Midterm 2

Question 1

Phylogeny (Intro)

Answer 1

• The evolutionary history of a group of organisms.
• Based on the idea that organism are related by evolution.
  –Phylogeny shows both the evoltuionary history and the relatedness of groups of organisms.
• Understnding these relationships is critical to our understand of both evoltion and how biological processes work.

Question 2

Phylogenic trees

Answer 2

• Reveal evolutionary history and relatedness among groups of organisms by comparing their anatomical physiology (aka morphology), or molecular features.
• Is a model of how a group of organisms descended from a common ancestor.
• It is all a hypothesis because they are the best explanation of existing data.

Question 3

Nodes

Answer 3

• Where groups split, which represents the most recent common ancestor of two descendant groups.

Question 4

Branches

Answer 4

• Where evolution occurs.

Question 5

Tips and taxa

Answer 5

• Tips represent observed taxa which are the endpoints of the process we are trying to model.

Question 6

Sister taxa

Answer 6

• Two species, or groups of species, are considered to be closest relatives if they share a common ancestor not shared by any other species or groups.
  EX. Frogs are more closed released to salamanders than to any other group of organs because frogs and salamanders share a common amphibian ancestor not shared by other groups.
• These are called SISTER TAXA
• The entire phylogenetic tree is simply a set of sister group relationships; adding a species to the tree entails finding its sister group in the tree.

Question 7

Equivalent groups

Answer 7

• The nodes of a tree can be rotated without changing the evolutionary relationship.

Question 8

Monophyletic group AKA clade

Answer 8

• All members share a single common ancestor that is not shared with any other species or group of species.
• Cladistic focuses specifically on derived similarities.
  – Defined by a single common ancestor where all descendants of the ancestor must be in the group.
  EX. The amphibians are monophyletic because all of the groups classified as amphibians share a common ancestor not shared by any other taxa.

Question 9

Constructing phylogenetic trees

Answer 9

• Phylogenetic tress are constructed by comparing characters shared among different groups of organism.
• CHARACTERS are the morphological, physiological, or molecular features that make up organisms.
• The infer the phylogenetic relationships.
  1. Phenetic approaches use measures of distance between organism.
  2. Cladistic approaches are based on modelling how evolution occurs on the tree.

Question 10

Morphological vs genetic characteristics

Answer 10

• We usually focus on genetic characteristics because it is easier to measure precisely.
• However, when we don’t have genetic information available, like in fossilized organism, we use the morphological approach.

Question 11

Phenetic vs. cladistic analysis

Answer 11

• Cladistic analysis makes use of the phylogenetic model of organisms evolving from each other to infer phylogenies.
• Phenetic analysis ignores the phylogenetic model of organisms evolving from each other while inferring phylogenies.
• Phenetics classifies organisms based on morphological and structural features while cladistics classifies organisms based on their ancestry and evolutionary relationships.
  — As a result cladistic is better because it is more accurate.

Question 12

Synapomorphies

Answer 12

• Classical cladistic analysis is based on synapomorphies…a shared, derived character as evidence that two taxa are related.
• We focus on synapomorphies because they evolved in the relevant context and because they must be things our model (the phylogenies) must explain.

Question 14

Basal vs derived

Answer 14

• BASAL are the characteristics of the common ancestors, while the DERIVED characters are those not shared by the common ancestor of the group that we are currently thinking about.
• Derived traits and basal characteristics are looked at as the same in phenetic analysis because they are they are looking at traits (the physical).

Basal and derived characteristics can be considered the same in phenetics because this approach primarily focuses on the overall similarity of organisms’ traits without making distinctions between primitive (basal) and advanced (derived) traits in terms of evolutionary history.

Basal characteristics: These are traits that are inherited from a common ancestor of a group of organisms. They are considered to be more ancient or primitive in the context of the group’s evolutionary history. Basal characteristics can help identify the common ancestry of a group of organisms and provide insights into their evolutionary relationships.

Derived characteristics: These are traits that have evolved or changed in a particular lineage or group of organisms since their divergence from a common ancestor. Derived characteristics can help researchers identify the unique features that distinguish one group of organisms from another and can be used to construct phylogenetic trees to represent evolutionary relationships.

The idea is to create clusters or groups of organisms that are most similar to each other, regardless of the evolutionary history of the specific traits being considered. This can lead to the grouping of organisms based on a combination of primitive and derived characteristics, without assigning them specific evolutionary significance.

