Abstract
The evolutionary analysis of DNA sequences bridges phylogenetics and population genetics. Ancient DNA (aDNA) allows the study of extinct genotypes, populations, and species, as well as dichronic comparisons of extant populations and species. Thus aDNA forges an empirical link between history and two inherently historical fields of research. Fortunately, the conceptual frameworks of phylogenetics and population genetics can easily be extended to encompass advances being made in the study of aDNA.
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References
Aquadro CF, Kaplan N, Risko KJ (1984) An analysis of the dynamics of mammalian mitochondrial DNA sequence evolution. Mol Biol and Evol 5:423–434
Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–521
Bibb M, Van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of the mouse mitochondrial DNA. Cell 26:167–180
Birky CW Jr (1991) Evolution and population genetics of organelle genes: mechanisms and models. In: Selander RK, Clark AG, Whittam TS (eds) Evolution at the Molecular Level. Sunderland Mass.: Sinauer, pp. 112–134
Birky CW Jr, Maruyama T, Fuerst P (1983) An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts and some results. Genetics 103:513–527.
Birky CW Jr, Fuerst P, Maruyama T (1989) Organelle gene diversity under migration, mutation and drift: equilibrium expectations, approaches to equilibrium, effects of heteroplasmic cells, and comparisons to nuclear genes. Genetics 121:613–627
Brown WM (1985) The mitochondrial genome of animals. In: MacIntyre RJ (ed) Molecular Evolutionary Genetics, New York: Plenum Press, pp. 95–130
Brown GG, Simpson MV (1982) Novel features of animal mtDNA evolution as shown by sequences of two cytochrome oxidase subunit II genes. Proc Natl Acad Sci USA 79:3246–3250
Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad USA 76:1967–1971
Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequence of primates: tempo and mode of evolution. J Mol Evol 18:225–239
Carpenter JM (1988) Choosing among multiple equally parsimonious cladograms. Cladistics 4:291–296
Carson HL (1975) The genetics of speciation at the diploid level. Am Naturalist 109:83–92
Carson HL (1982) Speciation as a major reorganization of polygenic balances. In: Barigozzi C (ed) Mechanisms of Speciation. New York: Alan R. Liss, pp. 411–433
Clegg MT, Learn GH, Golenberg EM (1991) Molecular evolution of chloroplast DNA. In: Selander RK, Clark AG, Whittam TS (eds) Evolution at the Molecular Level. Sunderland, Mass.: Sinauer, pp. 135–149
Cracraft J, Helm-Bychowski K (1991) Parsimony and phylogenetic inference using DNA sequences: some methodological strategies. In: Miyamoto MM, Cracraft J (eds) Phylogenetic Analysis of DNA Sequences. Oxford: Oxford Univ. Press, pp. 184–220
DeSalle R, Freedman T, Prager EM, Wilson AC (1987) Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J Mol Evol 26:157–164
Donoghue MJ, Doyle JA, Gauthier J, Kluge AG, Rowe T (1989) The importance of fossils in phylogeny reconstruction. Annu Rev Ecol Syst 20:431–460
Dover G (1987) DNA turnover and the molecular clock. J Mol Evol 26:47–58
Endler JA (1977) Geographic Variation, Speciation and Clines. Princeton, N.J.: Princeton Univ. Press
Farris JS (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in Cladistics, vol 2. New York: Columbia Univ. Press, pp. 7–36
Felsenstein J (1978) The number of evolutionary trees. Syst Zool 27:27–33
Felsenstein J (1979) Alternative methods of phylogenetic inference and their interrelationship. Syst Zool 28:49–62
Felsenstein J (1983) Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14:313–333
Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521–565
Felsenstein J (1989) PHYLIP 3.2 Manual. Berkeley, Cal.: Univ. of California Herbarium
Gillespie JH (1991) The Causes of Molecular Evolution. Oxford: Oxford Univ. Press
