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Unformatted text preview: ECOL 2007 Lecture 18
Phylogenetics 2: Phylogenies using different loci • In previous lectures we have considered how phylogenetic trees are constructed from sequence data • But we also know that:
– genes evolve at different rates – regions within genes may evolve at different rates – heritability of genes varies • We can therefore deduce that phylogenies constructed with sequence data from different loci will not necessarily be the same • Different Loci
– structural/functional genes, introns – differentially variable regions within genes – organelle genomes • More robust phylogenetic trees from multiple loci datasets Different loci evolve at different rates
• The rRNA gene complex is the most widely studied • Different genes/introns evolve at different rates
– Choice depends on resolution required – Ie: degree of relatedness betweeen samples • Also variable rates within genes
– Eg: the 5’ end of the 16S rRNA gene for bacteria is generally regarded as more informative than mid-gene regions Relatively low variability: broadest resolution Nb: In bacteria the SSU encodes a 16S rRNA Highest variability Genes encoding essential functions are highly conserved
• Structural genes such as the rRNA gene complex are highly conserved and so most useful in phylogenetic studies
– As are others such as RNA polymerase subunit B (rpoB) • Functional genes tend to be more variable but can be useful in studies related to physiological traits:
– Dsr – sulfide reductase – nifH – nitrogenase Organelle genomes evolve independantly
• mtDNA generally evolves much more rapidly that rDNA
– thought to be a consequence of less efficient repair mechanisms relative to nuclear DNA – useful for comparisons between closely related species or intraspecies populations • Haploid pattern of inheritance
– passed only by females to offspring – variability more vulnerable to loss than nuclear DNA by population bottlenecks, founder effects or selection – used to estimate divergence times for populations within species Can we combine sequence data from multiple loci?
• This is possible BUT…..
– Most sequence data exists for a single locus within a given group of taxa – Where multiple loci sequences are available these rarely overlap with existing data Research publications for fungi vs number of loci sequenced Number of published trees has increased, but the proportion based on one locus has remained fairly constant, with few multi-locus studies even recently For other organisms the situation is even worse! Single-locus trees can be a tool for taxonomic ‘splitters’! Multi-locus analysis gives better taxonomic resolution Also highlights study bias towards certain groups! Lutzoni et al, American Journal of Botany 91: 1446-1480 (2004) Multi-locus analysis gives better phylogeographic resolution The thermophilic archaeaon Sulfolobus is cosmopolitan yet habitats are highly isolated Sequence analysis of 9 chromosomal loci revealed distinct phylogeographic lineages
Whittaker et al, Science 301: 976-978 (2003) • Multi-locus phylogenetic analysis can identify errors in Genbank sequences or source material (eg: culture collections)
– Conflicts among loci indicate that at least one of the single-locus phylogenies must be wrong
• For a single loci this may suggest lab error • For all loci indicates misidentified taxa ...
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- Spring '10