3 schools of systematics

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Systematics Inferring Relationships

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SystematicsInferring Relationships

Three Schools of Systematics

• Phenetics

• Cladistics

• Evolutionary Classification

Phenetic analysis

• Phenetics also known as taximetrics, is an attempt to classifyorganisms based on overall similarity, usuallyin morphology or other observable traits, regardless of theirphylogeny or evolutionary relation.

• A numerical taxonomy which is concerned with the use ofnumerical methods for taxonomic classification. Many peoplecontributed to the development of phenetics, but the mostinfluential were Peter Sneath and Robert R. Sokal.

• Phenetic techniques include various forms of clustering andordination. These are sophisticated ways of reducing thevariation displayed by organisms to a manageable level. Inpractice this means measuring dozens of variables, and thenpresenting them as two- or three-dimensional graphs.

Phenetic analysis

Cladistic Analysis

• The Phylogeny of an organism is traced back,

it connects through shared ancestors to lineages of other organisms.

**phylogenetic tree

Cladistics or Phylogenetic Systematics

• Given that closely related species share acommon ancestor and often resemble eachother, it might seem that the best way to uncoverthe evolutionary relationships would be withoverall similarity.

• Q: In other words, out of a group of species, iftwo are most similar, can we reasonablyhypothesize that they are closest relatives?

YES or NO?

• Overall similarity may be misleadingbecause there are actually tworeasons why organisms have similarcharacteristics and only one ofthem is due to evolutionaryrelatedness.

• homologous feature (orhomology)- When two species havea similar characteristic because itwas inherited by both from acommon ancestor

• Ex: Morphological DivergenceAmong Vertebrate Forelimbs

• analogous feature (or homoplasy)- When twospecies have a similar characteristic because ofconvergent evolution

• Convergent evolution - when unrelated speciesadopt a similar way of life, their body parts maytake on similar functions and end up resemblingone another

• Only homologous similarity is evidence thattwo species are evolutionarily related.

• Q: If two animals share the highest number ofhomologies, can we reasonably assume theyare closest relatives?

• YES or NO?

• a homology may be recently derived or anancient retained feature; only shared recenthomologies (called synapomorphies) areevidence that two organisms are closelyrelated.

• Ex. The hand of the first vertebrates to live on land had fivedigits (fingers).

• Many living terrestrial vertebrates (such as humans, turtles,crocodiles and frogs) also have five digits because theyinherited them from this common ancestor. This feature isthen homologous in all of these species.

• In contrast, horses, zebras and donkeys have just a single digitwith a hoof.

• Clearly, humans are more closely related to horses, zebras anddonkeys, even though they have a homology in common withturtles, crocodiles and frogs.

• The key point is that the five digit condition is the primitivestate for the number of digits. It was modified and reduced tojust one digit in the common ancestor of horses, donkeys andzebras.

• In common cladistic usage, amonophyletic group is a taxon(group of organisms) which formsa clade, meaning that it containsall the descendants of the possiblyhypothetical closest commonancestor of the members of thegroup.

• The term is synonymous with theuncommon term holophyly.

• Monophyletic groups are typicallycharacterized by shared derivedcharacteristics (synapomorphies).

• In current usage, a paraphyletic groupconsists of all of the descendants of apossibly hypothetical closest commonancestor minus one or moremonophyletic groups (most usuallyone).

• A paraphyletic group is thus 'nearly'monophyletic (consistent with themeaning of the prefix 'para', namely'near' or 'alongside'.)

• A polyphyletic group is any groupother than a monophyletic group or aparaphyletic group, which like aparaphyletic group contains only someof the descendants of their closestcommon ancestor, but unlike aparaphyletic group is not characterizedby the missing descendants formingone (or more) monophyletic groups.

• A clade is a group of taxa consistingonly of an ancestor taxon and all ofits descendant taxa.

• It is hypothesized that allvertebrates, including ray-finnedfishes (Actinopterygii), had acommon ancestor all of whosedescendants were vertebrates, andso form a clade.

• Within the vertebrates, all tetrapods,including amphibians, mammals,reptiles (as traditionally defined) andbirds are hypothesized to have had acommon ancestor all of whosedescendants were tetrapods, and soalso form a clade.

