Pupko T, Pe'er I, Shamir R, Graur D (June 2000). "A fast algorithm for joint reconstruction of ancestral amino acid sequences". Molecular Biology and Evolution. 17 (6): 890–896. doi:10.1093/oxfordjournals.molbev.a026369. PMID10833195.
Ronquist F (September 2004). "Bayesian inference of character evolution". Trends in Ecology & Evolution. 19 (9): 475–481. doi:10.1016/j.tree.2004.07.002. PMID16701310.
Swofford DL, Maddison WP (1987). "Reconstructing ancestral character states under Wagner parsimony". Mathematical Biosciences. 87 (2): 199–229. doi:10.1016/0025-5564(87)90074-5. ISSN0025-5564.
Fitch WM (1971). "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology". Systematic Zoology. 20 (4): 406–416. doi:10.2307/2412116. ISSN0039-7989. JSTOR2412116.
Schluter D, Price T, Mooers AØ, Ludwig D (December 1997). "Likelihood of Ancestor States in Adaptive Radiation". Evolution; International Journal of Organic Evolution. 51 (6): 1699–1711. doi:10.2307/2410994. JSTOR2410994. PMID28565128.
Felsenstein J (1973). "Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters". Systematic Zoology. 22 (3): 240–249. doi:10.2307/2412304. ISSN0039-7989. JSTOR2412304.
Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N (August 2002). "A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families". Bioinformatics. 18 (8): 1116–1123. doi:10.1093/bioinformatics/18.8.1116. PMID12176835.
Finarelli JA, Flynn JJ (April 2006). "Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record". Systematic Biology. 55 (2): 301–313. doi:10.1080/10635150500541698. PMID16611601.
Albert JS, Johnson DM, Knouft JH (2009). "Fossils provide better estimates of ancestral body size than do extant taxa in fishes". Acta Zoologica. 90: 357–384. doi:10.1111/j.1463-6395.2008.00364.x. ISSN0001-7272.
Felsenstein J (1988). "Phylogenies and quantitative characters". Annual Review of Ecology and Systematics. 19: 445–471. doi:10.1146/annurev.ecolsys.19.1.445.
Garland Jr T, Dickerman AW, Janis CM, Jones JA (1993). "Phylogenetic analysis of covariance by computer simulation". Systematic Biology. 42 (3): 265–292. doi:10.1093/sysbio/42.3.265.
Griffith OW, Blackburn DG, Brandley MC, Van Dyke JU, Whittington CM, Thompson MB (September 2015). "Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles". Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 324 (6): 493–503. Bibcode:2015JEZB..324..493G. doi:10.1002/jez.b.22614. PMID25732809.
Erkenbrack EM, Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L (January 2016). "Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms". Development Genes and Evolution. 226 (1): 37–45. doi:10.1007/s00427-015-0527-y. PMID26781941. S2CID6067524.
Chang BS, Ugalde JA, Matz MV (2005). "Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins". Molecular Evolution: Producing the Biochemical Data. Methods in Enzymology. Vol. 395. pp. 652–670. doi:10.1016/S0076-6879(05)95034-9. ISBN9780121828004. PMID15865989.
Hodges WL (November 2004). "Evolution of viviparity in horned lizards (Phrynosoma): testing the cold-climate hypothesis". Journal of Evolutionary Biology. 17 (6): 1230–1237. doi:10.1111/j.1420-9101.2004.00770.x. PMID15525408. S2CID25069395.
Maddison WP (1991). "Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree". Systematic Biology. 40 (3): 304–314. doi:10.1093/sysbio/40.3.304.
Bonine KE, Gleeson TT, Garland T (December 2005). "Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states". The Journal of Experimental Biology. 208 (Pt 23): 4529–4547. Bibcode:2005JExpB.208.4529B. doi:10.1242/jeb.01903. PMID16339872.
Maddison WP (May 1990). "A Method for Testing the Correlated Evolution of Two Binary Characters: Are Gains or Losses Concentrated on Certain Branches of a Phylogenetic Tree?". Evolution; International Journal of Organic Evolution. 44 (3): 539–557. doi:10.2307/2409434. JSTOR2409434. PMID28567979.
Göbel U, Sander C, Schneider R, Valencia A (April 1994). "Correlated mutations and residue contacts in proteins". Proteins. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID8208723. S2CID14978727.
Shindyalov IN, Kolchanov NA, Sander C (March 1994). "Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?". Protein Engineering. 7 (3): 349–358. doi:10.1093/protein/7.3.349. PMID8177884.
Wienberg J (December 2004). "The evolution of eutherian chromosomes". Current Opinion in Genetics & Development. 14 (6): 657–666. doi:10.1016/j.gde.2004.10.001. PMID15531161.
Griffith OW, Blackburn DG, Brandley MC, Van Dyke JU, Whittington CM, Thompson MB (September 2015). "Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles". Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 324 (6): 493–503. Bibcode:2015JEZB..324..493G. doi:10.1002/jez.b.22614. PMID25732809.
Bonine KE, Gleeson TT, Garland T (December 2005). "Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states". The Journal of Experimental Biology. 208 (Pt 23): 4529–4547. Bibcode:2005JExpB.208.4529B. doi:10.1242/jeb.01903. PMID16339872.
Platnick NI, Cameron HD (1977). "Cladistic Methods in Textual, Linguistic, and Phylogenetic Analysis". Systematic Zoology. 26 (4): 380–385. doi:10.2307/2412794. ISSN0039-7989. JSTOR2412794.
Fitch WM (1971). "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology". Systematic Zoology. 20 (4): 406–416. doi:10.2307/2412116. ISSN0039-7989. JSTOR2412116.
