Post on 17-Jan-2016
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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