BI 215 Exam 2 Ch 4

phylogenetic systematics

an approach to classifying organisms based on their evolutionary histories

phylogeny

the branching tree in which the length of each branch represents the amount of evolutionary change that has occurred along that branch

characters

measurable aspects of an organism; may be anatomical, physiological, morphological, behavioral, developmental, molecular genetic, and more

traits

any observable characteristics of organisms, such as anatomical features, developmental or embryological processes, behavioral patterns, or genetic sequences

taxon

a group of related organisms

nodes

a branch point on a phylogenetic tree, representing an ancestral population or species that subsequently divided into multiple descendant populations or species

root

the basal (most ancestral) lineage on a phylogenetic tree

sister taxa

two taxa that are immediately derived from the same ancestral node on a phylogenetic tree

polytomy

a node on a phylogenetic tree that has more than two branches arising from it; are often used to represent uncertainty about phylogenetic relationships on a phylogenetic tree

monophyletic group

a group that consists of a unique common ancestor and each and every one of its descendant species, but no other species

clade

a taxonomic group including an ancestor and all of its descendants

polyphyletic group

a group that does not contain the common ancestor of its members and/or all descendants of that common ancestor

paraphyletic group

a group that includes the common ancestor of all its members but does not contain every species that descended from that ancestor

unrooted trees

a phylogenetic tree in which the root, and thus the direction of time, is unspecified

rooted trees

a phylogenetic tree in which the root in indicated and thus the direction of time is specified

cladograms

a phylogenetic tree in which cladistic (historical evolutionary) relationships are represented but in which branch lengths do not indicate the degree of evolutionary divergence

phylograms

a phylogenetic tree in which the length of each branch represents the amount of evolutionary change that has occurred along that branch

chronograms

a phylogenetic tree on which absolute time is denoted

homologous trait

a trait shared by two or more species because those species have inherited the trait from a shared common ancestor

analogous trait

a trait that is similar in two different species or taxa, not because of common descent, but rather as a result of natural selection operating in similar ways along separate evolutionary lineages

divergent evolution

the process in which natural selection operates in different ways in each of two or more taxa that share a recent common ancestor, leading to different traits in these taxa

convergent evolution

the process in which natural selection acts in similar ways in different taxa, driving the independent evolution of similar traits in each taxon

vestigial traits

traits that have no known current function that appear to have had a function in the evolutionary past

tree of life

classification of organisms into 3 domains, bacteria, archaea, eukaryota (rRNA)

Carolus Linnaeus

• systema naturae in 1735

• taxonomy and classification

• established binomial nomenclature system (hierarchial-inclusive groups)

• domain, kingdom, phylum, class, order, family, genus, species

2 million

___ described species

1 million

___ species of insects

350,000

species of beetles

human classification

eukaryota, animalia, chordata, mammalia, primates, hominidae, homo, H. sapiens

Darwin

classifications must reflect descent from a common ancestor dude

phylogenetics

building evolutionary trees

• cannot observe evolutionary history directly, but can reconstruct history and build evolutionary trees using character evidence and deductive logic

evolutionary trees

___ can be used to…

• infer relationships between organisms (classification)

• identify groups with common ancestry (classification)

• estimate the time in the past when a group evolved

modern evolutionary trees

Willi Hennig (1966)

• cladistics (phylogenetic systematics)

• used shared characters to construct accurate branching phylogenetic trees showing evolutionary history

• used principle of Parsimony to select best tree

• based classifications on groups with shared ancestry

• clades

clades

monophyletic groups

• on trees include common ancestors and all its descendants

DNA base

use ___ differences to build phylogenetic trees

shared

___ ancestry corresponds to different regions

• phylogeny of microbacterium tuberculosis isolates from humans with geographical areas

same

get ___ patterns of common ancestry whether use…

• morphological characters

• fossil evidence

• DNA sequence similarity

evolutionary

map traits on tree to infer ___ events

1. construct evolutionary tree using DNA characters

2. map morphological traits on tree (jaws, lungs, etc.)

3. this reveals the evolutionary origin of these traits

phylogenetic

reading ___ trees

• living species (human, mouse, fly, etc) at tips of branches

• internal nodes

• evolutionary changes happen along each branch

• branch length records number of evolutionary changes

internal nodes

common ancestors of monophyletic groups

node

common ancestor point on phylogenetic trees

adenine, thymine, cytosine, guanine

A, T, C, G (names)

phylogeny of vertebrates

nodes are common ancestor populations

phylogeny

ancestry of populations

clades

___ or monophyletic groups

• basis of classification

• members share a common ancestor

clades (monophyletic groups)

groups of species that share a common ancestor

• share node on the tree

monophyletic groups

• include all descendants of a common ancestor

• exclude all species not descended from this ancestor

• clades nest one within another (nesting dolls)

nested clades

phylogenetic tree comprises sets of ___

• a given species is a member of multiple clades at multiple levels

phylogenies

___ drawn as trees or ladders

time

___ runs left to right in phylogenies

branch tips at right

___ are current groups on trees

root

ancestral lineage from which all other lineages on tree are derived

interior nodes

___ common ancestral populations

phylogeny

rotating around any node leaves a ___ unchanged and the relationships remain unchanged

unrooted

___ phylogenetic trees show relationships

• doesn’t indicate direction of time, no ancestry assumption

• if cannot be assigned a root, then draw an unrooted tree

• branch tips represent recent species

• interior nodes represent earlier species

• does not indicate whether interior node A or B represents a more or less recent population

rooted

making ___ trees from unrooted trees can change relationships

• if root around a different interior node, get different relationships each time

