Molecular Phylogeny Analysis, Part I.

Molecular Phylogeny Analysis, Part I.
Mehrshid Riahi, Ph.D. Iranian Biological Research Center (IBRC), July 14-15, 2012

Molecular Phylogeny Analysis
Topics Introduction Four steps in Phylogenetic Inference Reading Phylogenetic Tree Tree interpretation in practice Reconstructing Evolutionary Trees Molecular Phylogeny Analysis

Introduction Taxonomy = the naming & grouping of creatures by characteristics Classification = the process of grouping things based on their similarities. * Biologists use it to organize living things into groups for easier study. Molecular Phylogeny Analysis

Man’s Early Systems of Classification:
* Aristole (Greek in 4th centrury B.C.) Three groups (Fly, Swim, Walk) * Linnaeus (1750’s) used a two-part naming system from Latin. (Dog = Canis familiaris) - Binomial Nomenclature = a two-part name 1. Genus = first part of the name (Capitalized) (Groups similar, related organisms) 2. Species = second part of the name. (Lowercase) (“species identifier”) (Groups similar organisms that can mate and produce fertile offspring) Molecular Phylogeny Analysis

Seven (7) Levels of Classification:
** For plants the phylum level is called “Division”. Kingdom – Phylum – Class – Order – Family – Genus – Species – “Kingdom” is the biggest and broadest. Each kingdom contains phyla – each phyla contains classes, etc. The more levels that two organisms share, the more characteristics they have in common. Molecular Phylogeny Analysis

Phylogeny and classification Hierarchy All taxonomic classifications are hierarchical – how does phylogeny differ? Class Order Order Family Family Family Genus Genus Genus Genus Species 1 Species 2 Species 3 Species 4 Species 1 Species 2 Species 1 Species 2 Species 3 Species 4 Species 5 Species 6 Species 7 Species 8 Species 9 Species 1 Species 2 Genus Species 1 Genus Species 1 Species 2 Species 3 Genus Species 1 Species 2 Species 3 Molecular Phylogeny Analysis

How can you identify an organism you find?
Field Guide = book with pictures and descriptions of organisms and characteristics Taxonomic Key = series of paired statements describing characteristics of organisms Molecular Phylogeny Analysis

Modern Phylogenetic Taxonomy
Systematics is the modern method of organizing “creatures” in the context of evolution. Phylogeny = the supposed evolutionary history of an organism Phylogenetics is the science of the pattern of evolution * Evolutionary theory now dominates the classification system, and assumes that similar organisms in a group evolved from a common ancestor. Phylogenetic Trees are family trees supposedly showing evolutionary relationships “thought to exist among groups of organisms”, “shows possible relationships”. Molecular Phylogeny Analysis

Phylogenetic tree of Kingdom Plantae
Molecular Phylogeny Analysis

Linnaeus “Lawn” His ‘lawn’ concept hypothesized that:
Each Genesis “kind” was unrelated to others Each “kind” stayed the same without variation Today’s species = the original “kinds” He was right about unrelated “kinds”. He was wrong about NO variation and species. Molecular Phylogeny Analysis

Evolutionary “Tree” This evolutionary ‘tree’ claims that:
all modern species are descended from a common ancestor Molecular Phylogeny Analysis

Phylogenetics The central problem of phylogenetics: how do we determine the relationships between taxa? in phylogenetic studies, the most convenient way of presenting evolutionary relationships among a group of organisms is the phylogenetic tree Molecular Phylogeny Analysis

Phylogenetic Taxonomy
Systematic taxonomists use several lines of evidence to construct a phylogenetic tree.” Fossil Record – “Billions of dead things buried in rock layers, laid down by water, all over the earth” (Ken Ham) Morphology – similar shape or form (homologous features) among different animals. Embryological Patterns of Development – (Ontogeny) Chromosomes and Macromolecules – Genetic similarities Molecular Phylogeny Analysis

What is molecular phylogeny?
phylon = Greek for “stem” genesis = Greek for “origin” molecular phylogeny = studying relationships among organisms using molecular markers (e.g. DNA or protein sequences) dissimilarities among sequences = genetic divergence caused by mutations during the course of time Molecular Phylogeny Analysis