Question 15

Inferring the common ancestor & Outgroup

Answer 15

• We want to know what the common ancestor was like, so we can tell which characters are derived (as opposed to basal)
• We can make use of an outgroup which is an organism closely related to, but outside, the group being studied.
  – We assume that the root or beginning, of the tree is where the outgroup branches from the group.
  – It is basically derived earlier than all the other organisms.

We begin with four species of animals (labeled “A” through “D”) for which we wish to build a phylogenetic tree. We will call this our ingroup, meaning it includes all of the groups for which we are interested in guring out relationships. For comparison, we also include a species that we believe is outside this ingroup – that is, it falls on a branch that splits o closer to the root of the tree – and so is called an outgroup (labeled “OG”).

Question 16

Convergent evolution, homogies, analogies

Answer 16

• Convergent evolution is a biological phenomenon in which distantly related species independently evolve similar traits, characteristics, or adaptations in response to similar environmental pressures or ecological niches.
• Convergent evolution often results in the development of analogous structures or functions that serve the same purpose but are not derived from a common ancestral trait. This can be seen in various aspects of an organism’s biology, such as morphology (physical appearance), behavior, or physiological adaptations.
• If similarities that are not homologies (i.e, not due to common ancestry), these are called analogies.

Question 17

Secondary loss

Answer 17

• Organism may lack a characters that its ancestors had.

Question 18

Parsimony

Answer 18

• The simplest tree, the one with the fewest evolutionary changes or character state transitions, is often considered the best representation of the evolutionary history.
• We take advantage that evolutionary change is typically rare.

Question 19

Why is genetic analysis more effective than the morphological analysis

Answer 19

• It can be hard to tell which traits are derived from a morphological perspective.
• Gene analysis typically allows us to analyze more traits.
• Down side is that it is more costly…so we can use morpholigcal groups if we have fossil records.

Question 20

Approximation of Phylogenetic trees

Answer 20

• Phylogenetic trees are tremendously useful and powerful tools for organizing, understanding and analyzing biological data. However, ther are limitations:
• The true history of life is not reflected and/or summerized in a single tree.
• Sex or other forms of gene transfer are not shown.
• Trees constructed by humans are not necessarily even the best apporiximation to the true history of life,
• Our guess often change overtime.

Question 21

History of life

Answer 21

• Big recent innovations have told us alot about the history of life.
• We have gained access to more detailed genetic information, sophisticated analysis techniques, and electronic computers.

Question 22

Bacteria

Answer 22

• No nuclei
• Small
• Most of the microorganisms that we see

Question 23

Archaea

Answer 23

• no nuclei
• mostly small
• rare, or live in more extreme conditions

Question 24

Eukarya / eukaryotes

Answer 24

• Large, nucleated cells with mitochondria
• mitochondria came after, and are captured bacteria

Early eukaryotic cells (the ancestors of modern eukaryotic organisms) are believed to have engulfed these aerobic bacteria through a process called endocytosis. Instead of being digested by the host cell, these bacteria formed a symbiotic relationship.

Question 26

When are trees a good approximation

Answer 26

• When populations are not mixing
• Geographical barrier
• Structural genetic exchange
• Populations have diverged enough to not have sex with each other (otherwise, we would need to make a tree of genes or genetic components instead of organisms)

Question 27

The fossil record

Answer 27

• A fossil is a physical trace of an organism from the past
• Intact fossils retain their form and substance
• Compression fossils are squashed into a thin film
• Cast fossils occur when the decomposing piece is replaced by minerals different from the surrounding ones.
• Premineralized fossils occur if minerals infiltrate cells as they decompose.

Question 28

Biases in the fossil records

Answer 28

• Very few things get fossiled and when they do, some are more fossiled than others.
• Habitat bias: eaier to find things that live in swampy areas, or unerground cuz they get buried…therefore bigger chance of finding fossils.
• Taxomomic bias: Hard things, or hard parts of things (ex. shells) are easier to find cuz when they die, we can see the hard shell
• Temporal bias: Things that lived more recently have had less time to be destoryed, or be buried too deep for recovery (more things to find that are recently dead)
• Adundance bias: things that are more abundant have more chance to be preserved
• SO! just because you dont see it, doesnt mean its not there. OR just because you see it more often, doesnt mean that there were a lot (relatively speaking)

Question 29

How to put fossil timeline together (3)

Answer 29

• Data of speciments can be inferred using radioactive isotopes (harder than it sounds)
• Geologic inference be made about the relative age of different things…depending if they how deep they are buried, you can tell they are older than the species above
• Molecular clocks are based on inferences about how fast are things evolving (DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms.)