• rooting point influences clades hypothesized to be monophyletic

  • tree A: species [1,2,3] = monophyletic group

  • tree B+C: species [1,2,3] = non-monophyletic group

cladograms and phylograms

___ and ___ both show evolutionary relations

• phylogram of primate lentiviruses

  • branch tips not aligned

  • different horizontal branch lengths show amount of sequence change along each branch

  • phylogram: branch lengths significant

human immunodeficiency virus

HIV

simian virus

SIV

longer

HIV-2/B branch ___ than HIV-2/A branch

• more sequence change in HIV-2/B

• faster rate of evolution on HIV-2/B

cladogram

shows branch order, but the branch lengths are meaningless

phylogram

shows branch order and branch lengths reflecting amount of evolutionary change

chronogram

branch tips aligned (present time)

• different horizontal branch lengths show actual time rather than amount of evolutionary change

65 mya

rapid speciation of orchids just after K-T (Cretaceous-Tertiary) mass extinction

size of clade

reflects number of genera in clade

80 mya

origin of orchids (only a few species)

25,000-30,000

species of orchids today

similarities

first classifications were based on ___ of appearances

two types of similarities

1. homologous characters

2. analogous characters

homologous characters

similar-looking; inherited from common ancestor

• good for classification

analogous characters

similar-looking; but not inherited from common ancestor

• NOT used for classification

related

two ___ species look alike because they share the same ancestor and then they diverge (become different) over time

unrelated

two ___ species look alike because they are adapted to similar conditions

• similarly due to similar adaptations to the same environment, not because of common ancestry

divergent evolution

wooly mammoth and modern elephants are linked through ___ from a common ancestor

tetrapod vertebrates

have 4 limbs and share common ancestors

350 mya

ancestry of tetrapod limbs dates back to the origin of tetrapods in ___

• product of divergent evolution

• shared ancestry good for classification

homologous

ancestry of tetrapod forelimbs are ___ traits

tetrapods

all ___ have same forelimb bone pattern because their common ancestor had these same bones

• forelimb bone pattern inherited from ancestor (not produced from scratch every time)

swimming

porpoise forelimb adapted for ___ (flipper)

running

horse forelimbs adapted for ___ (4 digits lost, fused)

flight

wings of birds, bats, and pterodactyls modified for ___

• bird wing (digits lost and fused)

• bats (long digits support flight membrane)

• pterodactyl (4th finger, supported flight membrane)

• wing bone pattern is homologous

homologous

wing bone pattern is ___

• the same in all tetrapod forelimbs

best

similarity not ___ indicator of relationships for lizards, crocs, and birds

• before: classify based on similarity: grouped lizards and crocs together

• now: classify based on relationships: grouped crocs and birds together

unnatural

classification based on morphological similarity is ___

natural

classification based on phylogenetic relationships is ___

best

similarity not ___ indicator of relationships for barnacles, limpets, and lobsters

• before: classify based on similarity: group barnacle and limpet together

• now: classify based on relationships: group barnacles and lobster together

trees

___ can detect homology and analogy

• if homologous: similar legs/tails inherited from shared common ancestry

• if analogous: similar legs/tails evolved independently from different ancestors (not inherited from shared common ancestor)

legs

long ___ are a homologous trait in birds

• both long ___ species share a common ancestor

tails

long ___ are an analogous trait

• both long ___ species have a different ancestor

• long ___ evolved separately in the 2 long ___ lineage

• their common ancestor had a short ___

analogy

when similarity is NOT an indicator of relationships

• similar-looking ears and legs of desert-adapted placental and marsupial mammals analogous traits-evolved independently

• NOT because inherited from common ancestor

• similar-looking dorsal fins of sharks (fish) and whales (mammals) are analogous traits-evolved independently

• NOT because inherited from common ancestor

analogous/convergent evolution

NOT used for classification

convergent/analogous

streamlined body shape is ___

• an adaptation for rapid swimming for prey capture in open water

similar

___ body form not result of shared common ancestry

400 mya

fish, ichthyosaurs, and mammals diverged from each other (time)

160 mya

marsupials and placental mammals evolved separately ___ (time)

placental and marsupial

similar-looking ___ and ___ mammals found on different continents have adapted to similar environments

• convergent evolution in unrelated saber-toothed carnivores

toxic

aposematic coloration means bright colors and ___

non-toxic

plain coloration means natural colors and ___

monophyletic group

everything within a ___ is the descendant of a single common ancestor

paraphyletic group

does not include all the descendants of a single common ancestor (only half of clades); excludes subset of ancestor’s descendants in the monophyletic group