Four steps in Phylogenetic Inference
Character (data) selection (not too fast, not too slow) 2. Alignment of Data (hypotheses of primary homology) 3. Analysis selection (choose the best model / method(s)) 4. Conduct analysis Molecular Phylogeny Analysis

Work- Flow aim: group of organisms or gene family
Choice of molecular marker(s) and Taxon sampling Extraction/Amplification/Sequencing Alignment Improvement of Choice of evolutionary model User- defined trees And topology testing Phylogenetic analyses Tree(s) Results Molecular Phylogeny Analysis

Types of Markers Marker is a piece of DNA molecule that is associated with a certain trait of a organism Morphological: Characters are selected based on appearance Disadvantage: lack of polymorphism Biochemical: Characters are selected based on biochemical properties Disadvantage: Age dependent, Influenced by environment It covers less than 10% of genome Chromosomal: Characters are selected based on Structural and Numerical Variations (Structural- Deletions, Insertions etc. Numerical- Trisomy, Monosomy, Nullysomy) Disadvantage: low polymorphism Genetic: Molecular Phylogeny Analysis

Molecular Marker Revealing variation at a DNA level Characteristics: Co-dominant expression Nondestructive assay Early onset of phenotypic expression High polymorphism Random distribution throughout the genome Assay can be automated Molecular Phylogeny Analysis

Methodological Advantages
DNA isolated from any tissue eg. Blood, hair etc. DNA isolated at any stage even during foetal life DNA has longer shelf-life readily exchangeable b/w labs Analysis of DNA carried out at early age/ even at the embryonic Stage irrespective of sex Molecular Phylogeny Analysis

Microsatellite Single locus marker RFLP STS Molecular Markers DNA Fingerprinting RAPD Multi-locus marker Molecular Phylogeny Analysis AFLP

Selection of characters
Morphologists typically choose: 1. Characters that are not constant 2. Characters that are not too variable Molecular systematists use the same criteria to select which gene(s) to sequence Genes that are virtually constant don’t have enough information Genes that are hypervariable have too much misinformation Molecular Phylogeny Analysis

Selection of Molecular characters
Character / discrete data: nucleotide or amino acid sequences (can be converted to distances) “fast & slow” genes: there is variation in the rate of change among regions of the genome e.g. rRNA (e.g. 18S) evolves slowly enough to hold information that is over 250 million years old - whereas mtDNA (e.g. COII) evolves much faster and most information over million yrs of age is probably gone (starts to go at my) Molecular Phylogeny Analysis

Higher-level phylogenetics: (families & above) use slower, conserved genes, nuclear genes - evolve slowly due to functional constraints: e.g. some proteins “still work” with many potential amino acids others won’t, e.g. histones are strongly conserved - faster evolving regions, e.g. mtDNA, -information is overwritten - back mutations - yield nonsense phylogenies for deep splits Molecular Phylogeny Analysis

Lower-level phylogenetics: (subfamilies & below) use faster, less-conserved genes, mtDNA because slower genes would be identical across your species - must select genes most appropriate for your study taxa Molecular Phylogeny Analysis

Typical structure of a eukaryotic gene
Flanking region Exon 1 Exon 2 Exon 3 Flanking region 5' 3' Intron I Intron II TATA Initiation Stop Poly (A) box codon codon addition site Transcription AATAA initiation Molecular Phylogeny Analysis

Three types of genes tRNA - transfer RNA (short) rRNA - ribosomal RNA (long, conserved) mRNA - messenger RNA - protein coding (exon) Also introns - non coding sequence sometimes inside a protein coding gene Can be Nuclear Typically slower evolving than mitochondrial better for deeper (older) divergences Can be Mitochondrial Better for shallow (recent) divergences Molecular Phylogeny Analysis

DNA Amplification Molecular Phylogeny Analysis

PHYLOGENETIC DATA ANALYSIS: THE FOUR STEPS
A straightforward phylogenetic analysis consists of four steps: 1. Alignment (both building the data model and extracting a phylogenetic dataset) 2. Determining the substitution model 3. Tree building 4. Tree evaluation Molecular Phylogeny Analysis

Reading Phylogenetic Tree

Assumptions Evolution produces dichotomous branching Evolution is simple – the best explanation assumes least mutations If we assume: 1. Our characters are independent 2. Our character states are homologous (& genes orthologous) 3. Evolution has happened We can infer the evolutionary relationships among organisms Molecular Phylogeny Analysis

