Evolution Must Happen, it is logical

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Ok, so item 8 isn't factual. Is there another way of getting there?

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Theoretically, the best way to construct phylogenies is to use genetic sequences that are strongly conserved and common to all species under investigation. Ribosomal RNA (rRNA) is one way in which scientists are now investigating the genetic relatedness of divergent species. Do a search for "rRNA phylogenies" and you will get a lot of hits. rRNA (or more accurately SSU rRNA phylogenies) research is still early in development but it does look promising.Here are a few abstracts dealing with rRNA and protein phylogenies. You will notice that rRNA phylogenies are useful for divergent species while other proteins are useful for finer-grade species:This abstract uses rRNA to counteract the occurence of horizontal gene transfer (genetic transfer between different species) in order to construct phylogenies within bacteria and how they relate to eukaryotes.
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Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response - PubMed
Mol Phylogenet Evol. 2005 Feb;34(2):371-81. Epub 2004 Dec 15. Related Articles, LinksReconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response.Briones C, Manrubia SC, Lazaro E, Lazcano A, Amils R.Centro de Astrobiologia, Carretera de Ajalvir Km. 4, 28850 Torrejon de Ardoz, Madrid, Spain.The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life.
----------------------------------------------------------------------This abstract demonstrates that other conserved proteins may be more useful in constructing phylogenies of species that are more closely related.
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Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms - PubMed
Genes Genet Syst. 2004 Oct;79(5):293-9. Related Articles, LinksMolecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms.Nagaraju J, Ranganath HA; Nagaraja.Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore.The nasuta subgroup is a cluster of morphologically almost similar forms with a wide range of geographic distribution. During the last three decades nature of inter-relationship among the members has been investigated at different levels of organization. The phylogenetic relationships of the members of the nasuta subgroup of the immigrans species group of Drosophila was made by employing Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeats-PCR (ISSR-PCR) polymorphisms, mitochondrial 12S rRNA, 16S rRNA and Cytochrome C Oxidase subunit I (CoI) gene sequences. The phylogenetic tree generated by RAPD analysis is in nearly complete congruence with the classification based on morphophenotypic characters. The 12S and 16S rRNA genes were highly conserved across the nasuta subgroup and revealed only 3 and 4 variable sites respectively, of which only one site was informative. The CoI gene, on the other hand, revealed 57 variable sites of which 25 sites were informative. All the three species of orbital sheen complex were included in a major cluster in the phylogenetic trees derived from mitochondrial gene sequence data consistent with the morphophenotypic classification. The CoI analysis placed two species of frontal sheen complex, D. n. nasuta and D. n. albomicans in two different clades and this is inconsistent with morphological classification. The molecular clock suggested that divergence between the kohkoa complex and the albomicans complex occurred ~2.2 MYA, indicating recent evolution of the nasuta subgroup. The higher transition bias in the mitochondrial genes reported in the present study also suggested recent evolution of the nasuta subgroup.
----------------------------------------------------------------------A great study that uses new methods of comparing rRNA. It shows that the genetic data independently verifies the phylogenies constructed through morphological traits within Insectevora (insects).
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Aligned 18S and insect phylogeny - PubMed
Syst Biol. 2004 Jun;53(3):506-14. Related Articles, LinksAligned 18S and insect phylogeny.Kjer KM.Department of Ecology Evolution and Natural Resources, 14 College Farm Road, Cook College, Rutgers University, New Brunswick, NJ 08901, USA. kjer@aesop.rutgers.eduThe nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.
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I need something to say that there are no really big gaps in spite of how different things look from Man to Mouse to fish to worm to...
Even tough I know that the time from some of the branch points may mean there are rather large genetic gaps between species today I am trying to see if you look at the tip of the branches now you can find nearby ones on the tree of life. And then go from branch tip to branch tip with smallish genetic differences.

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Ahh, I gotcha.What you should be looking for is mutation rates. Not only mutation rates, but the mutation rate of "junk DNA" vs. "transcribed DNA". Throughout genetics, it is observed that non-transcribed, non-regulatory DNA (ie junk DNA) contains more differences than transcribed DNA between species who share a recent common ancestor. This allows us to roughly estimate the occurrence of neutral and beneficial mutations within transcribed DNA. It is a very rough estimate, but junk DNA almost always contains more mutations than transcribed DNA, as would be expected.But this isn't the whole enchilada. The second mode of evolution, outside of mutation and selection, is speciation. This is a little harder to map. Mutations happen in a somewhat clockwork fashion. Speciation can happen quickly or not at all, depending on the situation. Mutations are related to biochemical processes while speciation relies on the environment and genetic flow within the population.Perhaps a good place to look is in comparing relatively stable environments with little immigration, such as the American Prairie, and areas with sudden immigration. One such place/species group are the cichlids. These fish speciated quickly once they entered into the Lake Victoria complex. Some estimate the number of new species at 250+, all of which occurred in less than 250,000 years. However, all 250 species differ very little genetically. This is in contrast to a more stable environment where species share far less genetic similarity and more distant common ancestors.I really don't have that many references on cichlids, so much of this is from memory. I do remember enough to know that this might fit into your ideas. Anyone else have good references for cichlids?

