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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