Monday, May 30, 2011

Another look at Bias and Prayer

I ran across this story today which I hadn't heard about before so I did some investigation and thought I would share my findings because it shows how Confirmation Bias leads to false conclusions.

Back in November 2007 Georgia (the whole southeast) had been experiencing a severe drought for some 18 months. So Georgia Gov. Sonny Perdue announced he would hold a public prayer to ask god for relief from the drought because, as we all know, "The only solution is rain, and the only place we get that is from a higher power," said Perdue spokesman Bert Brantley.

So the first question here (which apparently didn't occur to many in the media), is how many people, how many farmers prayed during that year for rain already over that year?  Keep in mind that those thousands upon thousands of prayers went unanswered.

Now read the very last line of this report about the upcoming event:
Now in Georgia, there is a little rain predicted, but not enough to end a drought.
"There is a little rain predicted," well now, isn't that convenient. Let's schedule a public prayer right around the time SCIENCE is already predicting precipitation. And if it so much as sprinkles on that day? Thank GOD we prayed.  I'm disgusted by this kind of duplicity honestly.  They wait 18 months to make a big deal out of a prayer meeting when meteorologists just happen to be predicting precipitation.  I'm also a little ashamed that people fall prey to such simplistic manipulation.

And then people (see this YouTube video) take ONE instance out of what could be tens of thousands and count that as a rousing success DESPITE the fact that the drought continued to worsen and lingered on through 2008, it got much WORSE in many locations after Nov 2007 and it was relieved only in late 2008 and 2009 for some regions.  This is a perfect example of Confirmation Bias

http://web.me.com/atlwx/wxhistory/files/20070501-drought.html
Drought conditions persisted and actually continued to worsen during December. This was especially true during the first half of the month when unseasonably warm, dry weather prevailed across the region
Lake Lanier in northeast Georgia and the main water supply for the Atlanta metropolitan area, dropped to its lowest level in history on December 28, 2007
Tell ya what, next time there is a drought, wait 6 years before praying and see if it corrects itself without the prayer and only then pray when meteorologists are predicting the weather to be the absolute worst, not when they are finally predicting some rain.

A detailed analysis of the 2006-2008 Drought: http://www.gawrc.org/2011paper_pdfs/7.3.4Kim.pdf

See also: http://ga.water.usgs.gov/

Monday, May 16, 2011

The Chicken-Egg problem, an evolutionary parable

Caveat: this is only slightly edited text, written very much off-the-cuff.  Please help me correct any errors you spot.

Overview


I made a twitter post today which read: "Evolutionary theory does NOT indicate a human male & female pair that is a bottleneck, common ancestor: True or False?"

That was the best I could do in 140 characters but I think I captured the essence of the question. The main purpose of this was to challenge people to think about how such evolutionary processes might work.

To explain in a bit more detail - the question is, for speciation to occur does a M/F pair of the NEW species need to pre-exist or not. If we cannot breach this barrier then evolution would be dead in the water.

I also have found this is an extremely common misconception amongst people who do not understand evolution that there is this requirement for a new species to be 'magically' created in pairs. They don't seem to understand that speciation happens in a population of viable procreation partners.

And while it is possible, in theory, that two individuals could just happen to have the SAME genetic mutation at the same time AND find each other it is simply not necessary for evolutionary speciation to occur (and co-mutation seems unlikely to be the norm).

So, the correct answer is True - evolutionary theory does NOT predict or require that there would be M/F pairs created for speciation to occur. Speciation is really the product of culling the population rather than procreation. That is, the isolated species is created when other 'bridge' members of the population die, rather than when it is born.

Thought Experiment:

If you isolated 2 groups of 100 rabbits (call them A and B) each then wait 200My with each group exposed to different selectivity criteria (e.g., group A in harsher, colder climates and group B in warmer) what would we expect to find? Well, the A' rabbits would all be fairly similar to each other but very different from the A rabbits - they might have smaller ears, warmer fur, cold-adapted respiratory systems, etc. Likewise, the B' rabbits would be similar to each other but again different from the original group B. They might have lost their dense fur for example.

And let's say that you saved some embryo's from the original population and raise them into 'normal' rabbits - these original rabbits might be completely unable to bred with either A' or B' (each generation spent in isolation would slightly increase this chance).

Each group will likely have speciated over that time but at no point would there be a unique M/F PAIR in the diverged lineages. They would ALL be related to each other with finer gradations of genetic variations.

Detailed Example

This next one is very technical but will demonstrate, I hope very clearly, what happens in a population leading up to speciation and why a M/F pair isn't required for the process.

First, please note that this account is FICTIONAL, although it is based on science I'm essentially paraphrasing. For example, there really IS an OCX family of genes which make Ovocalyxin proteins which are involved in egg-shell production (search for OCX-32, OCX-36, OCX-21 if you want to learn more). But I'm calling OCX1 my baseline and just numbering the successive mutations, I'm not using the SAME numbering scientists use.

We will look at three gene families (groups of genes) in a population of Gray junglefowl (the probable ancestor of the domesticated chicken) and we will crack the old chicken and egg problem (please hold your groans until the end).

Gene #1 will be OCX in the Ovocalyxin family of genes and is related to egg-shell production
Gene #2 will be SLIT, an axon guidance molecule in embryonic development (again, a real gene designation - but fictional mutations for purpose of demonstration)
Gene #3 will be MHC major histocompatibility complex - which controls the antigens affecting immune response; there are many possible sources of evolved sexual incompatibility; I'm using an antigen example

In each case, there exists a fairly large, and viable set of variants for these genes. We will number the variants start with 1 as the baseline for our population of Gray junglefowls as {1,1,1} which means OCX1, SLIT1, MHC1 while {1,1,2} has mutation variant MHC2.

In our make-believe world, the Gray junglefowls have softer-shelled eggs which are easily poached (no groans!) by snakes and other small animals, the eggs take 28 days to mature and hatch, and the animals have compatible antigen systems.

Also, imagine in our population there are 1000's of fowl although we will focus on just a few individuals. I will call each fowl F and a number (e.g., F1, F2, F3).

Our story begins when F1{1,1,1} mates with F2{1,1,1} and has offspring F3{1,2,1}. This lucky fowl develops and hatches in only 26 days, giving less time for predation to occur resulting in a slightly increased chance of survival.

F3{1,2,1} grows up and mates with F4{1,1,1} giving several Fn{1,1,1} offspring and two fowl F5{1,2,1} and F6{1,2,1}. The Fn's are eaten before they hatch but F5 & F6 survive due to the shorter 26 day incubation period thanks to the mutation to their SLIT gene complex. Hopefully it is easy to see how this trait could easily spread through the population. Year after Year, SLIGHTLY more of the {1,2,1} variants survive until finally the distribution is 95%{1,2,1} and only 5%{1,1,1}.

Is this minor mutation a new species? Well no, they can all freely interbred and while we think of Gray1 as having a 28 day incubation period and the 26 day incubation period of Gray2 alone doesn't seem like enough to call it a new species. Thanks only to the power of genetic sequencing we can SEE the exact change that occurred between the two groups in the population.

Possibly 100's of more years go by -- other genes mutate, maybe they get bigger or smaller feathers or their colors shift slightly - but still nothing we consider 'major' and still all sexually compatible with each other.

Finally, a single F7{2,2,1} is born and happens to survive. When F7 lays an egg is has a tougher shell than eggs from other Gray's! This harder shell thwarts several of the predators of the softer shells. The {2,2,1} mutation spreads quickly through the population as not only do these fowl survive predation it forces the predators to eat more of the {1,2,1} and {1,1,1} fowl.

The population quickly (in geological time) changes to 95%{2,2,1}, 3%{2,1,1}, 1.5%{1,2,1}, 0.5%{1,1,1} - almost all of the SLIT1 variants are now gone having been eaten before hatching either by taking too long or being easier targets.

There are likely MANY genetic variations which prove unviable, these fowl die before they are born or are unable to reproduce. Time marches forward. It is here where we need to understand that fowls are Diploid genetically (they have two copies) and thus can express dominate or recessive traits. I will mark genes which are different on the chromosome with a prime (e.g., 1'2 means it has both 1 and 2 variants).

Our next shift involves the MHC complex - this is the true beginning of our speciation event. F8{2,2,2'} is born, this minor shift in the MHC complex gives this variant a slightly lower chance of successful sexual reproduction (but possibly an increased resistance to a common disease).

F8{2,2,1'2} can then mate with F7{2,2,1}s giving both types of offspring (those like F8 and those like F7). At first, there would be no mating issue as MOST mates would be compatible, so the variant is not detrimental at this stage and it is over the long haul where genetic variations compete with one another. Even seemingly detrimental variants which do not prohibit reproduction can flourish for a time.

Eventually our fowl friend will meet another like itself and one F8{2,2,1'2} will mate with another giving three possible offspring:

F7{2,2,1} 25%
F8{2,2,1'2} 50% (1'2 and 2'1 are the same)
F9{2,2,2} 25%

And here is where our new variant encounters a slight challenge. F9's cannot mate successfully with F7 or lower (their MHC complexes are too incompatible due to the now dominate MHC2) and only half the time with F8's.

But we can see from the above that F8's are favored to become the most frequent so our fine feathered fowl has a decent chance of making it. And, unlike the mutation event itself, we do NOT have only one shot here. There can fairly quickly be 100's or thousands of F9's trying to mate and their chances are better than it might seem (50% chance with 50% of the population and 100% chance with 25%). And if there is some ancillary benefit to {2,2,2} like disease resistance that could kick it over the top.

Let's even say it has failed 1000 times before but THIS time it makes it. We suddenly have a very robust population of fowl with very diverse genomes but with a peak of 90%{2,2,2} and 8%{2,2,1'2} fowl.

So now you ask, where are the Chickens? These are all just Gray's right? Well, it is a Gray with a hardened shell, faster incubation, and sexual incompatibility with any {1,1,1} population that was perhaps isolated from our earlier group.

Let's say there are further enhancements {3,2,2} and {2,3,2} which result in a higher population of {3,3,2}'s and eventually {4,4,2}'s, {4,4,2'3}s and {4,4,3}s which are even more disease resistant. All these changes using the same processes above.

So now we have a fowl {4,4,3} with an extremely tough & bacteria resistant shell, a 21-day incubation period, and is more robust against diseases. This FIRST {4,4,3} is our first True Chicken. However, it is still sexually compatible, at various levels with the {4,4,2'3} fowl which are not quite True Chickens.

We now require only ONE more piece of information and we can resolve the famous Chicken vs Egg Dilemma. What do you mean by 'egg'?

a) An egg that CONTAINS a True {4,4,3} Chicken - the egg which contained the first True Chicken would have come from two {4,4,2'3}-Almost Chickens -- therefore the Egg would have come first.

b) An egg FROM a True {4,4,3} Chicken - then the True {4,4,3} Chicken must have come first

c) Any type of egg at all - eggs in general are much much older than chickens of all kinds

Supporting Data

If you chart out the allele frequencies over tme you get a graph that looks like this (from Wiki):


Here is a very nice study on allele frequency distribution in geographically diverse populations of mice.

