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Home , Basal (phylogenetics), Monophyly, Outgroup (cladistics)

Evolutionary relationships are defined in terms of descent from a common ancestor

Traits evolving on a tree A A is more closely related to B than to C E B because F 03‐327/727 Lecture 3 C • E, the common ancestor of A and B is more recent than D Time • F, the common ancestor of A and C.

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Traits evolving on a tree A character is a heritable trait or “well defined feature that … can assume one or more mutually exclusive states”*

* Graur and Li, Molecular , 2000 • Introduction to characters, character state matrices, and ancestral state reconstruction 1 Taxon 2 Taxon 3 … • Properties of characters Character 1 Character 2 Character‐states –Ancestral () and derived states Character 3 … – Monophyletic states

• Character States Examples: eye color blue, brown, green mammary glands present, absent number of legs 0, 2, 4, 6, 8, etc.

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1 Evolutionary change on a tree Evolutionary change on a tree

•Given •Given –a tree –a tree –a set of characters that are variable for these taxa, –a set of characters that are variable for these taxa, –a character state matrix for the leaf taxa –a character state matrix for the leaf taxa •infer •infer –the character states of each ancestral node and –the character states of each ancestral node and –the state changes along each branch –the state changes along each branch • such the number of changes required is minimal

Parsimony

* Graur and Li, Molecular Evolution,6 2000 * Graur and Li, Molecular Evolution,7 2000

No tool use Tool use Ancestral character states:

gain: tool use loss: tool use tool use tool use

Pattern Caudal Caudal Forehead Pattern Shape Bulge?

Striped Spot Round No

Barred None Forked No

Gorilla Chimp Chimp Human Tool Tool Barred None Forked No No Yes Yes No Yes Yes use use

Barred Round Yes There may be more than one None

most parsimonious solution. 9 10

2 Ancestral character states : Ancestral character states :

Character: Pattern Caudal Caudal Forehead Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge?

Striped Spot Round No Striped Spot Round No Striped Striped Spot Barred None Forked No Barred None Forked No

Barred None Forked No Barred None Forked No

Barred None Round Yes Barred None Round Yes

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Ancestral character states : Ancestral character states :

Note this history is equally parsimonious:

Character: Pattern Caudal Caudal Forehead Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge?

Striped Spot Round No Striped Spot Round No Barred Striped No spot Spot Barred Forked No Barred Forked No None None Round→Forked Round

Barred None Forked No Barred None Forked No

Barred None Round Yes Barred None Round Yes

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3 Ancestral character states : Questions to ask with character state analysis

•What were the properties of the ancestor?

Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge? •Which states are basal, which derived?

Striped Spot Round No Striped •Did certain character states arise more than once, Spot Barred Forked No independently? None Round→Forked Round No bulge – Parallel losses Barred Forked No None –, parallel gains

Barred None Round Yes

Gain bulge 15 16

Why is “basal” a loaded word? • Ancestral (basal) states: furry, light • Low body mass (~50kg) are early • Fur branching • Doesn’t use tools gain: tool use

gain: furry, light Monotremes are basal in body mass tool use the sense that they diverge loss: fur from the base of the tree Character state transitions Monotremes are not primitive species

Gorilla Chimp Human • Derived states Evolutionary change is occurring on this Fur Yes Yes No • High body mass (~175kg) branch, as well as other branches. • No fur Wt Heavy Light Light Tool • Tool use No Yes Yes Monotremes do not necessarily have the use properties of the ancestor of all 17 18

4 Traits evolving on a tree

Monotremes are not primitive species • Introduction to characters, character state matrices, and ancestral state reconstruction • Properties of characters Monotremes do not necessarily have the properties of the ancestor of all mammals – Ancestral (basal) and derived states  Monophyletic states For example, the platypus has the unique • Cladistics ability to finding things in the dark using electroreception.

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Monophyletic traits Monophyletic characters A two‐state character (trait) is monophyletic with respect to a tree, A trait is monophyletic if the taxa that possess the trait if it can be explained by a single state transition. • form a • constitute all the descendants of a common ancestor

A B C D • The orange trait was gained once • Taxa with the orange trait form a clade • The orange trait is monophyletic • The blue trait is not monophyletic

• The derived (orange) trait is monophyletic • The ancestral (blue) trait is not monophyletic 22 25

5 When is a trait not monophyletic? Which characters are monophyletic?

A two‐state character (trait) is monophyletic with respect to a tree, if it is ancestral & and was subsequently lost. Pattern Caudal Caudal Forehead Pattern Shape Bulge?

