Topic 08 Uses of Cladograms

1
Topic 08 Uses of Cladograms

• Taxonomy
• Classification
• e.g., cycad
• classification

2
Topic 08 Uses of Cladograms

• Taxonomy
• Classification
• e.g., cycad
• classification

1. Most parsimonious cladogram from Stevenson
(1992).
2. Classification based on cladogram.
3
Topic 08 Uses of Cladograms

• Taxonomy
• Classification
• e.g., recognition of new genus, Plowmanianthus,
  in Commelinaceae (2004).

• Timeline
• 1976 Strange Commelinaceae discovered at Field
  Museum Herbarium- were misplaced in
  Gesneriaceae indet folders
• Herbarium search turns up several more
• Ca. 1980 - Tim Plowman returns from S America w/
  living plant
• C-some counts, flower point to relationship with
  Cochliostema
• ...

4
Topic 08 Uses of Cladograms

• Taxonomy
• Classification
• e.g., recognition of new genus, Plowmanianthus,
  in Commelinaceae (2004).

Timeline (Continued) 5. 1995-2001 Fieldwork
in S America reveals new discoveries that
further support affinity w/ Cochliostema.
...
1 cm
5
Topic 08 Uses of Cladograms

• Taxonomy Classification Biogeography
  character states uniting differentiating
  Cochliostema and these new undescribed species.

• Cochliostema
• NW South America.
• n 19.
• Epiphytic in trees.
• Fringed petals.
• Reduction to 3 stamens.
• Filaments basally fused.
• Anthers concealed by fused filament hairs.
• Anthers spirally coiled.

3.
4-7.
4-8.

• Undescribed spp.
• NW South America.
• n19.
• Semi-terrestrial rooting only in leaf litter.
• Fringed petals.
• Reduction to 3 stamens.
• Filaments basally fused.
• Anthers concealed by unfused filament hairs.
• Anthers strongly curved, but not spirally
  coiled.

5-8.
4-8.
3.
6
Topic 08 Uses of Cladograms
New species 2
New species 4b
New species 5
New species 1
New species 4a
New species 3
Cochliostema odoratissimum
Cochliostema velutinum

• Taxonomy
• Classification

Cladistic analysis of Hardy (2001) provided
support for the recognition of two genera, with
the undescribed species comprising the second
genus, Plowmanianthus. Which of the following
three cladograms match the one obtained by
Hardy? Hint remember Hennigs principle that
only monophyletic groups should be named.
Cochliostema odoratissimum
Cochliostema velutinum
New species 5
New species 1
New species 2
New species 4b
New species 3
New species 4a
A
New species 2
New species 4b
New species 5
New species 1
New species 4a
New species 3
Cochliostema odoratissimum
Cochliostema velutinum
B
C
7
Topic 08 Uses of Cladograms

• Taxonomy Classification e.g., a new (sixth)
  species of Geogenanthus? Geo earth anthus
  flower.

