Ecology Exam 1

BIOL 312 Exam 1: Why study evolution, philosophy of science, line of evidence for evolution, phylogenetics, the origin of life, the history of life, diversity of life, history of science.

Three reasons why we study evolutionary biology

1. It is in interdisciplinary field and unifying field of study. 2. It has practical applications. 3. It has intellectual, philosophical, and spiritual significance.

Describe what makes a field of inquiry scientific versus inquiries that are not.

To be considered a scientific field of inquiry, The theory must be capable of being used to make predictions

The predictions must be falsifiable by some conceivable observation

Define homology and give an example.

Homology is similarity due to shared history or relatedness. For example, the wings of bats and forelimbs of humans although possess similar structures, are used to carry out different functions. This similarity is due to relatedness.

Define analogy and give an example.

Analogy refers to similarity due to convergent evolution, where different species evolve similar traits independently due to similar environmental pressures. An example is the wings of bats and birds; both are adaptations for flight but evolved separately.

Convergent evolution

is the evolution of similar traits in unrelated species due to adapting to similar environments or ecological niches. An example is the wings of birds and insects, which serve the same function but evolved independently.

Vestigial traits and how they support evolution.

Vestigial traits are structures that have lost much or all of their original function through the course of evolution. These traits, such as the human appendix or the pelvic bones in whales, provide evidence for evolutionary history by indicating common ancestry. These traits can be seen as “poorly designed”, and can be genetic (pseudogenes), structural (human tailbone), or developmental (development of human fetus has tail and loses it).

The half life t1/2

of a radioactive material is the time it takes for one half of the parent material to decay into a daughter product.

How do fossils justify evolution?

Fossils are evidence of change. The fossil record is full of beings that no longer live.

4 ways geologic record supports evolution.

1. Earth is old enough for evolution to have occurred.

2. Extinction has occurred.

3. Transitional forms have appeared in fossil records.

4. Geographic correlation between the living and the dead. (Fossil marsupials found in Australia and South America)

What are the 8 ecozones/biogeographic realms?

Nearctic, Palearctic, indomalaya, afrotropic, Australasia, Neotropic, Antarctic, Oceana

What are the 3 options that determine where living things live? What types of animals are generally the exception?

1. Randomly distributed

2. As appropriate ecologically (no penguins in the arctic and no polar bears in the antarctic)

3. Influenced by history of continental plates (should see sharp barriers that match)

Wallace’s Line in the Pacific

An example of sharp lines in species distribution. Placental mammals on West side and Marsupials on East side, despite only being 20 miles apart.

Tigon vs Liger

Tigon: Male tiger and female lion

Liger: Male lion and female tiger

Ring species

a connected series of populations that form a ring around an area of unsuitable habitat, where adjacent populations can interbreed, but the populations at the ends of the ring, where they overlap, cannot. This creates a situation where the populations at the ends of the ring may be so different that they are reproductively isolated, essentially forming two distinct species where they meet, while the populations in between remain connected through gene flow

Hybrids

Different individuals within a species are separated by a certain number of generations. Different species are separated by a greater number of generations. Where is the line? Many species are reproductively isolated but those that are not can sometimes create hybrids, either in nature or in captivity. For example, mules and hybrids between wheat and rye.

Direct observation of natural selection in peppered moths in industrial areas in England.

Peppered moths were historically white with black dots, the first melanic peppered moth was observed. Experiments showed higher relative survival rate for white moths in unpolluted areas and black moths in polluted areas.

Artificial selection

The repeated use of selective breeding

has created some very large changes

in the characteristics of domesticated

organisms.

Breeder’s Equation: Selection requires variation, selection must choose individuals with differences from others ... differences that are heritable.

R=h²S

R = response; is the change in overall mean of trait from parental generation to next generation.

S = the selection differential, is the difference in mean of trait between those selected and those in overall initial population.

h² = the narrow sense heritability of the trait - a measure of how much offspring resemble parents (between 0 and 1)

Linneaus’ Hierarchal classification system

Kingdom, Phylum, Class, Order, Family, Genus, Species

K P C O F G S

Taxon/Taxa

The singular and plural for group(s) of species.

Taxonomy

The study of how to classify species

Phylogeny OR Phylogenetic Tree (NOT phylogeny tree)

A representation of how organisms are related. Indicate relatedness due to common descent.

Synapomorphies

Shared derived traits, used to make trees

Symplesiomorphies

Shared ancestral traits, not used to make trees because they clump together taxa that are often not the most related.

Homoplasies and what cause them.

having the same character state for a reason other than ancestry. Can be caused by convergences and reversals. For example the lack of legs in caecilians and snakes.

Monophyletic groups

A group containing a common ancestor and all descendants.

Paraphyletic group

A group containing most, but not all of the descendants of an ancestor.

Polyphyletic group

Does not contain a common ancestor.

Outgroups importance in phylogenetics

Use of an outgroup allows us to locate evolutionary innovations on the tree

- provides direction of evolutionary change

- Innovations are synapomorphies if shared

Branch lengths meaning on a phylogenetic tree

Branch lengths: Represent measured divergence by lengths of the branches. Usually done for molecular data with clear distances.

