Bio 1M03 Midterm 2

Phylogeny

Phylogeny

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

Why is understanding phylogeny important

critical to our understanding of both evolution and how biological process work

phylogenetic tree

moel of how a group of orgamisms descended form a common ancestor

Nodes

where two or more groups split

branches

where evolution occurs

tips

represent observed taxa

taxa

endpoints of the process we are trying to model

monophyletic group

group defined by a single common ancestor, all descendants of the ancestor must be in the group

monophyletic groups can be called

clades or taxa

what are some prominent groups that are not clades

fish, bugs, vegetables, prokaryotes, reptiles, apes

sister taxa

two taxa that share a common node, at any scale, you need to take the whole taxon

lineage

tree indicates the pattern of branching lineage, model of how evolution occured

trees that correspond to the same model are considered______

equivalent

tips are ______ by the model to be monophyletic

assumed

except for _____________ we dont interpret anything about the _____ of the tree

branching pattern, anything

according to the tree:

no species are higher or lower than others, we’ve all been evolving for the same amount of time

how do we judge how closely related two organisms are according to a tree?

by looking for their common ancestor

constructing a phylogenic tree

1) measure characteristics of the taxa of interest(morphological or genetic)

2) infer the relationship

characteristics or character

anything that seems useful to measure, could be morphological(physical or genetic)

phrenetic approaches

use measure of distance between organisms, ignores the phylogenetic model of organisms evolving from each other while inferring phylogenies

cladistics approaches

makes use of the phylogenetic model of organisms evolving from each

other to infer phylogenies, based on modeling how evolution occurs on the tree

Should we use morphological or genetic characteristics to infer phylogenies?

We usually have more information from genetic characteristics, and this information is easier to measure precisely

When should we use morphological characteristics?

when genetic info isnt available, most fossil organisms

some viruses evolve so fast that morphological characteristics can be more stable than genetic characteristics

which is better cladistics or phenetic

cladistics

when should we use phenetic analysis

when our data is only distance, with no character available, eg certain molecular techniques

when we don’t have enough baseline info

synapomorphies

shared, derived characters as evidence that two taxa are related Classical cladistics analysis is based on

why do we focus on derived characters

These are things that evolved in the relevant context

So they are the things our model (the phylogenies) must explain

oaks and fish dont fly but birds do

We’re pretty sure that the common ancestor didn’t fly, No evidence (any model will have flight evolve once),Flight evolved once in either case

mosquitos and birds fly but fish dont

Evidence (flight might have evolved once or twice on this tree),But this evidence points in the wrong direction,This is why we combine evidence from different sources

derived compared to what

The common ancestor (characteristics of the common ancestor are called basal or ancestral characters

basal or ancestral characters

characteristics of the common ancestor are called

derived character

character not shared by the common ancestor of the group that we are currently thinking about

pheteic analysis treatment of traits

is that phenetic analysis treats derived and basal characters equally

why do we want to know what the common ancestor was like

so we can tell which characters are derived ( as opposed to basal)

can be done by common sense

inferring the common ancestor statistically is _______

difficult for technical reasons

outgroup

an organisms closley related to, but outside the group being studied, can be made use of to study a group

we assume that the root of the tree is where the ______ branches from the group

outgroup

convergent evolution

2 species might have the same trait b/c the trait evolved independently twice

flight, trees, dolphins and icthoysaurs

secondary loss

an organism might lack a character that its ancestor had

analogies

similarities that are not homologies( not due to common ancestor)

homology

due to common ancestor similarities

parsimoniously

with fewest number of changes necessary

classical cladistics analysis is based on searching for a tree that is the most this

How do we address the problem of convergent evolution and analogy?

Make use of many different characteristics, when possible

Look at characteristics in detail (break them up into smaller characteristics)

It may also help to use many different taxa

what is the effect of unique characteristics

they affect phenetic trees, not cladistic

as long as we are sure that they are derived

Why might whales have more derived characters than the other species?

Because they have had to adapt more since moving to the water

we except the pair with the _______ differences to match the pair with the ______ similarities

fewest, most

the conceptual difference between phenetic and cladistic is

cladistic focuses specifically on derived similarities

confirmation

Intermediate forms between hippo-like animals and whales

how to make a phenetic tree

1) join the two open nodes that are closest to each other, shortest distance

2) They are no longer active, made a new node halfway between them

(average the traits, this step is conceptually simple and practically tricky)

How to make a phenetic tree in this course

1) join the two open nodes that are closest to each other, shortest distance

phenetic analysis uses _____ info

less

to do a cladistic analysis inferences about the common ancestor can be____

crucial

why was the genetic analysis more effective than the morphological

It can be hard to tell which traits are derived, This can also be a problem with the genetic analysis, Genetic analyses typically allow us to analyze more traits!