Fact 1 Gentry (1991) includes an illustration of
a widespread Amazonian plant species,
Geogenanthus rhizanthus, with a plant possessing
rather large, complex inflorescences, and flowers
with very short pedicels.
Fact 2 A later monograph of Geogenanthus (Hardy
2001) suggests that plants with the larger
inflorescences and short pedicels (Fig. 1A below)
belong to a new species that is distinct from G.
rhizanthus, which has shorter inflorescences and
very long pedicels (Fig. 1B below).
Fig. 1. Inflorescences of (A) a putative new
species of Geogenanthus illustrated by Gentry
(1991) as G. rhizanthus, and (B) G. rhizanthus
(based on the type specimen for G. rhizanthus).
The distinctiveness of these inflorescences
suggests that the plant illustrated in Gentry
(1991) is not G. rhizanthus, but rather a new
species.
8
Fact 3 Application of the Phylogenetic Species
Concept indicates that the plants in question
actually belong to two separate species. Below, a
map showing vouchered populations of
Geogenanthus. All populations in red have short
inflorescences and long pedicels matching those
of the type specimen for G. rhizanthus. All
populations in white have the large
inflorescences and short pedicels of the putative
new species in question.
Geogenanthus new sp. 1 (i.e., G. pacificus
Geogenanthus new sp. 2 (i.e., G. bilsensis)
Geogenanthus ciliatus
Geogenanthus rhizanthus
Geogenanthus poeppigii
New species?
9
Fact 4 The cladistic analysis presented in the
monograph of the genus provides compelling
evidence for the distinctiveness of the putative
new species with larger inflorescences and short
pedicels. Below, populations of the putative new
species are shown in white, and the most
parsimonious cladogram depicting relationships
among the species of Geogenanthus based on DNA
and morphological data is drawn over the
distribution map.
Geogenanthus new sp. 1 (i.e., G. pacificus
Geogenanthus new sp. 2 (i.e., G. bilsensis)
Geogenanthus ciliatus
Geogenanthus poeppigii
Geogenanthus rhizanthus
New species?
10
Topic 08 Uses of Cladograms
II. Understanding the history of biological
diversification. -cladograms as the scaffold
for comparative biology, genomics, etc.
http//genetics.nbii.gov/systematics.html
11
Topic 08 Uses of Cladograms
II. Understanding the history of biological
diversification. -e.g., floral organ identity
genes. What are they doing in non-angiosperms?
When and how did they diversify?
12
Topic 08 Uses of Cladograms
II. Understanding the history of biological
diversification. -e.g., glutamate receptors
13
Topic 08 Uses of Cladograms
-e.g., glutamate receptors
http//genetics.nbii.gov/systematics.html
14
Topic 08 Uses of Cladograms
III. Disease Origins Disease Forensics e.g.,
HIV origins e.g., HIV infection histories
15
Topic 08 Uses of Cladograms
III. Disease Origins Disease Forensics e.g.,
HIV origins
Table 1. A comparison of species of Human
Immunodeficiency Virus (HIV).
16
Topic 08 Uses of Cladograms
e.g., HIV origins

• 1992 Rolling Stone, Tom Curtis
• HIV-1 (human immunodeficiency virus type 1) may
  have jumped into humans via OPV
• Chimps have related Simian IV (SIVcpz)
• Human HIV is clearly derived from SIVcpz
• Certain population of chimps in DR Congo were
  allegedly used to prepare OPV by Hilary Koprowski
  in the 1950s.
• Rolling stone retracts story.

1999 The River A Journey to the Source of HIV
and AIDS by Edward Hooper.
Map of the Democratic Republic of the Congo

• 7 yrs research.
• Good evidence for OPV-origin.
• http//www.aidsorigins.com/

17
Topic 08 Uses of Cladograms
e.g., HIV origins
Map of chimp subspecies Pan troglodytes
troglodytes (green) and P. t. schweinfurthii (red)
Worbley et al. 2004. Nature 428, 820.
Cladogram showing phylogenetic relation of HIV-1
types to SIV found in Ptt.
18
How are nucleic acid (DNA or RNA) sequences used
to infer phylogenies?
Grind up tissue, extract DNA
2
5
3
4
1
PCR DNA sequencing
Position 5 CgtU
Data matrix construction
Position 1 AgtG
Example Data Matrix Sp. 1 AGGUCCC Sp.
2 AGGUCUA Sp. 3 ACGUCUA Sp. 4 GCGUCUASp.
5 GCGUUUA
Position 2 GgtC
Position 6 CgtA
Cladistic Analysis e.g., application of
principle of parsimony.
19
Topic 08 Uses of Cladograms
e.g., HIV Infection Histories ( criminal
forensics)

• CDC Teams Up with Systematists
• 1990s Florida dentist was suspected of
  transmitting HIV to several of his patients.
• Several of his patients were indeed infected, but
  some had other risk factors as well.
• Conclusions?

20
Topic 08 Uses of Cladograms
e.g., HIV Infection Histories ( criminal
forensics)
Which patients were infected by dentist, which
were not?
21
Topic 08 Uses of Cladograms
Conservation Strategy Planning
2
5
3
4
1
22
Topic 08 Uses of Cladograms
Ancestor Reconstruction
23
Ancestor Reconstruction
Time (milliseconds)
24
Topic 08 Uses of Cladograms
Testing Adaptational Hypotheses e.g.,
succulence e.g., bromeliad evolution