• The tetrapod ancestor was adescendant of the original vertebrateancestor, but is not an ancestor ofany ray-finned fish living today.

The relationship between cladescan be described in severalways:

1. A clade is basal to another clade ifit contains that other clade as asubset within it.

• In the example, the vertebrateclade is basal to the tetrapod andray-finned fish clades.

Note:(Some authors have used "basal" differently to

mean a clade that is less species-rich than a sisterclade, with such a deficit being taken as anindication of 'primitiveness'. Others consider thisusage to be incorrect.)

• A clade located within a cladeis said to be nested within thatclade. In the diagram, thetetrapod clade is nestedwithin the vertebrate clade.

• Two clades are sisters if theyhave an immediate commonancestor.

• Terminology for characters

The following terms are used to identify sharedor distinct characters among groups:

• Plesiomorphy ("close form") or ancestralstate, also symplesiomorphy ("sharedplesiomorphy", i.e. "shared close form"), is acharacteristic that is present at the base of atree (cladogram).

• Since a plesiomorphy that is inherited fromthe common ancestor may appear anywherein a tree, its presence provides no evidenceof relationships within the tree. Thetraditional definition of reptiles (the bluegroup in the diagram) includes being cold-blooded (i.e. not maintaining a constant highbody temperature), whereas birds are warm-blooded. Since cold-bloodedness is aplesiomorphy, inherited from the commonancestor of traditional reptiles and birds, itshould not be used to define a group in asystem based on cladistics.

• Apomorphy ("separate form") orderived state is a characteristicbelieved to have evolved within thetree. It can thus be used toseparate one group in the treefrom the rest.

• Within the group which shares theapomorphy it is a synapomorphy("shared apomorphy", i.e. "sharedseparate form"). For example,within the vertebrates, alltetrapods (and only tetrapods)have four limbs; thus, having fourlimbs is a synapomorphy fortetrapods. All the tetrapods canlegitimately be grouped togetherbecause they have four limbs.

•Homoplasy is a characteristicshared by members of a treebut not present in theircommon ancestor.•It arises by convergence orreversion. Both mammals andbirds are able to maintain a highconstant body temperature (i.e.they are 'warm-blooded').However, the ancestors of eachgroup did not share thischaracter, so it must haveevolved independently.Mammals and birds should notbe grouped together on thebasis that they are warm-blooded.

• In an important work (first published inEnglish in 1966) by the German entomologistWilli Hennig, it was argued that only sharedderived characters could possibly give usinformation about phylogeny.

• The method that groups organisms that sharederived characters is called cladistics orphylogenetic systematics.

• Taxa that share many derived characters aregrouped more closely together than thosethat do not. The relationships are shown in abranching hierarchical tree called acladogram.

• If the character has only two states, then the task ofdistinguishing primitive and derived character states isfairly simple: The state which is in the outgroup isprimitive and the one found only in the ingroup isderived.

• It is common practice to designate the primitive statesas 0 (zero) and the derived states as 1 (one). If you aregoing to calculate trees by hand, this will certainlymake your calculations easier.

• On the other hand, if you are using a computerprogram to calculate a tree, it isn’t necessary todesignate the plesiomorphic state as 0 (zero):

• The first step in basic cladistic analysis is to determine whichcharacter states are primitive and which are derived.

• The outgroup comparison method is the primary one in use today.• In outgroup comparison, if a taxon that is not a member of the

group of organisms being classified has a character state that is thesame as some of the organisms in the group, then that characterstate can be considered to be plesiomorphic.

• The outside taxon is called the outgroup and the organisms beingclassified are the ingroup.

• The cladogram is constructed such that thenumber of changes from one character stateto the next is minimized. The principle behindthis is the rule of parsimony

• parsimony - any hypothesis that requiresfewer assumptions is a more defensiblehypothesis.

• the most parsimonious tree requires thefewest base changes.

0 1 2 3

0 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 1 step

0 to 2 = 2 steps

0 1 2 3

0 to 1 = 1 step 1 to 0 = 1 step 1 to 2 = 1 step

0 1 2 3

0 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step

0 1 2 3

0 to 1 = 1 step 1 to 0 = NA 1 to 2 = 1 step

• Maximum parsimony

– In the case of trees based on morphology, the most parsimonious treerequires the fewest evolutionary events, as measured by the origin ofshared derived morphological characters.