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When we look at extant life do we see any huge chasms anywhere?

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Boy, you really are going back to basics.The biggest division I see is the divide between prokaryote and eukaryote. This division was not caused by natural selection and mutation directly, but rather through endosymbiosis. The mitochondria, and later in plants the chloroplast, are captured organisms that made eukaryotes possible. The organisation of the nucleus and cytoplasmic space are also hurdles that may have been crossed through endosymbiosis. However, the root of the whole eukaryotic clade could have been a one time event, the engulfment of another organism. IMHO, the divide between plants and animals is not nearly as wide as the divide, or chasm, between prokaryotes and eukaryotes.

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Of course, if we pick an oak tree and an aardvark the genetic difference is very large. Is there, however, a path of organisms that are currently alive that connects the two without any very large chasms?

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I wrote a whole paragraph on "what I don't know about basal eukaryotes" before I started looking around and found the answer. That, and I hit myself in the head for forgetting the my first semester of Zoology class. The common ancestor to both plants and animals are (according to evolutionary theory) protists. Extant organisms include amoebas, euglenia, and quite a few others. Read more here: Introduction to the Basal EukaryotesABE: The homepage (Tree of Life Web Project) might be useful as well. I haven't looked at it in depth, but it seems pretty accurate and basic.ABE, again: Dammit, I no sooner post an edit than I find the answer you are looking for. Below are two trees that give the realationship between the major lineages (two different views). All of life can be categorized by one of those headings. You will notice that where the clades intersect there is not a lineage given. This is because there are no representatives of that common ancestor. For example, in the archaea tree, there is not an extant (or fossil I presume) species representing the common ancestor of eubacteria, archae, and eukaryotes. These are the chasms that you want to know about.The graph transfered over as ASCII. Check it out here: Life on EarthThis message has been edited by Loudmouth, 01-11-2005 20:47 AMThis message has been edited by Loudmouth, 01-11-2005 20:54 AM

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Even if you had 100's of species with only 0.5% genetic difference, however that was measured, between each adjacent one, you would still have a hard time convincing a 'true believer'.

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I think we all know that nothing will convince the "true believer" until they want to listen. I have even heard of creationists, once they have to face up to the fossil evidence, who proclaim that demons create fossils that look transitional. And I don't think we need to talk about the link between demons and gastro-intestinal emmissions . . . Anyway, you get my drift.Instead of focusing on the gradations between each fossil or extant species, I think it might be better to talk about the hierarchial structure of taxonomy. On another forum (username "Aaron-ra" at Christian Forums) had a great idea. He is walking people through the nested hierarchies of life, using humans as the guide.When one walks through these criteria of how life is organized, and how nested hierarchies are a real phenomena, it makes it hard to deny that evolution is not on to something. This covers some of the same ground that Ned is trying to cover, but it starts from the other end of the question. Instead of "Evolution must happen" it becomes "Common Ancestory had to have happened".Best of all, there are no gaps in nested hierarchies, no transitionals to find, no questionable fossils. All of the evidence for nested hiearchies is alive today, but fossil species don't hurt either.However, as well all know, common ancestory does not make evolution true. But, it does take us one step away from creationism.

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Would it be reasonable to say that if micro-evolution happens, then macro-evolution must also happen? Is there some logical reason why evolution would have to stop at the micro level?

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The scientific definition of macroevolution is speciation, or the creation of two gene pools from one gene pool. Evolution, as a process, does not absolutely require this to happen. However, given the characteristics of genetics and the environment, it is bound to happen. Also, we have observed this process happening in nature. Once there are two separate gene pools, there is nothing preventing these two species from acquiring completely different characteristics over time.Earth's environment makes speciation a necessary step in evolution. There are numerous niches that life can occupy, and these niches are so different that a single species would not be able to fill all of them. Therefore, speciation allows part of the population to specialize itself to one niche while another part of the population specializes itself to another niche. This process continues and continues until all of the niches are filled. Once a species is completely specialized to a particular niche, as long as that niche exists that species will not change much. In fact, natural selection will actually prevent the species from changing.So I guess the answer to your question is yes. The acquisition of mutations will tend to give some members of the population an edge in certain niches that are currently open. This first initial push will separate these individuals and their offspring from the rest of the population until there are two separate gene pools. This process then repeats itself. All of these separate gene pools will build up mutations that are specific to that gene pool, so the different species will tend to look quite different after a long period of time has passed.

Hey truthlover, you lurking rapscallion you. Nice to here from ya.It is Aron-Ra, sorry for the mix up.You can find the thread here. Aron-Ra does a great job but then the thread exploded and went off topic at about mssg #82. He got to phylum chrodata and then all hell broke loose, literally.Nice to here from ya big fella, hope things are going well.