Evolution3

• cladogenesis: branching or multiplication of lineages (each of which evolves by anagenesis)
• anagenesis: evolution within species along its own path

groups of actually or potentially interbreeding populations which are reproductively isolatedd from other such groups - several biological differences between teh populations greatly reduce gene exchange between them

this biological species concept takes in account teh individudal and geographic variation and is good for sexually reproducing and extant organisms (not asexual, not fossils)

reproductively isolated populations that are difficult or impossible to distinguish by morphological features, but are different in ecology, behavior, chromosomes, or other such characters

genetically distinct populations meet and interbreed to a limited extent, but in which there exist partial barriers to gene exchange (hybridizing entities may be calledd semi-species)

teh smallest monophyletic group of common ancestry

species are exclusive groups of organisms, where all the members of the group are more closely related to one another than to any organism outside teh group

barriers to gene flow - isolating mechanisms - biological differences

the origin of two species from a common ancestral species - consists of the evolution of biological barriers to gene flow

how can two different populations form without intermediates?

• prezygotic - prevent or reduce the likelihood of transfer of gametes to members of other species
• postmating - features that prevent successful formation of hybrid zygotes even if mating takes place
• postzygotic - reduced survival or reproductive rates of hybrid zygotes

• ecological isolation - seasonal isolation (breed at different times), isolatedd by habitat (wont even meet),
• behavioral isolation - sexual isolation or ethological isolation

specific mate recognition system: the signals and responses between potential mates - one sex (usually the females) will not respond to inappropriate signals

• mechanical - copulatory isolation: genitalia may differ between related species
• conspecific sperm precedence - if the female mates with both a heterospecific male and a conspecific - the conspecific males sperms will be successful in fertilizing her eggs

gametic isolation - games of different species fail to unite

• hybrid inviability
• hybrid sterility
• multiple isolating barriers

signals/responses between potential mates - one sex will not respond to inappropriate signals

a postzygotic barriers - structural differences between teh chromosomes that cause segregation of some anueploid gametes during meiosis or by differences between teh genes of teh two parents

Haldanes rule

• about hyrbid sterility
• sterility usually affects teh heterogametic sex (teh one with the two different sex chromosomes)

• single genes
• epistatic interactions of genes
• chromosome differences - alterations of chromosome structure and differences in the number of chromosome sets --> can cause aneuploidy! (or differences between the genes of the parent populations)

premating!

prezygotic isolation = stronger among sympatric than among allopatric pairs of taxa

in males! hybrid sterility/inviability is almost always seen in males only (female sterility seen when taxa are much older)

loss of all teh ancestral lineages of DNA sequence variants except one - coalescence to a common ancestral gene copy occurs in each species

occurs when offspring are produced by interbreeding between genetically distinct populations - may be the source of new adaptations or even new species

• primary: originate in situ as natural selection alters allele frequencies in a series of more/less continuously distributed populations (may correspond to a sharp change in an environmental factor)
• secondary: formed when two formerly allopatric populations that have become genetically differentiated expand so that they meet and interbreed

hyrbid zones when populations meet at secondary hybrid zones and have low intrinsic fitness (b/c of heterozygote disadvantage/breakdown of coadapted gene complexes)

hybrids have low fitness irrespective of variation in environmental conditions

• may persist indefinitely
• may favor alleles that enhance prezygotic isolation - may result in full reproductive isolation - extinction of hybrids
• alleles that improve fitness of hybrids may increase in frequency - postzygotic barreirs may break down - merging of species
• some hybrids may become reproductively isolated from teh parent forms and become a third species

• allopatric speciation - evolution of reproductive barriers in populations that are prevented by a geographic barrier from exchanging genes (gene flow = 0)
• parapatric speciation - spatially distinct populations between which there is some gene flow, diverge and become reproductively isolated
• sympatric speciation - evolution of reproductive barreirs within a single, initially randomly mating population (gene flow is maximum = 0.5)

• two forms of allopatric?
• vicariance - divergence of two large populations
• peripatric speciation - divergence of a small population from a widely distributed ancestral form

• populations that are geographically separated by a physical barrier (reduces gene flow)
• argued that it is the prevalent mode of speciation - at least in animals

if the barrier was removed or new species disperse over the barrier --> may become sympatric but without exchanging genes - they may form a hyrbidzone if incomplete reproductive isolation has occurred

the more geographically distant the populations, the more genetically different they were and the less likely they were to mate

as more allelic differences accumulate - later mutations have more opportunities to cause incompatibility and lower the fitness of hybrids

thought to be caused by natural selection, which causes the evolution of genetic differences that create prezygotic and/or postygotic incompatibility

• mutation/selection proceed independently - speciation is a side effect
• when they come back into contact the hybrids are sterile so natural selection favors prezygotic isolation

evolution of barriers to gene flow caused by divergent ecologically based selection