3 requirements for making accurate trees

1. Rarely changing characters (low chance of homoplasy due to reversals)

2. Knowledge of the characters and organisms (recognize homoplasy due to convergence)

3. Knowledge of tree construction and comparison methods and tools

Tree reconstruction vs tree comparison

Tree reconstruction: using an algorithm to make a tree

Tree comparison: using a criterion to decide between alternate trees

2 methods of tree reconstruction

Exhaustive search: Make ALL possible trees and comparing them to find the best one. Not feasible for more than 11-12 taxa. Number of possibilities growing faster than exponentially.

Using an algorithm to make a tree: Compute the distances between all the taxa and connecting 2 closest ones as a new taxa. Then, recompute the new distances between the taxa and connect the 2 closest…

Or, start with a good tree and swap branches randomly. Testing with each swap if the trees improves by criterion being used.

Tree comparison criteria: Parsimony

The tree with the fewest evolutionary events is the most likely one. Parsimony assumes evolutionary events are rare. However, does not take account into the the likelihood of each evolutionary event occuring.

Tree comparison criteria: Maximum Likelihood

compute the probability of seeing the data we observe given the tree we are assuming. Pick tree with highest probability.

P(data|tree)

Tree comparison criteria: Bayesian

compute the probability of getting the tree we assume given the data we have. Pick tree with highest probability.

P(tree|data)

Stochasticity definition and significance in constructing phylogenetic trees.

Randomness. How does stochasticity influence the patterns we see? Testing an observed pattern against randomness is central idea in

Robust definition and significance in constructing phylogenetic trees.

Repeatable, to determine the validity of the tree involves resampling to see how robust the tree is.

Methods to test robustness of the tree by resampling

Bootstrapping: resampling (with replacement) to create a new data set

• pick n characters from the set (may duplicate some and omit others)

• conceptually simulates robustness to gather even more data

Jacknifing: subsampling (without replacement) to create a smaller data set.

• Pick n characters from the set (will omit some)

• Conceptually simulates robustness to having gathered less data

The 4 Eons

Hadean, Archean, Proterozoic, Phanerozoic

Hellish Atmosphere Produces Plants

Why is the evidence for the earliest life circumstantial

Geologic turnover causes fossils to be almost impossible as very few rocks remain from this time.

Furthermore, early life forms would have eaten the precursors, and later life forms would have eaten the early life forms.

Properties of proteins

Chains of amino acids; provide structure, catalyze reactions, and not sensitive in water

Properties of RNA

Store genetic information; functional (tRNA and ribosomes); can catalyze various reactions (the breaking and forming of phosphodiester bonds like those found in RNA backbone); can evolve in the lab with the help of proteins; fragile in water

RNA vs DNA

RNA has an extral hydroxyl group on the ribose sugar. The difference between Uracil and Thymine is that Uracil is missing a methyl group.

Best current hypothesis for the origin of life

Simple inorganic compounds → complex organic compounds → replicating organic compounds → replicating RNA (this precursor explains why RNA is used in ribosomes and energy) → replicating DNA + proteins, cell membranes

Miller and Oro experiments

Miller: CH3 + NH3 + H2O + H2 → Amino Acids

Oro: HCN + NH3 + H2O → Amino Acids + Adenine

Out of all the possible amino acids, those that formed were the ones found in life.

What characterized each of the eons?

Hadean: Origin of life

Archean: Photosynthesis begins

Proterozoic: Multicellular Life begins

Phanerozoic: recognizable life begins

Hadean Eon

Formation of the solar system

Moon formed by Theia collides with Earth, bringing water and creating the 23.5 degrees axial tilt (cause of seasons)

Surface hot like Hades and generally unsuitable for life.

Origin of life ~4000 MYA, towards the end of the Hadean Eon

Archean Eon

Photosynthesis evolves, introducing oxygen to the atmosphere.

Life is single celled. Very few fossils from this time due to geologic turnover (oldest rocks from 4000 MYA)

Fossil ancient stromatolites, layered structures made by cyanobacteria (still seen today)

LUCA

MRCA of all currently existing life on Earth arose about 3.5 BYA. This organism would have DNA, ribosomes, tRNA, ATP and many genes (deep homologies of all life).

Proterozoic Eon

True multicellular life and eukaryotes evolve. Still very few fossils due to geologic turnover but they do exist. The Proterozoic Eon ends with the Cambrian Explosion 541 MYA.

Ediacaran Fauna

First fossils of multicellular life from 700 MYA during the Proterozoic eon. Predate familiar life forms.

Cambrian Explosion

541 MYA. Sudden appearance of many novel fossil species. Cause is hard to know, whether it is caused by true radiation of novel species, or simply evolution of fossil forming parts like shells. All 4 major arthropod groups are here, along with many other groups that are now extinct. Marks the end of the proterozoic and the start of the phanerozoic.

