CHARACTERS USED IN RECONSTRUCTING PHYLOGENETIC TREES

1. Morphological

“ Tiktaalik is the sister group of Acanthostega + Ichthyostega in one of the two most parsimonious trees, and clades with Elpistostege as sister to the tetrapods in the other. “Consistency index excluding uninformative characters = 0.7966”.”

“Consensus tree from a phylogenetic analysis of 114 characters and nine taxa”

Daeschler et al. Nature 440:757, 2006

Discovery of a Devonian fossil fish that is intermediate between fish with fins and tetrapods with limbs

2. Protein analysis

Allozymes - variant enzyme forms encoded by different alleles at a single locus

Electrophoretic profile of allozymic forms of six esterases from six individuals in Drosophila virilis population

Forms 2 & 4 show slow (S) and fast (F) migration

Avers Fig. 6.16

Mitochondrial DNA from 18 different eels cleaved with EcoRI

M

M = size marker

Avise,JC Fig. 3.8

(i) RFLPs (restriction fragment length polymorphisms)

Restriction maps of primate nuclear rRNA spacer region

(iii) AFLP (amplified-fragment length polymorphisms)PCR based methods

3. DNA analysis

How to choose which type of DNA sequence to use?

If comparing very divergent organisms:

- need ones “universally” present and highly conserved

otherwise possible errors in alignment, multiple sub…

eg. ribosomal RNAs

translation elongation factors, ribosomal proteins

glycolytic pathway enzymes

(ii) DNA sequencing – align sequences and score nt substitutions

Nature of nt substitutions in structural RNA genes

E.coli 16S rRNA

Brown Fig.11.11

- different functional constraints than for protein genes

RNA folding – 2o and 3o structure,interactions with proteins in ribosome…

- conservation of helical structureimportant (but not nt sequence in some cases)

C - GA - UU - AG - C

C - GG - CU - AG - C

compensatory base changes

If comparing very closely related organisms:

need rapidly evolving sequences

nuclear pseudogenes

mitochondrial genes in animals

Red – protein & rRNA genes

Blue – tRNA genes

Lewin Fig. 25.5

Human mitochondrial genome

Advantages of using animal mitochondrial sequences

High rate nt substitution

Maternally inherited, no recombination

Easy to isolate & assay - many identical copies per cell

Different regions evolve at different rates

ribosomal RNA

respiratory genes

replication origin (D-loop)

Biodiversity survey – mt DNA (COI) barcodes (P. Hebert)

Small, well-characterized genome, no repetitive DNA

Lewin Fig. 25.5

relatively slow

relatively fast

Fig. 5.37

Dusky seaside sparrow

1966 - A.m. nigrescens subspecies on Atlantic coast of Floridaendangered species

1980 - only 6 individuals (males) left

- artificial breeding program- chose A.m. peninsulae (female) on Gulf coast based onmorphological & behavioral characters

1989 – mitochondrial DNA restriction analysis for 39 individuals,11 subspecies

- Atlantic coast ones more similar to each other than to any GulfCoast subspecies- estimated divergence time consistent with change in sea levelcreating Florida peninsula ~ 0.5 Mya – reproductive barrier

1987 – last purebred sparrow died

Fig. 5.38

Moore Fig. 37.8

PHYLOGENETIC RELATIONSHIPS OF HUMANS AND APES

1950’s - morphological data

Human – gorilla split believed to be ~ 20 Mya

… and chimp – gorilla split much later

Human – gorilla – chimp trichotomy

1960’s – 1980’s

Protein & early molecular data

Freeman Fig. 14.2

Human-gorilla divergence time ~ 5 Mya

Freeman Fig. 14.4

1990’s – molecular data

Mitochondrial DNA sequences

Y chromosome gene

autosomal pseudogenes& nuclear non-coding

Human – chimp split morerecent than gorilla split

“statistically, this tree is about 10 23

times as likely as the alternative tree…”

Mitochondrial COII gene

- haplotypes cluster together by species

Branch lengths = minimum number of inferred changes

Maximum parsimony tree

Locke, Nature 469:529, 2011

Freeman Fig. 14.6

Scally, Nature 483:169, 2012

Langergraber PNAS 109:15706, 2012

Divergence times based on generation times of wild chimps & gorillas...

(ie. independent of fossil record or molecular data)

“Paler shading indicates the range of split times inferred in this study”

- compared average generation times among H, C, & G and applied “recent estimates of the human mutation rate per generation to derive estimates of split times of great apes and humans that are independent of fossil calibration.”

Kij = # sub per 100 sites between species i and j

** difference significant at 1% level

Are sequences from different primates evolving at same rate?

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