Another study in which e coli, under observed laboratory conditions, evolved the ability to process citrate with very detailed genomics data through the generations.

Learn about the HOX gene complex, which is a major factor in developmental morphology (and some cool examples in Drosophila).

Meet Prdm9 (PR domain-containing 9), the gene responsible for much of the genetic shuffling that is done when sperm eggs develop from germ cells (requires NewScientist account). This gene comes in many variations which alter how much shuffling is done and at which points (and some variations may be involved in certain kinds of genetic diseases) - more on Prdm9. Nature Genetics journal paper: doi:10.1038/ng.658

Learn about Histone and its role in shaping and regulating DNA expression.

A critical step in the fertilization process is Oocyte activation, within this process is the DNA synthesis from the two gametes (called syngamy, this combines the DNA from each gamete) and there are complexes of genes which must interlock or the synthesis will not happen, even if the DNA is otherwise compatible. This is one of the mechanisms of speciation by sexual incompatibility in complex organisms (penis shape and size is another in some species, e.g., ducks). Differences in these genes are involved in some cases of human infertility which could eventually lead to speciation in humans.

Interesting paper on the speciation of Yeast due to reproductive isolation:
Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species.

Saturday, May 7, 2011

Where is the evidence for Evolution?

Certain "types" of people seem to ask "Where is the evidence for Evolution?" persistently, apparently unaware of the hundreds of thousands of scholarly papers on the subject as well as untold numbers of books - which they are either allergic to or incapable of understanding.

What amazes me is that these people are apparently incapable of following the simplest arguments and yet, are simultaneously, smarter than the smartest people on earth who have been educated in this subject - despite not actually knowing a thing about the subject in question.  They cannot even seem to make honest claims about evolution  It's an extraordinary juxtaposition of traits but who am I to question such things. Ignorance truly works in mysterious ways.

So, here is just a TINY sampling of evidences for evolution. If you want to make a good argument that evolution is invalid, ALL you have to do it write a rebuttal on all of these papers, submit your brilliant rebuttals to the relevant, peer-reviewed journals and get it published.

Added:

Theobald, D. L.  2010.  A formal test of the theory of universal common ancestry.  Nature 465:219-223


