EVE 100 Midterm 2

what is a phylogeny

visual representation of evolutionary history of population genes, species, etc.

what does a phylogeny represent

a hypothesis of relationships between taxa

what is a rooted phylogeny

contains information about flow of time

what does rooted phylogenies allow us to discern

the pattern of descent from common ancestry and direction of trait evolution

what is a polytomy

indicates uncertainty in the correct branching pattern

what is a phylogram

branch lengths are proportional to the amount of change attributed to the branch

what is a ultrametric tree

rooted tree in which units of branch length accumulate evenly on all branches so that contemporaneous tips are equidistant from root

what is a transmission tree

pathogens that replicate and spread.

mutations used to track spread of outbreak

what is a common misinterpretation of phylogenies?

current existing species are not ancestral to other species (extant taza)

what is a derived vs basal?

only internal nodes can be referred to this with respect to the reference node

what is a monophyletic

a clade that includes an ancestral and all the descendants of that lineage ancestral lineage

what is a paraphyletic

not a clade such as reptiles that are lizards and crocodiles

what is the paraphyletic call that is characterized by shared ancestral characters

symplesiomorphies

what is a polyphyletic

united by similar but not homologous character states

what is apomorphy

a derived character state

what is plesiomorphy

ancestral character state

what is a synapomorphy

shared derived character state

what is symplesiomorphy

shared ancestral character state

what is a homoplasious character 

character state evolved around two + times = convergence

what is tree thinking

help organize species, populations, or genes according to relationships

what are meaningful taxonomic systems

relatedness in terms of common ancestry is the basics 

how do new genes arise

by duplication of existing genes followed by divergence of ones of the copies

how do we construct phylogenies

using traits/characters like shape, color, and dna sequence

whats an ingroup

group of taxa for which relationships will be analyzed

whats an outgroup

taxa that are more distantly related to the ingroup than any members of the ingroup are to each other

what are the methods to reconstruct phylogenic relationships

distance-based methods

maximum parsimony

maximum likelihood

bayesian

what is maximum parsimony

best estimate of true phylogeny

what is equally parsimonious

each involves the same number of evolutionary events

why can phylogenetics be difficult

the small number of taxa can have a very large number of possible phylogenies

what is a concensus tree

equally parsimonious trees can be combined to produce that represents uncertainty in relationships among taxa

what is strict concensus

a tree composed only of clades that occur on all input tree

what is a orthologous gene

homologous members of gene family in two or more species

separated by speciation

what is a paralogous gene

gene copies that originated via ancestral gene duplications

separated by duplication

what is a mutation

the change in the nucleotide sequence from parent to offspring

what is substitution 

a change between species at the dna level

what does higher sequence divergence percentage mean

its the most degenerate, what are the least constrained to evolve and exhibit highest substitution rates

what is non-synonymous substitutions

changes in protein sequence

what is synonymous substitutions

no changes in protein sequence

what does it mean when the dn/ds is less than 1

its consistent with purifying negative selection. and has a vast majority of nonsynonymous mutations that are deleterious and thus removed by natural selection

what does it mean when dn/ds = 1

consistent with neutral evolution which has no selection such as pseudogene

what does it mean when dn/ds is greater than 1

consistent with positive selection

what is a species concept

what we mean by species

what is a species diagnosis

defining criteria that can be used to delimit a particular species and the traits that separate the species from other similar species

what is biological species concept

groups of actually or potentially interbreeding populations in nature, reproductively isolated from other such groups

what are critical observation that contributed to the formulation of biological species concept

variation within species

geographic variation

existence of sibling [eg screech owl]

what is reproduction isolation

any of several biological difference between the groups greatly reduces gene exchange between them even it they aren’t geographically isolated

what is allopatric speciation

populations diverge while separated by a geographic barrier that prevents/reduces gene flow between populations

what is parapatric speciation

neighboring populations diverge while still exchanging some genes

why does gene flow reduce in parapatric speciation

due to strong selection preventing colonization of other habitat or formation of hybrids

how do adjacent populations adapt in parapatric speciation

to different habitats/niches and selection favors divergence

what is sympatric speciation

two new species emerge from a single ancestor without any geographic isolation and while exchanging genes freely

what does sympatric speciation require

extremely strong divergent selection and is highly unlikely to happen in nature

what is speciation

the evolution of biological barriers to gene flow

why would widely distributed species may become fragmented into allopatric population

