THE PHYLOGENETIC SYSTEM, ITS CLASSIFICATION,

TYPES

Submitted By: Arsalan Khan

Roll No 53611
Semester BS 4th

Submitted To: Dr. Sara Khan

DEPARTMENT OF BIOINFORMATICS
HAZARA UNIVERSITY MANSEHRA
2021
 TABLE OF CONTENTS
The phylogenetic system................................................................................................ 2

Botanist # 1. John Hutchinson (1884-1972): ................................................................. 2

Merits and Demerits Merits: ...................................................................................... 2

Demerits ..................................................................................................................... 2

Botanist # 2. Armen Takhtajan (1911) .......................................................................... 3

Merits ......................................................................................................................... 3

Botanist # 4. Arthur Cronquist (1919-1992) .................................................................. 4

Merits: ........................................................................................................................ 4

Demerits ..................................................................................................................... 4

Phylogenetic Classification ............................................................................................ 5

Types Of Phylogenetic ................................................................................................... 5

Cladograms................................................................................................................. 6

Phylograms ................................................................................................................. 7

Chronograms .............................................................................................................. 8

Phenograms ................................................................................................................ 8

References ...................................................................................................................... 9

1
The phylogenetic system

Botanist # 1. John Hutchinson (1884-1972):

John Hutchinson was a British botanist asso-ciated with Royal Botanic Gardens, Kew,

England. He developed and proposed his system based on Bentham and Hooker and

also on Bessey. His phylogenetic system first appeared as ―The Families of Flowering

Plants‖ in two volumes.The first volume contains Dicotyledons (published in 1926)

and second volume contains Monocotyledons (published in 1934). He made several

revisions in different years. The final revi­sion of ―The Families of Flowering Plants‖

was made just before his death on 2nd September 1972 and the 3rd i.e., the final

edition, was pub-lished in 1973.

Merits and Demerits Merits:

1. Hutchinson proposed the monophyletic origin of angiosperms from some

hypo-thetical Proangiosperms having Bennettitalean characteristics.

2. He made a valuable contribution in phylogenetic classification by his care-ful

and critical studies.

3. Monocots have been derived from Dicots.

4. According to him, the definitions of orders and families are mostly precise,

particularly in case of subphylum Monocotyledones.

Demerits

1. There is undue fragmentation of fami-lies.

2. Too much emphasis is laid on habit and habitat. Thus, creation of Lignosae

and Herbaceae is thought to be a defect reflecting the Aristotelean view.

2
 3. The origin of angiosperms from Bennettitalean-like ancestor is criticised by

many, because the anatomical struc-tures of the early dicotyledons are not

tenable with such ancestry.

Botanist # 2. Armen Takhtajan (1911)

Takhtajan was a reputed palaeobotanist of Komarov Botanical Institute of Leningrad,

U.S.S.R. (now in Russia). He also made great contributions in the field of angiosperm

taxo-nomy. In 1942, he proposed preliminary phylo-genetic arrangement of the orders

of higher plants, based on the structural types of gynoecium and placentation.

After 12 years i.e., in 1954, the actual system of classification was published in ―The

Origin of Angiospermous Plants‖ in Russian language. It was translated in English in

1958. Later on, in 1964, he proposed a new sys-tem in Russian language. To trace the

evolution of angiosperm, he was particularly inspired by Hallier’s attempt to develop

a synthetic evolu-tionary classification of flowering plants based on Darwinian

philosophy.

Merits

1. The classification of Takhtajan is more phylogenetic than that of earlier

sys-tems.

2. This classification is in a general agree-ment with the major contemporary

systems of Cronquist, Dahlgren, Thorne, and others. Both phylogenetic and

phenetic informations were adopted for delimination of orders and families.

3. Due to the abolition of several artificial groups like Polypetalae, Gamopetalae,

Lignosae, Herbaceae, many natural taxa came close together, viz. Lamiaceae

(earlier placed under Herbaceae) and Verbenaceae (placed under Lignosae)

are brought together under the order Lamiales.