Phanerozoic Eon

Recognizable life begins, marked by 3 eras:

Paleozoic: The transition onto land

Mesozoic: The age of reptiles

Cenozoic: The age of mammals

The 6 periods of the Paleozoic Era

Cambrian: maximum biodiversity

Ordovician: Land colonized

Silurian: Jawed Fish

Devonian: the age of fish

Carboniferous: Amniotic eggs

Permian: Pangaea forms

Cambrian Period of the Paleozoic Era

Many different phyla and some evolved mineralized shells, giving us good fossils. Mainly just microbes on land, but the ocean had many arthropods (trilobites). Burrowing evolves, breaking up seafloor microbial mats. Predation evolves, hard parts are useful (good fossils). Most land is Gondwanaland, oceans are warm. Oxygen levels fall and the Cambrian ends with extinction.

Ordovician Period of the Paleozoic Era

Second big diversification event. Arthropods still rule the sea but nautiloids > trilobites. Arthropods and plants approach land. Jawless fish diversify. Global temperatures drop (due to photosynthesis and volcanoes). Gondwanaland moves toward the South Pole (1st mass extinction event).

Silurian Period of the Paleozoic Era

Earth is warm again, life on land really begins, but Oceans are still primary. Jawed fish and bony fish arise and diversify. Vascular plants emerge on land. Arthropods begin to fully colonize land.

Devonian period of the Paleozoic Era

The age of fish: diversification of chondricthyes (cartilagenous fish), osteichthyes (bony fish), sarcopterygii (lobe finned fish). First trees, seeds, forests emerge. First tetrapods (amphibians). Pangaea starts to form. The second mass extinction at the end of the Devonian period, anoxia causes plant death and led to oil deposits (oil from plants not from dinosaurs).

Carboniferous period of the Paleozoic Era

Highest oxygen content in history with huge arthropods. Sharks and tetrapods diversify. Amnion evolves = reptiles and synapsids. Pangaea cools, “carboniferous rainforest collapse” creates most modern coal deposits.

Permian period of the Paleozoic Era

Pangaea is formed and dominates the Permian period. One singular continent with nice coasts and desert interior. Amphibian species decrease as diapsids and synapsids thrive. First cynodonts (ancestors of mammals) appear. About 90% of insects were blattopterans. Seed ferns and conifers diversify. Ends with the third and biggest extinction ever, wiping out over 70% of all species and completely wiping out the trilobites.

3 Periods of the Mesozoic Era (Age of Reptiles/Age of Dinosaurs)

Triassic Period: First dinosaurs/mammals

Jurassic Period: First birds

Cretaceous Period: first flowers and placentals

Triassic Period of the Mesozoic Era

The early Triassic period was reigned supreme by the lystrosaurus, accounting for 95% of all land vertebrates. Hot and dry with one continent — Pangaea. First dinos and mammals, seed plants dominate terrestrial flora. Modern corals, ray-finned fish diversify. Archosaurs and dinosaurs dominate, mammals go nocturnal. Ends with the 4th massive extinction but dinosaurs and mammals survive.

Jurassic Period of the Mesozoic Era

Warmer and more humid than present day. Pangaea began to break apart. First angiosperms and conifers diversify. Reptiles diversify and first birds emerge. Ichthyosaurs and plesiosaurs diversify. Moderate extinction at the end, dinosaurs and mammals survive.

Cretaceous Period of the Mesozoic Era

Pangaea fully separates, lots of coasts and nice and warm. Conifers decrease as angiosperms diversify. First placental and marsupial mammals. Ichthyosaurs go extinct, plesiosaurs and mosasaurs rule oceans. Insects diversify: moths, aphids, ants, termites, grasshoppers.

End of the Cretaceous Period and the Mesozoic Era

The asteroid that killed the dinosaurs ends the cretaceous and the mesozoic. Marking the beginning of the Cenozoic Era, the age of mammals

The 3 periods of the Cenozoic Era, the age of mammals

Paleogene: Birds, mammals

Neogene: Grass Mammals

Quaternary: Modern Humans

Paleogene Period of the Cenozoic Era

Mammals and birds diversify and dominate the world. Whales and large mammals. 3 modern mammal groups clearly separate (monotremes, placentals, marsupials). First primates, carnivora, and rodents. Angiosperm and insect co-evolution. Birds diversify due to abundant insects and lack of pterosaurs.

Neogene Period of the Cenozoic Era

Begin to resemble the modern world. Kelp forests evolve. Apes and artiodactyls (like deer and giraffes) evolve. Modern seed plants evolve and grasses replace forests. Near the end of the Neogene period, North and South America connect at Panama, leading to the extinction of many marsupials and terror birds. Some primates in Africa develop bipedal walking and larger brains.

The two major Epochs of the Quaternary Period

Pleistoscene: The longest epoch of the quaternary period. Characterized by multiple ice ages and extinction of many large mammals (Africa less affected). Homo sapiens spread as a drought in Africa ends. Around 100-200k years ago some homo sapiens left Africa.

Holoscene: “Recorded history” begins ~10,000 years ago. The 6th major extinction begins because of humans.