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Topic: Molecular phylogeny

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Phylogenetics

Molecular biology

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	Molecular Phylogeny
		Molecular sequencing illuminates the evolutionary history of the molecules themselves and, consequently, that of their host organisms.
		Molecular dating, while not always in agreement with fossil evidence, offers an opportunity for timing events that are otherwise unobservable.
		However, the molecular clock method must be applied with caution because molecular clocks are not nearly as constant as often believed.
	www.peripatus.gen.nz /Biology/MolPhy.html (2652 words)

	Molecular phylogeny - Definition, explanation
		Molecular phylogeny is the use of a gene's molecular characteristics to classify an organism and to place it on a map of evolutionary relationships known as the phylogenetic tree.
		Molecular phylogeny, caryology, and systematics of Gentianaceae at the University of Neuchatel, Switzerland.
		Molecular phylogeny, caryology, and systematics of Gentianaceae at the University...
	www.calsky.com /lexikon/en/txt/m/mo/molecular_phylogeny.php (609 words)

	Classification - Carnivorous Plant by Makoto Honda
		Molecular phylogenetic analyses continue to provide quantitative data for objective inference of angiosperm phylogeny, largely eliminating room for subjective interpretations that have resulted in differing taxonomic views in the past.
		Molecular systematics relies on gene sequencing which allows the determination of the exact sequence of nucleotides in DNA and RNA.
		Molecular evidence shows these species are closely related, with Aldrovanda being sister to Dionaea, suggesting a common ancestral origin of these snap-traps.
	www.honda-e.com /A03_Classification/PhylogeneticTreeText.htm (1222 words)

	Molecular systematics Summary
		Molecular systematics is a phrase used to indicate a branch of the traditional field of systematics that utilizes molecular biology techniques.
		Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be at least paraphyletic and preferably monophyletic.
		Molecular systematics often uses the molecular clock assumption that quantitative similarity of genotype is a sufficient measure of the recency of genetic divergence.
	www.bookrags.com /Molecular_systematics (3648 words)

	Cytochrome b sequence variation and a molecular phylogeny of the live bearing fish genus Gambusia (Cyprinodontiformes: ...
		Cytochrome b sequence variation and a molecular phylogeny of the live bearing fish genus Gambusia (Cyprinodontiformes: Poeciliidae).
		Cytochrome b sequence variation and a molecular phylogeny of the live-bearing fish genus Gambusia (Cyprinodontiformes: Poeciiiidae)
		As with other fishes, the overall rate of divergence appeared to be slower than that of other vertebrates and the overall replacement/substitution pattern was suggestive of nonrandom evolutionary input.
	www.uga.edu /srel/Reprint/1973.htm (205 words)

	Molecular phylogeny
		To fully grasp molecular phylogeny one should know basic genetics, including DNA replication, protein synthesis, mutation, recombination, etc.
		Molecular phylogeny employs nucleotide sequences (or some character depending on sequences) from several organisms to compute the tree requiring the fewest of steps.
		Evolution required molecular phylogeny to be consistent with classical phylogeny.
	www.geocities.com /lclane2/phylo.html (279 words)

	- Välkommen till Bergianska Trädgården -
		Phylogeny of the complex Vanguerieae (Rubiaceae) genera Fadogia, Rytigynia, and Vangueria with close relatives and a new circumscription of Vangueria.
		Molecular Phylogenetics and Evolution 34: 334-354, and 37: 938-939.
		Molecular phylogeny of the extinct cave lion Panthera leo spelaea.
	www.bergianska.se /forskning_publikationer.html (851 words)

	Livingunderworld.org Works Cited
		A molecular phylogenetic perspective on the origins of morphological novelties in the salamanders of the tribe Plethodontini (Amphibia, Plethodontidae).
		Molecular phylogeny of the genus Paramesotriton (Caudata: Salamandridae).
		Molecular phylogeny of the salamandrid genus Neurergus: evidence for an intrageneric switch of reproductive biology.
	www.livingunderworld.org /works_cited (1908 words)

	Prion Molecular Phylogeny
		Molecular phylogeny based on aligning single genes gives erratic results, depending on assumptions, methodologies, and weighting schemes.
		This turns conventional molecular phylogency on its head -- instead of trying to deduce the tree and dates from prion sequences, we use a consensus tree derived from many genes and fossils and ask where, how fast, and when mutations in the prion gene become accepted as dominant alleles.
		A partial prion sequence has been completed from a dolphin (toothed whale); from molecular taxonomy, it is expected to have features in common with giraffe, deer, cow, and oryx lacking in pig or camel (one expects closest of all to hippo, then chevrotain).
	www.mad-cow.org /moly_phylo.html (1760 words)