Schluter D, Price T, Mooers AØ, Ludwig D (December 1997). "Likelihood of Ancestor States in Adaptive Radiation". Evolution; International Journal of Organic Evolution. 51 (6): 1699–1711. doi:10.2307/2410994. JSTOR2410994. PMID28565128.
Felsenstein J (1973). "Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters". Systematic Zoology. 22 (3): 240–249. doi:10.2307/2412304. ISSN0039-7989. JSTOR2412304.
Maddison WP (May 1990). "A Method for Testing the Correlated Evolution of Two Binary Characters: Are Gains or Losses Concentrated on Certain Branches of a Phylogenetic Tree?". Evolution; International Journal of Organic Evolution. 44 (3): 539–557. doi:10.2307/2409434. JSTOR2409434. PMID28567979.
Pupko T, Pe'er I, Shamir R, Graur D (June 2000). "A fast algorithm for joint reconstruction of ancestral amino acid sequences". Molecular Biology and Evolution. 17 (6): 890–896. doi:10.1093/oxfordjournals.molbev.a026369. PMID10833195.
Ronquist F (September 2004). "Bayesian inference of character evolution". Trends in Ecology & Evolution. 19 (9): 475–481. doi:10.1016/j.tree.2004.07.002. PMID16701310.
Schluter D, Price T, Mooers AØ, Ludwig D (December 1997). "Likelihood of Ancestor States in Adaptive Radiation". Evolution; International Journal of Organic Evolution. 51 (6): 1699–1711. doi:10.2307/2410994. JSTOR2410994. PMID28565128.
Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N (August 2002). "A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families". Bioinformatics. 18 (8): 1116–1123. doi:10.1093/bioinformatics/18.8.1116. PMID12176835.
Finarelli JA, Flynn JJ (April 2006). "Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record". Systematic Biology. 55 (2): 301–313. doi:10.1080/10635150500541698. PMID16611601.
Griffith OW, Blackburn DG, Brandley MC, Van Dyke JU, Whittington CM, Thompson MB (September 2015). "Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles". Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 324 (6): 493–503. Bibcode:2015JEZB..324..493G. doi:10.1002/jez.b.22614. PMID25732809.
Erkenbrack EM, Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L (January 2016). "Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms". Development Genes and Evolution. 226 (1): 37–45. doi:10.1007/s00427-015-0527-y. PMID26781941. S2CID6067524.
Chang BS, Ugalde JA, Matz MV (2005). "Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins". Molecular Evolution: Producing the Biochemical Data. Methods in Enzymology. Vol. 395. pp. 652–670. doi:10.1016/S0076-6879(05)95034-9. ISBN9780121828004. PMID15865989.
Hodges WL (November 2004). "Evolution of viviparity in horned lizards (Phrynosoma): testing the cold-climate hypothesis". Journal of Evolutionary Biology. 17 (6): 1230–1237. doi:10.1111/j.1420-9101.2004.00770.x. PMID15525408. S2CID25069395.
Bonine KE, Gleeson TT, Garland T (December 2005). "Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states". The Journal of Experimental Biology. 208 (Pt 23): 4529–4547. Bibcode:2005JExpB.208.4529B. doi:10.1242/jeb.01903. PMID16339872.
Maddison WP (May 1990). "A Method for Testing the Correlated Evolution of Two Binary Characters: Are Gains or Losses Concentrated on Certain Branches of a Phylogenetic Tree?". Evolution; International Journal of Organic Evolution. 44 (3): 539–557. doi:10.2307/2409434. JSTOR2409434. PMID28567979.
Göbel U, Sander C, Schneider R, Valencia A (April 1994). "Correlated mutations and residue contacts in proteins". Proteins. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID8208723. S2CID14978727.
Shindyalov IN, Kolchanov NA, Sander C (March 1994). "Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?". Protein Engineering. 7 (3): 349–358. doi:10.1093/protein/7.3.349. PMID8177884.
Wienberg J (December 2004). "The evolution of eutherian chromosomes". Current Opinion in Genetics & Development. 14 (6): 657–666. doi:10.1016/j.gde.2004.10.001. PMID15531161.
Erkenbrack EM, Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L (January 2016). "Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms". Development Genes and Evolution. 226 (1): 37–45. doi:10.1007/s00427-015-0527-y. PMID26781941. S2CID6067524.
Hodges WL (November 2004). "Evolution of viviparity in horned lizards (Phrynosoma): testing the cold-climate hypothesis". Journal of Evolutionary Biology. 17 (6): 1230–1237. doi:10.1111/j.1420-9101.2004.00770.x. PMID15525408. S2CID25069395.
Göbel U, Sander C, Schneider R, Valencia A (April 1994). "Correlated mutations and residue contacts in proteins". Proteins. 18 (4): 309–317. doi:10.1002/prot.340180402. PMID8208723. S2CID14978727.
Swofford DL, Maddison WP (1987). "Reconstructing ancestral character states under Wagner parsimony". Mathematical Biosciences. 87 (2): 199–229. doi:10.1016/0025-5564(87)90074-5. ISSN0025-5564.
Fitch WM (1971). "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology". Systematic Zoology. 20 (4): 406–416. doi:10.2307/2412116. ISSN0039-7989. JSTOR2412116.
Felsenstein J (1973). "Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters". Systematic Zoology. 22 (3): 240–249. doi:10.2307/2412304. ISSN0039-7989. JSTOR2412304.
Albert JS, Johnson DM, Knouft JH (2009). "Fossils provide better estimates of ancestral body size than do extant taxa in fishes". Acta Zoologica. 90: 357–384. doi:10.1111/j.1463-6395.2008.00364.x. ISSN0001-7272.