envs lecture 3 Flashcards
taxonomy
science of describing, naming, classifying organisms
taxon
unit of taxonomic classification
plural of taxon
taxa
systematics
study of biological diversity and evolutionary relationships among organisms
extinct
no longer present
extant
taxa that exist today
phylogeny
history of descent of a group of taxa from their common ancestors
phylogenetics
study of phylogenies
phylogenetic trees
diagrams taht depict phylogenies
what is taxonomy
used to organize groups of species into progressively smaller hierarchical groups
originally what was the most inclusive taxonomic group
kingdom
what system was used for many years
5 kingdom system
what are the 5 kingdoms
monera, protista, fungi, plantae, animalia
monera
single celled prokaryotic organisms (cells don’t have nucleus) w/ no true nuclear membrane
example of monera
bacteria
protists
mostly single celled eukaryotic organisms (meaning cell has a nucleus),
examples of protists
amoebas
multicellular protists
kelp, red algae, slime molds
fungi
eukaryotic organisms with chitin in cell wallys
examples of fungi
yeasts, molds, mushrooms
what are fungi
heterotrophs (liike animals)
how do heterotrophs take in food
take in food, don’t make food; do this by secreting digestive enzymes and absorbing nutrients
plantae
multicellular eukaryotes
how do plantae make their living
photosynthesis
do plantae make their own food
yuh
animalia
multicellular eukaryotes
how do animalia make their living
consuming organic material
how do animalia reproduce
sexually (unique development)
3 domain system
eukarya, prokarya/bacteria, archaea
eukarya
multicellular eukaryotes
bacteria
prokaryotes
archaea
single celled prokaryotes
another name for archaea
extremophiles
one purpose of taxonomy
to name species
who did modern species taxonomy start with
Carl Linnaeus
what did Linnaeus do
introduced binomial nomenclature in 1753 ‘species plantarum’ and ‘systema naturae’
describe binomial nomenclature
each species has two parts, a genus and a species
how is studying systematics interesting
relatedness
describe relatedness
who is most closely related to who; are dogs more closely related to cats or pigs, etc.
eagles and falcons
due to molecular phylogenetic data, falcons are more closely related to parrots and songbirds than hawks
shrews
elephant shrews are more closely related to elephants than shrews
why else is studying systematics interesting
trait evolution and comparative biology
trait evolution and comparative biology
phylogenetic trees provide a foundation for understanding many aspects of evolutionary history, like pathways thru which various characters evolved [how many times did wings evolve? etc.]
another reason why studying systematics is interesting
cutting edge technology
cutting edge technology
use of molecular data, including whole genome sequences
yet another reason why its interesting
detective work
detectie work
we can’t observe evolutionary history, must infer it by phylogenetic methods [use characters on living organisms, fossils, DNA to give clues]
tree of life metaphor
200 yrs before darwin they used tree as a representation of the history of life
what is tree of life/universal tree of life used for
metaphor, model, research tool used to explore evolution of life and describe relationships b/w organisms, living and extinct
basically what do trees show
ancestor, descendant relationships; history of evolutionary lineages that have branched over time
root
common ancestor of all taxa
node
a branchpoint in a tree
clade
a group of two or more taxa that includes both their common ancestor and all their descendents
what do phylogenetic trees do
depict lines of descent from common ancestors; hierarchical in pattern
monophyletic group
includes ALL the descendants of a common ancestor
another way to describe monophyletic group
a taxon that is a clade
what is in monophyletic group
most recent common ancestor of a group of organisms and all its descendants
basically what does monophyletic mean
the group of descendants in question share a common ancestor
what are trees formed from
nested monophyletic groups
are phylogenetic trees hierarchical
yeah
how do we know if a group is monophyletic
rotate the node, see if highlighted box will fit the same taxa inside
what is a clade
monophyletic group; includes ALL and ONLY the descendants of a particular ancestor
what are groups that are non-monophyletic?
