MEGA 11 GEN11306
TA geeft de aminozuren op alle posities weer
Color cells (Display) chemisch dezelfde aminozuren hebben dezelfde kleur
C= conserved sites plekken/sites die gedurende de evolutie niet zijn veranderd
V= variable positions Met V kun je de genen bepalen met de hoogste evolutionary rate.
Bijvoorbeeld V=(52/58) dan is heeft het gen 98% evolutionary rate, dat is hoog.
Pi= parsimony informative potential synapomophies: Gedeelde trait door 1 of meerdere
afstammelingen
S= Singleton = autapomophy unique trait
1
,Term Definition
Taxon A group of organisms. They are defined by
being monophyletic
Monophyletic group A group of organisms with the same ancestor
Synapomorphy shared trait (apomorphy) by two or more
taxa/species. It’s a shared derived character.
Are the stuff that keeps the tree together.
autapomorphy unique changes, only found in one species on
the tree.
Symplesiomorphy / Plesiomorphy a character that all species in the tree share
Cladistics is an approach to biological classification in
which organisms are categorized in groups
("clades") based on hypotheses of most recent
common ancestry
Homoplasy A feature has been lost or gained independently
in separate lineages over the course of
evolution
Homology term used to characterize the similarity of
features that can be parsimoniously explained
by common ancestry
Reversal A loss of derived trait present in ancestor and
the reestablishment of a plesiomorphic trait
Convergence independent evolution of a similar trait in two
or more taxa
Apomorphy a derived trait or novel (nieuwe) eigenschap
Autapomorphy a distinctive derived trait that is unique to a
given taxon or group
Clade group defined by most recent common
ancestor. Same as a monophyletic group.
Paraphyletic group a group with the group’s last common ancestor
and most of its descendants.
Bootstrap Measuring confidence indicates how many
times out of 100 (in your case) the same branch
was observed when repeating the phylogenetic
reconstruction on a re-sampled set of your
data. Used to asses the support for nodes in
your phylogenetic tree.
polyphyletic group voltures for example, convergent evolution.
MRCA = most recent common ancestor
monophyletic if all organisms for example are
birds and share the same ancestor. If a turtle
has the same ancestor then it becomes
paraphyletic.
Anagenesis Evolutie van soorten waarbij een soort in zijn
geheel evolueert
Monisme filosofisch standpunt dat zegt dat er slechts één
van iets is. For example one species definitions
would fit all species. (most people disagree).
Pluralist een systeem dat stelt dat de werkelijkheid
2
, bestaat uit een veelheid aan principes en niet
herleid kan worden tot één enkel principe zoals
bij het monisme.
Cladogram consists statements on which species are sister
species
classification Tree tells where traits changed
Scenario what happened over time
Lecture 1 Conceptual overview and historic account
3
, Comparative Biology: Uses natural variation and disparity to understand the patterns of life at all
levels – from genes to communities – and the critical role of organisms in ecosystems. It
encompasses (omvat) evolutionary biology.
comparing different things within different systems, as long as it is linked to historic approaches.
comparing lineages implies taking history in account.
A trait is variable within species. With phylogenetics you want to look a differences between species
(not within) therefore you talk about characters.
Synapomorphy is a shared derived character. NOT unique (shared)
Clade a group that is defined by its most recent common ancestor. It is the same as a monophyletic
group.
Bootstrapping is measuring confidence. Assessing support for the nodes in your phylogenetic tree.
NOT for the branches.
Picture above shows a phylogenetic tree:
1 = monophyletic
2 = paraphyletic group; a MRCA and not all its descendants
3 = polyphyletic: multiple MRCA’ers. Vultures for example, African vulture are related to storks and
American vultures are related to birds of prey.
Synapomorphies are the ‘stuff’ that keeps a tree together.
Systematics is across species and evolutionary biology is within species.
Sympleseiomorphy: a character that all species share.