Golenberg EM (1991) Amplification and analysis of Miocene plant fossil DNA. Phil Trans R Soc Lond B 333:419–426
Gyllensten U. Wharton D, Joseffson A, Wilson AC (1992) Paternal inheritance of mitochondrial DNA in mice. Nature (London) 352:255–357
Hafner JC, Hafner MS (1983) Evolutionary relationships of heteromyid rodents. Great Basin Naturalist Memoirs 7:3–29
Harrison RC (1990) Hybrid zones: windows on evolutionary processes. In: Futuyama D, Antonovics J (eds) Oxford Surveys in Evolutionary Biology, vol 7. Oxford: Oxford Univ. Press, pp. 69–128
Hendy MD, Penny D (1989) A framework for the quantitative study of evolutionary trees. Syst Zool 38:297–309
Hennig W (1965) Phylogenetic systematics. Annu Rev Entomol 10:97–116
Hey J (1991) The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations. Genetics 128:831–840
Hillis DM (1991) Discriminating between phylogenetic signal and random noise in DNA sequences. In: Miyamoto MM, Cracraft J (eds) Phylogenetic Analysis of DNA Sequences. Oxford: Oxford Univ. Press, pp. 278–294
Hillis D, Huelsenbeck J (1992) Signal, noise, and reliability in molecular phylogenetic analysis. Jour Hered 83:189–195
Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J (eds) Oxford Surveys in Evolutionary Biology, vol. 7. Oxford: Oxford Univ. Press, pp. 1–44
Irwin D, Kocher TD, Wilson AC (1991) Evolution of the cytochrome b gene of mammals. J Mol Evol 32:128–144
Kaplan NL, Hudson RR, Langley CH (1989) The “hitchhiking effect” revisited. Genetics 123:887–899
Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge Univ. Press
Kocher TD, Wilson AC (1991) Sequence evolution of mitochondrial DNA in humans and chimpanzees: control region and a protein coding region. In: Osawa S, Honjo T (eds) Evolution of Life. Tokyo: Springer-Verlag, pp. 391–413
Kreitman M (1991) Detecting selection at the level of DNA. In: Selander RK, Clark AG, Whittam TS (eds) Evolution at the Molecular Level. Sunderland, Mass.: Sinauer, pp. 204–221
Lessa EP (1992) Rapid surveying of DNA sequence variation in natural populations. Mol Biol Evol 9:323–330
Lewontin RC (1985) Population genetics. In: Greenwood PJ, Harvey PH, Slatkin M (eds) Evolution: Essays in the Honor of John Maynard Smith. Cambridge: Cambridge Univ. Press, pp. 3–18
Lewontin RC (1991) Twenty-five years ago in genetics: electrophoresis in the development of evolutionary genetics—milestone or millstone? Genetics 128:657–662
Maddison WP, Donoghue MJ, Maddison DR (1984) Outgroup analysis and parsimony. Syst Zool 33:83–103
Mayr E (1954) Change of genetic environment and evolution. In: Huxley J, Hardy AC, Ford EB (eds) Evolution as a Process. New York: MacMillan, pp. 157–180
Mayr E (1963) Animal Species and Evolution. Cambridge, Mass.: Harvard Univ. Press
Miyamoto MM, Boyle SM (1989) The potential importance of mitochondrial DNA sequences to eutherian mammal phylogeny. In: Fernholm B, Bremer K, Jörnvall H (eds) The Hierarchy of Life. Amsterdam: Elsevier, pp. 437–450
Moritz C, Dowling TE, Brown WM (1987) Evolution of mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst 18:269–292
Nei M (1987) Molecular Evolutionary Genetics. New York: Columbia Univ. Press
Ohta T (1987) Very slight deleterious mutations and the molecular clock. J Mol Evol 26:1–6
Orrego C (1990) Organizing a laboratory for PCR work. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: A Guide to Methods and Applications. San Diego: Academic Press, pp. 447–454
Pääbo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86:1939–1943
Pääbo S (1990) Amplifying ancient DNA. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols: A Guide to Methods and Applications. San Diego: Academic Press, pp. 159–166
Pääbo S, Wilson AC (1988) Polymerase chain reaction reveals cloning artefacts. Nature (London) 334:387–388
