Test 2

Phylogeny

Phylogeny

evolutionary history of a group of organisms, based on idea that organisms are related by evolution

phylogenetic tree

model of how group of organisms descend from a common ancestor, model consists of nodes, branches, and tips

nodes

where groups split on a phylogenetic tree

branches on a phylogenetic tree

where evolution occurs

tips on a phylogenetic tree

representing observed taxa, assumed to be monophyletic

taxa on a phylogenetic tree

the endpoints of the process we are trying to model

clades

group defined by single common ancestor, all descendants of that ancestor must be in it, can also be called monophyletic groups or taxa

sister taxa

useful way of thinking about the phylogenetic trees, two taxa that share common ancestor at any scale, and you would need to take the whole taxon

lineages on a phylogenetic tree

the tree indicates the pattern of these branching, the tree is a model of how evolution occured

equivalent for phylogenetic trees

trees that correspond to the same model, all same common ancestors, just telling us who split from who

order of species on a phylogenetic tree

we don’t interpret anything about the order of a tree, no species are higher or lower than others (according to tree), we’ve all been evolving for same amt of time

how closely related two organisms are

we look at common ancestor on tree

characteristics/ characters

the describing phenotypes that make species look/ act similar

morphological

physical or genetic, looks like, or blood, genetic sequence, etc.

phenetic approach

use measures of distance between organisms

cladistic approach

based on modeling how evolution occurs on the tree

morphological or genetic for phlyogenies

usually more info from genetic, and easier to measure precisely, but can use morphological when less resources like when genetic info is not available (most fossils)

cladistic analysis

makes use of phylogenetic model of organisms evolving from each other to infer phylogenies, making use of how we think evolution happened. preferred model

phenetic analysis

ignores phylogenetic model of organisms evolving from each other while inferring phylogenies, just using those that look similar. not preferred, we use thing when not enough time money etc, only distance info no genetics, not enough baseline info. looks at derived and basal characters equally

synapomorphies

has to be different as opposed to homologies, classical cladistic analysis is based on this; shared, derived characteristics, evidence that two clades are related

derived characteristics

character not shared by the common ancestor of the group that you are looking at

flight as evidence

oaks and fish don’t fly, but birds do. Does that make oaks and fish closely related? no, theres no evidence

basal/ancestral characters

the common ancestor, characteristics of the common ancestor

inferring common ancestor

want to know to tell what characters are derived vs basal. sometimes common sense, but difficult statistically, make use of outgroup

outgroup

organism closely related to, but outside, of group being studied, you have to be confident about what you call this. we assume that the root of the tree is where it branches from the group

convergent evolution

two species may have the same trait because the trait evolved twice independently

secondary loss

lack a characteristic that its ancestors had, can get confusing and make unsimilar organisms look similar

analogous

similarities that are not homologous

parsimony

fewest number of changes necessary, classical cladistic analysis is based on the tree that can explain this way

how to address convergent evolution and analogy

use as many different characteristics as possible and look at them, may also help to use many different taxa. modern approaches w genetic data use more sophisticated models

genetic vs morphological

genetic analysis more effective than morphological bc it can be hard to tell which traits are actually derived, genetic allows for greater trait analysis (more data)

limits of phylogenetic trees

cannot really summarize true history of life, different types of gene combination, our guesses change over time

the three domains

bacteria, archaea, and eukarya

bacteria as a domain

no nuclei, mostly small, most of the seen microorganisms, hard to tell apart from archaea even w microscope, need to see niche

archaea as a domain

no nuclei, mostly small, rare, live in extreme environments, hard to tell apart from bac even on microscope, need to see niche

eukarya as a domain

large, nucleated cells. plants, animals, fungi, and then all sorts of protozoa. seem to be sisters w archaea based on most key genes, characterized by nuclei & mitochondria (endosymbiosis theory)

web of life

if genes or even whole bacteria (like the mitochondria) can be transferred, as well as reuniting of species, life is not really a tree

the five kingdoms

an old approach to seeing life, does not describe the correct evolution, more useful for genera understanding of difference bw types of eukaryota.