• founder effect speciation - restricted distributions, isolated, peripheral to the parent species, highly divergent - genetic change can be rapid when only a few individuals move!
• snowballing of genetic change -- reproductive isolation
• foundation for the idea of punctuated equilibrium

• speciation in neighboring populations
• higher rate of gene flow - force of selection is stronger to create genetic differences for reproductive isolation
• occurs when gene flow is much weaker than divergent selection for different gene combos

• controversial - can it really happen?
• biological barrier to gene exchange arose within an initially randomly mating population wihtout any segregation of the species (speciation despite initially high gene flow) - how are the intermediates reduced then?
• diversifying selection
• divergent adaptation to two distinct resources (ecological speciation - or temporal speciation)
• 2 models of mating - assortative (individuals prefer mates that match own phenotype) and trait preference (genes control female preference and male trait)
• recombination = huge obstacle!

• organism with more than two complements of chromosomes - isolated by postzygotic barriers
• instantaneous speciation by single genetic event
• may be important in plant evolution

• auto - formed by union of unreduced gametes from genetically and chromosomally compatible individuals that belong to the same species
• allo - derivative of a diploid hybrid between two species (or two ancestors that form hybrids that are sterile b/c of genetic/chromosomal incompatibility)

• hybrid speciation
• hybridization can give rise to distinct species with same ploidy as their parents
• generates diverse gene combos on which selection can act

• transition time (time for speciation) - time for reproductive isolation to evolve once process has started
• biological speciation interval - average time between origin of a new species and when that species speciates again

generation time, envirionmental factors, mating systems

two species evolve in response to each other

when several species are involved - effects are not independent

species evolves a defense against enemies and is thereby enabled to proliferate into a diverse clade

• could continue indefinitely - unending escalation of evolutionary arms race
• could result in stabel equilibrium
• cause continual cycles (or irregular fluctations) in the genetic composition of both species
• may leadd to extinction of one/both species
• gene for gene interactions

• model of enemy-victim coevolution
• example: host as R that confers resistance to the parasite, but in the parasite v confers infectivity (ability to infect/grow in host with R allele) - can become frequency dependent

those that reduce the survival/reproduction of their hosts

• greater virulence is expected to evolve in parasite species in which multiple infection is frequent
• if hosts rapidly become immune to the parasite slection favors rapid reproduction to outrun the host's immune system
• if horizontally transmitted - their fitness does not depend on reproduction of host - more virulent in horizontal transmitted parasites

• interactions between species that benefit individuals of both species
• symbiotic - individuals are intimately associated for much of their lifetimes
• reciprocal exploitation
• always a chance of cheaters - selection favors protective mechanisms to punish cheaters
• important basis for adaptation and complexity - provides one or both partners with new capabilities

• competition is one of hte major causes of adaptive radiation - divergence in resource use (competition for resoruce within species)
• density-dependent diversifying slection - two species

divergence in response to competition between species - process of divergence that is due to competition

• a species/population exhibits greater variation in resource use and phenotypic characters if it occurs alone that if it coexits with competing species
• alleviation of competition may enhance rates of speciation/diversification

• if a predators presence increases with the abundance of one prey, another species of prey may suffer heavier predation and decline
• one or both prey may be selected to diverge from the other in characteristics of susceptibility to the predator (can also converge if it lowers risk of predation)

a mimic resemples a dangerous species (the model)

two or more dangerous species are co-mimics (or co-models) that jointly reinforce aversion learning by predators

• comparative study of whole genomes
• to reveal major life history events

finding htat organismal complexity and total genome size dod not display a tight correlation

• a way in which protein-coding genes evolve
• measure of the departure from equality of the frequency of synonymous codons for a given amino acid in proteins
• codon usage is uneven

the measure of how dispensable certain genes are (can be deleted from genome or not)

ability of an amino acid sequence to maintain its proper protein folding in the face of ongoing mutations

lateral gene transfer, from noncoding regions, exon shuffling, gene chimerism, motif multiplication/exon loss, gene duplication

horizontal gene transfer between lineages - can arise in the origin of new genes

• produces truly new genes -
• domain accretion - new genes are produced by the addition of domains to teh beginnings/ends of ancestral genes

one that consists of pieces derived from two or more different ancestral genes (by exon shuffling, or by retrotransposition - can result in pseudogenes)

larger groups of genes, related to one anotehr by clear ancestry/descent, have diverse functions that have a common theme

new genes arise as copies of pre-existing genes

• paralogous - members of multigene families, originated from a common ancestral gene by gene duplication
• orthologous - found in different species have diverged from a common ancestral gene by phylogenetic splitting at the organismal level

emerging as an important source of variation in the human genome

• may diverge in sequence and function
• one copy may remain functional while the other becomes nonfunctional pseudogene (or deleted)
• undergo gene conversion

when sequence information from locus is transferred unidirectionally to other membres of hte gene family so that all acquire essentially the same sequence - causes concerted evolution of the gene family - causes the production of the same gene product from multiple loci

one of the gene duplicates retains original function and the other acquires a new function because of fixation of new mutations

each gene duplicate becomes specialized for a subset of functions originally performed by teh ancestral single-copy gene

seeks to understand teh mechanisms by which development has evolved in terms of developmental processes and evolutionary processes