Pääbo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–4721
Palumbi SR (1989) Rates of molecular evolution and the number of nucleotide positions free to vary. J Mol Evol 29:180–187
Pamilo P, Nei M (1988) Relationship between gene trees and species trees. Mol Biol Evol 5:568–583
Runnegar B (1991) Nucleic acid and protein clocks. Phil Trans R Soc Lond B 333: 391–397
Sanderson MJ, Donoghue DJ (1989) Patterns of variation in levels of homoplasy. Evolution 43:1781–1795
Slatkin M (1985) Gene flow in natural populations. Annu Rev Ecol Syst 16:393–430
Slatkin M (1987) The average number of sites separating DNA sequences drawn from a subdivided population. Theor Popul Biol 32:42–49
Slatkin M (1989) Detecting small amounts of gene flow from phylogenies of alleles. Genetics 121:609–612
Slatkin M (1991) Inbreeding coefficients and coalescence times. Genet Res Camb 58:167–175
Slatkin M, Maddison WP (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123:602–613
Sokal RR, Rohlf FJ (1981) Biometry, 2nd ed. New York: Freeman, W.H.
Spaulding WG (1990) Vegetational and climatic development of the Mojave Desert: the last glacial maximum to the present. In: Betancourt JL, Van Devender TR, Martin PS (eds) Packrat Middens, Tucson: Univ. of Arizona Press, pp. 166–199
Swofford DL (1989) Phylogenetic analysis using parsimony (ver. 3.0). Illinois Natural History Survey
Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular Systematics. Sunderland Mass: Sinauer, pp. 411–501
Tajima F (1983) Evolutionary relationship of DNA sequences in a finite population. Genetics 105:437–460
Tajima F (1989a) Statistical method for testing the neutral mutation hypothesis of DNA polymorphism. Genetics 123:585–595
Tajima F (1989b) The effect of change in population size on DNA polymorphism. Genetics 123:597–601
Takahata N (1987) On the overdispersed molecular clock. Genetics 116:169–179
Takahata N, Slatkin M (1990) Genealogy of neutral genes in two partially isolated populations. Theor Popul Biol 38:331–350
Thomas RH, Schaffner W, Wilson AC, Pääbo S (1989) DNA phylogeny of the extinct marsupial wolf. Nature (London) 340:465–467
Thomas WK, Pääbo S, Villablanca FX, Wilson AC (1990) Spacial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. J Mol Evol 31:101–112
Villablanca FX, Thomas WK (1993) Empirical limits to the phylogenetic utility of DNA sequences. M.S. submitted
Walsh SP, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10:506–513
Watrous LE, Wheeler QD (1981) The outgroup comparison method of character analysis. Syst Zool 30:1–11
Wiley EO (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics. New York: Wiley
Wilson AC, Cann RL, Carr SM, George M, Gyllensten UR, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26:375–400
Wilson AC, Zimmer EA, Prager EM, Kocher TD (1989) Restriction mapping in the molecular systematics of mammals: a retrospective salute. In: Fernholm B, Bremer K, Jörnvall H (eds) The Hierarchy of Life. Amsterdam: Elsevier, pp. 407–419
Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058
Wood AE (1935) Evolution and relationships of the heteromyid rodents with new forms from the Tertiary of western North America. Ann Carnegie Mus 24: 73–262
Wright S (1969) Evolution and the Genetics of Populations, vol 2. Chicago: University of Chicago Press
Zuckerkandl E (1987) On the molecular evolutionary clock. J Mol Evol 26:34–46
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Villablanca, F.X. (1994). Spatial and Temporal Aspects of Populations Revealed by Mitochondrial DNA. In: Herrmann, B., Hummel, S. (eds) Ancient DNA. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-4318-2_3
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DOI: https://doi.org/10.1007/978-1-4612-4318-2_3
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