Adl, S., Leander, B.S., Simpson, A.G.B., Archibald, J.M., Anderson, O.R., Bass, D., Bowser, S.S., Brugerolle, G., Farmer, M.A., Karpov, S., Kolisko, M., Lane, C.E., Lodge, D.J., Mann, D.G., Meisterfeld, R., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S.E., Smirnov, A.V., and Spiegel, F. (2007) Diversity, nomenclature, and taxonomy of protists. Syst. Biol., 56, 684-689.
Adl, S.M., Simpson, A.G., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, O., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W. and Taylor, M.F. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.
Adoutte, A., G. Balavoine, N. Lartillot, O. Lespinet, B. Prud'homme, and R. de Rosa. 2000. The new animal phylogeny: Reliability and implications. Proceedings of the National Academy of Sciences (USA) 97:4453-4456.
Ahmad, S., A. Selvapandiyan, and R. K. Bhatnagar. 1999. A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene. International Journal of Systematic Bacteriology 49:1387-1394.
Anderson, C. L. 1998. Phylogenetic relationships of the Myxozoa. Pages 341-350 in Evolutionary Relationships among Protozoa (G.H. Coombs, K. Vickerman, M.A. Sleigh, and A. Warren, eds.) Chapman & Hall, London.
Anderson, C. L., E. U. Canning, and B. Okamura. 1998. A triploblast origin for Myxozoa? Nature 392:346-347.
Andersson, S. G. E., A. Zomorodipour, J. O. Andersson, T. Sicheritz-Ponten, U. C. M. Alsmark, R. M. Podowski, A. K. Naslund, A. S. Eriksson, H. H. Winkler, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.
Andersson, S.G. and Kurland, C.G. (1999) Origins of mitochondria and hydrogenosomes. Curr. Opin. Microbiol., 2, 535-541.
Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends in Genetics 14:442-444.
Archibald, J.M. (2005) Jumping genes and shrinking genomes.probing the evolution of eukaryotic photosynthesis with genomics. IUBMB Life, 57, 539-547.
Archibald, J.M., Longet, D., Pawlowski, J. and Keeling, P.J. (2002) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20, 62-66.
Arisue, N., Hasegawa, M., and Hashimoto, T. (2005) Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Molecular Biology and Evolution, 22(3), 409-420.
Ayala, F. J., A. Rzhetsky, and F. J. Ayala. 1998. Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates. PProceedings of the National Academy of Sciences (USA) 95:606-611.
Baguñà, J., P. Martinez, J. Paps, and M. Riutort. 2008. Back in time: a new systematic proposal for the Bilateria. Philosophical Transactions of the Royal Society Series B 363(1496):1481-1491
Baldauf, S. L. (1999) A search for the origins of animals and fungi: Comparing and combining molecular data. American Naturalist, 154(suppl.), S178-S188.
Baldauf, S. L., J. D. Palmer, and W. F. Doolittle. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proceedings of the National Academy of Sciences of the United States of America 93:7749-7754.
Baldauf, S.L. and Doolittle, W.F. (1997) Origin and evolution of the slime molds (Mycetozoa). Proceedings of the National Academy of Sciences (USA), 94, 12007-12012.
Baldauf, S.L. and Palmer, J.D. (1993) Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA, 90, 11558-11562.
Baldauf, S.L., Roger, A.J., Wenk-Siefert, I. and Doolittle, W.F. (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science, 290, 972-977.
Balows, A., H.G. Träper, M. Dworkin, W. Harder, and K.-H. Schleifer (eds.). 1992. The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. Second edition, Volumes I-IV. Springer Verlag, New York.
Bapteste, E., Brinkmann, H., Lee, J., Moore, D., Sensen, C., Gordon, P., Durufle, L., Gaasterland, T., Lopez, P., Muller, M. and Philippe, H. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostellium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. U S A, 99, 1414-1419.
Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proceedings of The National Academy of Sciences (U.S.A.) 93:9188-9193.
Barns, S. M., R. E. Fundyga, M. W. Jeffries and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proceedings of the National Academy of Sciences of the United States of America 91(5): 1609-1613.
Bass, D., Moreira, D., Lopez-Garcia, P., Polet, S., Chao, E.E., von der Heyden, S., Pawlowski, J. and Cavalier-Smith, T. (2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist, 156, 149-161.
Battistuzzi, F. U. and A. B. Hedges. 2009. A major clade of prokaryotes with ancient adaptations to life on land. Molecular Biology and Evolution 26(2):335-343; doi:10.1093/molbev/msn247
Battistuzzi, F. U., A. Feijao, and A. B. Hedges. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary Biology 4:44-.
Becerra, A., L. Delaye, S. Islas, and A. Lazcano. 2007. The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annual Review of Ecology, Evolution, and Systematics 38:361-379.
Benachenhou, L. N., P. Forterre and B. Labedan. 1993. Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. Journal Of Molecular Evolution 36(4): 335-346.
Benachenhou, L. N., P. Forterre and B. Labedan. 1993. Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. Journal Of Molecular Evolution 36:335-346.
Bern, M. and D. Goldberg. 2005. Automatic selection of representative proteins for bacterial phylogeny. BMC Evolutionary Biology 5:34-.
Berney, C. and Pawlowski, J. (2006) A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Proceedings of the Royal Society Series B, 273(1596), 1867-1872.
Boone, D. R., R.W. Castenholz, and G.M. Garrity. 2001. Bergey's Manual of Systematic Bacteriology. Springer, New York.
Borchiellini C., Boury-Esnault, N., Vacelet, J., and Le Parco, Y. (1998) Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of metazoa and specific phylogenetic relationships between animals and fungi. Molecular Biology and Evolution, 15, 647-655.
Borchiellini, C., M. Manuel, E. Alivon, N. Boury-Esnault, J. Vacelet, and Y. Le Parco. 2001. Sponge paraphyly and the origin of Metazoa. Journal of Evolutionary Biology 14:171-179.
Briggs, D. E. G., D. H. Erwin, and F. J. Collier. 1994. The Fossils of the Burgess Shale. Smithsonian Institution Press, Washingthon, D.C.
Brinkmann, H. and H. Phillippe. 1999. Archaea sister group of bacteria? Indications from Tree Reconstruction Artifacts from ancient Phylogenies. Molecular Biology and Evolution 16:817-825.
Brochier, C., E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational apparatus proteins.
Brocks, J. J., G. A. Logan, R. Buick, and R. E. Summons. 1999. Archean molecular fossils and the early rise of eukaryotes. Science 285:1033-1036.
Brown, J. R. , C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nature Genetics 28:281-285.
Brown, J. R. 2001. Genomic and phylogenetic perspectives on the evolution of prokaryotes. Systematic Biology 50:497-512.
Brown, J. R. and W. F. Doolittle. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proceedings of the National Academy of Sciences of the United States of America 92:2441-2445.
Brown, J. R. and W. F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiology and Molecular Biology Reviews 61:456-502.
Brusca, R. C. and G. J. Brusca. 2002. Invertebrates. Second Edition. Sinauer Associates, Inc., Sunderland, Massachusetts.
Budd, G. E. 2008. The earliest fossil record of the animals and its significance. Philosophical Transactions of the Royal Society Series B 363(1496):1425-1434.
Budin, K. and Philippe, H. (1998) New insights into the phylogeny of eukaryotes based on Ciliate Hsp70 sequences. Molecular Biology and Evolution, 15, 943-956.
Burki, F. and Pawlowski, J. (2006) Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts. Molecular Biology and Evolution, 23(10), 1922-1930.
Burki, F., Shalchian-Tabrizi, K. and Pawlowski, J. (2008) Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol. Lett., 4(4), 366-369.
Burki, F., Shalchian-Tabrizi, K., Minge, M., Skjaeveland, A., Nikolaev, S.I., Jakobsen, K.S. and Pawlowski, J. (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE, 2, e790.
Bustard, K. and R. S. Gupta. 1997. The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus-Thermus group and cyanobacteria. Journal of Molecular Evolution 45:193-205.
Caetano-Anolles, G. 2002. Evolved RNA secondary structure and the rooting of the universal tree of life. Journal of Molecular Evolution 54: 333-345.
Calisher, C. H., M. C. Horzinek, M. A. Mayo, H. W. Ackermann, and J. Maniloff. 1995. Sequence analyses and a unifying system of virus taxonomy - consensus via consent. Archives of Virology 140 (11):2093-2099.
Cammarano, P., P. Palm, R. Creti, E. Ceccarelli, A. M. Sanangelantoni, and O. Tiboni. 1992. Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the Archaeal domain. Journal Of Molecular Evolution 34:396-405.
Cammarano, P., R. Creti, A. M. Sanangelantoni, and P. Palm. 1999. The archaean monophyly issue: a phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions. Journal Of Molecular Evolution 49:524-537.
Canning, E.U. (1998) Evolutionary relationships of Microsporidia. Pages 77-90 in Evolutionary Relationships among Protozoa (G. H. Coombs, K. Vickerman, M .A. Sleigh, and A. Warren, eds.) Chapman & Hall, London.
Carroll, S. B., J. K. Grenier, and S. D. Weatherbee. 2001. From DNA to Diversity. Molecular Genetics and the Evolution of Animal Design. Blackwell Science, Malden, Massachusetts.
Castro, H. F., N. H. Williams, and A. Ogram. 2000. Phylogeny of sulfate-reducing bacteria. FEMS Microbiology Ecology 31:1-9.
Cavalier-Smith, T. (1987) The origin of fungi and pseudofungi. In Rayner, A.D.M., Brasier, C.M. and Moore, D. (eds.), Evolutionary biology of the fungi. Cambridge University Press, Cambridge, pp. 339-353.
Cavalier-Smith, T. (1993) Kingdom Protozoa and its 18 phyla. Microbiol. Rev., 57, 953-94.
Cavalier-Smith, T. (1998) A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc., 73, 203-266.
Cavalier-Smith, T. (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J. Eukaryot. Microbiol., 46, 347-366.
Cavalier-Smith, T. (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Sys. Evol. Microbiol., 52, 297-354.
Cavalier-Smith, T. (2003) Protist phylogeny and the high-level classification of Protozoa. Eur. J. Protistol., 39, 338-348.
Cavalier-Smith, T. (2004) Chromalveolate diversity and cell megaevolution: interplay of membranes, genomes and cytoskeleton. In Hirt, R.P. and Horner, D. (eds.), Organelles, Genomes and Eukaryotic Evolution. Taylor and Francis, London, pp. 71-103.
Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionay Microbiology 52:7-76.
Cavalier-Smith, T. and Chao, E.E. (1995) The opalozoan Apusomonas is related to the common ancestor of animals, fungi and choanoflagellates. Proceedings of the Royal Society of London Series B, 261, 1-6.
Cavalier-Smith, T. and Chao, E.E. (2003) Phylogeny and classification of phylum Cercozoa (Protozoa). Protist, 154, 341-358.
Cavalier-Smith, T., M. T. E. P. Allsopp, E. E. Chao, N. Boury-Esnault, and J. Vacelet. 1996. Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S rRNA evidence. Canadian Journal of Zoology 74:2031-2045.
Chen, J.-Y., P. Oliveri, C.-W. Li, G.-Q. Zhou, F. Gao, J. W. Hagadorn, K. J. Peterson, and E. H. Davidson. 2000. Precambrian animal diversity: Putative phosphatized embryos from the Doushantuo Formation of China. Proceedings of the National Academy of Sciences (U.S.A.) 97:4457-4462.
Ciccarelli, F. D., T. Doerks, C. von Mering, C. J. Creevey, B. Snel, and P. Bork. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311(5765):1283-1287.
Clark C.G. and Roger, A.J. (1995) Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proceedings of the National Academy of Sciences (USA), 92, 6518-6521.
Coenye, T. and P. Vandamme. 2004. A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria. Syst Appl. Microbiol. 27:313-322.
Collins, A. G. 1998. Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence. Proceedings of the National Academy of Sciences (U.S.A.) 95:15458-15463.
Collins, A. G. and J. W. Valentine. 2001. Defining phyla: evolutionary pathways to metazoan body plans. Evolution & Development 3:432-442.
Conway Morris, S. 1993. The fossil record and the early evolution of the Metazoa. Nature 361:219-225.
Conway Morris, S. 1998. The Crucible of Creation: The Burgess Shale and the Rise of Animals. Oxford University Press, Oxford, UK.
Copeland, H.F. (1956) The Classification of Lower Organisms. Pacific Books, Palo Alto, California.
Copley, R. R. 2008. The animal in the genome: comparative genomics and evolution. Philosophical Transactions of the Royal Society Series B 363(1496):1453-1461.
Creti, R., E. Ceccarelli, M. Bocchetta, A. M. Sanangelantoni, O. Tiboni, P. Palm and P. Cammarano. 1994. Evolution of translational elongation factor (EF) sequences: Reliability of global phylogenies inferred from EF-1-alpha(Tu) and EF-2(G) proteins. Proceedings of the National Academy of Sciences of the United States of America 91:3255-3259.
Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Research 2(7):1080-1090.