• regulate teh patterning of specific body structures- homeobox genes (with homeobox- in the gene), homeodomian - in the protein)
• morphological differences is caused by changes in expression of genes that the Hox genes regulate

• thsoe that are inherited, with more/less modification froma common acnestor in which teh feature first evolved (synapomorphies)
• similarity in position, structural features, intermediate forms,

share same developmental genetic machinery in their ontogeny but are not historically homologous within a species

a features may be homologous among species at oen level of organization but not at another level

• with different enhancers on genes
• enables evolutionary changes in development of specific tissues/bodyd structures

novel uses of pre-existing morphological traits

refers to teh evolution of novel functions for preexisting genes and developmental pathways

evolutionary changes in the timing of development

differential growth rates of different parts of the body

• phsyical constraints (properties of biological materials do not permit them to evolve)
• selective (functional) constraints - some features may not appear b/c they are always disadvantageous
• genetic contraints - varying degrees of tolerance for variation
• developmental constraints - bias on the production of various phenotypes caused by the structure, character, composition, or dynamics of the developmental system

• absence of features in certain lineages
• directional trends
• parallel evolution of traits in independent lineages
• reduction of morphological variation of traits (canalization - most highly advantageous phenotype is mroe reliably produced)
• morphological stasis over long periods
• similarities in embryological stages among higher taxa

• internal genetic/developmental contraints
• stabilizing selection for a constant optimum phenotype (more common explanation)

teh shifting of the geographic distributions of species in concert with teh distribution of their typical habitat

• punctuated equilibrium - passed through intermediates but it was so fast taht the fossil record makes it appear like a discontinuous change
• saltation - intermediates never existed - mutatnt individuals differ drastically from their parents

idea that the production of genetic and phenotypic variation may be structured in a way that makes adaptive evolution more likely

• trend: persistent directional change in teh average values of a feature over a course of time
• progress: implies betterment

• lineages in teh clade evolve in both directions, but if there is a boundary on one side, teh variation can only expand in the other direction - mean increases but some lineages remain near the ancestral value
• the boundaries may be due to functional/developmental genetic constraints

changes within lineages in one direction are more likely that changes in the other direction

• efficiency/adaptedness
• complexity
• diversity/disparity

increases in phenotypic variation among species

GOd established natural laws (like natural selection) and then let the universe run on its own without further supernatural intervention

each species was created independently by GOd essentially in its present form

attacks on, and scientific disputes of evolution

• do no invoke special creation
• argue that many biological phenomen are too complicated to have arisen by natural processes - can only be explained by an intelligent designer (ID is a scientific not religious concept)

• hypothesis: proposition
• fact: hypothesis that has become so supported by evidence
• theory: big idea that encompasses other ideas/weaves them into coherent fabric

• fossils
• phylogenetic and comparative studies
• genes and genomes (molecular clocks)
• biogeography

evolutionary science that was misappropriated to jsutify racism and domination - genetic inferiority for superior people

the joint evolution of ecologically interacting species, each of which evolves in response to selection imposed by the other(s)

• virulence - effect on host
• infectivity - transmission

• formation of truly new genes through exon shuffling
• new genes produced by addition of domains to the beginnings/ends of ancestral genes

consists of pieces derived from two or more different ancestral genes - by exon shuffling or by retrotransposition

results in processed pseudogenes sometimes

can give rise to new genes ith new functions - multiplication of specific motifs

• orthologous: found in different species ahve diverged from a comon ancestral gene by phylogenetic splitting at the organismal level
• paralogous: like members of multigene families - have a common ancestral gene by gene duplication

the genes that regulate morphogenesis function in heirarchies or netowrks

• enhancers for each gene (bind to one or more transcription factors)
• genes have different enhancers - regulatory modularity
• changes in enhancers = phenotypic adaptations
• or in teh transcription factor itself

• the degree to which teh development of different body structures is independent
• individual structures/units seen as modules

non-genetically based polymorphism in which environmental differences cause development to produce a small set of (usually two) alternative states

jump

have changed so littler since millions of years ago

• how there are living fossils - they have changed so little since millions of eyars ago
• hypotheses for it include stabilizing selection or internal contraints

• logn dependence of related species on the same resources/environmental conditions
• caused because maybe another species will prevent a species from shifting/expanding or because stabilizing selection or ancestral character states because a majority of the population occupies the ancestral environment, not the new one

• the argument against evolution that a complex feature cannot function effectively except with coordination of all componenets - so intermediates couldn't have worked
• and the entire complexity couldn't have arisen by a single mustational step
• BUT intermeditaes are function (like the eye)

• teh core processes of protein activity and cell/organ development, with the establishment of regulatory interactions among ancient genes causes variation to arise that facilitates for evolution
• facilitates the evolution of complex characters