On Aug 16, 2012, at 2:21 PM, Jeffry Ricker, Ph.D. wrote: > all I can say is this: estimating genetic similarities/differences is > complex, and it will "hurt your brain real bad" once you start trying to > figure it out. :-)
So of course, I've spent the rest of the day hurting my brain. I doubt that many of you want a detailed description of the complexities (and I'm not sure I can give a coherent description anyways); so I decided to provide some references along with their abstracts (in chronological order) so you can scan them if you wish. I chose papers from 2001 to 2005 because these were often cited in later papers, and also because they provide what I was looking for: some details about the various ways of estimating the degree of genetic divergence among related species. 1. Chen, F-C, & Li, W-H (2001). Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics, 68, 444-456. Available online at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1235277/pdf/AJHGv68p444.pdf Abstract To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of humans and chimpanzees, we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan. The average sequence divergence was only 1.24% ± 0.07% for the human-chimpanzee pair, 1.62% 0.08% for the human-gorilla pair, and 1.63% ± 0.08% for the chimpanzee-gorilla pair.... The average sequence divergences between orangutans and humans, chimpanzees, and gorillas were 3.08% ± 0.11%, 3.12% ± 0.11%, and 3.09% ± 0.11%,..... The sequence divergences in other regions between hominoids were estimated ... and Alus showed the highest divergence, followed in order by Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites.... 2. Britten, R. J. (2002). Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proceedings of the National Academy of Sciences, 99 (21), 13633–13635. http://dx.doi.org/10.1086%2F406830 Abstract Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best match-ing regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences... 3. The Chimpanzee Sequencing and Analysis Consortium (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69-87. doi:10.1038/ Abstract Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution. 4. Cheng, Z., Ventura, M., She1, X., Khaitovich, P., Graves, T., Osoegawa, K., et al. (2005). A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature, 437, 88-93. doi:10.1038/nature04000 We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (>94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4–5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post- speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (>100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%). -- --------------------------------------------------------------------------------- Jeffry Ricker, Ph.D. SCC: Professor of Psychology MCCCD: General Studies Faculty Representative PSY 101 Website: http://sccpsy101.wordpress.com/ --------------------------------------------------------------------------------- Scottsdale Community College 9000 E. 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