Reading phylogenetic trees: A quick review (Adapted from evolution.berkeley.edu) A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon) that are believed to have a common ancestor. Molecular Phylogeny Analysis

Tips, Internal Nodes, Edges
The tips of the phylogenetic tree represent groups of descendent taxa (often species) The internal nodes of the tree represent the common ancestors of those descendents. The tips are the present and the internal nodes are the past. The edge lengths in some trees correspond to time estimates – evolutionary time. Molecular Phylogeny Analysis

Parts of a phylogenetic tree
Internal Nodes or Divergence Points (represent hypothetical ancestors of the taxa) Branch , Lineages : defines the relationship between the taxa in terms of descent and ancestry Topology: the branching patterns of the tree Branch length (scaled trees only): represents the number of changes that have occurred in the branch Root: the common ancestor of all taxa Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains Branch Node Clade Root Molecular Phylogeny Analysis

Sister Groups and a common ancestor
Two descendents that split from the same node are called sister groups. In the trees above, species A & B are sister groups — they are each other's closest relatives; which means that: i) they have a lot of evolutionary history in common and very little evolutionary history that is unique to either one of the two sister species and ii) that they have a common ancestor that is unique to them. Molecular Phylogeny Analysis

Equivalent trees For any speciation event on a phylogeny, the choice of which lineage goes to the right and which one goes to the left is arbitrary. These three phylogenies are therefore equivalent. Molecular Phylogeny Analysis

Phylogenetic trees There are many ways of drawing a tree E D C B A = = Molecular Phylogeny Analysis

Phylogenetic trees There are many ways of drawing a tree Molecular Phylogeny Analysis

Phylogenetic trees There are many ways of drawing a tree = = no meaning Molecular Phylogeny Analysis

Outgroup Many phylogenies also include an outgroup — a taxon outside the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees. Molecular Phylogeny Analysis

Branches and clades Evolutionary trees depict clades. A clade is a group of organisms that are all descendent from a common ancestor; thus a clade includes an ancestor and all descendents of that ancestor. You can think of a clade as a branch on the tree of life. Some examples of clades and non-clades in a phylogenetic tree are shown here Molecular Phylogeny Analysis

More on clades. Nested clades
Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few. Some examples of clades at different levels are marked on the phylogenies above. Notice how clades can be nested within larger clades. Molecular Phylogeny Analysis

Types of trees: unrooted vs rooted
A rooted phylogenetic tree is a tree with a unique root node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves (aka tips) of the tree. A rooted tree is a binary tree. Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about common ancestry. An unrooted tree has a node with three edges; the rest of the nodes have up to two edges. Molecular Phylogeny Analysis

Rooting the Tree In an unrooted tree the direction of evolution is unknown The root is the hypothesized ancestor of the sequences in the tree The root can either be placed on a branch or at a node You should start by viewing an unrooted tree Molecular Phylogeny Analysis

Positioning Roots in Unrooted Trees
We can estimate the position of the root by introducing an outgroup: Proposed root Falcon Aardvark Bison Chimp Dog Elephant Molecular Phylogeny Analysis

Rooting Using an Outgroup
1. The outgroup should be a sequence (or set of sequences) known to be less closely related to the rest of the sequences than they are to each other 2. It should ideally be as closely related as possible to the rest of the sequences while still satisfying condition 1 The root must be somewhere between the outgroup and the rest (either on the node or in a branch) Molecular Phylogeny Analysis

Dendrogram, cladogram, phylogram
Dendrogram is the ‘generic’ term applied to any type of diagrammatic representation of phylogenetic trees. All four trees depicted here are dendrograms. Cladogram (to some biologists) is a tree in which branch lengths DO NOT represent evolutionary time; clades just represent a hypothesis about actual evolutionary history TREE1 and TREE2 are cladograms and TREE1 = TREE2 Phylogram (to some biologists) is a tree in which branch lengths DO represent evolutionary time; clades represent true evolutionary history (amount of character change) TREE3 and TREE4 are phylograms and TREE3 ≠ TREE4 Molecular Phylogeny Analysis

