Chapter 2:Phylogenetic Systematics

The objective of systematics: infer phylogenetic relationships

E.g., what is Cynomorium (“Maltese mushroom”) related to?

Balanophoraceae?

Cladogram: representation of

evolutionary history

What is phylogeny?

Evolutionary history or pattern of descent

What is phylogenetic systematics (cladistics)?

Branch of systematics concerned with inferring phylogeny

Lines on cladogram?

Lineage = sequence of ancestral-descendent populations through time; represent descent

Descent

The origin of new life from pre-existing life by transfer of DNA from parent to offspring generation after generation.

Time

Descent results in a

lineage (clade)!

• Lineage or clade= a sequence of ancestors (parents) and descendants (offspring)

• Involves transfer of DNA through space and time

Split, from one lineage into two?

Divergence, which may lead to speciation

Pre-existing feature?

Plesiomorphy (ancestral feature)

New feature?

Apomorphy (derived feature)

Autapomorphy?

Apomorphy for a single lineage

Synapomorphy?

Apomorphy for two or more lineages

Topology?

Structure of branching diagram; how branches are connected together

Group as a whole? Individual taxa?

Ingroup O.T.U.’s (Operational Taxonomic Units)

What is homology?

Similarity due to common ancestry

Intra-individual homology?

Similarity by common ancestry of features within an individual, e.g., carpels and leaves (common ancestry by genes)

What is homoplasy?

Similarity not by common ancestry.

Types?

Convergence - independent evolution of a similar feature in 2 or more lineages.

Reversal - loss of a derived feature with re-establishment of ancestral feature.

Convergence - Stem succulence and “spines” in Cactaceae and Euphorbia spp.

Reversal - Loss of perianth in Lemna, Wolffia.

How is homology assessed?Beware of terminology!

Similarly termed features may not be homologous!

Look carefully at structure, position, development.

E.g., “spines” of cacti & euphorbs differ in position and development: leaf spines vs. stipular spines

euphorb spines

cactus spines

Convergent evolution:spines of cacti &

euphorbs

Hypotheses of homology are tested in cladistic analysis

What is a transformation series?Sequence of character states

Represent hypothesized sequence of evolution

Binary: Two states A <–––> B

What is state polarity?

Determination of direction of transformation.

Character X Taxon Matrix?

Recency of common ancestry?

Premise: All forms of life share a common ancestor.

Taxa which share a common ancestor more recent in time are more closely related to one another than they are to a taxon whose common ancestor is further back in time.

Primary tenet of phylogenetic systematics?

Taxa (O.T.U.’s) can be grouped by apomorphies,

because these represent unique evolutionary events.

Is C most closely related to D or to F?

Is C most closely related to E or to B?

Is C most closely related to A or to B?

Monophyletic Group

A common ancestor and all (and only all) descendents of

that common ancestor.

ApomorphiesBasis for grouping taxa together because

they represent the product of aunique evolutionary event

Sister Taxa?

Each of two descendent lineages from one common ancestor.

Plumbaginaceae and Polygonaceae (Caryophyllales) are sister taxa.

Paraphyletic Group?

A group consisting of a common ancestor but not all descendents of that common ancestor.

Polyphyletic Group?

A group consisting of two or more common ancestors, does not have a single common ancestor that is part of

the group.

“DICOTS” are paraphyletic.

A group consisting of the Grewioideae &

Dombeyoideae is polyphyletic.

Principle of Parsimony

The cladogram that is shortest – has the fewest number of steps (character state changes) – is accepted as most probable,

because it minimizes the number of ad hoc hypotheses.

“Entia non sunt multiplicanda praeter necessitatem.”

(That does not exist which multiplies more than necessary.)

Of two or more competing hypotheses, the simplest one is accepted.

Outgroup Comparison

Outgroup – taxon that is not a member of the ingroup.

Closest outgroups are considered to have ancestral features.

Why? Related to the principle of parsimony.