– For phylogenies based on DNA, the most parsimonious tree requires thefewest base changes.

Maximum Parsimony

Applying Parsimony

Applying Parsimony

Applying Parsimony

Applying Parsimony

Applying Parsimony

WHAT A CLADOGRAM ACTUALLY SAYS ABOUT RELATIONSHIPS• The trees that result from cladistic

analysis are relative statements ofrelationship and do not indicateancestors or descendants.

• For example in the tree above,Prorodon teres and Prorodon marinaare hypothesized to be sister taxaand to share a more recent commonancestor with each other than withColeps; but the prorodontids (P.teres+ P. marina+ Coleps) all share amore recent common ancestor withone another than with the Placidae(Placus + Spathidiopsis).

• The tree does not explicitlyhypothesize ancestor-descendantrelationships. In other words, the treehypothesizes that Prorodon andColeps are related, but not thatProrodon evolved from Coleps or thatColeps evolved from Prorodon.

Sample Exercise

You have discovered the skeletons of five new fossil animals, and you would like toinvestigate their phylogenetic relationships. After being told that species "A" isvery primitive, you decide to use it as the outgroup for a phylogenetic analysis.

Sample Exercise

You have constructed the following character matrix:

Sample Exercise

1

2

3

45

67

7 character changes

Sample Exercise

1

2

3

45

6 7

33

45

11 character changes

Sample Exercise

Which is the most parsimonious tree?

A B

Monophyly of Endomychidae

Consensus Tree

Length: 89 CI: 57 RI: 81

Monophyly of Endomychidae

Nelsen Consensus Tree

Length: 89 CI: 57 RI: 81

Monophyly Supported by:Fronto-clypeal ridge present

Monophyly of Endomychidae

Nelsen Consensus Tree

Length: 89 CI: 57 RI: 81

Monophyly Supported by:Fronto-clypeal ridge present Head without antennal grooves Tarsi 4-segmented, simple

Monophyly of Endomychidae

Nelsen Consensus Tree

Length: 89 CI: 57 RI: 81

Monophyly Supported by:Fronto-clypeal ridge present Head without antennal grooves Tarsi 4-segmented, simple

Phenogram

A C B D

A B C D

Cladogram

• Like the phenetic/cladistic system, thisclassification groups organisms according tobasic similarity, but unlike the two, it demandsan evolutionary explanation for thesesimilarities.

• Evolutionary taxonomists regard phenotypicspecialization and degree of change afterdivergence from a common ancestor asimportant components of classification.

• Traditionally, classical evolutionary taxonomistshave considered a taxon worthy of separatestatus if its members show a high degree ofspecialization relative to those of a closelyrelated taxon.

• The problem arises in the subjectivity of thisjudgment.

• Ex. Genetic and ontogenetic data indicate that birds share a most recent common ancestor with crocodilians.

• The Traditional Phylogeny diagram shows that some unknown commonancestor evolved into mammals and another unknown common ancestor.That second unknown ancestor evolved into turtles and a third unknownancestor. The third unknown ancestor evolved into the common ancestorof birds and crocodiles and the common ancestor of tuataras andsquamates. Turtles evolved early, and have remained unchanged for along time.

• But DNA evidence (“molecular phylogeny”) shows a different picture. Itshows, for example, that turtles and crocodiles evolved recently from acommon ancestor that also had birds for descendants.

• However, because birds havefeathers, are "warm blooded",and are superficially very differentfrom crocodilians, the classicalevolutionary biologist places themin Class Aves, and the crocodiliansin Class Reptilia.

• This means that Class Reptiliadoes not include all the speciesthat descended from the originalancestral reptile that gave rise tolizards, snakes, crocodilians, andbirds. Such an artificial taxon,which does not include alldescendants of a single ancestor,is said to be paraphyletic

• Similarly, Homo sapiens has traditionally beenassigned to its own family (Hominidae),although there is no objective reason totaxonomically separate it from the great apes(Pongidae). Like Reptilia, Pongidae notincluding Homo sapiens is paraphyletic.