson 4: Evidence of common ancestry Theory of special creation-species are connected by descend -species have geological relationships that are analogous to family tree **Phylogenetic tree-** evolutionary relationships between species; came out on Darwin's origin of species-bottom to top; shows species diversifying over time **Cladogram-** a diagram used to represent a hypothetical relationships between groups of organisms **-**used by scientist studying phylogenetic systematics to visualize groups of organisms being compared, how they related and their most common ancestors **-**arbitrary branch legs where length doesn't matter A thought experiment: history of a population of **imaginary snails as they evolved and spread across a chain of four islands** a. A population of snails on island 1 b. Elongated shells appear and become common, replacing uncoiled shells c. Snails from island 1 colonize island 2 d. Island 2 population evolves pink shells due to mutation or vegetation in area closer to color pink and later, island 2 snails colonize island 3 e. Island 1 snails evolve banded shells ; island 3 snails evolve high spire f. Island 2 population genes extinct due to anthropogenic factors, human factors, toxic chemicals ; island 3 snails colonize island 4 g. Island 3 snails evolve spiked shells Six different coat patterns in living species of felid **Evidence of Descent with Modification** **Ring species-**provide evidence of common ancestry and a situation that a new population do not interbreed are living in the same region and connected by geographic chains of population that can interbreed **Ensatina eschscholtzii** **Greenish warblers-**songbirds **Homology-** the same organ but variety of forming function **Homologous structures-** similar in related organism because they were inherited from **common ancestors**; may or may not have the same functions as the descendants. Example is **the embryos** from different vertebrates show striking similarities in development by the presence of notochord, post anal tail and gill's slits evolved to lungs **-**All embryos look the same because they evolved from the same common ancestors and some developmental stages have remain similar as they diversify over time **Analogous structures-** similar in unrelated organisms; **similar because they perform similar function** **Molecular Homology-** A genetic flaw that humans share with chimpanzees **-**invention of PCR **-**all organism have inherited their genetic codes from their common ancestors **-**CMTIA repeat/chromosome 17 **-**Peripheral Myelin Protein-peripheral nerves or myelin sheath **-Chimpanzees, bonobos and humans all share genetic flaws;** all species inherited proximal CMTIA repeat from a descent common ancestors Proximal repeat misaligns