when can trees be used to approximate

when pops are not mixing, we can do this by geographical separation, or otherwise make a tree of genes instead of traits

how fossils can form

compression squashes them into thin film, cast fossils from decomposition replacing minerals different from surrounding ones, permineralized if minerals infiltrate cells as they decompose

biases in fossil record

you can’t always rely on the given information of fossils. Habitat bia, taxonomic bias, temporal bias, abundance bias

habitat bias

things that live in swampy areas or underground may not fossilize, so we never knew they existed

taxonomic bias

hard things, or hard parts of things like microorganisms w shells harder to fossilize

temporal bias

things that lived more recently had less time to be destroyed, or to be buried too deep for recovery

abundance bias

things more abundant likely to be perserved, does that mean that something significant isnt important if there is less of it?

accounting for bias in fossils

just because you don’t see it, doesn’t mean it wasn’t there. just because you see alot, doesn’t mean that there were alot (relatively)

how to put timeline of fossils together

dates can be inferred using radioactive isotopes, geologic inferences (one fossilized on top of the other), molecular clocks (how fast things evolve)

radiation events

dramatic diversity at one time (one species diverges into 10)

mass extinction

species that disappear dramatically

process of diversification

diversity can arise and decline gradually, or arise and decline dramatically

adaptive radiation

occurs when single lineage produces many descendant species in a short period of time. triggered by ecological opportunity, morphological innovation, and co-evolution. Makes their living different

ecological opportunity

organism arrives in new area w no similar organisms or competition drives or kills a species away

morphological innovation

new adaptive mutation can open up further possibilities for adaptation. legs in arthropods

co-evolution

evolution of one group creates new niches for another group and vice versa (insects and flowering plants)

gene duplication

one or more genes may be accidentally duplicated so that the genome has two copies of each gene (polyploidy is an example). could make organism less efficient and be selected against, but could also allow for innovation

innovation from gene duplication

one copy of the gene would continue to do the task while the copy can evolve to perform a new function

mass extinction events

five major ones so far, last one was the one that wiped out the dinosaurs, we could be in the middle of a mass extinction right now! (hunting/ exploiting/ overfishing, deforestation/ urbanization, introduction of species from one place to another, global warming/ pollution, water overuse, etc. (don’t need to be memorized, just some examples))

humans as an example of evolution

it is known that humans evolved from other primates due to our large similarities

what is different about people from other organisms

opposable thumbs + tool use, long development time, communication, culture, language, technology, complex thoughts

what is the same between humans and other organisms

genetic code, biochemical processes, common ancestor, successful reproduction, if our current reproductive success depends on heritable variation in traits, then were gonna keep evolving (smarter, dumber, bigger, smaller)

context for evolution

adaptations build on existing adaptations often in unexpected ways, evolution doesn’t know where it is going, it moves from one thing to the next as it reaches a “goal”

issue of a constant environment

species can only improve with gradual adaptations to the same environment and will be in danger of getting “stuck” (vertebrate eyes), a changing environment provides opportunities to try new combinations and build in unexpected directionss

physical changes

often provide species w new adaptive challenges and opportunities. global climate change, continental drift, geological changes, vicariance events

changing ecosystems

taxa can be dramatically impacted by changes in other taxa (flowering plants and their bees), co-evolution is a driver of diversity

therapsids

mammalian ancestors, radiated and dominated many environments before even dinosaurs, they were largely replaced by the dinosaurs during the age of the dinosaurs, but some survived and radiated after the mass extinciton

radiation and contraction

gain and then loss of species diversity. radiation gives chance for adaptation. contraction may occur due to changing conditions, competition from other clades and competition from same clade

interpreting patterns

we see many clades w history of radiation but we can’t confirm this because of bias of seeing what still exists (survivors bias)