Phylogenetic trees Molecular Phylogeny Analysis

Phylogenetic Trees and classification
Phylogenetic trees classify organisms into clades. By contrast, the Linnaean system of classification assigns every organism a kingdom, phylum, class, order, family, genus, and species. The phylogenetic tree depicted here identifies four clades To build a phylogenetic tree biologists collect data about the characters of each organism they are interested in. Characters are heritable traits that can be compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits. Some molecular biologists (like C. Woese) build phylogenetic trees from genetic sequences alone. Molecular Phylogeny Analysis

Phylogenetic trees Bifurcation versus Multifurcation (e.g. Trifurcation) Multifurcation (also called polytomy): a node in a tree that connects more than three branches. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation) = / Bifurcation Trifurcation Molecular Phylogeny Analysis

Completely unresolved bifurcating phylogeny
The goal of phylogeny inference is to resolve the branching orders of lineages in evolutionary trees: Completely unresolved or "star" phylogeny Partially resolved phylogeny Fully resolved, bifurcating phylogeny A B C E D Polytomy or multifurcation A bifurcation Molecular Phylogeny Analysis

Phylogenetic trees Trees can be scaled or unscaled (with or without branch lengths) Molecular Phylogeny Analysis

Tree interpretation in practice

1) By reference to the tree above, which of the following is an accurate statement of relationships? a) A green alga is more closely related to a red alga than to a moss b) A green alga is more closely related to a moss than to a red alga c) A green alga is equally related to a red alga and a moss d) A green alga is related to a red alga, but is not related to a moss Molecular Phylogeny Analysis

2) By reference to the tree above, which of the following is an accurate statement of relationships? a) A crocodile is more closely related to a lizard than to a bird b) A crocodile is more closely related to a bird than to a lizard c) A crocodile is equally related to a lizard and a bird d) A crocodile is related to a lizard, but is not related to a bird Molecular Phylogeny Analysis

3) By reference to the tree above, which of the following is an accurate statement of relationships? a) A seal is more closely related to a horse than to a whale b) A seal is more closely related to a whale than to a horse c) A seal is equally related to a horse and a whale d) A seal is related to a whale, but is not related to a horse Molecular Phylogeny Analysis

4) Which of the five marks in the tree above corresponds to the most recent common ancestor of a mushroom and a sponge? Molecular Phylogeny Analysis

5) If you were to add a trout to the phylogeny shown above, where would its lineage attach to the rest of the tree? Molecular Phylogeny Analysis

6) Which of trees below is false given the larger phylogeny above? Molecular Phylogeny Analysis

7) Which of the four trees above depicts a different pattern of relationships than the others? Molecular Phylogeny Analysis

8) Which of the four trees above depicts
a different pattern of relationships than the others? Molecular Phylogeny Analysis

9) In the above tree, assume that the ancestor had a long tail, ear flaps, external testes, and fixed claws. Based on the tree and assuming that all evolutionary changes in these traits are shown, what traits does a sea lion have? a) long tail, ear flaps, external testes, and fixed claws b) short tail, no ear flaps, external testes, and fixed claws c) short tail, no ear flaps, abdominal testes, and fixed claws d) short tail, ear flaps, abdominal testes, and fixed claws e) long tail, ear flaps, abdominal testes, and retractable claws Molecular Phylogeny Analysis

10) In the above tree, assume that the ancestor was a herb (not a tree) without leaves or seeds. Based on the tree and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit and lacks true leaves? a) Lepidodendron b) Clubmoss c) Oak d) Psilotum e) Fern Molecular Phylogeny Analysis

Tree structure A tree can be also presented in a text format: (A(B(C,D))) The graphic structure can be difficult to interpret (2-dimentional) Molecular Phylogeny Analysis

Visualising trees Treeview You can change the graphic presentation of a tree (cladogram, rectangular cladogram, radial tree, phylogram), but not change the structure of a tree Molecular Phylogeny Analysis

Reconstructing Evolutionary Trees

Recall The phylogeny of a group of taxa (species, etc.) is its evolutionary history A phylogenetic tree is a graphical summary of this history — indicating the sequence in which lineages appeared and how the lineages are related to one another Because we do not have direct knowledge of evolutionary history, every phylogenetic tree is an hypothesis about relationships Of course, some hypotheses are well supported by data, others are not Molecular Phylogeny Analysis

