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Phylogeny:Reconstructing Evolutionary Trees

Chapter 14

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Phylogenetic trees

• 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

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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?

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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

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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

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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

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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

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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)

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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

ACTT

ACCT

ACCT

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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)

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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

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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

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A tree for [dogs, humans, lizards] – 1

lizard human dog

hair

backbone

• The TWO major assumptions that we are making when we build this tree are:

1) hair is homologous in humans and dogs2) hair is a derived trait within tetrapods

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A tree for [dogs, humans, lizards] – 2

lizard human dog

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.

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A tree for [dogs, humans, lizards] – 3

• 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

human lizard dog

hair

backbone

hair

dog lizard human

hair

backbone

hair

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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

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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)

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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

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A tree for [dogs, humans, lizards] – 4

• The presence of hair is apomorphic (derived) because no amphibians have hair

lizard human dog

hair

backbone

Amphibia

amniotic egg

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Cladistic methodology

• Determine character state polarity by reference to outgroup or fossil record

• Construct all possible trees for the taxa in the in group

• Map evolutionary transitions in character states onto each tree

• Find the most parsimonious tree — the one with the fewest evolutionary changes

• Only synapomorphies are informative

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A tree for [dogs, humans, lizards] – 5

• Tree (a) is most parsimonious, so we’ll take that as our best estimate of the true phylogeny of [dog, human, lizard]

• Of course, if we studied different characters, or used a different outgroup, our phylogenetic tree could change

human lizard dog

hair

backbone

hair

dog lizard human

hair

backbone

hairlizard human dog

hair

backbone

(a)

(b)

(c)

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The phylogeny of whales

• Based on skeletal characteristics, several studies have placed whales (Cetaceans) as close relatives of ungulates (hoofed mammals) – Cetaceans are possibly the sister group of the even-toed ungulates (Artiodactyla) – “Artiodactyla hypothesis”

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The Artiodactlya hypothesis for the evolutionary relationships of Cetacea (Fig. 14.4 a)

Odd-toed ungulates (Perissodactyla [horses, rhinos]) are the outgroup

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The whale + hippo hypothesis for the evolutionary relationships of Cetacea (Fig. 14.4 a)

This tree was proposed based on nucleotide sequence of a milk protein gene

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Sequence data for

parsimony analysis

(Fig. 14.6)Blue shaded bars

represent invariant (uninformative

sites, but note error for site 192), and red shaded bars

represent synapomorphies

(note, site 177 does not agree with tree as drawn). Tree is

based on parsimony

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Which phylogeny for whales, if either, is correct?

• According to the whale + hippo hypothesis, whales are artiodactyls – not the sister group to artiodactyls

• Artiodactyls are defined by a particular adaptation of the astragalus, an ankle bone

• Since modern whales don’t have legs, they don’t have ankle bones, so without more data it’s hard to resolve the conflict between these two phylogenetic hypotheses

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Whale phylogeny – more molecular data(Nikaido et al. 1999)

• SINEs and LINEs — Short Interspersed Elements and Long Interspersed Elements

• Transposable elements present in hundreds of thousands of copies in mammalian genomes – transposition is relatively infrequent

• Independent transposition into the same location in two different genomes is unlikely (homoplasy)

• Therefore, if SINEs and LINEs are present at the same location in two taxa, it is most likely homologous.

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Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls

(Nikaido et al. 1999) (Fig. 14.8)

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Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls

(Nikaido et al. 1999) (Fig. 14.8)

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Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls

(Nikaido et al. 1999) (Fig. 14.8)

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Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls

(Nikaido et al. 1999) (Fig. 14.8)

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Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls

(Nikaido et al. 1999) (Fig. 14.8)

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Whale phylogeny – more fossilsIchthyolestes, Pakicetus, Ambulocetus, Rhodocetus: whale-like ear bones; artiodactyl-like astragalus

Whales are an evolutionary line of artiodactyls

The whale + hippo tree is supported by additional data