DeLong E. F. and N. R. Pace. 2001. Environmental diversity of Bacteria and Archaea. Systematic Biology 50: 470-478.
DeLong E. F. and N. R. Pace. 2001. Environmental diversity of Bacteria and Archaea. Systematic Biology 50:470-478.
Deeds, E. J., H. Hennessey, and E. I. Shakhnovich. 2005. Prokaryotic phylogenies inferred from protein structural domains. Gen. Res. 15:393-402.
Dellaporta, S. L., A. Xu, S. Sagasser, W. Jakob, M. A. Moreno, L. W. Buss, and B. Schierwater. 2006. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proceedings of the National Academy of Sciences (U.S.A.) 103(23):8751-8756.
Delong, E. F. 1992. Archaea in coastal marine environments. Proceedings of The National Academy of Sciences (U.S.A.) 89: 5685-5689.
Delwiche, C.F. (1999) Tracing the thread of plastid diversity through the tapistry of life. American Naturalist, 154 (suppl.), S164-S177.
Des Marais, D. J. 1999. Astrobiology: Exploring the origins, evolution, and distribution of life in the universe. Annual Review of Ecology and Systematics 30:397-420.
Dewel, R. A. 2000. Colonial origin for Eumetazoa: Major morphological transitions and the origin of Bilaterian complexity. Journal of Morphology 243:35-74.
Doolittle, W. F. 1998. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307-311.
Doolittle, W. F. 1999. Lateral genomics. Trends in Biochemical Sciences 24: M5-M8.
Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.
Doolittle, W. F. 2000. Uprooting the tree of life. Scientific American 282:90-95.
Doolittle, W. F. and J. M. Logsdon. 1998. Archaeal genomics: Do archaea have a mixed heritage? Current Biology 8: (6) R209-R211.
Doolittle, W. F. and J. R. Brown. 1994. Tempo, mode, the progenote, and the universal root. Proceedings of the National Academy of Sciences of the United States of America 91:6721-6728.
Douzery, E.J.P., Snell, E.A., Bapteste, E., Delsuc, F., and Philippe, H. (2004) The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proceedings of the National Academy of Sciences (USA), 101(43), 15386-15391.
Dunn, C. W., A Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen, S. H. D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. doi:10.1038/nature06614
Edlind, T.D. (1998) Phylogenetics of protozoan tubulin with reference to the amitochondriate eukaryotes. Pages 91-108 in Evolutionary Relationships Among Protozoa (Coombs, G.H., Vickerman, K., Sleigh, M.A. and Warren, A., eds.) Chapman & Hall, London.
Edlind, T.D., Li, J., Visvesvara, G.S., Vodkin, M.H., McLaughlin, G.L., and Katiyar, S.K. (1996) Phylogenetic analysis of beta-tubulin sequences from amitochondrial protozoa. Molecular Phylogenetics and Evolution, 5, 359-367.
Eernisse, D. J. and K. J. Peterson. 2004. The history of animals. Pages 197-208 in Assembling the Tree of Life, J. Cracraft and M. J. Donoghue, eds. Oxford University Press, New York.
Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species. Journal of Molecular Evolution 41:1105-1123. Molecular Biology and Evolution 21(9):1643-1660.
Embley, T. M., M. van der Giezen, D. S. Horner, P. L. Dyal, S. Bell, and P. G. Foster. 2003. Hydrogenosomes, mitochondria and early eukaryotic evolution. International Union of Biochemistry and Molecular Biology: Life 55(7):387-395.
Embley, T.M. (2006) Multiple secondary origins of the anaerobic lifestyle in eukaryotes. Philos. Trans. R. Soc. Lond. B Biol. Sci., 361, 1055-1067.
Embley, T.M. and Hirt, R.P. (1998) Early branching eukaryotes? Curr. Opinion Gen. Dev., 8, 624-629.
Emelyanov, V. V. and B. V. Sinitsyn. 1999. A groE-based phylogenetic analysis shows very close evolutionary relationship between mitochondria and Rickettsia. Russian Journal of Genetics 35:618-627.
Ender, A. and B. Schierwater. 2003. Placozoa are not derived cnidarians: Evidence from molecular morphology. Molecular Biology and Evolution 20(1):130-134.
Erwin, D. H. 1993. The origin of metazoan development: A palaeobiological perspective. Biological Journal of the Linnean Society 50: 255-274.
Esser, C., N. Ahmadinejad, C. Wiegand, C. Rotte, F. Sebastiani, G. Gelius-Dietrich, K. Henze, E. Kretschmann, E. Richly, D. Leister, D. Bryant, M. A. Steel, P. J. Lockhart, D. Penny and W. Martin. 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.
Fast, N.M., Kissinger, J.C., Roos, D.S. and Keeling, P.J. (2001) Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol., 18, 418-426.
Fast, N.M., Logsdon, J.M., and Doolittle, W.F. (1999) Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a microsporidia-fungi relationship and spliceosomal intron loss. Molecular Biology and Evolution, 16, 1415-1419.
Fauquet, C. M., M. A. Mayo, J. Maniloff, U. Desselberger, and L. A. Ball (Eds.). 2005. Virus Taxonomy. Elsevier, San Diego.
Feng, D.-F., G. Cho, and R.F. Doolittle. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proceedings of the National Academy of Sciences of the United States of America 94:13028-13033.
Ferrier, D. E. K. and P. W. H. Holland. 2001. Ancient origin of the Hox gene cluster. Nature Reviews Genetics 2:33-38.
Fields, B. N., D. M. Knipe, and P. M. Howley (eds.) 1996. Fields Virology, 3rd ed. Lippincott-Raven Publishers, Philadelphia, Pa.
Finnerty, J. R., K. Pang, P. Burton, D. Paulson, and M. Q. Martindale. 2004. Origins of bilateral symmetry; Hox and dpp expression in a sea anemone. Science 304:1335-37.
Forterre, P. 2001. Genomics and early cellular evolution. The origin of the DNA world. Comptes Rendus de l'Academie des Sciences Serie III-Sciences de la Vie 324:1067-1076.
Forterre, P. and H. Philippe. 1999. Where is the root or the universal tree of life? BioEssays 21:871-879.
Forterre, P., Benachenhou-Lahfa, N., Confalonieri, F., Duguet, M., Elie, C., and Labedan, B. (1992) The nature of the last universal ancestor and the root of the tree of life, still open questions. Biosystems, 28, 15-32.
Fox, G. E., E. Stackebrandt, R. B. Hespell, J. Gibson, J. Maniloff, T. A. Dyer, R. S. Wolfe, W. E. Balch, R. S. Tanner, L. J. Magrum, L. B. Zablen, R. Blakemore, R. Gupta, L. Bonen, B. J. Lewis, D. A. Stahl, K. R. Luehrsen, K. N. Chen, and C. R. Woese. 1980. The phylogeny of prokaryotes. Science 209:457-463.
Garrity, G. M., J. A. Bell, and T. G. Lilburn. 2004. Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition. Release 5.0.
Germot, A., Philippe, H., and Le Guyader, H. (1997) Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Molecular and Biochemical Parasitology, 87, 159-168.
Gibbs, A. J. 2000. Virus nomenclature descending into chaos. Archives of Virology 145:1505-1507.
Giribet, G. 2002. Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Molecular Phylogenetics and Evolution 24:345-357.
Giribet, G., C. W. Dunn, G. D. Edgecombe, and G. W. Rouse. 2007. A modern look at the Animal Tree of Life. Pages 61-79 in: Zhang, Z.-Q. & Shear, W.A., eds. Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Zootaxa 1668:1-766.
Gogarten, J. P. and L. Taiz. 1992. Evolution of proton pumping ATPases: Rooting the tree of life. Photosynthesis Research 33:137-146.
Gogarten, J. P., E. Hilario, and L. Olendzenski. 1996. Gene duplications and horizontal gene transfer during early evolution. Pages 267-292 in Evolution of Microbial Life (D. McL. Roberts, P. Sharp, G. Alderson, and M. Collins, eds.) Symposium 54. Society for General Microbiology. Cambridge University Press, Cambridge.
Gogarten, J.P. (2003) Gene transfer: Gene swapping craze reaches eukaryotes. Curr Biol., 13, R53.54.
Gogarten, J.P., Kiblak, H., Dittrich, P., Taiz, L., Bowman, E.J., Bowman, B.J., Manolson, N.F., Poole, R.J., Date, T., Oshima, T., Konishi, J., Denda, K. and Yoshida, M. (1989) Evolution of the vacuolar H+-ATPase: inplications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA, 86, 6661-6665.
Golding, G.B. and Gupta, R. S. (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Molecular Biology and Evolution, 12, 1-6.
Golding, G.B. and R.S. Gupta. 1995. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Molecular Biology and Evolution 12:1-6.
Gould, S. J. 1989. Wonderful Life: The Burgess Shale and the Nature of History. Norton, New York.
Gould, S.B., Waller, R.F. and McFadden, G.I. (2008) Plastid evolution. Annu. Rev. Plant. Biol., 59, 491-517.
Gouy, M. and W.-H. Li. 1989. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature 339:145-147.
Gouy, M. and W.-H. Li. 1990. Archaebacterial or eocyte tree? Nature 343:419.
Graham, D. E., R. Overbeek, G. J. Olsen, and C. R. Woese. 2000. An archaeal genomic signature. Proceedings of The National Academy of Sciences (U.S.A.) 97:3304-3308.
Gray, M. W., G. Burger, and B. F. Lang. 1999. Mitochondrial evolution. Science 283:1476-1481.
Gray, M.W. and Doolittle, W.F. (1982) Has the endosymbiont hypothesis been proven? Microbiol Rev., 46, 1-42.
Gray, M.W., Burger, G. and Lang, B.F. (1999) Mitochondrial evolution. Science, 283, 1476-1481.
Gray, M.W., Lang, B.F. and Burger, G. (2004) Mitochondria of protists. Annu. Rev. Genet., 38, 477-524.
Gribaldo, S. and P. Cammarano. 1998. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. Journal of Molecular Evolution 47:508-516.
Griffiths, E. and R. S. Gupta. 2004. Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales. Int Microbiol. 7:41-52.
Grosberg, R.K. and Strathmann, R.R. (2007) The evolution of multicellularity: a minor major transition? Annual Review of Ecology, Evolution, and Systematics, 38, 621-654.
Gruber, T. M. and D. A. Bryant. 1997. Molecular systematic studies of eubacteria, using sigma(70)-type sigma factors of group 1 and group 2. Journal of Bacteriology 179:1734-1747.
Gupta, R. S. 1997. Protein phylogenies and signature sequences: Evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 72:49-61.
Gupta, R. S. 1998. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiology and Molecular Biology Reviews 62:1435-1491.
Gupta, R. S. 1998. What are archaebacteria: Life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Molecular Microbiology 29:695-707.
Gupta, R. S. 2000. The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiology Reviews 24(4):367-402.
Gupta, R. S. 2004. The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes. Critical Reviews in Microbiology 30(2):123-143.
Gupta, R. S. and G. B. Golding. 1993. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. Journal of Molecular Evolution 37:573-582.
Gupta, R. S., T. Mukhtar, and B. Singh. 1999. Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Molecular Microbiology 32:893-906.
Gupta, R.S. and E. Griffiths. 2002. Critical issues in bacterial phylogeny. Theoretical Population Biology 61(4):423-434.
Gupta, R.S., K. Bustard, M. Falah, D. Singh. 1997. Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes. Journal of Bacteriology 179:345-357.
Hackett, J.D., Yoon, H.S., Li, S., Reyes-Prieto, A., Rummele, S.E. and Bhattacharya, D. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol. Biol. Evol., 24, 1702-1713.
Haen, K. M., B. F. Lang, S. A. Pomponi, and D. V. Lavrov. 2007. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? Molecular Biology and Evolution 24(7):1518 - 1527.
Hagopian, J.C., Reis, M., Kitajima, J.P., Bhattacharya, D. and de Oliveira, M.C. (2004) Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. J. Mol. Evol., 59, 464-477.
Halanych, K. 2004. The new view of animal phylogeny. Annual Review of Ecology, Evolution, and Systematics 35:229-256.
Hampl, V., Horner, D.S., Dyal, P., Kulda, J., Flegr, J., Foster, P.G., and Embley, T.M. (2005) Inference of the phylogenetic position of oxymonads based on nine genes: Support for Metamonada and Excavata. Molecular Biology and Evolution, 22(12), 2508-2518.
Hanelt B., D. VanSchyndel, C. M. Adema, L. A. Lewis, E. S. Loker. 1996. The phylogenetic position of Rhopalura ophiocomae (Orthonectida) based on 18S ribosomal DNA sequence analysis. Molecular Biology and Evolution 13:1187-1191.
Hanson, E.D. (1977) The Origin and Early Evolution of Animals. Wesleyan University Press, Middletown, Conn.
Harper, J.T. and Keeling, P.J. (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol., 20, 1730-1735.
Hashimoto, T., Nakamura, Y., Kamaishi, T., and Hasegawa, M. (1997) Early evolution of eukaryotes inferred from protein phylogenies of translation elongation factors 1 alpha and 2. Archiv für Protistenkunde, 148, 287-295.
Hendrix, R. W. 1999. The long evolutionary reach of viruses. Current Biology 9:R914-R917.
Hendrix, R. W., J. G. Lawrence, G. F. Hatfull, and S. Casjens. 2000. The origins and ongoing evolution of viruses. Trends in Microbiology 8:504-508.
Hendrix, R. W., M. C. M. Smith, R. N. Burns, M. E. Ford, and G. F. Hatfull. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proceedings of the National Academy of Sciences (USA) 96:2192-2197.
Herrmann, K.M. and Weaver, L.M. (1999) The Shikimate Pathway. Annu. Rev. Plant Physiol. Plant Mol. Biol., 50, 473-503.