3
 4. Nomenclature adopted in this system is in accordance with the ICBN, even at

the level of division.

Botanist # 4. Arthur Cronquist (1919-1992)

Arthur Cronquist was the Senior Curator of New York Botanic Garden and Adjunct

Professor of Columbia University. He presented an elabo-rate interpretation of his

concept of classification in ―The Evolution and Classification of Flowering

Plants‖(1968). The further edition of his classi­fication was published in ―An

Integrated System of Classification of Flowering Plants‖ (1981).

The latest rvision was published in the 2nd edition in 1988 in ―The Evolution and

Classification of Flowering Plants‖. He discussed a wide range of characteristics

important to phylogenetic system. He also provided synoptic keys designed to bring

the taxa in an appropriate alignment.

Merits:

1. There is general agreement of Cronquist’s system with that of other

contemporary systems like Takhtajan, Dahlgren and Thorne.

2. Detailed information on anatomy, ultra- structure phytochemistry and

chromo-some — besides morphology — was presented in the revision of the

classi-fication in 1981 and 1988.

3. The system is highly phylogenetic.

4. Nomenclature is in accordance with the ICBN.

Demerits

1. Though highly phylogenetic and popu-lar in U.S.A., this system is not very

use-ful for identification and adoption in Herbaria since Indented keys for

genera are not provided.

4
 2. Dahlgren (1983, 89) and Thorne (1980, 83) treated angiosperms in the rank of

a class and not that of a division.

3. Superorder as a rank above order has not been recognised here, though it is

present in other contemporary classifi-cations like Takhtajan, Thorne and

Dahlgren.

4. The subclass Asteridae represents a loose assemblage of several diverse

sympetalous families.

Phylogenetic Classification

1. Treats all levels of a cladogram as equivalent.

2. Places no limit on the number of levels in a ladogram.

3. Primary goal is to show the process of evolution.

4. It is limited to organisms that are related by ancestry.

5. Does not include a method for naming species.

Types Of Phylogenetic

This post has two motivations. First, it can serve as a future reference point if I need

to mention tree types again, and of course it can be found via search engine by

anybody who needs to look this stuff up. The second is my recent observation that

some 'evolutionary' systematists have the tendency to call all phylogenetic trees

cladograms, perhaps conflating ways of displaying evolutionary relationships with

their dubious claim that cladists do not accept the existence of ancestors. I would like

to take the opportunity to explain the different ways we can draw trees, what they

mean, and what a cladogram really is.

Phylogenetic trees are simple non-cyclical graphs connecting terminals - often species

- to show how the terminals are related. In species trees, the internal internodes are

common ancestors, and the nodes where branches meet are speciation events. In gene

5
trees, they would be ancestral alleles and mutation events, respectively.

Perhaps the oldest truly phylogenetic tree was drawn by Charles Darwin in his

notebook, the famous "I think" diagram. But it was in that case an abstract model to

help him visualise for himself common descent, not yet a concrete hypothesis about

any specific organisms.

So we have a tree connecting terminals. I will further assume that the tree is outgroup-

rooted, so that it has an explicit directionality: In the following examples, the arrow of

time points from the left to the right. It could be different. All that follows would

work just as well if the trees were turned by 90 degrees and the arrow of time pointed

from bottom to top, or if the tree was circular as in the case of Darwin's sketch. What

this post is about is simply what the branch lengths on the tree diagram mean, if

anything.

Cladograms

The least informative way of depicting a phylogenetic tree is as a cladogram. All that

it shows is how the terminals are assumed to be related, nothing else. The branch

lengths are meaningless and could be drawn with arbitrary length. But to show that

this is the case, in practice people draw them either equal length or, as in the case of

my example tree here, as all ending flush. If you are unsure if you are dealing with a

cladogram, it might be useful to check if there is a scale bar on the diagram. If there

isn't, it is probably a cladogram.However, the author may still opt to put ticks onto the

cladogram branches to illustrate where character changes took place. In that case, you

will have the same information as provided by the phylogram (see below) but without

meaningful branch lengths, so you are still dealing with a cladogram view of the tree.