Questions How do we make phylogenetic trees? Cladistic methodology Similarity (phenetics) What kinds of data do we use? Morphology Physiology Behavior Molecules How do we decide among competing alternative trees? Molecular Phylogeny Analysis

Similarity The basic idea of phylogenetic reconstruction is simple: Taxa that are closely related (descended from a relatively recent common ancestor) should be more similar to each other than taxa that are more distantly related — so, all we need to do is build trees that put similar taxa on nearby branches — this is the phenetic approach to tree building Consider, as a trivial example, leopards, lions, wolves and coyotes: all are mammals, all are carnivores, but no one would have any difficulty recognizing the basic similarity between leopards and lions, on the one hand, and between wolves and coyotes, on the other, and producing this tree; which, it would probably be universally agreed, reflects the true relationships of these 4 taxa leopard lion wolf coyote Molecular Phylogeny Analysis

Causes of similarity Things are seldom as simple as in the preceding example We need to consider the concept of biological similarity, and the way in which similarity conveys phylogenetic information, in greater depth: Homology Homoplasy Molecular Phylogeny Analysis

Homology A character is similar (or present) in two taxa because their common ancestor had that character: In this diagram, wings are homologous characters in hawks and doves because both inherited wings from their common winged ancestor cat hawk dove wings Molecular Phylogeny Analysis

Homoplasy A character is similar (or present) in two taxa because of independent evolutionary origin (i.e., the similarity does not derive from common ancestry): In this diagram, wings are a homoplasy in hawks and bats because their common ancestor was an un-winged tetrapod reptile. Bird wings and bat wings evolved independently. hawk bat cat wings Molecular Phylogeny Analysis

Types of homoplasy Convergence Independent evolution of similar traits in distantly related taxa — streamlined shape, dorsal fins, etc. in sharks and dolphins Parallelism Independent evolution of similar traits in closely related taxa — evolution of blindness in different cave populations of the same fish species Reversal A character in one taxon reverts to an earlier state (not present in its immediate ancestor) Molecular Phylogeny Analysis

Reversal A character is similar (or present) in two taxa because a reversal to an earlier state occurred in the lineage leading to one of the taxa: In this diagram, hawks and cats share the ancestral nucleotide sequence ACCT, but this is due to a reversal on the lineage leading to cats hawk bat cat ACCT ACTT ACCT Molecular Phylogeny Analysis

Cladograms Within a tree a clade is defined as a group that includes an ancestral species and all of its descendants. Cladistics is the science of how species may be grouped into clades. Molecular Phylogeny Analysis

Cladistics By definition, homology indicates evolutionary relationship — when we see a shared homologous character in two species, we know that they share a common ancestor Build phylogenetic trees by analyzing shared homologous characters Of course, we still have the problem of deciding which shared similarities are homologies and which are homoplasies (to which we shall return) Molecular Phylogeny Analysis

Two kinds of homology – 1 Shared ancestral homology — a trait found in all members of a group for which we are making a phylogenetic tree (and which was present in their common ancestor) — symplesiomorphy For example: a backbone is a shared ancestral homology for dogs, humans, and lizards Symplesiomorphies DO NOT provide phylogenetic information about relationships within the group being studied Molecular Phylogeny Analysis

Two kinds of homology – 2 Shared derived homology — a trait found in some members of a group for which we are making a phylogenetic tree (and which was NOT present in the common ancestor of the entire group) — synapomorphy For example: hair is (potentially) a shared derived homology in the group [dogs, humans, lizards] Synapomorphies DO provide phylogenetic information about relationships within the group being studied In this particular case, if hair is a synapomorphy in dogs and humans, then dogs and humans share a common ancestor that is not shared with lizards, and the common dog-human ancestor must have lived more recently than the common ancestor of all three taxa Molecular Phylogeny Analysis

A tree for [dogs, humans, lizards] – 1
hair backbone The TWO major assumptions that we are making when we build this tree are: hair is homologous in humans and dogs hair is a derived trait within tetrapods Molecular Phylogeny Analysis

hair backbone In the absence of other information, the assumption of homology of hair in humans and dogs is justified by parsimony (fewest number of evolutionary steps is most likely = simplest explanation) Also we can check to see that hair is formed in the same way by the same kinds of cells, etc. Molecular Phylogeny Analysis

hair backbone dog lizard human hair backbone These trees (in which hair is considered a homoplasy in dogs and humans) are less parsimonious than the one on the previous slide, because they require two independent evolutionary origins of hair Molecular Phylogeny Analysis

