the gradualist point of view
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Transcript of the gradualist point of view
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the gradualist point of viewEvolution occurs within populations where the fittest organisms have a selective advantage. Over time the advantages genes become fixed in a population and the population gradually changes.
See Wikipedia on the modern synthesis http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis
Processes that MIGHT go beyond inheritance with variation and selection? •Horizontal gene transfer and recombination •Polyploidization (botany, vertebrate evolution) see here or here•Fusion and cooperation of organisms (Kefir, lichen, also the eukaryotic cell) •Targeted mutations (?), genetic memory (?) (see Foster's and Hall's reviews on directed/adaptive mutations; see here for a counterpoint) • Random genetic drift • Mutationism •Gratuitous complexity •Selfish genes (who/what is the subject of evolution??) •Evolutionary capacitors•Hopeless monsters (in analogy to Goldschmidt’s hopeful monsters)
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Other ways to detect positive selection
Selective sweeps -> fewer alleles present in population (see contributions from archaic Humans for example)
Repeated episodes of positive selection -> high dN
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Variant arose about 5800 years ago
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The age of haplogroup D was found to be ~37,000 years
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Adam and Eve never met Albrecht Dürer, The Fall of Man, 1504
MitochondrialEve
Y chromosomeAdam
Lived approximately
40,000 years ago
Lived 166,000-249,000
years ago
Thomson, R. et al. (2000) Proc Natl Acad Sci U S A 97, 7360-5
Underhill, P.A. et al. (2000) Nat Genet 26, 358-61
Mendez et al. (2013) American Journal of Human Genetics 92 (3): 454.
Cann, R.L. et al. (1987) Nature 325, 31-6
Vigilant, L. et al. (1991) Science 253, 1503-7
The same is true for ancestral rRNAs, EF, ATPases!
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From: http://www.nytimes.com/2012/01/31/science/gains-in-dna-are-speeding-research-into-human-origins.html?_r=1
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The multiregional hypothesis
From http://en.wikipedia.org/wiki/Multiregional_Evolution
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Ancient migrations.The proportions of Denisovan DNA in modern human populations are shown as red in pie charts, relative to New Guinea and Australian Aborigines (3). Wallace's Line (8) is formed by the powerful Indonesian flow-through current (blue arrows) and marks the limit of the Sunda shelf and Eurasian placental mammals.
Did the Denisovans Cross Wallace's Line?Science 18 October 2013: vol. 342 no. 6156 321-323
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From: http://en.wikipedia.org/wiki/Archaic_human_admixture_with_modern_Homo_sapiens
Archaic human admixture with modern Homo sapiens
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For more discussion on archaic and early humans see: http://en.wikipedia.org/wiki/Denisova_hominin
http://www.nytimes.com/2012/01/31/science/gains-in-dna-are-speeding-research-into-human-origins.html
http://www.sciencedirect.com/science/article/pii/S0002929711003958 http://www.abc.net.au/science/articles/2012/08/31/3580500.htm
http://www.sciencemag.org/content/334/6052/94.full http://www.sciencemag.org/content/334/6052/94/F2.expansion.html
http://haplogroup-a.com/Ancient-Root-AJHG2013.pdf
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Finding transferred genes
Screening in the wet-lab and in the computer
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Finding transferred genes
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Taxplot at NCBI
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Taxplot at NCBI
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Other approaches to find transferred genes
• Gene presence absence data for closely related genomes (for additional genes)
• Phylogenetic conflict (for homologous replacement (e.g. quartet decompositon spectra)
• Composition based analyses (for very recent transfers).