Hilario, E. and J. P. Gogarten. 1993. Horizontal transfer of ATPase genes: The tree of life becomes a net of life. Biosystems 31:111-119.
Hirt, R.P. and Horner, D. (eds.) (2004) Organelles, Genomes and Eukaryote Evolution. Taylor & Francis, London.
Hirt, R.P., Healy, B., Vossbrinck, C.R.,Canning, E.U., and Embley, T. M. (1997) A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: Molecular evidence that microsporidia once contained mitochondria. Current Biology, 7, 995-998.
Hirt, R.P., Logsdon, Jr., J.M., Healy, B., Dorey, M.W., Doolittle, W.F., and Embley, T.M. (1999) Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings of the National Academy of Sciences (USA), 96, 580-585.
Hoppenrath, M. and Leander, B.S. (2006) Dinoflagellate, euglenid or cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp. J. Eukaryot. Microbiol., 53, 327-342.
Huang, J., Xu, Y. and Gogarten, J.P. (2005) The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol., 22, 2142-2146.
Huang, W. M. 1996. Bacterial diversity based on type II DNA topoisomerase genes. Annual Review of Genetics 30:79-107.
Huang, Y. P. and J. Ito. 1999. DNA polymerase C of the thermophilic bacterium Thermus aquaticus: Classification and phylogenetic analysis of the family C DNA polymerases. Journal of Molecular Evolution 48:756-769.
Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer, and K. O. Stetter. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67.
Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180:4765-4774.
Iwabe, N., K.-I. Kuma, M. Hagesawa, S. Osawa, T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proceedings of the Natural Academy of Sciences (USA) 86:9355-9359.
Iyer, L. M., L. Aravind, and E. V. Koonin. 2001. Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses. Journal of Virology 75(23):11720-11734.
Jeffares, D. C., A. M. Poole, and D. Penny. 1998. Relics from the RNA world. Journal of Molecular Evolution 46:18-36.
Jenner, R. A. 2004. The scientific status of metazoan cladistics: why current research practice must change. Zoologica Scripta 33(4):293-310.
Jenner, R. A. 2004. When molecules and morphology clash: Reconciling conflicting phylogenies of the Metazoa by considering secondary character loss. Evolution & Development 6(5):372-378.
Jenner, R. A. and D. T. J. Littlewood. 2008. Problematica old and new. Philosophical Transactions of the Royal Society Series B 363(1496):1503-1512.
Jenner, R.A. and Schram, F.R. (1999) The grand game of metazoan phylogeny: rules and strategies. Biological Reviews, 74, 121-142.
Jiménez-Guri, E., H. Philippe, B. Okamura, P. W. H. Holland. 2007. Buddenbrockia is a cnidarian worm. Science 317(5834):116-118.
Johnson, M.D., Oldach, D., Delwiche, C.F. and Stoecker, D.K. (2007) Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra. Nature, 445, 426-428.
Kamaishi, T., Hashimoto, T., Nakamura, Y., Nakamura, F., Murata, S., Okada, N., Okamoto, K., and Hasegawa, M. (1996) Protein phylogeny of translation elongation factor EF-1alpha suggests microsporidians are extremely ancient eukaryotes. Journal of Molecular Evolution, 42, 257-263.
Kamm, K., B. Schierwater, W. Jakob, S. L. Dellaporta, and D. J. Miller. 2006. Axial patterning and diversification in the Cnidaria predate the Hox system. Current Biology 16:920-926.
Kandler, O. 1994. Cell wall biochemistry and three-domain concept of life. Systematic and Applied Microbiology 16:501-509.
Katz, L. A. 1998. Changing perspectives on the origin of eukaryotes. Trends in Ecology and Evolution 13:493-497.
Katz, L. A. 1999. The tangled web: gene genealogies and the origin of eukaryotes. Am. Nat. 154 (suppl.):S137-S145.
Katz, L.A. (1998) Changing perspectives on the origin of eukaryotes. Trends Ecol. Evol., 13, 493-497.
Katz, L.A. (1999) The tangled web: gene genealogies and the origin of eukaryotes. American Naturalist, 154(suppl.), S137-S145.
Keeling, P.J. (1998) A kingdom's progress: Archezoa and the origin of eukaryotes. BioEssays, 20, 87-95.
Keeling, P.J. (2001) Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol., 18, 1551-1557.
Keeling, P.J. (2004) The diversity and evolutionary history of plastids and their hosts. Am. J. Bot., 91, 1481-1493.
Keeling, P.J. (2009) Chromalveolates and the evolution of plastids by secondary endosymbiosis. J. Eukaryot Microbiol., in press.
Keeling, P.J. and Doolittle, W.F. (1996) Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Molecular Biology and Evolution, 13, 1297-1305.
Keeling, P.J. and McFadden, G.I. (1998) Origins of microsporidia. Trends Microbiol., 6, 19-23.
Keeling, P.J. and Palmer, J.D. (2000) Phylogeny - Parabasalian flagellates are ancient eukaryotes. Nature, 405, 635-637.
Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol., 20, 670-676.
Keeling, P.J., Luker, M.A., and Palmer, J.D. (2000) Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Molecular Biology and Evolution, 17, 23-31.
Kim, J., W. Kim, and C. W. Cunningham. 1999. A new perspective on lower metazoan relationships from 18S rDNA sequences. Molecular Biology and Evolution 16:423-427.
Kim, J.,Kim, W., and Cunningham, C.W. (1999) A new perspective on lower metazoan relationships from 18S rDNA sequences. Molecular Biology and Evolution, 16, 423-427.
Kjems, J., N. Larsen, J. Z. Dalgaard, R. A. Garrett and K. O. Stetter. 1992. Phylogenetic relationships amongst the hyperthermophilic Archaea determined from partial 23S rRNA gene sequences. Systematic and Applied Microbiology 15(2): 203-208.
Klenk, H. P., C. Schleper, V. Schwass and R. Brudler. 1993. Nucleotide sequence, transcription and phylogeny of the gene encoding the superoxide dismutase of Sulfolobus acidocaldarius. Biochimica Et Biophysica Acta 1174(1): 95-98.
Knoll, A. H. and S. B. Carroll. 1999. Early animal evolution: emerging views from comparative biology and geology. Science 284:2129-2137.
Knoll, A.H. (1992) The early evolution of eukaryotes: a geological perspective. Science, 256, 622-627.
Koonin, E. V., A. R. Mushegian, M. Y. Galperin, and D. R. Walker. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Molecular Microbiology 25:619-637.
Kruse, M., S. P. Leys, I. M. Mueller, and W. E. G. Mueller. 1998. Phylogenetic position of the hexactinellida within the phylum porifera based on the amino acid sequence of the protein kinase C from Rhabdocalyptus dawsoni. Journal of Molecular Evolution 46:721-728.
Kumar, S. and Rzhetsky, A. (1996) Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular Evolution, 42, 183-193.
Kunisawa, T. 2006. Dichotomy of major bacterial phyla inferred from gene arrangement comparisons. J. of Theor. Biol. 239:367-375.
Kyrpides, N. C. and C. A. Ouzounis. 1999. Transcription in Archaea. Proceedings of The National Academy of Sciences (U.S.A.) 96:8545-8550.
Kyrpides, N. C. and G. J. Olsen. 1999. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends in Genetics 15:298-299.
Lake, J. A. 1990. Archaebacterial or eocyte tree? Nature 343:418-419.
Lake, J. A. and M. C. Rivera. 1996. The prokaryotic ancestry of eukaryotes. Pages 87-108 in Evolution of Microbial Life (D. McL. Roberts, P. Sharp, G. Alderson, and M. Collins, eds.) Symposium 54. Society for General Microbiology. Cambridge University Press, Cambridge.
Lake, J. A., M. W. Clark, E. Hendeson, S. P. Fay, M. Oakes, A. Scheinman, J. P. Thornber and R. A. Mah. 1985. Eubacteria, halobacteria and the origin of photosynthesis: The photocytes. Proceedings of the National Academy of Sciences (USA) 82:3716-3720.
Lake, J.A. and Rivera, M.C. (1994) Was the nucleus the first endosymbiont? Proceedings of the National Academy of Sciences (USA), 91, 2880-2881.
Lake, J.A., E. Henderson, M. Oakes, M.W. Clark. 1984. Eocytes: a new ribosome structure indicates a kingdom with close relationship to eukaryotes. Proceedings of the National Academy of Sciences (USA) 81:3786-3790.
Lang, B.F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Turmel, M., and Gray, M. W. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature, 387, 493-497.
Lang, B.F., Gray, M.W. and Burger, G. (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet., 33, 351-397.
Lawrence, J. G. and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proceedings of the National Academy of Sciences of the United States of America 95:9413-9417.
Lawrence, J. G., G. F. Hatfull, and R. W. Hendrix. 2002. Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches. Journal of Bacteriology 184(17):4891-4905.
Lawson, F. S., R. L. Charlebois, and J.-A. R. Dillon. 1996. Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the Tree of Life. Molecular Biology and Evolution 13:970-977.
Leander, B.S. (2004) Did trypanosomatid parasites have photosynthetic ancestors? Trends Microbiol., 12, 251-258.
Leander, B.S. (2008) A hierarchical view of convergent evolution in microbial eukaryotes. J. Eukaryot. Microbiol., 55, 59-68.
Leander, B.S. (2008) Different modes of convergent evolution reflect phylogenetic distances. Trends Ecol. Evol., 23, 481-482.
Leander, B.S. and Keeling, P.J. (2003) Morphostasis in alveolate evolution. Trends Ecol. Evol., 18, 395-402.
Leander, B.S. and Keeling, P.J. (2004) Early evolutionary history of dinoflagellates and apicomplexans (Alveolata) as inferred from hsp90 and actin phylogenies. J. Phycol., 40, 341-350.
Leipe, D., Gunderson, J.H., Nerad, T.A., and Sogin, M. L. (1993) Small subunit ribosomal RNA of Hexamita inflata and the quest for the first branch in the eukaryotic tree. Mol. Biochem. Parasitol., 59, 41-48.
Levin, H. L. 1999. Ancient Invertebrates and Their Living Relatives. Prentics Hall, Upper Saddle River, New Jersey.
Liao, D. and P. P. Dennis. 1994. Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences. Journal of Molecular Evolution 38:405-419.
Lipscomb D.L., Farris, J.S., Kallersjo, M., and Tehler, A. (1998) Support, ribosomal sequences and the phylogeny of the eukaryotes. Cladistics, 14, 303-338.
Liu, R. and H. Ochman. 2007. Stepwise formation of the bacterial flagellar system. Proceedings of the National Academy of Sciences of the United States of America 104(17):7116-7121.
Longet, D., Archibald, J.M., Keeling, P.J. and Pawlowski, J. (2003) Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol., 53, 1735 - 1739.
Lopez, P., P. Forterre, and H. Philippe. 1999. The root of the tree of life in the light of the covarian model. Journal of Molecular Evolution 49:496-508.
Lovisolo, O., R. Hull, and O. Rösler. 2003. Coevolution of viruses with hosts and vectors and possible paleontology. Advances in Virus Research 62:325-379.
Ludwig, W., J. Neumaier, N. Klugbauer, E. Brockmann, C. Roller, S. Jilg, K. Reetz, I. Schachtner, A. Ludvigsen, M. Bachleitner, U. Fischer, and K. H. Schleifer. 1993. Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 64:285-305.
Ludwig, W., O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger , J. Neumaier, M. Bachleitner, and K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554-568.
Macario, A. J. L. and E. C. de Macario. 1999. The archaeal molecular chaperone machine: Peculiarities and paradoxes. Genetics 152:1277-1283.
Makarova, K. S., L. Aravind, M. Y. Galperin, N. V. Grishin, R. L. Tatusov, Y. I. Wolf, and E. V. Koonin. 1999. Comparative genomics of the archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell. Genome Research 9:608-628.
Maldonado, M. (2004) Choanoflagellates, choanocytes, and animal multicellularity. Invertebrate Biology, 123, 1-22.
Margulis, L. (1970) Origin of Eukaryotic Cells. Yale University Press.
Margulis, L. (1981) Symbiosis in cell evolution. W. H. Freeman and Co., San Francisco.
Margulis, L. 1996. Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proceedings of the Natural Academy of Sciences (USA) 92:1071-1076.
Margulis, L., Chapman, M., Guerrero, R., and Hall, J. (2006) The last eukaryotic common ancestor (LECA): Acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proceedings of the National Academy of Sciences (USA), 103(35), 13080-13085.
Margulis, L., Corliss, J.O., Melkonian, M., and Chapman, D.J. 1990. Handbook of Protoctista. Jones and Bartlett Publishers, Boston.
Martin W. and M. Müller. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
Martin, W. 1999. Mosaic bacterial chromosomes: a challenge on route to a tree of genomes. BioEssays 21:99-104.
Martindale, M. Q., J. R. Finnerty, and J. Q. Henry. 2002. The Radiata and the evolutionary origins of the bilaterian body plan. Molecular Phylogenetics and Evolution 24:358-365.
Matte-Tailliez, O., C. Brochier, P. Forterre, and H. Philippe. 2002. Archaeal phylogeny based on ribosomal proteins. Molecular Biology and Evolution 19:631-639.
Matus, D. Q., K. Pang, H. Marlow, C. W. Dunn, G. H. Thomsen, and M. Q. Martindale. 2006. Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proceedings of the National Academy of Sciences (USA) 103(30):11195-11200.
McClendon, J. H. 1999. The origin of life. Earth-Science Reviews 47:71-93.