Character Polarity What’s the basis for our second major assumption – that hair is a derived trait within this group (and that absence of hair is primitive)? Fossil record Outgroup analysis Molecular Phylogeny Analysis

Outgroups – 1 An outgroup is a taxon that is related to, but not part of the set of taxa for which we are constructing the tree (the “in group”) Selection of an outgroup requires that we already have a phylogenetic hypothesis A character state that is present in both the outgroup and the in group is taken to be primitive by the principle of parsimony (present in the common ancestor of both the outgroup and the in group and, therefore, homologous) Molecular Phylogeny Analysis

Outgroups – 2 In the present example, [dog, human, lizard] are all amniote tetrapods. The anamniote tetrapods (amphibia) make a reasonable outgroup for this problem No amphibia have hair, therefore absence of hair [amphibia, lizards] is primitive (plesiomorphic) and presence of hair [dogs, humans] is derived (apomorphic) So, presence of hair is a shared derived character (synapomorphy), and dogs and humans are more closely related to each other than either is to lizards Molecular Phylogeny Analysis

hair backbone Amphibia amniotic egg The presence of hair is apomorphic (derived) because no amphibians have hair Molecular Phylogeny Analysis

Theories of taxonomy There are two current major theories of taxonomy: Traditional Evolutionary Taxonomy Phylogenetic Systematics (Cladistics) Both based on evolutionary principles, but differ in the application of those principles to formulate taxonomic groups. Molecular Phylogeny Analysis

Theories of taxonomy There are three different ways a taxon may be related to a phylogentic tree. The taxon may be a monophyletic, paraphyletic or polyphyletic grouping Molecular Phylogeny Analysis

Monophyletic Group A monophyletic taxon includes the most recent common ancestor of a group and all of its descendents. Molecular Phylogeny Analysis

Paraphyletic group A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all of its descendents. Molecular Phylogeny Analysis

Polyphyletic grouping
A taxon is polyphyletic if it does not contain the most recent common ancestor of all members of the group. This situation requires the group to have had independent evolutionary origin of some diagnostic feature. E.g. If you grouped birds and bats into a group you called “WingedThings” it would be a polyphyletic group because birds and bats evolved wings separately. Molecular Phylogeny Analysis

Theories of taxonomy Both traditional evolutionary taxonomy and cladistics reject polyphyletic groups. They both accept monophyletic groups, but differ in their treatment of paraphyletic groupings. Molecular Phylogeny Analysis

Phylogeny and classification Monophyly Each of the colored lineages in this echinoderm phylogeny is a good monophyletic group Asteroidea Ophiuroidea Echinoidea Holothuroidea Crinoidea Each group shares a common ancestor that is not shared by any members of another group Molecular Phylogeny Analysis

Paraphyletic groups Foxes Paraphyly “Foxes” are paraphyletic with respect to dogs, wolves, jackals, coyotes, etc. This is a trivial example because “fox” and “dog” are not formal taxonomic units, but it does show that a dog or a wolf is just a derived fox in the phylogenetic sense Molecular Phylogeny Analysis Lindblad-Toh et al. (2005) Nature 438:

Paraphyletic groups Fry et al. (2006) Nature 439: Snakes are just derived, limbless lizards Lizards Paraphyly “Lizards” (Sauria) are paraphyletic with respect to snakes (Serpentes) Serpentes is a monophyletic clade within lizards Squamata (lizards + snakes) is a monophyletic clade sister to sphenodontida Molecular Phylogeny Analysis

Traditional Evolutionary Taxonomy
TET uses two principles for designating taxa. Common descent Amount of adaptive evolutionary change The second criterion leads to the idea that groups may be designated as higher level taxa because they represent a distinct “adaptive zone” (Simpson) because they have undergone adaptive change that fits them to a unique role (e.g. penguins, humans). Molecular Phylogeny Analysis

Molecular Phylogeny Analysis, Part I.

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