Autapomorphy: a unique character that only one organism/species has
Homoplasy: the multiple occurrence of a character on a tree
4
TA geeft de aminozuren op alle posities weer
Color cells (Display) chemisch dezelfde aminozuren hebben dezelfde kleur
C= conserved sites plekken/sites die gedurende de evolutie niet zijn veranderd
V= variable positions Met V kun je de genen bepalen met de hoogste evolutionary rate.
Bijvoorbeeld V=(52/58) dan is heeft het gen 98% evolutionary rate, dat is hoog.
Pi= parsimony informative potential synapomophies: Gedeelde trait door 1 of meerdere
afstammelingen
S= Singleton = autapomophy unique trait
1
,Term Definition
Taxon A group of organisms. They are defined by
being monophyletic
Monophyletic group A group of organisms with the same ancestor
Synapomorphy shared trait (apomorphy) by two or more
taxa/species. It’s a shared derived character.
Are the stuff that keeps the tree together.
autapomorphy unique changes, only found in one species on
the tree.
Symplesiomorphy / Plesiomorphy a character that all species in the tree share
Cladistics is an approach to biological classification in
which organisms are categorized in groups
("clades") based on hypotheses of most recent
common ancestry
Homoplasy A feature has been lost or gained independently
in separate lineages over the course of
evolution
Homology term used to characterize the similarity of
features that can be parsimoniously explained
by common ancestry
Reversal A loss of derived trait present in ancestor and
the reestablishment of a plesiomorphic trait
Convergence independent evolution of a similar trait in two
or more taxa
Apomorphy a derived trait or novel (nieuwe) eigenschap
Autapomorphy a distinctive derived trait that is unique to a
given taxon or group
Clade group defined by most recent common
ancestor. Same as a monophyletic group.
Paraphyletic group a group with the group’s last common ancestor
and most of its descendants.
Bootstrap Measuring confidence indicates how many
times out of 100 (in your case) the same branch
was observed when repeating the phylogenetic
reconstruction on a re-sampled set of your
data. Used to asses the support for nodes in
your phylogenetic tree.
polyphyletic group voltures for example, convergent evolution.
MRCA = most recent common ancestor
monophyletic if all organisms for example are
birds and share the same ancestor. If a turtle
has the same ancestor then it becomes
paraphyletic.
Anagenesis Evolutie van soorten waarbij een soort in zijn
geheel evolueert
Monisme filosofisch standpunt dat zegt dat er slechts één
van iets is. For example one species definitions
would fit all species. (most people disagree).
Pluralist een systeem dat stelt dat de werkelijkheid
2
, bestaat uit een veelheid aan principes en niet
herleid kan worden tot één enkel principe zoals
bij het monisme.
Cladogram consists statements on which species are sister
species
classification Tree tells where traits changed
Scenario what happened over time
Lecture 1 Conceptual overview and historic account
3
, Comparative Biology: Uses natural variation and disparity to understand the patterns of life at all
levels – from genes to communities – and the critical role of organisms in ecosystems. It
encompasses (omvat) evolutionary biology.
comparing different things within different systems, as long as it is linked to historic approaches.
comparing lineages implies taking history in account.
A trait is variable within species. With phylogenetics you want to look a differences between species
(not within) therefore you talk about characters.
Synapomorphy is a shared derived character. NOT unique (shared)
Clade a group that is defined by its most recent common ancestor. It is the same as a monophyletic
group.
Bootstrapping is measuring confidence. Assessing support for the nodes in your phylogenetic tree.
NOT for the branches.
Picture above shows a phylogenetic tree:
1 = monophyletic
2 = paraphyletic group; a MRCA and not all its descendants
3 = polyphyletic: multiple MRCA’ers. Vultures for example, African vulture are related to storks and
American vultures are related to birds of prey.
Synapomorphies are the ‘stuff’ that keeps a tree together.
Systematics is across species and evolutionary biology is within species.
Sympleseiomorphy: a character that all species share.
Autapomorphy: a unique character that only one organism/species has
Homoplasy: the multiple occurrence of a character on a tree
4