Striped Spot Round No • The red trait was lost once

• Taxa lacking the red trait (i.e., blue taxa) Barred None Forked No form a clade • The blue trait (i.e, the absence of red) is Barred None Forked No monophyletic

• The red trait is not monophyletic Barred None Round Yes

• The derived trait (lack of red) is monophyletic • The ancestral red trait is not monophyletic 26 27

Pattern Caudal Caudal Forehead Pattern Caudal Caudal Forehead Pattern Shape Bulge? Pattern Shape Bulge?

Striped Spot Round No Striped Spot Round No

Barred None Forked No Barred None Forked No

Barred None Forked No Barred None Forked No

Barred None Round Yes Barred None Round Yes

Gain bulge • The forehead bulge was gained once • The tail spot was lost once • The forehead bulge is monophyletic • The “spot free” tail is monophyletic

• The “bulge free” profile is not monophyletic • The caudal spot is not monophyletic

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6 When is a trait not monophyletic? Is blood‐squirting a monophyletic trait? No

Independent gains or losses Hypothesis 1: Independent losses

Reversal: A trait is gained and The species possessing the orange later lost (or vice versa). trait are not monophyletic, because Blood‐squirting? No Yes of two independent gains

Loss of orange

Gain of orange

The species possessing the blue trait are not monophyletic, because of two independent losses

30 31 Data: A single character with two states: orange and blue.

Is blood‐squirting a monophyletic trait? No Which of the following geographic Hypothesis 2: Blood‐squirting was gained twice traits are monophyletic? independently and lost once (a reversal).

A Blood‐squirting? No Yes Highland Mexico Southwestern USA Eastern and Central USA Other South American Caribbean B

32 33 Matsuoka et al. (2002)

7 Traits evolving on a tree Is social behavior in sweat monophyletic? • Introduction to characters, character state matrices, and If not, why not? ancestral state reconstruction • Properties of characters – Ancestral (basal) and derived states – Monophyletic states • Cladistics

Source: Brady, S.G., S. Sipes, A Pearson, B. Danforth. 2006. Proceedings of the Royal Society B. doi:10.1098/rspb.2006.3496 36 37

Phylogeny and classification Cladistic approach to evolutionary trees ( 1966) Monophyletic group Includes an ancestor and all of its descendants •Gather data on characters to be used • Establish the character states • Determine which states are ancestral (polarize the A B C D characters) • Select (s) with all ancestral states • Taxonomic groups are based on shared, derived characters •Apply the principle of parsimony to obtain a hierarchical organization of taxa that minimizes state transitions Only monophyletic groups () are recognized in cladistic classification

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8 Terminology not required for this course Cladistic approach to evolutionary trees (but that you may encounter in your reading) (Willi Hennig 1966)

Plesiomorphy Character state found in ancestor of group •Gather data on characters to be used Apomorphy Derived character state in descendants of group • Establish the character states Symplesiomorphy Shared, ancestral character state  Determine which states are ancestral (polarize the Synapomorphy Shared, derived character state characters)  Select outgroup(s) with all ancestral states A B C D  Taxonomic groups are based on shared, derived “Blue” and “square” are plesiomorphic monophyletic characters “Small size” is an apomorphy for A •Apply the principle of parsimony to obtain a hierarchical “Red” is a synapomorphy for A + B organization of taxa that minimizes state transitions “Circle” is a synapomorphy for A + B + C …but a symplesiomorphy for A + B 43 44

In this example, the outgroup has all the ancestral character states A tree based on cladistic principles

Character: Pattern Caudal Caudal Forehead Pattern Shape Bulge?

Striped Spot Round No Striped Spot Barred Forked No None Round→Forked Round No bulge Barred None Forked No • Each clade is defined by a single derived trait

Barred None Round Yes • No parallel gains, no reversals

Gain bulge 45 46

9 A Deuterostome cladistic tree

The traits mapped onto the phylogeny were Problems with the cladistics carefully chosen to be derived states that define these groups.  Determine which states are ancestral (polarize the characters) – Difficult to know whether a trait is ancestral  Select outgroup(s) with all ancestral states –How to find such an outgroup?  Taxonomic groups are based on shared, derived monophyletic characters –Many traits are gained and lost or gained multiple times independently.

