1. Chapter 2: Phylogenetic Systematics

2. The objective of systematics: infer phylogenetic relationships
E.g., what is Cynomorium (“Maltese mushroom”) related to?

3. Balanophoraceae?

4. Cladogram: representation of evolutionary history

5. What is phylogenetic systematics (cladistics)?
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

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

7. 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

9. Split, from one lineage into two?
Divergence, which may lead to speciation
Pre-existing feature?
Plesiomorphy (ancestral feature)
New feature?
Apomorphy (derived feature)

11. Autapomorphy? Synapomorphy?
Apomorphy for a single lineage
Synapomorphy?
Apomorphy for two or more lineages

13. Group as a whole? Individual taxa?
Topology?
Structure of branching diagram; how branches are connected together
Group as a whole? Individual taxa?
Ingroup O.T.U.’s (Operational Taxonomic Units)

14. Intra-individual homology?
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)

15. Similarity not by common ancestry.
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.

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

17. Reversal - Loss of perianth in Lemna, Wolffia.

18. 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

19. Convergent evolution: spines of cacti & euphorbs
Hypotheses of homology are tested in cladistic analysis
euphorb spines
cactus spines
Convergent evolution: spines of cacti & euphorbs

20. 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.

21. Character X Taxon Matrix?

22. Recency of common ancestry?
Primary tenet of phylogenetic systematics?
Taxa (O.T.U.’s) can be grouped by apomorphies, because these represent unique evolutionary events.
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.

23. 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?

24. Monophyletic Group
A common ancestor and all (and only all) descendents of that common ancestor.

26. Apomorphies
Basis for grouping taxa together because they represent the product of a unique evolutionary event

27. Sister Taxa? Each of two descendent lineages from one common ancestor.
Plumbaginaceae and Polygonaceae (Caryophyllales) are sister taxa.

28. Paraphyletic Group? Polyphyletic 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.

29. “DICOTS” are paraphyletic.

30. A group consisting of the Grewioideae & Dombeyoideae is polyphyletic.

31. 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.

33. For 54 OTUs, no. trees = 3 x 10 84, > no. atoms universe

35. 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.

36. Outgroup Comparison

37. Consensus trees used to summarize “best” or most probable tree.
Phylogenetic analyses may result in 100s or 1000s of equally parsimonious trees.
Consensus trees used to summarize “best” or most probable tree.

38. Two most common 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.

39. OTHER ALGORITHMS FOR INFERRING PHYLOGENY
Maximum Likelihood:
Considers probability of trees, given a particular model of evolution

40. Generally, any pp >90% good support
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

41. Anything >70% good support.
Cladogram Robustness
Bootstrap:
resamples matrix at random (with replacement), then 50% majority tree generated
Anything >70% good support.

42. Phylogenetic Classification
Indented
Annotated
Annotated, rankless

43. Phylogenetic Classification

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

45. ancestral state reconstruction
Optimization
Maximum likelihood
ancestral state reconstruction

46. Geography
Vicariance versus
dispersal
Habitat

47. Heterochrony Peramorphosis Paedomorphosis Neotony
evolutionary change in the rate or timing of development
Peramorphosis
derived type of heterochrony
Paedomorphosis
adult stage resembles juvenile stage
Neotony
adult stage resembles juvenile stage by decrease in rate of development

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

49. C. albida, C. circumscissa, C. maritima,
Cryptantha s.l.
197 species total
N. America species
California - 66 species
S. America - 70 species
3 species,
C. albida, C. circumscissa, C. maritima,
in both N. & S. America

50. Gynobase = expanded basal axis attached to nutlet(s)
stigma
style
gynobase

51. Nutlet Morphology C. holoptera C. dumetorum C. ganderi C. micromeres
C. hoffmannii
C. nevadensis

52. 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 smooth or rough **
can be heteromorpic with 1 smooth & 1 rough nutlet

53. Nutlets 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

54. Nutlets heteromorphic
SBBG 46949
SDSU 18852
J. angelica
J. angustifolia SD SD
SD 62789
J. echinosepala
J. fastigiata

55. Phylogenetic systematic study
This is an example of a phylogenetic systematic study that mike just published. This is a good example of a paper that contains both a molecular phylogeny and a taxonmic revision. The paper shows that Cryptantha is polyphyletic and then splits the group into 5 genera.

56. Cryptantha s.l. is polyphyletic! Cryptantha s.s. 1 Greeneocharis
Johnstonella
Cryptantha s.s. 2
Oreocarya
Eremocarya

57. Example: Pogogyne Mostly restricted to vernal pools
Trichomes
Pogogyne nudiuscula A. Gray
courtesy of Scott McMillan

58. Vernal Pools Ephemeral wetland Different phases throughout year
Wetting
Inundated
Waterlogged
Drought
Suite of organisms adapted

59. Fertile Stamen Number & Flower Insertion correlated: Related to
Subgenus Hedeomoides
Fertile Stamen Number &
Flower Insertion correlated:
Related to
autogamy?
Apomorphies uniting hedeo
Shift from outcrossing to self-polination
Pog ab only one studied
many (if not most) vernal pool are selfing (spencer and reisberg 1998)
Future studies of pollination mechanisms
Relative corolla length and fertile stamen number changes likely happened along same branch

60. Biogeography: some correlations

61. Species of Pogogyne – short branches

62. BEAST Analysis: Rates of nrDNA and cpDNA in angiosperms
5.1–7.7 Ma

63. BEAST Analysis: Rates of nrDNA and cpDNA in angiosperms
5.1–7.7 Ma
0.9–1.9 Ma
A strict clock with a mean rate of 0.2% for the trnQ-rsS16 data and 0.45% for the ITS data were used, based on average divergence rates in angiosperms of 0.1– 0.3% per million years for non-coding cpDNA (Wolfe et al. 1987; Muse 2000)
and 0.1–0.8% per million years for non-coding nrDNA (Kay et al. 2006). The analysis was run for 10 million generations.

64. Rapid divergence: adaptation to ephemerally aquatic habitats
Ephermerally
Aquatic habitat
0.6-4 million years: vernal pool soils (Harden 1987)