McCormack, G. P. and J. P. Clewley. 2002. The application of molecular phylogenetics to the analysis of viral genome diversity and evolution. Reviews in Medical Virology 12(4):221-238.
McFadden, G.I. (1999) Endosymbiosis and evolution of the plant cell. Curr. Opin. Plant. Biol., 2, 513-519.
McFadden, G.I., Gilson, P.R., Douglas, S.E., Cavalier-Smith, T., Hofmann, C.J. and Maier, U.G. (1997) Bonsai genomics: sequencing the smallest eukaryotic genomes. Trends Genet., 13, 46-49.
Medina, M., A. G. Collins, J. D. Silberman, and M. L. Sogin. 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proceedings of the National Academy of Sciences (U.S.A.) 98:9707-9712.
Mendoza, L., Taylor, J.W., and Ajello, L. (2002) The class mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Annual Review of Microbiology, 56, 315-44.
Mindell, D. P., J. S. Rest, and L. P. Villarreal. 2004. Viruses and the tree of life. Pp. 107-118 in Cracraft, J. and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford University Press, New York.
Minelli, A. 2007. Invertebrate taxonomy and evolutionary developmental biology. Pages 55-60 in: Zhang, Z.-Q. & Shear, W.A., eds. Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Zootaxa 1668:1-766.
Minge, M.A., Silberman, J.D., Orr, R.J., Cavalier-Smith, T., Shalchian-Tabrizi, K., Burki, F., Skjaeveland, A. and Jakobsen, K.S. (2008) Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc. Biol. Sci., 276, 597-604.
Monteiro, A. S., B. Okamura, and P. W. H. Holland. 2002. Orphan worm finds a home: Buddenbrockia is a Myxozoan. Molecular Biology and Evolution 19:968-971.
Moran, N. and P. Baumann. 1994. Phylogenetics of cytoplasmically inherited microorganisms of arthropods. Trends in Ecology and Evolution 9:15-20.
Moreira, D. and P. Lopez-Garcia. 1998. Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. Journal of Molecular Evolution 47:517-530.
Moreira, D., Le Guyader, H. and Phillippe, H. (2000) The origin of red algae and the evolution of chloroplasts. Nature, 405, 69-72.
Moreira, D., von der Heyden, S., Bass, D., Lopez-Garcia, P., Chao, E. and Cavalier-Smith, T. (2007) Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol. Phylogenet. Evol., 44, 255-266.
Morin, L. (2000) Long branch attraction effects and the status of "basal eukaryotes": Phylogeny and structural analysis of the ribosomal RNA gene cluster of the free-living diplomonad Trepomonas agilis. Journal of Eukaryotic Microbiology, 47, 167-177.
Morris, P.J. (1993) The developmental role of the extracellular matrix suggests a monophyletic origin of the Kingdom Animalia. Evolution, 47, 152-165.
Müller, M. (1993) The hydrogenosome. J. Gen. Microbiol., 139, 2879-2889.
Narbonne, G.M. (2004) Modular construction of early Ediacaran complex life forms. Science, 305(5687), 1141-1144.
Nealson, K. H. and P. G. Conrad. 1999. Life: past, present and future. Philosophical Transactions of the Royal Society of London Series B 354:1923-1939.
Nielsen, C. 2001. Animal Evolution: Interrelationships of the Living Phyla. Second Edition. Oxford University Press, Oxford.
Nielsen, C., N. Scharff, and D. Eibye-Jacobsen. 1996. Cladistic analyses of the animal kingdom. Biological Journal of the Linnean Society 57:385-410.
Nikolaev, S.I., Berney, C., Fahrni, J.F., Bolivar, I., Polet, S., Mylnikov, A.P., Aleshin, V.V., Petrov, N.B. and Pawlowski, J. (2004) The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc. Natl. Acad. Sci. USA, 101, 8066-8071.
Nowack, E.C., Melkonian, M. and Glockner, G. (2008) Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr. Biol., 18, 410-418.
Nozaki, H., Iseki, M., Hasegawa, M., Misawa, K., Nakada, T., Sasaki, N., and Watanabe, M. (2007) Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Molecular Biology and Evolution, 24, 1592-1595.
Nozaki, H., Matsuzaki, M., Takahara, M., Misumi, O., Kuroiwa, H., Hasegawa, M., Shin-i, T., Kohara, Y., Ogasawara, N., and Kuroiwa, T. (2003) The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. Journal of Molecular Evolution, 56(4), 485-497.
Ochman, H., S. Elwyn, and N. A. Moran. 1999. Calibrating bacterial evolution. Proceedings of the National Academy of Sciences of the United States of America 96:12638-12643.
Okamoto, N. and Inouye, I. (2005) A secondary symbiosis in progress? Science, 310, 287.
Okamura, B., A. Curry, T. S. Wood, and E. U. Canning. 2002. Ultrastructure of Buddenbrockia identifies it as a myxozoan and verifies the bilaterian origin of the Myxozoa. Parasitology 124:215-223.
Olsen, G. J. and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEB Journal 7:113-23.
Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. Journal of Bacteriology 176:1-6.
Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
Pace, N. R. 1999. Microbial ecology and diversity. ASM News 65:328-333.
Patron, N.J., Inagaki, Y. and Keeling, P.J. (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr. Biol., 17, 887-891.
Patron, N.J., Rogers, M.B. and Keeling, P.J. (2004) Gene replacement of fructose-1,6-bisphosphate aldolase (FBA) supports a single photosynthetic ancestor of chromalveolates. Eukaryot. Cell, 3, 1169-1175.
Patterson, D.J. (1994) Protozoa: Evolution and Systematics. Pages 1-14 in Progress in Protozoology. Proceedings of the IX International Congress of Protozoology, Berlin (1993) (K. Hausmann and N. Hülsmann, eds.) Gustav Fischer Verlag, Stuttgart, Jena, New York.
Patterson, D.J. (1999) The diversity of eukaryotes. American Naturalist, 154(suppl.), S96-S124.
Patterson, D.J. and Sogin, M.L. (1992) Eukaryote origins and protistan diversity. Pages 13-46 in The Origin and Evolution of Prokaryotic and Eukaryotic Cells (H. Hartman and K. Matsuno, eds.) World Scientific Pub. Co. NJ.
Pennisi, E. 1998. Genome data shake the tree of life. Science 280:672-674.
Pennisi, E. 1999. Is it time to uproot the tree of life? Science 284:1305-1307.
Penny, D. and A. Poole. 1999. The nature of the last universal common ancestor. Current Opinion in Genetics and Development 9:672-677.
Peterson, K. J. and D. J. Eernisse. 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evolution & Development 3:170-205.
Peterson, K. J. and E. H. Davidson. 2000. Regulatory evolution and the origin of bilaterians. Proceedings of the National Academy of Sciences (U.S.A.) 97:4430-4433.
Peterson, K. J. and N. J. Butterfield. 2005. Origin of the Eumetazoa: Testing ecological predictions of molecular clocks against the Proterozoic fossil record. Proceedings of the National Academy of Sciences (USA) 102(27):9547-9552.
Peterson, K. J., J. A. Cotton, J. G. Gehling and D. Pisani. 2008. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society Series B 363(1496):1435-1443.
Peterson, K. J., J. B. Lyons, K. S. Nowak, C. M. Takacs, M. J. Wargo and M. A. McPeek. 2004. Estimating metazoan divergence times with a molecular clock. Proceedings of the National Academy of Sciences (USA) 101(17):6536-6541.
Philip, G.K., Creevey, C.J., and McInerney, J.O. (2005) The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Molecular Biology and Evolution, 22(5), 1175.1184.
Philippe, H. and Adoutte, A. (1998) The molecular phylogeny of Eukaryota: solid facts and uncertainties. Pages 25-56 in Evolutionary Relationships among Protozoa (G. H. Coombs, K. Vickerman, M. A. Sleigh, and A. Warren, eds.) Chapman & Hall, London.
Philippe, H. and Germot, A. (2000) Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution. Molecular Biology and Evolution, 17, 830-834.
Philippe, H. and M. J. Telford. 2006. Large-scale sequencing and the new animal phylogeny. Trends in Ecology & Evolution 21(11):614-620.
Philippe, H. and P. Forterre. 1999. The rooting of the universal tree of life is not reliable. Journal of Molecular Evolution 49:509-523.
Philippe, H., Lopez, P., Brinkmann, H., Budin, K., Germot, A., Laurent, J., Moreira, D., Muller, M., and Le Guyader, H. (2000) Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proceedings of the Royal Society of London Series B, 267, 1213-1221.
Philippe, H., Snell, E.A., Bapteste, E., Lopez, P., Holland, P.W.H., and Casane, D. (2004) Phylogenomics of eukaryotes: impact of missing data on large alignments. Molecular Biology and Evolution, 21(9), 1740-1752.
Pierson, B. K. 1994. The emergence, diversification, and role of photosynthetic bacteria. Pages 161-180 in Early Life on Earth, Nobel Symposium No. 84 (Bengtson, S., ed.). Columbia University Press, New York.
Polet, S., Berney, C., Fahrni, J. and Pawlowski, J. (2004) Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria. Protist, 155, 53-63.
Poole, A., D. Jeffares, and D. Penny. Early evolution: prokaryotes, the new kids on the block. BioEssays 21:880-889.
Putnam, N. H., M. Srivastava, U. Hellsten, B. Dirks, J. Chapman, A. Salamov, A. Terry, H. Shapiro, E. Lindquist, V. V. Kapitonov, J. Jurka, G. Genikhovich, I. V. Grigoriev, S. M. Lucas, R. E. Steele, J. R. Finnerty, U. Technau, M. Q. Martindale, and D. S. Rokhsar. 2007. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317(5834):86-94.
Ragan, M.A. and Gutell, R.R. (1995) Are red algae plants? Botanical Journal of the Linnean Society, 118, 81-105.
Ragan, M.A., Goggin, C.L., Cawthorn, R.J., Cerenius, L., Jamieson, A.V., Plourde, S.M., Rand, T.G., Soderhall, K. and Gutell, R.R. (1996) A novel clade of protistan parasites near the animal-fungal divergence. Proc. Natl. Acad. Sci. USA, 93, 11907-11912.
Rappé, M. S. and S. J. Giovannoni. 2003. The uncultured microbial majority. Annual Review of Microbiology 57:369-394.
Rasmussen, B. 2000. Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature 405:676-679.
Reichert, A.S. and Neupert, W. (2004) Mitochondriomics or what makes us breathe. Trends Genet., 20, 555-562.
Reyes-Prieto, A., Weber, A.P. and Bhattacharya, D. (2007) The origin and establishment of the plastid in algae and plants. Annu. Rev. Genet., 41, 147-168.
Reysenbach1, A. L. and E. Shock. 2002. Merging genomes with geochemistry in hydrothermal ecosystems. Science 296:1077-1082.
Ribeiro, S. and G. B. Golding. 1998. The mosaic nature of the eukaryotic nucleus. Molecular Biology and Evolution 15:779-788.
Ribeiro, S. and Golding, G.B. (1998) The mosaic nature of the eukaryotic nucleus. Molecular Biology and Evolution, 15, 779-788.
Rice, D.W. and Palmer, J.D. (2006) An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol., 4, 31.
Rice, G., L. Tang, K. Stedman, F. Roberto, J. Spuhler, E. Gillitzer, J. E. Johnson, T. Douglas, and M. Young. 2004. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proceedings of the National Academy of Sciences (USA) 101(20):7716-7720.
Richards, T.A. and Cavalier-Smith, T. (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature, 436, 1113-1118.
Richards, T.A. and van der Giezen, M. (2006) Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes. Molecular Biology and Evolution, 23, 1341-1344.
Rivera, M. C., R. Jain, J. E. Moore, and J. A. Lake. 1998. Genomic evidence for two functionally distinct gene classes. Proceedings of the National Academy of Sciences (USA) 95:6239-6244.
Rivera, M. C., and J. A. Lake. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155.
Robinson, R. 2005. Jump-starting a cellular world: Investigating the origin of life, from soup to networks. PLoS Biol 3(11): e396. http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030396
Rodriguez-Ezpeleta, N., Brinkmann, H., Burey, S.C., Roure, B., Burger, G., Loffelhardt, W., Bohnert, H.J., Philippe, H. and Lang, B.F. (2005) Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol, 15, 1325-1330.
Rodriguez-Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A.J., Gray, M.W., Philippe, H. and Lang, B.F. (2007) Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol., 17, 1420-1425.
Roger, A.J. (1999) Reconstructing early events in eukaryotic evolution. Am. Nat., 154, S146-S163.
Roger, A.J., Sandblom, O., Doolittle, W. F., and Philippe, H. (1999) An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. Molecular Biology and Evolution, 16, 218-233.
Rogers, M.B., Gilson, P.R., Su, V., McFadden, G.I. and Keeling, P.J. (2007) The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol. Biol. Evol., 24, 54-62.
Ruiz-Trillo, I., A. J. Roger, G. Burger, M. W. Gray, and B. F. Lang. 2008. A phylogenomic investigation into the origin of Metazoa. Molecular Biology and Evolution 25:664-672.
Ruiz-Trillo, I., Lane, C.E., Archibald, J.M. and Roger, A.J. (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Eukaryot. Microbiol., 53, 379-384.
Ruppert, E. E., R. S. Fox, and R. D. Barnes. 2004. Invertebrate Zoology, a Functional Evolutionary Approach. 7th ed. Brooks/Cole-Thomson Learn, Belmont, CA.
Sapp, J. 2005) Microbial Phylogeny and Evolution: Concepts and Controversies. Oxford University Press, New York.
