Ch. 14 - 18 Flashcards
phylogeny
hypothesis about the evolutionary relationship of genes, cells, individuals, populations, species
root
the common ancestor of all species under discussion
node
the most recent common ancestor of a subgroup
clade
monophyletic group
monophyletic group
a group of organisms that consists of their common ancestor and all descendants, nothing extraneous or missing
tips/terminal nodes
the end of a branch, a species/group depending on tree
tree topology
branching order, idea that taxa can be rotated around nodes and still depict the same relationship
sister group
the closest relatives of a given unit in a tree, each node defines a sister group
3 types of groups in phylogenetic tree
monophyletic, paraphyletic, polyphyletic
non-monophyletic groups:
paraphyletic and polyphyletic
paraphyletic group
a common ancestor and some, but not all, descendants
polyphyletic group
a grouping of species that does not include their common ancestor
myth of ‘ancestral living species’
no currently existing species is ancestral to any other, a trait can be ancestral as they all evolved at different times but a living species cannot be ancestral
there can be primitive traits/adaptations within a species, but not primitive taxa, as there are always some traits that are shared by most/all lineages (such as cells, multicellularity, vertebrate, placenta, bipedalism…etc)
apomorphy
a derived character
novel character trait that evolved from a plesiomorphy (ancestral form)
synapomorphy
shared derived character
plesiomorphy
ancestral, pre-existing character
what defines a clade/monophyletic group?
synapomorphy
convergent evolution
the independent appearance in different lineages of similar derived characteristics
reversal
the loss of derived characters/traits in a lineage, causes a return to the ancestral condition
homoplasy
similarity in character states due to convergence or reversal i.e. they have different ancestry but arrived at the same/similar trait
homology
homologous traits are ___ traits
similarity in character states due to common ancestry
analogous
analogous structures
traits arising through convergent evolution
ex: bat wings, bird wings, insect wings
homoplasy causes ___ structures
analogous
what is the outgroup? (as compared to the ingroup)
the ingroup is the species whose relationships are in question, outgroup is relatives of the ingroup
principle of parsimony
the idea that the simplest explanation is the best evolutionary hypothesis, the one that requires the least changes
outgroup analysis
use an outgroup member in phylo. analysis, ensures that the finished reconstruction is monophyletic (nothing in what is considered outgroup/relative only is also in the ingroup)
transitions
evolutionary modification
polytomy
a three-way split in a phylogenetic tree (rather than just two), represents lingering uncertainty about the evolutionary relationships
uninformative characters
traits shared by all members of the group, don’t add any information to a parsimony analysis because the number of changes is equal or there is no difference at all
how does homoplasy come about?
homoplasy: morphological similarities that evolved out of convergent evolution/reversal, meaning the species that present the trait do not share ancestry
these arise independently when lineages experience similar environmental pressures –> similar patterns of natural selection
benefits of using DNA/protein sequence to test evo. relationships:
new tech makes sequencing faster and less expensive
there are sophisticated models to analyze sequences
downsides to using DNA/protein sequence to test evo. relationships:
molecular data is only readily available for extant/recently extinct taxa
only 4 states that can be studied - ATCG
homoplasy can be difficult to recognize
aligning DNA sequences
must be done for sequence analysis,
means that any insertions or deletions that have occurred in some lineages but not all have been identified, and sequences are shifted to account for those differences (basically you want to make sure you are comparing the DNA/protein that is coding for the same things
polytomy
a node or branch point on a phylogeny with more than 2 descendant lineages emerging
3 types of mutation and their fate
deleterious: tend to be eliminated by NS rapidly
neutral: tend to rise and fall due to genetic drift
beneficial: either lost to drift at while at a low freq., or rise by NS
mutation
creation of a new allele
substitution
fixation of a new allele (mutation) in a population
‘the neutral theory of molecular evolution’ (kimura 1968)
nearly neutral mutations that are able to rise to fixation via drift vastly outnumber beneficial mutations that rose to fixation via NS
molecular clock
if substitutions in alleles occurs at a relatively constant rate, we can estimate the divergence time btwn two taxa (based on # of allele differences)
redundancy of genetic code
many codons may code for the same amino acid (prevents deleterious mutations from single base mutations)
synonymous vs nonsynonymous substitutions
when the wrong nucleotide is placed in a sequence, it may or may not affect the amino acid formed, and thus, the protein:
Synonymous: Same amino acid formed
Nonsynonymous: wrong amino acid formed
synonymous and nonsynonymous substitutions evolve at a constant rate, but _____ sites ‘tick’ faster than _____ sites
synonymous ; nonsynonymous
subs that resulted in the same amino acid to be prod. occur more often than ones that do not
why do nonsynonymous sites evolve slower than synonymous sites?
