Download Only(features(that(result(from(common(ancestry(reflect( evolutionary

• Only(features(that(result(from(common(ancestry(reflect(
evolutionary(changes(
• Homologies:(phenotypic(and(genetic(similarities(from(a(shared(
ancestry(
• Analogy:(similarity(between(2(species(that(is(due(to(convergent(
evolution(rather(than(common(ancestors((homology)(
• Analogous(structures(that(arose(independently(are(also(called(
homoplasies(
• The(more(elements(that(are(similar(in(2(complex(structures,(the(
greater(the(chance(of(homology((
• Molecular(homoplasy:(coincidental(matches(
• Molecular(systematics:(uses(DNA(data(of(the(molecules(to(
determine(evolutionary(relationships(
• Cladistics:(place(species(into(groups((clades)(which(includes(an(
ancestral(species(and(all(its(descendants((((
• A(taxon(only(equals(a(clade(if(it’s(monophyletic:(consists(of(an(
ancestral(species(and(all(its(descendants(
• Paraphyletic:(an(ancestral(species(and(some((not(all)(of(its(
descendants(
• Polyphyletic:(taxa(with(different(ancestors(
• Phyletic=(tribe(
• Shared(ancestral(character:(character(that(originated(in(an(
ancestor(of(the(taxon(
• Shared(derived(character:(shared(by(all(taxa(but(not(found(in(
their(ancestors,(evolutionary(novelty(unique(to(a(clade(
• Outgroup:(species/group(of(species(from(an(evolutionary(
lineage(that(is(known(to(have(diverged(before(the(lineage(that(
includes(the(species(we(are(studying(
• Branching(patterns(are(all(relative(
• Maximum(parsimony:(first(investigate(the(simplest(explanation(
that(is(consistent(with(the(facts(
• Phylogenies(based(on(DNA;(most(parsimonious(tree(requires(
the(fewest(base(changes(
• Maximum(likelihood:(given(certain(probability(rules(about(how(
DNA(sequences(change(over(time,(a(tree(can(be(formed(that(
reflects(the(most(likely(sequence(of(evolutionary(events(
(usually(complex)(
• Likelihood(of(a(tree(depends(on(the(assumptions(on(which(it’s(
based(
• Phylogenetic(trees(represent(hypothesis(
• Gene(duplication:(more(genes(in(the(genome,(therefore(more(
opportunities(for(further(evolutionary(change(
• Orthologous(genes:(found(in(different(species,(and(their(
divergence(tracks(back(to(the(speciation(events(that(produced(
the(species(
• Paralogous(genes:(results(from(gene(duplication,(multiple(
copies(of(these(genes(have(diverged(from(one(another(within(a(
species(
• Molecular(clock:(measurement(of(the(absolute(time(of(
evolutionary(change(based(on(the(observation(that(some(genes(
and(other(regions(of(genomes(appear(to(evolve(at(constant(
rates(
• Average(rate(of(evolution:(number(of(genetic(differences(
against(the(dates(of(evolutionary(branch(points(that(are(known(
from(the(fossil(record(
• Possibility(that(some(mutations(have(become(fixed(by(genetic(
drift((neither(beneficial(or(detrimental)(
• Neutral(theory:(much(evolutionary(change(in(genes(and(
proteins(have(no(effect(on(fitness(and(therefore(is(not(
influenced(by(natural(selection(
• Molecular(clock(assumes(that(the(estimated(evolutionary(
divergence(has(been(constant(all(along(
• Horizontal(gene(transfer:(genes(are(transferred(from(one(
genome(to(another(through(mechanisms,(such(as(exchange(of(
transposable(elements(and(plasmids,(viral(infection(and(fusion(
of(organisms(
(
• Linnaeaus’(binomial(classification(system(gives(organisms(2(
part(names:(a(genus(and(a(epithet(part(
• In(the(Linnaean(system,(species(are(grouped(in(increasingly(
broad(taxa:(related(genera(are(place(in(the(same(family,(
families(in(orders,(orders(in(classes(etc(
• Systematists(depict(evolutionary(relationships(as(branching(
phylogenetic(trees.(Many(systematists(propose(that(
classification(be(based(entirely(on(evolutionary(relationships(
• Unless(branch(lengths(are(proportional(to(time(or(amount(of(
genetic(change,(a(phylogenetic(tree(indicates(only(patterns(of(
descent(