the habitat on which its depends on becomes fragmented by climate change

what are types of barriers

geographic and reproductive that work together during the speciation process

what are the reproductive barriers to gene flow

prezygotic and postzygotic

what is pre-mating, prezygotic isolation

organisms occur in the same area but dont mate

what are potential mates that dont meet in the premating prezygotic isolation

different habitats and different mating seasons and times

what are potential mates meet but dont mate in premating prezygotic isolation

different mating behavior in animals and different pollinators in plants

what is post mating prezygotic

potential mates try to mate but cant form a zygote

what are post mating prezygotic potentials

have incompatible genitalia and gametes

what is postzygotic isolation

hybrids are formed but have low fitness

what are intrinsic mechanisms in postzygotic isolation

hybrid lethality and sterility

what are extrinsic mechanisms in postzygotic isolation

ecological isolation where hybrids dont fit into either ecological niche

mate recognition where mating behavior is not appropriate for either species

what is gametic incompatibility in post mating, prezygotic barriers

sperm or pollen from one species fails to fertilize the egg or ovule of another species

what is the dobzhansky-muller in the intrinsic mechanism for the postzygotic isolation

based on differences at two or more loci that have complementary effects on fitness

substitutions at two or more loci can generate incompatible genotypes

what is haldanes rule

when in the f1 offspring of two different species a sex is absent, rare, or sterile, that the sex is the heterogametic sex

what are heterogametic hybrids

affected by all X-linked alleles that causes incompatibilities

what are homogametic hybrids

only affected by dominant deleterious x-linked alleles

what is reinforcement

an adaptation to prevent the production of low fitness hybrids

how does reinforcement generate selection favors

by the evolution of stronger prezygotic reproductive barriers between emerging species

what is the first step in evolution of reinforcement

populations diverge in allopatry

what is the second step in evolution of reinforcement

the two divergent populations come back in secondary contact

what is the third step in the evolution of reinforcement

selection acts against interbreeding because hybrids have flower fitness

selection favors the evolution of greater reproductive isolation

what is sex

fusion of 2 gamets that are the combinig of 2 genomes into one cell and subsequent segregation by meiosis

what is the basic definition of anisogamy

a large immobile egg

small mobile sperm

what is isogamy

gametes that look alike that are classified as + and - 

what does meiosis involve

recombination which reshuffles alleles created by mutation

how do most eukaryotes reproduce

sexually

what kind of animal is a simultaneous hermaphrodite

leopard slug that has no separate sexes

what kind of animal is sequential hermaphrodites

clownfish which first mature as male and later change sex to female

what is one of the few species that self fertilize to reproduce

cactus which has flower that do not open

what uses conjugation and other mechanism to exchange genetic material

bacteria such as e. coli

what is the persistance of asexual reproduction in bdelloid rotifers

an entire clade of over 400 species of animals that have survived without sex for 80 million years

what are the high costs of sex

1. finding and attracting mates can be costly and dangerous

2. sexual reprod. breaks up winning genotypes

3. sexual reprod. halves relateness between parents and offspring

4. two-fold cost of sex

what is two-fold cost of sex

production of males in sexual population reduces reproduction potential by a factor of 2

what happens to clonal and sexual population if each individual has 2 offspring

clonal doubles

sexual remain constant

what is clonal interference

asexual species forced to fix advantageous mutations sequentially 

how do asexual species accumulate deleterious mutations 

by the mullers ratchet and ruby-in-the-rubbish

whats is mullers ratchet in asexual reproduction

progressive loss by drift of haplotype with lowest number of deleterious alleles that results in lower fitness of population

what is mullers ratchet in sexual reproduction

organisms avoid the effects, loss of haplotype with zero deleterious alleles which recombination can restore

what is ruby-in-the-rubbish effect

loss of benefiticial mutations as the result of linkage to deleterious mutations

what does ruby-in-the-rubbish favor

sexual reproduction

what is heteromorphic

one chromosome is much reduced in function and size and does not recombine

how does the degeneration of neo-sex chromosomes occur

due to mullers ratchet and the hitchhiking of deleterious alleles

what is the evolution of sex chromosomes

1. pair of ancestral autosomes

2. evolve a sex determining locus

3. suppression of recombination evolves between x and y

4. degeneration of y chromosomes due to mullers ratchet and hitchhiking of deleterious alleles

what is the red queen effect hypothesis

species have to run or evolve in order to stay in the same place or else they go extinct