paraphyletic
paraphyletic group
group that includes some but not all of the descendants of a common ancestor
polyphyletic group
members of multiple evolutionary lineages, but don’t include the most recent common ancestor + descendants
does length of branches matter
no; don’t tell us anything about evolutionary descent
does order of letters matter
no; rotating the branches doesn’t change relationships
why are phylogenies important
provide objective criterion for organizing biodiversity, framework for posing and testing biological questions, predictive power
synapomorphies
shared derived traits
what diagnoses monophyletic groups
synapomorphies
how do we infer phylogeny
synapomorphies
what are newly evolved characters that are shared
synapomorphies
apomorphy
newly evolved character that ISNT shared
do apomorphies tell us about evolution
nope
homologous characters
characters that a given set of organisms have inherited from their common ancestor
character
particular trait of interest (number of digits on the forelimb)
character state
a given character can have many different character states (5 digits on forelimb, one digit on forelimb, etc.)
ingroup
the group on interest, assumed to be monophyletic w/r to outgroup
what is ingroup w/r to outgroup
assumed to be monophyletic
what is outgroup
group of taxon related to ingroup
steps
number of inferred changes in character state on a tree
most parsimonious tree
tree w/ shortest number of steps or changes
plesiomorphy
ancestral character state
symplesiomorphy
shared ancestral characters, not phylogenetically informative
apomorphy
derived character state
synapomorphy
shared derived character, most useful for inferring phylogenetic relatedness
autapomorphy
unique derived character state, not useful for inferring relationships, but helpful for identification of species
what does cladistics use
parsimony/occam’s razor
what is occam’s razor
among competing hypotheses, the one w/ fewest assumptions should be selected
homoplasy
convergence
what happens when there’s a lot of homoplasy/convergence in characters
parsimony does a poor job of reconstructing phylogenetic relationships; model based statistical approaches are better
convergent evolution
homoplasy
what is best option for dealing w/ long branches
model based methods able to take into account probability of reversals in character states
maximum likelihood (ML)
given a specific model of evolution and a possible tree, this method calculates the likelihood of observing the data, and the algorithms used in analysis calculate this likelihood score across many trees and optimize that likelihood to determine which tree is best
bayesian
maximized the probability of observing a particular tree, given the model and the data, unlike the ML method, Bayesian analysis provides the probability of a set of different trees so that they can be compared and summarized
what else can we use phylogenies for besides species
to shed light on the history among individuals and populations wihtin a single species
what else can phylogenies use to make (what kinda trees)
gene trees, gene geneologies
what are gene trees
shows which haplotypes are more closely related within a region
what is gene duplication followed by
speciation
orthologous genes
loci in diff species descended from same locus in most recent ancestor
paralogous genes
loci in same/diff species descended from diff duplicate genes in ancestral species
are orthologs homologous loci
yes
who is more closely related orthologs or paralogous loci
orthologs/ homologous loci
what does each branching event in a tree denote
gene duplication event
what does gene phylogeny tell us
about relative timing of these events, helps us infer when duplications occur (creating alpha and beta hemoglobin families and within these gene subfamilies)
what else can we use phylogenies to do
to make inferences about evolution of physical traits (ex. evolution of opposable toes in hominids)
what else can molecular phylogenetic studies do
study timing of diversification and events
what do differences in sequences in concert w/ estimates of timing of splits do
serve as molecular clock, used to calibrate evolutionary trees to absolute time
homoplasy
independent evolution of a character/character state on a phylogenetic tree
three classes of homoplasy
convergent evolution, parallel evolution, evolutionary reversal
what else can we use evolutionary trees to do
help tease apart evolution of similarities among species due to independent evolution of similar characters over evolutionary time
convergent evolution
ex. hummingbirds and sunbirds independently evolving long, slender bills for feeding
what do phylogenies describe
patterns of diversification
what can phylogenies be used to reconstruct
history of adaptive radiations