Schierwater, B., M. Eitel, W. Jakob, H.-J. Osigus, H. Hadrys, S. L. Dellaporta, S.-O. Kolokotronis, and R. DeSalle. 2009. Concatenated molecular and morphological analysis sheds light on early metazoan evolution and fuels a modern .Urmetazoon. hypothesis. PLoS Biol 7(1): e1000020. doi:10.1371/journal.pbio.1000020.
Schlegel, M. (2003) Phylogeny of Eukaryotes recovered with molecular data: highlights and pitfalls. European Journal of Protistology, 39, 113-122.
Schlegel, M., J. Lom, A. Stechmann, D. Bernhard, D. Leipe, I. Dykova, and M. L. Sogin. 1996. Phylogenetic analysis of complete small subunit ribosomal RNA coding region of Myxidium lieberkuehni: Evidence that Myxozoa are Metazoa and related to the Bilateria. Archiv für Protistenkunde 147:1-9.
Schopf, J. W. 2006. Fossil evidence of Archaean life. Philos. T. R. Soc. B 361:869-85.
Schütze J., Krasko, A., Custodio, M.R., Efremova, S.M., Müller, I.M. and Müller, W.E.G. (1999) Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera. Proceedings of the Royal Society of London Series B, 266, 63-73.
Sicheritz-Ponten, T., C. G. Kurland, and S. G. E. Andersson. 1998. A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae. Biochimica et Biophysica Acta Bioenergetics 1365:545-551.
Siddall, M. E. and M. F. Whiting. 1999. Long-branch abstractions. Cladistics 15:9-24.
Siddall, M. E., D. S. Martin, D. Bridge, S. S. Desser, and D. K. Cone. 1995. The demise of a phylum of protists: Phylogeny of myxozoa and other parasitic cnidaria. Journal of Parasitology 81:961-967.
Siddall, M.E., Martin, D.S., Bridge, D., Desser, S.S., and Cone, D.K. (1995) The demise of a phylum of protists: phylogeny of Myxozoa and other parasitic Cnidaria. J. Parasitol., 81, 961-967.
Simpson, A.G. (2003) Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int. J. Syst. Evol. Microbiol., 53, 1759-1777.
Simpson, A.G. and Patterson, D.J. (2001) On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata. J. Eukaryot. Microbiol., 48, 480-492.
Simpson, A.G. and Roger, A.J. (2002) Eukaryotic evolution: getting to the root of the problem. Curr Biol, 12, R691-693.
Simpson, A.G., Inagaki, Y. and Roger, A.J. (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol. Biol. Evol., 23, 615-625.
Simpson, A.G., Roger, A.J., Silberman, J.D., Leipe, D.D., Edgcomb, V.P., Jermiin, L.S., Patterson, D.J. and Sogin, M.L. (2002) Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol. Biol. Evol., 19, 1782-1791.
Simpson, A.G.B. and Patterson, D.J. (1999) The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the "Excavate hypothesis". Eur. J. Protistol., 35, 353-370.
Skophammer, R. G., C. W. Herbold, M. C. Rivera, J. A. Servin, and J. A. Lake. 2006. Evidence that the Root of the Tree of Life Is Not within the Archaea. Molecular Biology and Evolution 23(9):1648-1651.
Smothers, J. F., C. D. von Dohlen, L. H. Smith, Jr., and R. D. Spall. 1994. Molecular evidence that the myxozoan protists are metazoans. Science 265:1719-1721.
Smothers, J.F., van Dohlen, C.D., Smith, L.H., and Spall, R. D. (1994) Molecular evidence that the myxozoan protists are metazoans. Science, 265, 1719-1721.
Sogin, M.L. (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Amer. Zool., 29, 487-499.
Sogin, M.L. (1991) Early evolution and the origin of eukaryotes. Current Opinion in Genetics and Development, 1, 457-463.
Sogin, M.L. and Silberman, J.D. (1998) Evolution of the protists and protistan parasites from the perspective of molecular systematics. International Journal of Parasitology, 28, 11-20.
Sogin, M.L., Elwood, H.J. and Gunderson, J.H. (1986) Evolutionary diversity of eukaryotic small-subunit rRNA genes. Proc. Natl. Acad. Sci. USA, 83, 1383-1387.
Sogin, M.L., Morrison, H.G., Hinkle, G., and Silberman, J. D. (1996) Ancestral relationships of the major eukaryotic lineages. Microbiologia SEM, 12, 17-28.
Staley, J. T. and J. J. Gosink. 1999. Poles apart: Biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology 53:189-215.
Stanier, R.Y. (1970) Some aspects of the biology of cells and their possible evolutionary significance. Symp. Soc. Gen. Mircrobiol., 20, 1-38.
Stechmann, A. and Cavalier-Smith, T. (2002) Rooting the eukaryote tree by using a derived gene fusion. Science, 297, 89-91.
Stechmann, A. and Cavalier-Smith, T. (2003) The root of the eukaryote tree pinpointed. Curr. Biol., 13, R665-666.
Stechmann, A. and T. Cavalier-Smith. (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91.
Steenkamp, E.T., Wright, J. and Baldauf, S.L. (2006) The protistan origins of animals and fungi. Mol. Biol. Evol., 23, 93-106.
Stetter, K. O. 1996. Hypterthermophilic procaryotes. FEMS Microbiology Reviews 18:149-158.
Stiller, J.W. and Hall, B.D. (1997) The origin of red algae: Implications for plastid evolution. Proceedings of the National Academy of Sciences (USA), 94, 4520-4525.
Stiller, J.W. and Hall, B.D. (1999) Long-branch attraction and the rDNA model of early eukaryotic evolution. Molecular Biology and Evolution 16:1270-1279.
Stiller, J.W., Duffield, E.C.S., and Hall, B.D. (1998) Amitochondriate amoebae and the evolution of DNA-dependent RNA polymerase II. Proceedings of the National Academy of Sciences (USA), 95, 11769-11774.
Stiller, J.W., Riley, J., and Hall, B. D. (2001) Are red algae plants? A critical evaluation of three key molecular data sets. Journal of Molecular Evolution, 52(6), 527-539.
Syvanen, M. and C. I. Kado (eds.) 1998. Horizontal Gene Transfer. Chapman & Hall, London.
Takai, K. and K. Horikoshi. 1999. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297.
Taylor F.J.R. (1999) Ultrastructure as a control for protistan molecular phylogeny. American Naturalist, 154(suppl.), S125-S136.
Taylor, F.J. (1978) Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes. Biosystems, 10, 67-89.
Teichmann, S. A. and G. Mitchison. 1999. Is there phylogenetic signal in prokaryote proteins? Journal of Molecular Evolution 49:98-107.
Tidona, C. A. and G. Darai. 2000. Iridovirus homologues of cellular genes -- implications for the molecular evolution of large DNA viruses. Virus Genes 21:77-81.
Tourasse, N. J. and M. Gouy. 1999. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Molecular Phylogenetics and Evolution 13:159-168.
Tovar, J., Fischer, A. and Clark, C.G. (1999) The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol. Microbiol., 32, 1013-1021.
Trends in Genetics 18:1-5.
Turner, S. (1997) Molecular systematics of oxygenic photosynthetic bacteria. Pl. Syst. Evol. [Suppl.], 11, 13-52.
Turner, S., Pryer, K.M., Miao, V.P. and Palmer, J.D. (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J. Eukaryot. Microbiol., 46, 327-338.
Valentine, J. W., D. Jablonski, D. H. Erwin. 1999. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126:851-859.
Van de Peer, Y. and de Wachter, R. (1997) Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. Journal of Molecular Evolution, 45, 619-630.
Van de Peer, Y., Ben Ali, A., and Meyer, A. (2000) Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. Gene, 246, 1-8.
Van de Peer, Y., Van der Auwera, G. and DeWachter, R. (1996) The evolution of stramenopiles and alveolates as derived by 'substitution rate calibration' of small ribosomal subunit RNA. Journal of Molecular Evolution, 42, 201-210.
Vellai T. and Vida, G. (1999) The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proceedings of the Royal Society of London Series B, 266, 1571-1577.
Vellai, T. and G. Vida. 1999. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proceedings of the Royal Society of London Series B 266:1571-1577.
Viale, A. M. and A. K. Arakaki. 1994. The chaperone connection to the origins of the eukaryotic organelles. FEBS Letters 341:146-151.
Viale, A. M., A. K. Arakaki, F. C. Soncini, and R. G. Ferreyra. 1994. Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparison. International Journal of Systematic Bacteriology 44:527-533.
Villarreal, L. P. 2005. Viruses and the Evolution of Life. ASM Press. Washington DC.
Villarreal, L. P. and V. R. DeFilippis. 2000. A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. Journal of Virology 74:7079-7084.
Vishwanatha, P., P. Favaretto, H. Hartman, S. C. Mohr, and T. F. Smith. 2004. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Molecular Phylogenetics and Evolution 33(3):615-625.
Wagner, M. and M. Horn. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotech. 17:241-249.
Wainright, P.O., G. Hinkle, M.L. Sogin, and S.K. Stickel. 1993. Monophyletic origins of the Metazoa: an evolutionary link with Fungi. Science 260: 340-342.
Wainright, P.O., Hinkle, G., Sogin, M.L. and Stickel, S.K. (1993) Monophyletic origins of the metazoa: an evolutionary link with fungi. Science, 260, 340-342.
Wainright, P.O., Patterson, D.J., and Sogin, M.L. (1994) Monophyletic origin of animals: a shared ancestry with fungi. Pages 39-53 in Molecular Evolution of Physiological Processes. Society of General Physiologists Series No. 49. (D. M. Farmborough, ed.) Rockefeller Press, New York.
Wallberg, A., M. Thollesson, J. S. Farris, and U. Jondelius. 2004. The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling. Cladistics 20(6):558-578.
Wang, D. Y.-C., S. Kumar, and S. B. Hedges. 1999. Divergence time estimates for the early history of animal phyla and the origin of plants, animals, and fungi. Proceedings of the Royal Society London Series B 266:163-171.
Ward, C. W. 1993. Progress towards a higher taxonomy of viruses. Research in Virology 144(6):419-453.
Williams, B.A.P. and Keeling, P.J. (2003) Cryptic organelles in parasitic protists and fungi. Adv. Parasitol., 54, 9-67.
Wilson, R.J. (2002) Progress with parasite plastids. J. Mol. Biol., 319, 257-274.
Woese, C. 1998. The universal ancestor. Proceedings of the National Academy of Sciences (USA) 95:6854-6859.
Woese, C. R. 1987. Bacterial evolution. Microbiological Reviews 51:221-271.
Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences (USA) 87:4576-4579.
Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA, 87, 4576-4579.
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evolutionary Biology 1:8-.
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479.
Wolf, Y. I., L. Aravind, N. V. Grishin, and E. V. Koonin. 1999. Evolution of aminoacyl-tRNA synthetases: analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Reserarch 9:689-710.
Wolters, J. and V. A. Erdmann. 1986. Cladistic analysis of 5S rRNA and 16S rRNA secondary and primary structure -- the evolution of eukaryotes and their relation to Archaebacteria. Journal of Molecular Evolution 24:152-166.
Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G.J., and Woese, C. R. (1985) Mitochondrial origins. Proceedings of the National Academy of Sciences (USA), 82, 4443-4447.
Yang, S., R. F. Doolittle, and P. E. Bourne. 2005. Phylogeny determined by protein domain content. Proceedings of the National Academy of Science USA 102(2):373-378 .
Yoon, H.S., Grant, J., Tekle, Y.I., Wu, M., Chaon, B.C., Cole, J.C., Logsdon, J.M., Patterson, D.J., Bhattacharya, D., and Katz, L.A. (2008) Broadly sampled multigene trees of eukaryotes. BMC Evolutionary Biology, 8, 14. doi:10.1186/1471-2148-8-14
Yoon, H.S., Hackett, J.D., Pinto, G. and Bhattacharya, D. (2002) A single, ancient origin of the plastid in the Chromista. Proc. Natl. Acad. Sci. USA, 99, 15507-15512.
Yutin, N., K. S. Makarova, S. L. Mekhedov, Y. I. Wolf, and E. V. Koonin. 2008. The deep archaeal roots of Eukaryotes. Molecular Biology and Evolution 25(8):1619-1630; doi:10.1093/molbev/msn108
Zanotto, P. M. D., M. J. Gibbs, E. A. Gould, and E. C. Holmes. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. Journal of Virology 70(9):6083-6096.
Zrzavy, J. 2001. The interrelationships of metazoan parasites: a review of phylum- and higher-level hypotheses from recent morphological and molecular phylogenetic analyses. Folia Parasitologica 48:81-103.
Zrzavy, J. and V. Hypsa. 2003. Myxozoa, Polypodium, and the origin of the Bilateria: The phylogenetic position of "Endocnidozoa" in light of the rediscovery of Buddenbrockia. Cladistics 19(2):164-169.
Zrzavy, J., S. Mihulka, P. Kepka, A. Bezdek, and D. Tietz. 1998. Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics 14:249-285.
van Regenmortel, M. H. V. 2004. Viruses are real, virus species are man-made, taxonomic constructions. Archives of Virology 148(12):2481-2488.
van Regenmortel, M. H. V. and B. W. J. Mahy. 2004. Emerging issues in virus taxonomy. Emerging Infectious Diseases 10(1):8-13.
van Regenmortel, M. H. V., C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner (eds.) 2000. Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego.
van Regenmortel, M. H. V., M. A. Mayo, C. M. Fauquet, and J. Maniloff. 2000. Virus nomenclature: consensus versus chaos. Archives of Virology 145(10):2227-2232.
van der Giezen, M. and Tovar, J. (2005) Degenerate mitochondria. EMBO Rep., 6, 525-530.
van der Giezen, M., Tovar, J. and Clark, C.G. (2005) Mitochondrion-derived organelles in protists and fungi. Int. Rev. Cytol., 244, 175-225.