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Examples of groups that do not fit the cladistic framework Examples of groups that do not fit the cladistic framework

“” (Sauria) are not “Lizards” (Sauria) are not monophyletic monophyletic

Snakes (Serpentes) are monophyletic within lizards

Squamata (lizards + ) form a clade that is sister to sphenodontida

(Snakes are derived, limbless lizards .)

51 52 Fry et al. (2006) Nature 439: 584-588 Fry et al. (2006) Nature 439: 584-588

10 Examples of groups that do not fit the cladistic framework Common ancestry versus similarity Reptilia are similar to are more closely related to crocodilians than to other lizards because the share extant basal characters (green)

We think of as , lizards, snakes, and crocodiles, but reptilia is not a clade unless it includes Aves Birds Crocs Lizards Turtles scales, skales, shell, External feathers skin skin skin Body temp warm cold cold cold Legs two four four four

Gait upright semi-erect sprawling sprawling

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Common ancestry versus similarity Common ancestry versus similarity

Crocodiles differ from birds Derived characters shared by due to derived characters birds and crocodiles (yellow) (pink) unique to birds support the of birds and crocodiles

Birds Crocs Lizards Turtles Birds Crocs Lizards Turtles scales, skales, shell, External feathers scales, shell, skin skin skin External feathers skin skales, skin skin Body temp warm cold cold cold Body temp warm cold cold cold Legs two four four four Legs two four four four Gait upright semi-erect sprawling sprawling Antorbital fenestra yes yes no no Gait upright semi-erect sprawling sprawling Mandibular fenestra yes yes no no Builds/defends nests yes yes no no 55 56

11 Problems with the cladistics

•Requires traits that have been gained only once.

•It is difficult to know which traits are ancestral and which are derived Species evolution

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A species tree represents the evolution of A species tree represents the evolution of populations populations

Individual

Population at Speciation Time Time generation gt

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12 Biological Species Concept • A species is a group of individuals capable of interbreeding to produce fertile offspring. Close-up view of divergence Many definitions of species. All have problems.

Process of reproductive isolation

Modified from Hennig, W. (1966) Phylogenetic 62 63

One Problem in the Biological Species Concept How Do Species Arise?

The key to speciation is reproductive isolation of populations.

There are extrinsic and intrinsic reproductive isolating mechanisms.

Geographic isolation is the primary extrinsic reproductive isolating For asexually‐reproducing , like these bacteria, what mechanism. constitutes a species?

13 Reproductive Isolation May Occur With or Without Geographic Isolation Harris’ antelope White‐tailed antelope squirrel

Allopatric speciation occurs when geographic isolation creates a reproductive barrier (an extrinsic mechanism).

Sympatric speciation occurs when a reproductive barrier is created by something other than geographic Two species of are postulated to have descended isolation (intrinsic from a common ancestral population that was separated by formation mechanisms). of the Grand Canyon.

Many Intrinsic Reproductive Isolating Many Intrinsic Reproductive Isolating Mechanisms Drive Speciation Mechanisms Drive Speciation

Ecological Isolation: Behavioral isolation: Individuals from separate species do not Individuals from separate species do not mate mate because they do not come into contact because they are not attracted to one another. (e.g., different habitats within an overlapping range).

Temporal isolation: Individuals from separate species do not Courtship rituals are mate because they breed at different times. • critical for within a species • ineffective for attracting members of other species.

14 Many Intrinsic Reproductive Isolating Many Intrinsic Reproductive Isolating Mechanisms Drive Speciation Mechanisms Drive Speciation

Hybrid inviability or infertility: Mechanical isolation: Even if fertilization occurs successfully, the offspring Individuals from separate species do not mate may not survive, or be infertile (e.g., mule). because they are not physically compatible.

Gametic isolation: In this course, Even if they are physically compatible, an • we will consider speciation as a separation of populations embryo will not form if the egg and sperm with reproductive isolation; do not fuse properly. • species concepts and process of speciation are not the focus.

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