	Phylogeny of the family Cichlidae
		Efforts to use molecular markers have not involved any comprehensive treatment of the group, and were usually limited to a few species and left many recognized groups unrepresented.
		Phylogenies for the group based on molecular characters are partial and not comprehensive, usually part of a phylogeny of larger groups of cichlids or of Cichlidae in general.
		The gene for ependymin is presumed to be a good molecular marker for this group since it is a single-copy nuclear gene and previous studies in other groups of fish have shown that ependymin has a good phylogenetic signal over a wide range of taxonomic distance and divergence time.
	golab.unl.edu /projects/Cichlidae (1488 words)

	Spartanburg SC \| GoUpstate.com \| Spartanburg Herald-Journal (Site not responding. Last check: )
		Molecular phylogeny is the use of the structure of molecules to gain information on an organism's evolutionary relationships.
		Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms.
		Another application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
	www.goupstate.com /apps/pbcs.dll/section?category=NEWS&template=wiki&text=molecular_phylogeny (265 words)

	Molecular phylogeny of nitrogen-fixing unicellular cyanobacteria (Site not responding. Last check: )
		Molecular phylogenetic study was conducted using maximum likelihood tree inference methods with small subunit ribosomal RNA sequence data to ascertain the evolutionary relationships among sheathless, single-cell cyanobacteria capable of nitrogen fixation.
		The halotolerance and phylogeny of cyanobacteria with tightly coiled trichomes (Spirulina Turpin) and the description of Halospirulina tapeticola gen. nov., sp.
		Wilmotte, A.P. Molecular evolution and taxonomy of the cyanobacteria.
	ejournal.sinica.edu.tw /bbas/content/2001/3/bot423-04.html (3281 words)

	Teaching Animal Molecular Phylogenetics
		The molecular phylogeny of 10 strains of laboratory mice inferred from chromosomal differences agreed exactly with the known phylogeny (Fitch and Atchley 1987).
		Molecular phylogenetics correctly reconstructed the branching pattern and branch lengths for a virus serially propagated in the presence of a mutagen (Hillis et al.
		Phylogenies of birds and mammals based on different molecules were more nearly in agreement with each other than were phylogenies based on different morphological characters (Bledsoe and Raikow 1990).
	www.mhhe.com /biosci/pae/zoology/animalphylogenetics/section01.mhtml (5259 words)

	MOLECULAR PHYLOGENY (Site not responding. Last check: )
		An early study using amino acid of the VWF nuclear gene and local molecular clock methodology was conducted as a first attempt to specify the timing of their radiation with special emphasis on the status of the controversial fossil Eurotamandua.
		Delsuc F. Catzeflis F.M., Stanhope M.J. and Douzery E.J.P. The evolution of armadillos, anteaters, and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua.
		Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes.
	www.isem.univ-montp2.fr /PPP/PM/RES/Phylo/Xen/@Xenarthra.php (1076 words)

	Molecular Systematics
		Second, if previous molecular studies are any indication, the molecular phylogeny will differ from morphological phylogenies in several respects, and this will inspire careful examination of molecular and morphological evidence.
		If no potential source of bias in the molecular data can be found, this should inspire morphologists to carefully reevaluate the characters underlying that part of their phylogeny.
		Molecular data consistently fails to support this clade, instead suggesting a close relationship between Macroscelidea and paenungulate taxa.
	www.bio.umass.edu /biology/adkins/Systematics.html (2774 words)

	The Role of Morphological Data in Phylogeny Reconstruction - Science - RedOrbit (Site not responding. Last check: )
		Second, until we reach the stage where all molecular phylogenies are reconstructed without error, it is still important to have rigorous, morphology-based phylogenies as a "reality check" for molecular results (e.g., Doyle, 1992; Hillis and Wiens, 2000; Jenner, 2004).
		If students are trained exclusively in molecular techniques, the next generation of systematists may be incapable of identifying the species in their study groups, and phylogenetic progress in these groups may quickly "grind" to a halt.
		SEA suggest that the best approach for integrating molecular and morphological data is to map a limited number of "unambiguous" morphological characters onto the molecular phylogeny.
	www.redorbit.com /news/display?id=92556 (5331 words)

	Molecular Phylogeny of Parasitic Zygomycota (Dimargaritales, Zoopagales) Based on Nuclear
		Molecular evidence for the early colonization of land by fungi and plants.
		Phylogeny of discomycetes and early radiations of the apothecial ascomycotina inferred from SSU rDNA sequence data.
		The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides.
	www.biology.duke.edu /fungi/phylogeny/references.html (1535 words)

	Molecular Phylogeny
		Phylogenies, or evolutionary trees, are the basic structures necessary to reveal the differences among species, and to analyze those differences statistically.
		Generally speaking, a problem in molecular phylogeny starts from the identification of a sequence (DNA, RNA, or Protein) that is of particular interest to the researchers.
		It does not assume a molecular clock (i.e., all species evolve with the same rate) and instead assumes the minimum evolution model, that is, at each step of the algorithm (which will be given later), the topology that gives the least branch length is preferred.
	darwin.nmsu.edu /~molb470/fall2005/projects/pan (1097 words)