the vast majority of euk. genome is noncoding, so any mutations that occur there will be ‘neutral’, introns mutate much faster than coding sites (because mutations that affect dev/on coding DNA are usually bad and so will be selected out right away)
dN /dS ratio:
rate of nonsynonymous substitution per site / rate of synonymous sub. per site
if dN/dS > 1
if dN/dS =1
if dN/dS < 1
substitution is advantageous
substitution is neutral
substitution is deleterious
the probability that a given allele will be the one that drifts to fixation is equal to that allele’s:
initial frequency
drift is especially important for molecular mutations because:
most mutations are neutral, meaning they have an equal chance of being fixed/NS is not acting on them
genetic drift is faster in ____ sized populations and slower in ____ sized populations
smaller ; bigger
what process is responsible for the rapid, clocklike sequence change observed in the molecular clock theory?
genetic drift
why does genetic drift seem to act more strongly on neutral substitutions than on positive or negative substitutions?
positive/negative substitutions are also affected by NS, and because populations are not infinite, it takes much longer for them to reach fixation because there are always other forces at work that may counteract each other
neutral substitutions should, in theory, only be affected by genetic drift since they offer no benefit/weakness, so they will reach fixation/loss faster
C-value paradox, and what explains it?
C-value is the total amount of DNA found in a cell
little correlation between DNA quantity and an organism’s perceived morphological complexity
explained by: whole-genome duplications resulting in polyploidy & the existence of large portions of noncoding genes/genes that are functionless to the organism’s survival
relationship between genome size and protein coding DNA
protein coding DNA and genome size increase proportionally up until a certain size, when the amount of coding DNA plateaus but size increases (that is to say, organisms with huge genomes have a larger proportion of noncoding DNA than organisms with smaller genomes)
part of DNA that we used to believe was noncoding is actually there to:
regulate coding DNA transcription
mobile genetic elements
replicate and insert themselves in an organism’s genome by hijacking the same cellular machinery that normally replicates/transcribes protein-coding DNA
usually: have no effect on an organism’s phenotype
sometimes: can disrupt the function of protein-coding genes because they insert themselves in the middle of that important sequence –> creates changes in the organism’s phenotype
mobile genome elements are much more common in __ than in ___
eukaryotes ; prokaryotes
regions of the genome:
coding
noncoding
intergenic
intergenic regions of the genome
the space between protein-coding genes
introns:
occur within the coding regions of genes, are transcribed into mRNA, but are spliced out before protein translation
retrotransposans
transposans/transposable elements which leave a copy of themselves behind when they move
in these types, this transposition event leads to an increase in that element’s abundance (there are now 2 copies)
examples of human diseases caused by transposable elements
(which land in the the middle of a coding region, disrupting the proteins that should have been coded):
cystic fibrosis, hemophilia, cancer
mobile genetic elements are often called ____ because they can disrupt coding sequences and place an energetic burden on the cell
genome parasites
the effects of mobile elements in the genome are either:
neutral or maladaptive
mobile elements favored by NS are:
elements that can replicate themselves efficiently and with the least fitness cost to the host genome
methylation of DNA:
addition of a methyl group to DNA nucleotides that prevents transcription of DNA to RNA, especially common in regions associated with mobile elements
form of pre-transcriptional silencing
mechanisms of defense in host organism against mobile elements:
methylation
RNA interference/RNAi
RNA interference/RNAi/small RNAs
short sequences of complementary RNA can silence the expression of a certain DNA gene
form of post-transcriptional silencing
2 types of gene duplication
whole genome duplication: polyploidization
segmental duplication (smaller sections duplicated)
2 most common molecular mechanisms that causes segmental duplication:
unequal cross-over between chromosomes during meiosis
& mobile genetic elements
when a duplicated gene becomes fixed, then mutates so that the copy performs a new function that increases fitness
neofunctionalization
4 mechanisms by which a duplicated gene would be preserved:
neofunctionalization
subfunctionalization
gene conservation
nonfunctionalization
a gene with two functions is duplicated, then mutates so that one of the functions is preserved and one is lost (in both the original and the duplicate)
ie: both versions (og and dup) only perform one out of original 2 functions
subfunctionalization