survivorship bias

bias arises from the fact that we’re much more likely to observe successful taxa, unlikely adaptive radiation, weird speciation events like hybridization, polyploidy + other duplications, and combination of species (eukaryota absorbing mitochondria and choloroplast)

advantages of previous radiation

even if it contracts, they’ve explored a new environment, more chance to adapt (only few successful species)

primates

characterized by: highly developed stereoscopic vision, versatile limbs (grasping hands + feet, nails instead of claws), and large brains (compared to other mammals)

stereoscopic vision

eyes close together, face forward, used together, 3-d visualization

observer bias

since we are human, it gives us a particular perspective when studying humans

angiosperm explosion

flowering plants that diversified very rapidly around 100mya. radically changed ecology of the world, opened up new niches

primate adaptations

each step favoured adaptively by pressures: leaping from branches, climbing on trees, exploiting new resources, catching insects, adaptive foraging

adaptive foraging

ability to switch bw types of food and learn to use new types of food from others, then teaching that

adaptive looping

sometimes adaptions reinforce each other; bigger brain for adaptive foraging→ process more types of food for clever hands→ clever hands increase selection for stereoscopic vision→ ability to see and manipulate things may increase selection for bigger brains→ back to start

apes

more adapted for swinging through trees rather than climbing and leaping (monkeys). more upright, better at hanging, worse at sitting on trees

patterns of replacement

apes radiated into many habitats before monkeys did, many apes replaced by old world monkeys. this could have happened because of: competition w other taxa, changing environment, change in plants + insects, adaptive innovations by the monkeys

chimps vs humans

everything says 1%, but it is actually a 4% difference. This is because the different number of chromosomes is not accounted for. the 96% is probably metabolic function organs and cells

hominins

people and other upright ancestors, changes in jaw and chewing, more social. very specific splitting bw genus and species because of observers bias

upright posture

unknown for sure, but could have been due to: adaptation to walking on ground instead of tree swinging (climatic change, less trees), adaptation to keep cool (less sun on back, only on head), adaptation for harvesting and carrying food

Modern humans

probablyu replaced H. egaster through competition. characterized by: small face + mouth, less robust skeletal features, evolved in Africa around 200tya, took over most of world in last 50tya

complex foraging

our ancestors went beyond adaptive strategies of other hominins and found various ways to feed: cooking, tools for hunting animals and digging for tubers, selecting plants. likely built on existing traits of adaptive looping

brain and body size of humans

compared to graph showing what average human brain size should be, it is very large, this is part of the looping effect

new adaptive loops for modern humans

social interactions → big brains → communication → culture → long development period

slow rate of development for humans

could be due to many reasons: lots to learn, social skills are important to survive so those must be present, could also be a tradeoff for bigger brains

strategies for early primates for eating

frugivory, folivory, insectivory

frugivory

eating fruits and sometimes flowers

folivory

eating leaves

insectivory

eating insects

teeth

very important for food processing, they help scientists understand what extinct animals ate, often preserved and highly adapted

orbits

skeletal cavities where the eyes are, they tell us the size shape and position of eyes from fossils

advantages and disadvantages of forward-facing and large eyes

forward facing is good for 3D visualization and precision, but worse for predators as we cannot see around us. large eyes may be better for night vision but may be more costly and harder to protect.

sexual dimorphism

in species with more dimorphism there is more variation in male success and competition bw males for females

human sexual competition

compared to other apes, humans have big penises and small testicles. could be because less sperm is needed because less partners, and large penis because of larger competition for sexual success

population ecology

stage of evolution rather than evolution itself

defining a population in ecology

individuals of the same species living together, all individuals of a given species that live and reproduce in a particular place and time

Population size

can size be estimated if a population is not defined? When we're told a population is a certain number it is never exact because it can change from year to year

population range

the area in which a population lives, not proportional in all areas because of resources existing in different areas and climates best for certain members of the population

population density

We can do the math to give us the exact number, but this is not accurate because of the range