limitations for phylogenetic trees

history of life cant really be summarized by a tree ( sex and other forms of combo or gene transfer)

trees constructed by humans are not necessarily even the best approximations to the true history of life our guesses often change over time

recent innovations have told us a lot about the history of life

detailed genetic info, sophisticated analysis techniques, electronic computers

3 domains

bacteria, archea, eukarya

bacteria

no nuclei, mostly small, most of the micro organisms you see

archaea

no nuclei, mostly small, rarer or live in more extreme environments

eukarya

large, nucleated cells sisters to archaea characterized by nuclei and mitochondria, mitochondria came later captured from bacteria but nobody knows where nucleus comes from

the web of life

if genes, can be transferred life isnt really a tree

reuniting can create new species

hybridization, allopolyploidy

5 kingdoms

fungi, plants, animals, protists

not a good way to describe the evolution of life

why has the idea of the 5 kingdoms persisted for so long

matches the way the world works, some branches have organism that are much smaller or just have many fewer organisms, archaea and bacteria are difficult to tell apart even with a microscope

when are trees a good approximation

when populations not mixing, geographical barriers, structured genetic

exchange, populations have diverged enough to not have sex with each other

otherwise we may need to make trees of genes or genetic components instead of organisms

fossil

physical trace of an organism from the past

intact fossils

retain their form and substacne

compression fossils

squashed into a thin film

cast fossils

occur when the decomposed piece is replaced by minerals different from surrounding ones

per-mineralized fossils

occur if minerals infiltrate cells as they are decomposing

bias in the fossil record

care is needed, few things fossilized and some things more likely to fossilize than others

habitat bias

things that live in swampy areas or undergound

taxonomic bias

hard things or hard parts of things

temporal bias

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

abundance bias

things that are more abundant have more chances to be preserved

accounting for bias

just b/c you dont see it doesnt mean that it wasnt there

just b/c you see it a lot doesnt mean that there were a lot

trying to figure out what happened based on what kind of fossils we have happen to find is tricky

putting timeline together

1) dates- radioactive isotopes

2) geological inferences can be made about relative age of different things

3) molecular clocks are based on inferences about how fast things are evolving

radiation events

diversity that arises dramatically are called

mass extinction event

species sometimes disappear gradually, sometimes dramatically

adaptive radiation

occurs when a single lineage produces many descendant species in a short period of time that make their living in a variety of different ways, triggered by opportunity either in environment or b/c the evolution of the organisms themselves

ecological opportunity

an organisms arrives in an area with no similar organisms, group of competing species is driven extinct or nearly extinct by some other cause

morphological innovation

an organisms comes up with a good new idea, legs in tetrapods, new body plans in the Cambrian explosion, multi-cellularity

co-evolution

evolution of one group creates new niches for another group, and vice versa

what did well after dinos

mammals

we have seen major tree species driven near extinction by intro disease in the last century

This opens up ecological niches, Species may diverge to fill these niches, Or spread around the world to fill them

morphological innovation

a new adaptive mutation can open up further possibilities for adaptation

flowering plants opened many new opportunities for everyone not just the innovators

animals evolved to exploit the flowering plants, flowering plants and animals co evolved, natrual defenses and ways to exploit them

gene duplication

One or more genes may be accidentally duplicated so that the genome has two copies of each gene

– Chromosomal duplication by polyploidy is one way this can happen

ˆ This may make the organism less efficient, and thus be selected against

ˆ It may also allow for innovation. Why?

– Answer: Because one copy can continue to do the old function, while the other

evolves a new function

how many mass extinction

5 so far, last one by a cosmic impact

Are we in the middle of a mass extinction now?

Extinction rate very high over the last 400 years, Many scientists believe that we are likely to cause a geologically significant mass extinction

how are people causing extinctions

over harvesting, land use, climate change, overusing resources, intro of species

what is different about people

complex thoughts, culture, language, tech

what is the same humans and animals

genetic code, biochemical process, reproduction, still evolving

adaptations build on___

existing adaptations in unexpected ways often

In a constant environment species can only improve with ____ adaptations to the same environment

gradual

a changing environment provide opportunties to

try new combo and build in unexcpeted directions

Physical changes often provide species with

new adaptive challenges and opportunitie, climate change, continentak drift, geological changes

Taxa can be dramatically affected by

changes in other taxa Due to evolution or to colonization

Interactions with other organisms are _____to most ecological niches

key

Co-evolution is a key driver of

diversity, Plants evolve new ways to use insects for sex, or vertebrates for dispersal, Animals evolve new ways to benefit from plant resources