Question 30

Processes of diversification

Answer 30

• Diversity sometimes arises gradually and sometimes dramatically (radication event).

Question 31

Adaptive radiations

Answer 31

• Occurs when a single lineage produces many descendant species, in a short period of time.
• Triggered by opportunity, either in the environment or because of the evoltuon of the organisms themselves.
• biotic and abiotic

Question 32

Biotic adaptive radiation

Answer 32

Biotic adaptive radiation, also known as ecological adaptive radiation, occurs when a single ancestral species diversifies into a variety of forms as a result of interactions with other living organisms and their environments. This type of adaptive radiation is often driven by ecological factors and interactions with other biotic components of an ecosystem. Here are some key factors and mechanisms involved in biotic adaptive radiation:

Resource Partitioning: In a given ecosystem, species may diversify to exploit different resources, reducing competition among them. This resource partitioning allows each species to occupy a unique ecological niche and utilize specific resources, leading to the coexistence and diversification of species.

Question 33

Abiotic adapative radiation

Answer 33

Abiotic adaptive radiation, also known as non-ecological adaptive radiation, occurs when a single ancestral species undergoes rapid diversification into different forms due to adaptation to non-living environmental factors. Unlike biotic adaptive radiation, which is driven by interactions with other living organisms, abiotic adaptive radiation is influenced primarily by physical and environmental factors. Here are some key mechanisms and factors involved in abiotic adaptive radiation:

Geographic Isolation: Physical barriers, such as mountain ranges, rivers, or islands, can lead to the isolation of populations of a species. Different isolated populations may face distinct environmental conditions, promoting divergence and adaptation to local abiotic factors.

Climate Changes: Shifts in climate can lead to the adaptation and radiation of species. For example, as climate conditions change, populations may evolve traits that allow them to thrive in different temperature ranges, precipitation levels, or other climatic variables.

Question 34

Triggers of adaptive radiation

Answer 34

1. Morphological innovation: a new adapative mutation can open up further possibilies for adaptive.
   EX. Anthropod body plan created new species of insects, arachnidsd and crustaceans.
2. Gene duplication: One or more genes may be accidentally duplicated so that the genome has two copies of each gene (can occur through polypolidy). This can be less efficient and selected against but it can also providethe opportunity for one copy to continue to do the old function, while the other copy evolves to do a new function.
3. Co-evolution: The evolition of one group creates a new nich for another group and vice versa. Flower will arrange pettle but birds will evolve beak to still reach.
4. Mass extinction: gives opportunity for other species to radiate

Question 35

Physical changes

Answer 35

• Physical changes often provide species with new adaptive challenges and opportunties.
• Climate change, continental drift, geological change, new environment arise (geology may change connections between two populations without a large effect on how they live….via river chanign course, moutainint ranges

Question 36

Changing ecosystems

Answer 36

• Taxa can be dratmatically affected by changes in other taxa (like co-evolution)
• Interactions with other organisms is key (who do i eat? Who will try to eat me? how do i reproduce? –> if organisms around you evolve, you are likely to evolve)
• As a result, coevolution drives diversity (plants evolve new ways to use insects or vertebrates for sex)

Question 37

Mammalian ancestors

Answer 37

• The therapsids radicated and dominated many terrestiral enviroment before dinosaurs did BUT they were largely replaced by the age of the dinosaurs.
• Therapsids are the branch of mammalian ancestor right before us but didnt yet have milk.

Question 38

Radiation and contraction

Answer 38

• Many clades seem to go through periods of radiation and contractions AKA the loss and gain of species diversity.
• Some reasons for contraction are:
  change in conditions (climate, continents moving), competition with other clades (therapsids vs dinosaurs), competition from a successful memebr (people vs other hominins), bottleneck effect (driven to low numbers –>Overall, the bottleneck effect is a key factor in the contraction of species because it can result in a loss of genetic diversity and compromise the adaptive potential of the population )

Environmental Changes: Shifts in environmental conditions, such as changes in climate, can have a profound impact on a diverse clade. Species within the clade may be adapted to specific ecological niches, and alterations in temperature, precipitation, or other environmental factors can threaten their survival.