Outgroup Comparison

Phylogenetic analyses may result in 100s or 1000s of equally parsimonious trees.

Consensus trees used to summarize “best” or most probable tree.

Consensus Trees:combining features in common between two or

more trees.

Two most common consensus trees:

Strict consensus tree: only those clades in common among all trees are retained.

50% majority tree: clades retained if occur in 50% (or greater) of all trees.

OTHER ALGORITHMS FOR INFERRING PHYLOGENY

Maximum Likelihood:Considers probability of trees, given a

particular model of evolution

OTHER ALGORITHMS FOR INFERRING PHYLOGENY

Bayesian Analysis:Considers posterior probability (pp) of trees,

can also use model of evolution

Generally, any pp >90% good support

Cladogram Robustness

Bootstrap:resamples matrix at random (with replacement),

then 50% majority tree generated

Anything >70% good support.

Phylogenetic Classification

Indented

Annotated Annotated, rankless

Phylogenetic Classification

Parsimony Optimization

Representation of character state changes on cladogram in most parsimonious way.

Optimization

Maximum likelihood

ancestral state reconstruction

Geography

Habitat

Vicariance versus

dispersal

Heterochronyevolutionary change in the rate or

timing of development

Peramorphosis

Paedomorphosis

Neotony

derived type of heterochrony

adult stage resembles juvenile stage

adult stage resembles juvenile stage by decrease in rate of

development

Example: Cryptantha“Cats eyes” / “Popcorn flowers”

Cryptantha s.l.197 species total

N. America - 130 species

S. America - 70 species

3 species,C. albida, C. circumscissa, C. maritima,

in both N. & S. America

California - 66 species

Gynobase = expanded basal axis attached to nutlet(s)

gynobase

style

stigma

Nutlet Morphology

C. ganderi

C. hoffmannii

C. micromeres

C. nevadensis

C. holoptera

C. dumetorum

Nutlets smooth

C. affinis C. clevelandii C. flaccida C. ganderi C. glomeriflora C. gracilis C. hispidula C. incana C. leiocarpa

C. mariposae C. maritima C. microstachys C. milobakeri C. mohavensis C. nemaclada C. torreyana C. watsonii

* **

**can be heteromorpic with 1 smooth & 1 rough nutlet

* can be smooth or rough

C. ambigua C. angustifolia C. barbigera C. costata C. crinita C. decipiens C. dumetorum C. echinella

C. excavata C. holoptera C. hooveri C. intermedia C. mariposae* C. maritima C. micromeres C. muricata

C. nevadensis C. pterocarya C. racemosa C. recurvata C. scoparia C. simulans C. traskiae C. utahensis

Nutlets rough

Nutlets heteromorphic

J. angelica J. angustifolia

J. echinosepala

SBBG 46949

SD 190348 SD 153717

SDSU 18852

J. fastigiata

SD 62789

Phylogenetic systematic study

Cryptantha s.s. 1

Greeneocharis

Johnstonella

Oreocarya

Eremocarya

Cryptantha s.s. 2

Cryptantha s.l.is

polyphyletic!

Example: PogogyneMostly restricted to vernal pools

courtesy of Scott McMillan

Trichomes

Pogogyne nudiuscula A. Gray

Vernal Pools

• Ephemeral wetland• Different phases

throughout year– Wetting– Inundated– Waterlogged– Drought

• Suite of organisms adapted

Relative corolla length and fertile stamen number changes likely

happened along same branch

Subgenus Hedeomoides

Fertile Stamen Number &

Flower Insertioncorrelated:

Related to

autogamy?

Biogeography: some correlations

Species of Pogogyne – short branches

BEAST Analysis: Rates of nrDNA and cpDNA in angiosperms

5.1–7.7 Ma

BEAST Analysis: Rates of nrDNA and cpDNA in angiosperms

5.1–7.7 Ma 0.9–1.9 Ma

Ephermerally

Aquatic habitat

Rapid divergence: adaptation to ephemerally aquatic habitats