Maximum parsimony (phylogenetics) (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Maximum parsimony (phylogenetics)" in English language version.

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archive.org

De Laet J (2005). "Parsimony and the problem of inapplicables in sequence data.". In Albert VA (ed.). Parsimony, phylogeny and genomics. Oxford University Press. pp. 81–116. ISBN 978-0-19-856493-5.

doi.org

Farris JS (March 1970). "Methods for computing Wagner trees". Systematic Biology. 19 (1): 83–92. doi:10.1093/sysbio/19.1.83. JSTOR 2412028.
Fitch WM (1971). "Toward defining the course of evolution: minimum change for a specified tree topology". Systematic Zoology. 20 (4): 406–416. doi:10.2307/2412116. JSTOR 2412116.
Felsenstein J (1978). "Cases in which parsimony and compatibility methods will be positively misleading". Systematic Zoology. 27 (4): 401–410. doi:10.1093/sysbio/27.4.401.
Brower AV (October 2018). "Statistical consistency and phylogenetic inference: a brief review". Cladistics. 34 (5): 562–7. Bibcode:2018Cladi..34..562B. doi:10.1111/cla.12216. PMID 34649374.
Farris JS (October 2008). "Parsimony and explanatory power". Cladistics. 24 (5): 825–47. doi:10.1111/j.1096-0031.2008.00214.x. S2CID 32931349.
De Laet J (2014). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Goloboff, Pablo; De Laet, Jan; Ríos-Tamayo, Duniesky; Szumik, Claudia (2021). "A reconsideration of inapplicable characters, and an approximation with step-matrix recoding". Cladistics. 37 (5): 596–629. doi:10.1111/cla.12456. PMID 34570932. S2CID 234846773.
Sober E (1983). "Parsimony in Systematics: Philosophical Issues". Annual Review of Ecology and Systematics. 14 (1): 335–357. Bibcode:1983AnRES..14..335S. doi:10.1146/annurev.es.14.110183.002003.
Wiens, John J. (2001). "Character Analysis in Morphological Phylogenetics: Problems and Solutions". Systematic Biology. 50 (5): 689–699. doi:10.1080/106351501753328811. ISSN 1076-836X. PMID 12116939.
Grand, Anaïs; Corvez, Adèle; Duque Velez, Lina Maria; Laurin, Michel (2001). "Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements". Biological Journal of the Linnean Society. 110 (4): 914–930. doi:10.1111/bij.12159. ISSN 0024-4066.
Rineau, Valentin; Grand, Anaïs; Zaragüeta, René; Laurin, Michel (2015). "Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes". Contributions to Zoology. 84 (2): 129–148. doi:10.1163/18759866-08402003. ISSN 1875-9866.
Rineau, Valentin; Zaragüeta, René; Laurin, Michel (2018). "Impact of errors on cladistic inference: simulation-based comparison between parsimony and three-taxon analysis". Contributions to Zoology. 87 (1): 25–40. doi:10.1163/18759866-08701003. ISSN 1875-9866.
Bremer K (July 1988). "The limits of amino acid sequence data in angiosperm phylogenetic reconstruction". Evolution; International Journal of Organic Evolution. 42 (4): 795–803. doi:10.1111/j.1558-5646.1988.tb02497.x. PMID 28563878. S2CID 13647124.
Bremer KR (September 1994). "Branch support and tree stability". Cladistics. 10 (3): 295–304. doi:10.1111/j.1096-0031.1994.tb00179.x. S2CID 84987781.
Brower AV, Garzón-Orduña IJ (April 2018). "Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined". Cladistics. 34 (2): 151–66. Bibcode:2018Cladi..34..151B. doi:10.1111/cla.12198. PMID 34645081.
Steel, M. A.; Hendy, M. D.; Penny, D. (1 December 1993). "Parsimony Can Be Consistent!". Systematic Biology. 42 (4): 581–587. doi:10.1093/sysbio/42.4.581.
Day WH (1987). "Computational complexity of inferring phylogenies from dissimilarity matrices". Bulletin of Mathematical Biology. 49 (4): 461–7. doi:10.1007/BF02458863. PMID 3664032.
Puttick, Mark N.; O'Reilly, Joseph E.; Tanner, Alastair R.; Fleming, James F.; Clark, James; Holloway, Lucy; Lozano-Fernandez, Jesus; Parry, Luke A.; Tarver, James E.; Pisani, Davide; Donoghue, Philip C. J. (2017). "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data". Proceedings of the Royal Society B: Biological Sciences. 284 (1846): 20162290. doi:10.1098/rspb.2016.2290. ISSN 0962-8452. PMC 5247500. PMID 28077778.
O'Reilly, Joseph E.; Puttick, Mark N.; Parry, Luke; Tanner, Alastair R.; Tarver, James E.; Fleming, James; Pisani, Davide; Donoghue, Philip C. J. (2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. ISSN 1744-9561. PMC 4881353. PMID 27095266.
Goloboff, Pablo A.; Torres, Ambrosio; Arias, J. Salvador (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Garwood, Russell J; Knight, Christopher G; Sutton, Mark D; Sansom, Robert S; Keating, Joseph N (2020). "Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. ISSN 1063-5157. PMC 7440746. PMID 32073641.
Goloboff, Pablo A.; Pittman, Michael; Pol, Diego; Xu, Xing (2019). "Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model". Systematic Biology. 68 (3): 494–504. doi:10.1093/sysbio/syy077. ISSN 1076-836X. PMID 30445627. S2CID 53567539.
Rindal E, Brower AV (2011). "Do model-based phylogenetic analyses outperform parsimony? A test with empirical data". Cladistics. 27 (3): 331–4. doi:10.1111/j.1096-0031.2010.00342.x. PMID 34875779. S2CID 84907350.
Kolaczkowski B, Thornton JW (October 2004). "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous". Nature. 431 (7011): 980–4. Bibcode:2004Natur.431..980K. doi:10.1038/nature02917. PMID 15496922. S2CID 4385277.
Catanzaro D (2009). "The minimum evolution problem: Overview and classification". Networks. 53 (2): 112–125. doi:10.1002/net.20280. S2CID 6018514.
Desper R, Gascuel O (March 2004). "Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting". Molecular Biology and Evolution. 21 (3): 587–98. doi:10.1093/molbev/msh049. PMID 14694080.

