-groups of interbreeding natural populations that are reproductively isolated from other such groups

-main criterion=reproductive isolation

-reduced gene flow (fundamental step in cladogenesis)

-good= clear emphasis of cladogenetic process; widely used concept

-bad= difficult to apply; not apply to asexual lineages/organisms; difficult to measure for animals that can't interbreed due to *allopatry* (geographical separation)

-species defined by morphological similarities

-main criterion= morphological differentiation

-good= intuitive, widely applicable (dead/alive, sexual/asexual)

-bad= arbitrary, overlook other important traits e.g. behavior, ecology

=homoplasy

-smallest monophyletic group of common ancestry

-main criterion= monophyly

-good= widely applicable, methodically rigorous

-bad= historical, not mechanistic; arbitrary depending on what DNA seq compared

-natural part of speciation

-difficult to cleanly demarcate species boundaries

-studying hybrids help us understand how species arise

1. Anagenesis= change in evolutionary lineage without splitting (chronospecies)

2. Cladogenesis= splitting of one evolutionary lineage into 2 separate, independent ones; cessation of gene flow (ensure independent evolutionary trajectory)

-definition= splitting of 1 lineage into two independent ones

-species is the smallest evolutionarily independent unit

(smallest grouping of organisms with independent evolutionary trajectory

-cladogenesis result in divergence - both processes are ongoing

-key component of speciation

-cause genetic isolation and prevent gene flow 

-genetic isolation= allow independent evolutionary trajectory and allow populations to diverge

1) extrinsic (geographical/environmental) physical separation

2) intrinsic (biological/organismal) habitat specialization, mating preferences, hybrid incompatibilities; evolutionary divergence prevents gene flow

-allopatric speciation= species diverge due to complete geographical/physical separation of populations

-barrier create two genetically isolated population that diverge over time

-separated population become new populations

1) vicariance= separation of organisms by geographical barrier resulting in differentiation (split for longer= more differentiation)

2) dispersal= movement of a part of population to another isolated location (ex island hopping)

-strong differential selection across an environmental gradient

-this selection causes local adapatation and creates genetic isolation between geographically adjacent populations

-genetic isolation and divergence occur without extrinsic barrier

-disruptive selection forms two subpopulations= they use diff. resources and occupy diff. niches=> genetic isolation

e.g. ploidy mutation of plants

e.g. mice on the island of madeira with karyotype differences

-drift allows isolated small populations to diverge

e.g. rhagoletis flies on apple and hawthorne fruits

-different species= fidelity to fruit type provide genetic isolation

=return to larval fruit for mating

=genetically distinguishable

-hybrids are inferior (so selected out)

-differences in courtship and mating preferences emerge due to drift/selection

-can lead to extrinsic reproductive isolation without intrinsic isolation

-rapid speciation

e.g. bird courtship, jumping spiders, cichlid fish coloration, plant traits change for pollinator visitation

-differentiated populations come into secondary contact

-what happened?=>1)allopatry (vicariance/dispersal) 2)divergence (drift/selection) 3)secondary contact (amt of dispersal into/out of hybrid zone;selection on hybrid relative to parent)

-outcomes

1) hybrids equally or more fit everywhere than parents= merge (because of increased fitness)

2) hybrids less fit in parental ranges but equally or more fit than parents in hybrid zone= stable hybrid zone

3) hybrids less fit than parents everywhere= selection reinforce reproductively isolating mechanisms (complete speciation)

*** if hybrids less fit in in hybrid zone than species don't merge (postzygotic isolation)

-selection increases reproductive isolation especially when hybrids less fit

-way of forming a full species barrier where the hybrid zone was

-postzygotic to prezygotic 

-act on mating preference =ex. females in sympatry more choosy about selecting own species (avoiding heterospecific males)

-formed by selection in a continguous population (adjacent) along an environmental gradient

-parapatry is taking place

-cline= transition in allele frequency (genotype or phenotype) along a geographical transect

-secondary = clines for different allele frequencies match up (overlap at the point of population contact) & for neural/adaptive traits

-primary= clines for diff. allele frequencies not necessarily match up (only reflect ecological gradient- which have differential effects on different traits) & neural traits not show cline

-inherited trait that increases the ability of an animal to survive/reproduce in an environment compared to other animals without the trait

-the trait is shaped by natural selection and it allows individuals to perform a particular function

-same genotype, different phenoype b/c live in different environment

e.g. hemoglobin increase at higher alt. (not genetic)

**adaptation (HIF pathway change)

-drift

-necessary consequences of physical laws

-exaptation (trait predate the function- exist before it was known for some function)

differential mating success (associated with phenotype/genotype)

-sexual dimorphism:

1)females invest more in offspring- limited by access to resources; therefore are choosy for good genes (handicap principle), runaway sex. selection- sexy sons

2)males reproductive success (tied to mating success) is very variable- limited by number of mates; therefore compete (intrasexual)e.g. sperm competition (have sex immediately in retaliation); infanticide

** sexual selection and natural selection oppose each other

-whose evolution is the study of reproductive and life strategies

-life history= lifetime pattern of an individual's allocation of resources (time and energy) to fundamental activities such as growth, repair, and reproduction

-growth, survivorship, reproduction

**tradeoffs= growth vs. reproduction/ current vs. future offspring

-accumulation of cell damage and metabolic by-product

why?

1) Theory: rate of living= higher METABOLIC RATE= more damage = NO lifespan not correlate with MR

=repair mechanisms already perfected?= NO just tradeoff between repair and reproduction

2)Theory: evolutionary tradeoff= selection on age of reproduction= change lifespan (late reproduction= increase lifespan)

=lifespan relate to species level traits and extrinsic sources of mortality 

** accumulation of deleterious mutations (not selected out b/c occurs after reproduction) (no selection against late bad alleles)

**antagonistic pleiotropy (alleles good early will be favored even if bad later) (positive selection for alleles that are good early on but bad later on)

1) Mutualism= all benefit; behaving like a pack

2) Reciprocity= benefit is delayed; repaid later; no cheating b/c repeated interactions and punishment

3) Altruism= risk oneself for benefit of others; happen b/c of inclusive fitness of relatives

=rB>C

4) Eusociality= cooperative care of offspring; some are non-reproductive; generations overlap

5) Haplodiploidy= fertilized eggs (diploid)-females; unfertilized eggs (haploid)- males

**haplodiploidy does not explain eusociality b/c of multiple mating 

-genome size not correlate with complexity

-1.2% of genome = protein coding

-genetic variation in non-coding region

-repetitive DNA= repeats throughout the genome 50% (transposable element)= closely related to viruses= selfish b/c repeatedly replicate (LINE (RNA)/SINE)

**variation in genome size correspond to differences in cell size

-neutral theory of molecular evolution= rate of silent change > or equal to rate of replacement change

=purifying selection dominate and DNA evolution is from genetic drift of mutations (not from fitness)

=more variation at less constrained region= evolutionary constraint dn<ds

-adaptive evolution= when replacement rate greater than silent (speciation) dn>ds