If they are so uninformative, then why are cladograms used at all? As far as I can tell,

in contemporary practice it has nothing to do with cladists' supposed dogmatic

6
rejection of ancestors. Cladogram views are pragmatically used in phylogenetic

publications when showing true branch lengths would lead to a very untidy and

confusing looking tree or when there are no meaningful branch lengths. The latter is

the case with consensus trees summarising a number of equally parsimonious trees or

the results of bootstrapping or jackknifing. Each of the trees they are the consensus of

had branch lengths, but the consensus tree itself shows only what relationships they

agree on. It doesn't have well defined branch lengths on its own.

Phylograms

A phylogram is a phylogenetic tree whose branch lengths are proportional to how

many character changes have been inferred along the branches. If the tree you are

looking at has branches that do not end flush and a scale bar you are most likely

dealing with a phylogram.

If the branch lengths are multiples of one, it is most parsimonious to assume that the

tree is the result of a parsimony analysis. A length of one then means that one

character change took place along the branch, two means two, and so on. If the branch

lengths are tiny fractions of one, on the order of 0.004, the tree is most likely the

result of a likelihood or Bayesian analysis. The length then means what fraction of the

characters changed along the branch. I have no idea why parsimony and model-based

phylogenies have such different conventions, but if you want to make them directly

comparable you merely have to multiply all branch lengths in the likelihood tree with

the number of characters in the original data matrix.

Note that in a phylogram view a zero length branch indicates that the common

ancestor below that branch has been reconstructed to have the same characters as the

descendant at the end of the branch. In my example tree, the common ancestor

7
of Planta arvensis and Planta vulgaris would have been indistinguishable

from Planta arvensis by the character set used in the analysis. An 'evolutionary'

systematist is now free to pull a "this chimpanzee over there is my ancestor" and

consider Planta arvensis to be the ancestor of Planta vulgaris. I do not think that

makes sense, but the point is this is a question of approaches to classification. It is not

a question of phylogenetic trees or cladistic analyses as such not allowing this

interpretation.

Chronograms

A chronogram is a phylogenetic tree whose branch lengths are proportional to time. If

the tree you are looking at is ultrametric, that is all branches end flush, and it has a

full-length scale bar, you may be dealing with a chronogram. If the scale bar is in

units of "Myr" or suchlike and starts with zero in the present you are definitely

dealing with a chronogram.Some chronograms may not be ultrametric because they

contain extinct species, but the kind of fancy analysis that produces these kinds of

trees is still rarely used, not least because many groups don't have decent fossils

available anyway.

Phenograms

Another term that you may run into is phenogram, but this one is not about the

meaning of branch lengths. Many systematists do not consider clustering by similarity

to have a true phylogenetic logic whereas others disagree and consider it simply

another tool in the phylogentic toolbox. The former accordingly use phenogram to

differentiate the results of distance based, clustering, phenetic analyses from the

phylogenetic trees resulting from what they consider to be actual phylogenetic

analyses. Similarly, one would then call a group in a phenogram a cluster as opposed

to clade, reserving the latter word for phylogenetic trees.

8
References

Letunic, Ivica; Bork, Peer (1 January 2007). "Interactive Tree Of Life (iTOL): an

online tool for phylogenetic tree display and annotation" (PDF).

Bioinformatics. 23 (1): 127–128. doi:10.1093/bioinformatics/btl529. ISSN

1367-4803. PMID 17050570. Archived (PDF) from the original on

November 29, 2015. Retrieved 2015-07-21.

Ciccarelli, F. D.; Doerks, T.; Von Mering, C.; Creevey, C. J.; Snel, B.; Bork, P.

(2006). "Toward automatic reconstruction of a highly resolved tree of life"

(PDF). Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C.

CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982.

S2CID 1615592.

Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.

Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette.

ISBN 978-2010035289. OCLC 461974285.

Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Archived

from the original on April 21, 2014. Retrieved March 2, 2018.