Phylogenies

EEB 390 - Exam 2

biogeography

improved phylogenetic inference ratites clarified role of continental drift (vicariance vs dispersal) in biogeography

viruses

phylogenies can track the evolution of virus to figure out how they have travelled and spread.

phylogeny

a visual representation of the relationship between entities (species, taxa, individuals, populations, etc). constructed from data and models. can be made from many types of data: morphology, DNA, other molecules - or a mix of types

speciation

the process by which new species are formed

tip

species, individual, or other entity that we are studying

node

hypothetical ancestor to descendent tips (denotes a speciation or divergence event)

branch

represents the evolution of lineage; length proportional to amount of change

root

common ancestor to all tips

topology

pattern and arrangement of branch structure

how to create phylogenies

1. collect charcter data from each taxon

2. align those characters into a matrix showing similarity

3. use some method of inferring relationships from the matrix data (which taxa share more informative characters than others)

maximum parsimony

minimize the number of changes needed to produce the observed tip states

simple molecular phylogenies

commonly a mitochondrial gene in animals or a chloroplast gene in plants. use just one gene

distance methods

directly calculate a tree based on genetic distance between species

heuristic methods

search across many trees to find the best

maximum likelihood

statistical approach to find the model that maximizes the likelihood of the data given the model

bayesian inference

statistical approach to find the model that maximizes the likelihood of the model given the data and prior expectations

genetic distance

a measure of divergence between two species based on DNA differences.

basic parsimony algorithim

1. start with one tree

2. calculate the score (how many steps are required for the data to fit that tree)

3. look at another tree and calculate the score

4. keep the tree that has the better score

5. repeat 3-4 as much as you like

maximum likelihood for phylogenetics

statistical approach used to find the best phylogenetic tree that uses an explicit model of molecular evolution
parsimony ranks trees by how many changes were required. tomake the tree fit the data

ML ranks tree by the likelihood of the data given the tree and model of molecular evolution

different scoring mechanism and computation but similar concept

Bayesian inference

calculates the probability of the model given the data P(M|D). describes the probability of an event, based on prior knowledge of conditions that might be related to the event

branch lengths

you may have noticed that some trees have variable branch lengths. longer branch = more change.

bootstrapping analyses

a statistical techniques involving the resampling of data to assess the confidence in a phylogeny

bridging population genetics and phylogeny building

species level phylogenies are made from genetic information from individuals. different genes can have unique histories of ancestry and descent

incomplete lineage sorting

when ancestral genetic variation is retained through speciation events

coalescent theory

developed to study gene-genealogical relationships by tracing the ancestry of gene copies in populations. individual genes may or may not reflect the history of population splitting.

coalescent process

different genes have different histories of ancestry and descent in a population. This process relies on two things: stochasticity and finite sampling

coalescence point

the point on a gene tree ( the ancestral gene copy) that is the most recent common ancestor of the genes being studied in a population

estimating population divergence histories

4N(1-(1/k). k is the number of gene copies of interest. N is the number of organisms in the population

discordance

when different genes tell distinct stories even though they evolved under a shared history. especially common between mitochondrial and nuclear loci

Hadean Earth

4.5-4.1 billion years ago first and oldest the four known geologic eons of earth’s history

life properties

organization - maintenance of parts (whether cells or more complex)

metabolism - control of chemical reactions to sustain life

growth and reproduction - creation of offspring

homeostasis - the ability to regulate one’s internal environmental conditions

external response - response to external environment and stimuli

microfossils

microscopic fossils (typically < 1-4 nm)

biomarkers

molecular evidence of life in fossil record

steps for life to evolve

generation of simple organic molecules from inorganic molecules, origin of self replication, moving from RNA. toDNA and creation of cells (compartmentalization)

prebiotic soup hypothesis

the idea that the earliest life emerged in a soup-like liquid environment, drawing upon energy from solar energy, volcanic eruptions and the Earth internal heat

Miller-Urey experiment

1952. simulated ocean and atmosphere interface. Methane, ammonia, and hydrogen mixed with boiling water and simulated lightning. reactions produced over 20 amino acids

RNA

RNA has diverse roles that include catalyst and temporary information carrier: ribozymes. RNA was a carrier and catalyst

ribozymes

RNA molecules with enzymatic function

RNA World

4-3.5 billion years ago. a potential early stage in the history of life in which RNA was the fundamental unit upon which life was based, fulfilling both an information role (as DNA does today) and a catalytic role (as proteins do today)

DNA replaces RNA

RNA replaced by DNA (probably around 3.5 bya). proteins for catalytic functions can be more complex and diverse. DNA is more stable, RNA is more reactive (which is why it can be a good catalyst)

protocell

a cell-like entity that predated cellular life-forms in the history of life

LUCA

last universal common ancestor (3.5-3.8 bya)

early prokaryotes

3.9 bya. prokaryotic cells have no nucleus or organelles (chloroplast, mitochondria). -the first single-celled life was prokaryotic

minimal gene sets

hypothetical minimal number of genes necessary to allow for cellular-based life

horizontal gene transfer

movement of genetic material between individuals (not parents/offspring). was more prevalent in the early tree of life: early cells swapped DNA frequently. this makes LUCA difficult to reconstruct

origin of photosynthesis

cyanobacteria arose following sulfur-reducing bacteria (anaerobic). cyanobacteria did photosynthesis

stromatolites

sedimentary layers of cemented microbial mats of cyanobacteria

oxygen crisis

cyanobacteria and photosynthetic organism release oxygen which is toxic and killed most organisms on earth. organisms evolve oxygen metabolism and there is max extinction of anaerobic life.

snowball earth

2.4 bya. oxidative photosynthesis removes methane which causes massive global cooling for 300-400 million years.

eukaryotes

cells have a nucleus and other organelles enclosed within membranes (can be uni- or multicellular organisms)

major groups of eukaryotes

animals and fungi are more closely related to amoebozoic protists than to other eukaryotes

eukaryotic timeline

first eukaryotes - 1.8 bya
initial radiation of animals - 800 mya

initial radiation of land plants - 500 mya

endosymbiosis

lynn margulis. mutually beneficial relationship in which one organism lives within the body often within the cell of another

origin of mitochondria

mitochondria fall within a clade of proteobacteria that includes Rickettsia (pathogens) and SAR 11 (most common oceanic bacteria)

origin of chloroplasts

chloroplasts fall within a clade of cyanobacteria

multicellularity

at least 1.2 billion years old

advantages due to increased size - response to environmental cues, disperse further, protection from predation
advantages due to division of labor - specialization and regrowth

multicellularity origin hypothesis

(a) colonial group of single cells coming together

(b) cells remaining together after replication. - studies support b

slime molds

unicellular protists with facultative sociality (paraphyletic). spend most of their lives as single-celled amoebas. under nutrient depletion they aggregate into slugs and fruiting bodies

taphonomy

the study of fossilization process

fossil

any trace left by an organism that lived in the past. commonly mineralization but also amber/freexing, molds/casts, and trace fossils

lagerstatten fossils

amazing preservation of entire organisms and ecosystems in incredible detail

burgess shale

cambrian explosion discovered in Canadian Rockies that is a prime example of lagerstatten

fossil formation

abundance, durability, burial environment, and lack of oxygen. Each of these factors slows decomposition and makes fossilization more likely

sedimentation gaps

sedimentation is discontinuous and episodic at all scales. erosion can contribute to gaps. Michigan basin: thousands of feet of sediment that built up during the Paleozoic

fossil record

an incomplete physical record of the existence of organisms that lived in the past. young fossils are overrepresented