Question 39

Interpreting patterns

Answer 39

• we see alot of clades with a history of radiation…does that make they most clades radiate?
  -Maybe because they are the ones we notice the most, because the other species are exitinct or with very little population. Or because the clades that radiate are more successful

Question 40

Survivorship bias

Answer 40

• Biases arise from the fact that we’re much more likely to observe successful taxa. So we miss:
  Unlikely adaptive muations, weird specifiation events, polypoloidy and other duplication.

Answer 41

• a clade that has undergone adaptive radiation in the past may retain several advantages, even if it later experiences a contraction in its population or diversification.
• Retention of Specialized Traits: Traits evolved during adaptive radiation, such as specialized morphologies, behaviors, or physiological adaptations, may persist within the clade. These traits can continue to provide advantages in specific ecological niches, contributing to the clade’s survival and success.
• Unique Reproductive Strategies: The marsupial reproductive strategy, characterized by the birth of relatively undeveloped young that continue their development in a pouch, is a unique adaptation. This strategy allows marsupials to reproduce rapidly and efficiently, which can be advantageous for population recovery after contractions.

Question 42

Our recent history

Answer 42

• Primates (apes, new/ old world moneky, lemures)

HUMANS
Highly developed stereoscopic vision
- Eyes are close together, face forward, and are used together
- Allows 3-d visualization
–Trade off: eyes close together so we don’t see a large range
Versatile limbs
Grasping hands and feet
Nails and fingertips (instead of claws)
- Large brains
–Compared to related groups of mammals (whoever are our close mammalian relatives)

Question 43

Obersever bias between primates

Answer 43

1. Obeserver bias: scientists view humans with a particular perspective because we are humans.
   2.Phenetic approaches show that humans have lots of adapations
   – like humans look different to us but penguins all look the same to us too, so maybe we think we have lots of adaptations compared to chimps and gorillas. OR we have adapted to communicate with others while chimps and gorillas have not.

Question 44

Angiosperm explosion

Answer 44

• Flowering plants radiated and look over lots of niches in the world.
• This radically changed the ecology of the world, and opened up many new niches, apparently including space for primates (Source of food, shelter)

Question 45

Primate adaptations

Answer 45

• There are a variety of theories of how characterisitc primate. Likey something that has to do with processing and handling angiosperm fruit and flowers.
• Suggests that the diversification and evolution of primates are closely tied to their adaptations to specific ecological niches and environmental conditions. This theory emphasizes the role of environmental factors in shaping primate characteristics, behaviors, and evolutionary trajectories.

Question 46

Adaptive theory of primate

Answer 46

tThere are many theories for why primate traits might have been adaptively favored in our ancestors.
- Primate traits might good for monkeys to Leap from branch to branch
-Lead to stereoscopic vision to have an idea of where the branches are
-Climbing and balancing on trees, lead to grasping
- Exploiting new plant resources
- Catching insects
–With clever hands and stereoscopic vision would be good
- Adaptive foraging: the ability to switch between types of food, and to learn to use new types of food. To try things, and observe things, and to have the brain power to switch from one type of food to other and to learn things and learn from each other

Question 47

Adaptive looping

Answer 47

Sometimes adaptations can reinforce each other:
- Bigger brains may increase selection for adaptive foraging
- Needing to process more types of food my increase selection for clever hands
- More clever hands may increase selection for good stereoscopic vision
- Ability to see and manipulate things may increase selection for bigger brains to process what we see . . .

Question 48

Apes

Answer 48

• Apes are more adapted for swinging thorugh tress, wheras monkeys are more adapted for climbing
• They are more upright
• They have mobile arm joints that may have evolved to help heavy animals specifically climb down from trees.
• This adapatation when humans evolved helped us with other tasks, like adpative ofraging or using tools, playing games and cooking
• Many ape speices were replaced by OLD WORLD MONKEYS…why is this if apes adapted so well?
• Competition with other taxa of apes
• Changing climate conditions
• Changes in plantsand insects (plants evolved to be more resistat to be eaten by acient apes)
• If ape radiation did not happen, there would be less diversity/ possibily no humans.

• Basically, apes were in the environment and they radiated…it could be possible that monkey’s radiated ALOT BETTER than apes to overtake apes…or that apes radiated at a much slower rate.
• Abiotic factors can also come into to play that constricted apes…the new world monekys replaced them because there was space in the niche.