• Much(information(can(be(learned(about(species(from(its(
evolutionary(history;(hence,(phylogenies(are(useful(in(a(wide(
range(of(applications((
• Organisms(with(similar(morphologies(or(DNA(sequences(are(
likely(to(be(more(closely(related(than(organisms(with(very(
different(structures(and(genetic(sequences(
• Computer(programs(are(used(to(align(comparable(DNA(
sequences(and(to(distinguish(molecular(homologies(from(
coincidental(matches(between(taxa(that(diverged(long(ago(
• Branch(lengths(can(ne(drawn(proportional(to(the(amount(of(
evolutionary(change(or(time(
• Among(phylogenies,(the(most(parsimonious(tree(is(the(one(that(
requires(the(fewest(evolutionary(changes.(The(most(likely(tree(
is(the(one(based(on(the(most(likely(pattern(of(changes(
• Well]supported(phylogenetic(hypothesis(are(consistent(with(a(
wide(range(of(data(
• Distnaly(related(species(can(have(orthologous(genes.(The(small(
variation(in(gene(number(in(organisms(of(varying(complexity(
suggests(that(genes(are(versatile(and(may(have(multiple(
functions(((
• Past(classification(systems(have(given(way(to(the(current(view(
of(the(tree(of(life,(which(consists(of(3(domains(
1. Bacteria(
2. Archaea(
3. Eukarya(
• Phylogenies(based(on(rRNA(genes(suggest(that(eukaryotes(are(
most(closely(related(to(archaea,(while(data(from(some(other(
genes(suggests(a(closer(relationship(to(bacteria(
• Other(genetic(analyses(suggest(that(eukaryotes(arose(as(a(
fusion(between(a(bacterium(and(an(archaean,(leading(to(a(“ring(
of(life”(in(which(eukaryotes(are(equally(closely(related(to(
bacteria(and(archaea(
(
CHAPTER(27:(BACTERIA(AND(ARCHAEA(
• Many(prokaryotes(can(tolerate(extreme(environments(
• Ability(to(adapt(to(a(broad(range(of(environments(explains(why(
they(are(so(abundant(
• Prokaryote(populations(have(been(subject(to(natural(selection(
in(all(kinds(of(environments,(resulting(in(their(enormous(
diversity(today(
• Prokaryotes:(mostly(unicellular(although(the(cells(of(some(
species(remain(attached(to(each(other(after(cell(division(
• Much(smaller(than(eukaryotic(cells((
• Well]organised,(achieving(all(of(an(organisms(life(functions(
within(a(single(cell(
1. Sphereical(
2. Rod]shaped(
3. Spiral((
• In(a(hypertonic(environment(most(prokaryotes(lose(water(and(
shrink(away(from(their(wall((they(lay(dormant)(
• Salt(can(be(used(as(a(preservative(as(it(causes(prokaryotes(to(
lose(water,(preventing(them(from(rapidly(multiplying(
• Eukaryote(cell(wall:(cellulose(or(chitin(
• Prokaryote(cell(wall((bacteria):(peptidodglycan:(polymer(of(
modified(sugars(cross]linked(by(short(polypeptides(
• Archaeal(cell(wall:(variety(of(polysaccharides(and(proteins((no(
peptidoglycan)(
• Gram(stain:(classification(of(many(bacterial(species(into(2(
groups(based(on(differences(in(cell]wall(composition(
• Stained(with:(
1. Crystal(violet(dye(and(iodine(
2. Rinsed(in(alcohol(
3. Stained(with(red(dye((eg(safranin)(
• Gram]positive:(simpler(walls(with(a(relatively(large(amount(of(
peptidoglycan(
• Gram]negative:(less(peptidoglycan,(structurally(more(complex,(
outer(membrane((lipopolysaccharides)((
• More(resistant(to(antibiotics((due(to(wall)(
• Cell]wall(of(many(prokaryotes(are(surrounded(by(a(sticky(layer(
of(polysaccharides(and(protein(called(a(capsule(
• Fimbriae:(hair]like(appendages(that(allow(prokaryotes(to(stick(
together(
• About(50%(of(prokaryotes(are(capable(of(taxis:(directed(
movement(towards(or(away(from(a(stimulus(
• Prokaryote(flagella(are(1/10(the(size(of(eukaryotic(flagella(and(
are(not(covered(by(an(extension(of(the(plasma(membrane(
• Bacteria(flagellum:(motor,(hook,(filament((42(kinds(of(proteins)(
• Only(half(of(these(are(necessary(for(function(
• Exaptation:(existing(structures(take(on(new(functions(through(
descent(with(modification((
• Prokaryotes(lack(compartmentalisation(found(in(eukaryotes(
• Prokaryotes(have(less(DNA(than(eukaryotes(