	Wayne Maddison
		Phylogeny of salticid spiders — The handful of systematists who have worked on salticid phylogenetics over the last century have begun to resolve the outlines of groups, but considerable work remains.
		A better resolved phylogeny and the corresponding classification of subfamilies and genera would facilitate efforts to discover new species and distinguish among them, and would also open the group to phylogenetically-based studies of evolutionary processes.
		Recently we completed a first molecular phylogeny for the family, but continued sampling is needed to fill in the phylogeny with many more genera, especially from Asia, Oceania, and Africa.
	salticidae.org /wpm (968 words)

	Kathleen Pryer's Lab
		A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera.
		Molecular phylogenetic relationships and morphological evolution in the heterosporous fern genus Marsilea.
		Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences.
	www.pryerlab.net /publication (1012 words)

	BioMed Central \| Full text \| Molecular phylogeny and taxonomic revision of the sportive lemurs (Lepilemur, Primates)
		Based on molecular data we propose to recognize the sportive lemur populations from north of the Tsiribihina River, south of the Betsiboka River, and from the Sahamalaza Peninsula, as distinct species.
		Molecular studies, especially the sequencing of mitochondrial genes, have expanded enormously during the last decade and have helped to characterise biodiversity and biogeographic patterns of Malagasy lemurs [10-19].
		In contrast, cytogenetics or molecular methods such as sequencing of marker genes offer powerful tools that lead to important insights into the diversity and phylogeny of several Malagasy lemur genera [17,19,28,29].
	www.biomedcentral.com /1471-2148/6/17 (5746 words)

	Molecular Phylogeny (Site not responding. Last check: )
		Although the morphologies and physiologies of prokaryotes are much simpler than those of eukaryotes, there is a large amount of information in the molecular sequences of their DNA, RNAs and proteins.
		Thus, it is possible to use molecular similarities to infer the relationships of genes, and, by extension, to learn the relationships of the organisms themselves.
		In principle, the range accessible to molecular analysis could be increased by looking at specific genes with above average conservation.
	lecturer.ukdw.ac.id /dhira/ClassAndPhylo/molPhylogeny.html (934 words)

	A Global Molecular Phylogeny of the Small Puffinus Shearwaters and Implications for Systematics of the Little-Audubon's ... (Site not responding. Last check: )
		A molecular phylogeny based on 917 base pairs (bp) of the mitochondrial (mt) DNA cytochrome-b gene was used to test and reassess the systematics and conflicting taxonomic treatments of the small, fl-and-white Puffinus shearwaters, including the P. assimilis-lherminieri species complex.
		Phylogenies derived separately from the three overlapping cytochrome-fc subfragments amplified from most museum specimens were congruent with the topology derived from the complete 917 bp (data not shown), indicating that the sequences are not chimeric.
		In addition, molecular data from unsampled taxa and populations and from multiple nuclear genes (Prychitko and Moore 1997, Lovette and Bermingham 2000, Shapiro and Dumbacher 2001) are required to refine and confirm the current mtDNA-based phylogeny.
	www.redorbit.com /news/display?id=76547 (6438 words)

	Lesson: Molecular Biology & Phylogeny
		Relationship patterns derived from molecular structure are consistent with those derived from anatomical structure.
		As in other characteristics, we would expect those organisms with fewer differences in their protein amino-acid sequences to be derived from common ancestors more recently, and therefore to be more closely related.
		Based on the molecular data, make a general statement about the "human-monkey" relationship as compared to the "duck-chicken" relationship (which shows three differences in their amino acids).
	www.indiana.edu /~ensiweb/lessons/mol.bio.html (1975 words)

	Molecular Phylogeny
		Molecular identification of the maternal parent of hybrids and hybridogenous species
		Maternal inheritance of the chloroplast DNA in this group was ascertained by the analysis of progeny from reciprocal crosses using parents of known distinct haplotypes (Fehrer et al.
		Ongoing research is aimed at a molecular phylogeny of the whole genus on a coarse taxonomical level.
	www.ibot.cas.cz /hieracium/studygroup/phylogeny.html (512 words)

	Molecular Phylogeny
		Molecular biology often helps in determining genetic relationships between different organisms.
		In particular, the sequence of the small-subunit ribosomal RNA (rRNA) is widely used in molecular phylogeny.
		One advantage of the molecular approach in determining phylogenetic relationships over the more classical approaches, such as those based on morphology or life cycle traits, is that the differences are readily quantifiable.
	www.tulane.edu /~wiser/protozoology/notes/tree.html (540 words)

	MOLECULAR EVOLUTION
		MOLECULAR EVOLUTION: Phylogenetic analysis and evolutionary processes (Information on molecular evolution relevant to this section is in Freeman and Herron (2001) Chapter 18; information on mutation that is relevant to this section is in Freeman and Herron Chapter 4.
		One major difficulty in the study of phylogeny is the existence of convergent evolution.
		You would like to use the molecular clock to estimate the times of speciation of the clam species, and you have a date of speciation for two species from the fossil record.
	www.utm.edu /departments/cens/biology/rirwin/391/391ManChXII.htm (1670 words)

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