Question 49

Chimps vs humans

Answer 49

• Chimps and humans have only 1% genetic difference
• Humans have 46 chromosome, chimps have 48. what they’re doing is they’re finding pieces of DNA that will fuse together and then they’re seeing how similar they are (this is the same thing we would do with a banana plant)…The concept of a 1% difference in homologous sequences refers to the genetic divergence or variation observed between two species in specific regions of their DNA that are considered homologous.
• This number is 4% on a broader scale: meaning that small changes can have large effects…We’re very complicated biochemical machines, so small chances in our genes can lead to a large change in how they work -> how they’re expressed
  EX. we may have the same protein as chimps but the base pairs that make up the protein is different.

Question 50

Hominins

Answer 50

• Refer to people and our upright ancestors
  – Adaptive looping of being upright gave opportunity to use hands which increased selection of upright taits.
• Changes in chewing design (teeth, jaw, skull)

Question 51

More on upright posture

Answer 51

Some theories:
- adapation to walking on the ground instead of swining through trees (might be due to climate change where enviornments have less forest, more savanas)
- Adaptions of keeping cool (Idea is that there is less surface for the sun to beat down on your back if you stand up)
- Adaptation for harvesting food
- Adaptation for carrying food

Question 52

Complex foraging

Answer 52

Our ancestors went beyond the adaptive strategies of their relatives and found a tremendous variety of ways to feed themselves:
Cooking and fire
Weapons and hunting
Tools and digging
Selecting plants

These strategies likely built on, and also favored, existing traits:
Big brains, clever hands, mobile arms, stereoscopic vision, uprightness
This is an example of: adaptive looping

Question 53

Co-operation and sociality

Answer 53

• Complex foraging can lead to selection for more co-operation…people with different skills sets can achieve different tasks.
• This leads to factors like social interactions, bigger brains, communication, culture and long develoment periods and maturation.

Question 54

Rate of development

Answer 54

• Why do human children develope so slowley?
• This may be because of trade off to attain a bigger brain which takes longer to develop.
• Alot to learn and development of social skills.

Question 55

Teeth

Answer 55

• Teeth are very important for processing food
• We have two sets of teth because it makes it more likely that our teeth will last aka why wisdom teeth come later.
• They help scientist understand what extinct animals ate.

Question 56

Eyes

Answer 56

• Eye orbits are the skeletal cavits where eyes are.
• The orbits tell us size, shape and position of eyes from fossil animals.

What are the advantages and disadvantages of more forward-facing eyes?
- Better for precise tasks three-dimensional visualization
- Not as good for looking around, being alert (things sneaking up on you)

What are the advantages and disadvantages of larger eyes?
Better for night vision
More costly? Harder to protect? Might be hard to design? There’s always a trade-off
Are small (or deep) eyes better for day vision?

Question 57

Dimorphism and sexual strategies

Answer 57

• Gorillas live in male centered groups (one adult male, several adult females)
• Chimps live in large, well-mixed groups with lots of interactions between males and females
• Therefore, gorillas have more sexual dimorphism because they are huge and strong to compete for females by displaying and compete by females by displaying and fighting. A dominant male has exclusive access to a group of females

Question 58

Gentials

Answer 58

• Chimps have larger
  1. To attract females
  2. female can reproduce with others and it means that she can have multiple sperm donors in her which would be another form of competition so they have more sperm to be more likely to have the female have their child and not someone else so they can pas on traits
• Gorillas don’t use genitals as part of sexual competition, they don’t need to further compete after determining the strongest

Question 59

Human sexual competition

Answer 59

• gentials are likely imporant in copetition for sexual access
  Probably less sperm competition than chimps (more stable relationships, not someone reproducing with someone reproducing with someone where the female now has a mix of sperms)

Question 60

Species richness

Answer 60

Species Richness:

Definition: Species richness refers to the total number of different species present in a particular area or community.
Measurement: It is a simple count of the number of species.
Example: If a forest has 10 different species of birds, 15 species of plants, and 5 species of mammals, the total species richness of that ecosystem would be 30.

Question 61

Species evenness

Answer 61

Species Evenness:

Definition: Species evenness refers to the relative abundance of each species in a community.
Measurement: It takes into account not only the number of species but also how evenly distributed the individuals are among those species.
Example: In a hypothetical community with two species of birds, if there are 100 individuals of species A and 10 individuals of species B, the community is not very even. However, if there are 55 individuals of species A and 45 individuals of species B, the community is more even.

The importance of species evenness is highlighted, as a community dominated by a single species may be more vulnerable to environmental changes.
- This means that