Wednesday, May 4, 2011

Response: Rabbi Eric H. Yoffie: The Sad, Naive Atheism of Christopher Hitchens

Response to: Rabbi Eric H. Yoffie: The Sad, Naive Atheism of Christopher Hitchens

The biggest problem with Yoffie's claims are passages such as these in his own, supposed, "Holy" books.
Deuteronomy 7
1 When the LORD thy God shall bring thee into the land whither thou goest to possess it, and hath cast out many nations before thee, the Hittites, and the Girgashites, and the Amorites, and the Canaanites, and the Perizzites, and the Hivites, and the Jebusites, seven nations greater and mightier than thou;
2 And when the LORD thy God shall deliver them before thee; thou shalt smite them, and utterly destroy them; thou shalt make no covenant with them, nor shew mercy unto them
Deuteronomy 13
6 If thy brother, the son of thy mother, or thy son, or thy daughter, or the wife of thy bosom, or thy friend, which is as thine own soul, entice thee secretly, saying, Let us go and serve other gods, which thou hast not known, thou, nor thy fathers;
7 Namely, of the gods of the people which are round about you, nigh unto thee, or far off from thee, from the one end of the earth even unto the other end of the earth;
8 Thou shalt not consent unto him, nor hearken unto him; neither shall thine eye pity him, neither shalt thou spare, neither shalt thou conceal him:
9 But thou shalt surely kill him; thine hand shall be first upon him to put him to death, and afterwards the hand of all the people.
10 And thou shalt stone him with stones, that he die; because he hath sought to thrust thee away from the LORD thy God, which brought thee out of the land of Egypt, from the house of bondage.
...
14 Then shalt thou enquire, and make search, and ask diligently; and, behold, if it be truth, and the thing certain, that such abomination is wrought among you;
15 Thou shalt surely smite the inhabitants of that city with the edge of the sword, destroying it utterly, and all that is therein, and the cattle thereof, with the edge of the sword.
16 And thou shalt gather all the spoil of it into the midst of the street thereof, and shalt burn with fire the city, and all the spoil thereof every whit, for the LORD thy God: and it shall be an heap for ever; it shall not be built again.
Deuteronomy 20
16 But of the cities of these people, which the LORD thy God doth give thee for an inheritance, thou shalt save alive nothing that breatheth
Either these books are lies (leaving nothing supporting claims about god) or you believe that god commands genocide from time-to-time (in which case you are sick and need professional help). I've read the apologetics and they should sicken any rational human being.

If these passages are taken to be historical, then men took swords and SLICED OPEN infant after infant after infant. To even HINT that a god would command such a thing is the most vile lie ever to leave mans lips or his quill. It sickens me to think of the atrocities that men have committed solely because it was CLAIMED that god willed it so. And no, it is not a sufficient defense to claim that these children will go to an imaginary heaven - so that makes it ok. Reverse the situation - have someone murder YOUR CHILD and THEN I want to see you excuse their actions because your child will go to heaven. You KNOW it's wrong.

Various (unsubstantiated) claims have been levied at these people in order to try to justify the atrocities apparently commanded by god in the bible. They worshiped a different god, they had the wrong kinds of sex with each other, they didn't love the way the authors of the bible thought people should love, they committed child sacrifices (kind of like god supposedly commanded of Abraham? IF they were committing child sacrifices then WHY didn't god just intervene in the Hittite ritual like he did for Abraham? Clearly he CAN if he feels like it). But no, this time god said the punishment for those adults who had committed these sins was for their CHILDREN to be hacked to pieces with a sword - and wasn't that a convenient justification for those who would take their land afterwards? I call such a god utterly unworthy of worship. If that really IS the god that exists then it is no wonder his own creations supposedly revolted against him.

I prefer to think that reality is not nearly that evil or stupid. I don't think there is a god at all, least of all a personal god as concieved by warmongering, goat herding, misogynists.

I have no issue with someone who wants to believe in a good higher power as long as they STOP there - once you start making claims about what this god commands or wills then you better have something better than 3000 year old drek about a war god who wills humans to stone each other to death, cut off part of their child's genitalia, and murder entire populations of other people because they are 'bad' (without ever enumerating any crimes which could possibly morally justify such an atrocity).

And you DARE to ask where MY morals come from? -- I ask where YOUR morals come from because they are clearly lacking. My morals come from the evolutionary processes which yielded my ability to observe and predict the consequences of actions. The fact that I CAN make reasoned choices based on knowledge and prediction is what gives me the moral responsibility to make some choices over others.

Don't get me wrong, I don't mean to be picking on Judaism here - Christianity and Islam are all equally vile -- Their disgusting and all too human treatment of one another should be all the evidence anyone needs that there is no god at work behind any of these religions.

You don't need a god to exist to see that we need to work together to make the world a better place for our selves and our children. I applaud all those good people who have been deluded by the call of religious surety and false promises of justice and peace only in a future world and yet remain good people in spite of it. And I condemn all those people who commit ill, some in the name of religious dogma and some in the name of ideological dogma - but all as a result of fallacious logic, incorrect facts, and a fundamental lack or denial of their own humanity.

I do not believe in god but I HOPE a god exists - a just and moral god that had nothing to do with Judaism, Christianity, or Islam. If I am to be punished for trying to live a good life and being HONEST about the evidence before me, then so be it - I welcome it because I would have NOTHING to do with such a petty, jealous, petulant god.

And I do not wish to scapegoat the punishment for my sins onto another either. I'll have nothing to do with the cannibalistic and sick worship of the torture and murder of another human being whom was (at best) mislabeled Christ. [There is simply not sufficient evidence to believe a Jesus person actually existed as described in the Christian bible - but neither is there sufficient evidence to support the claims of Exodus].

So yes, I believe I am more moral than the average religious person BECAUSE I refuse to accept some foolish authority which makes blatantly HORRENDOUS claims about what is supposedly moral.

I have sound logical justifications for my ethical beliefs AND I am open to questioning them in light of new evidence or argument. The crime of the religious believer is that they form their ethical beliefs in a near vacuum of data (save the appeal to authority of some book) and then proceed to commit crimes against humanity wearing the blinders of righteous indignation. Nothing makes a non-believer more sure of their choices than the statements and action of such a hypocrite.