handle.net

hdl.handle.net

Goloboff, Pablo A.; Torres, Ambrosio; Arias, J. Salvador (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.

harvard.edu

ui.adsabs.harvard.edu

Brower AV (October 2018). "Statistical consistency and phylogenetic inference: a brief review". Cladistics. 34 (5): 562–7. Bibcode:2018Cladi..34..562B. doi:10.1111/cla.12216. PMID 34649374.
Sober E (1983). "Parsimony in Systematics: Philosophical Issues". Annual Review of Ecology and Systematics. 14 (1): 335–357. Bibcode:1983AnRES..14..335S. doi:10.1146/annurev.es.14.110183.002003.
Brower AV, Garzón-Orduña IJ (April 2018). "Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined". Cladistics. 34 (2): 151–66. Bibcode:2018Cladi..34..151B. doi:10.1111/cla.12198. PMID 34645081.
Kolaczkowski B, Thornton JW (October 2004). "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous". Nature. 431 (7011): 980–4. Bibcode:2004Natur.431..980K. doi:10.1038/nature02917. PMID 15496922. S2CID 4385277.

jstor.org

Farris JS (March 1970). "Methods for computing Wagner trees". Systematic Biology. 19 (1): 83–92. doi:10.1093/sysbio/19.1.83. JSTOR 2412028.
Fitch WM (1971). "Toward defining the course of evolution: minimum change for a specified tree topology". Systematic Zoology. 20 (4): 406–416. doi:10.2307/2412116. JSTOR 2412116.

kuleuven.be

lirias.kuleuven.be

De Laet J (2014). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.

nih.gov

pubmed.ncbi.nlm.nih.gov

Brower AV (October 2018). "Statistical consistency and phylogenetic inference: a brief review". Cladistics. 34 (5): 562–7. Bibcode:2018Cladi..34..562B. doi:10.1111/cla.12216. PMID 34649374.
De Laet J (2014). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Goloboff, Pablo; De Laet, Jan; Ríos-Tamayo, Duniesky; Szumik, Claudia (2021). "A reconsideration of inapplicable characters, and an approximation with step-matrix recoding". Cladistics. 37 (5): 596–629. doi:10.1111/cla.12456. PMID 34570932. S2CID 234846773.
Wiens, John J. (2001). "Character Analysis in Morphological Phylogenetics: Problems and Solutions". Systematic Biology. 50 (5): 689–699. doi:10.1080/106351501753328811. ISSN 1076-836X. PMID 12116939.
Bremer K (July 1988). "The limits of amino acid sequence data in angiosperm phylogenetic reconstruction". Evolution; International Journal of Organic Evolution. 42 (4): 795–803. doi:10.1111/j.1558-5646.1988.tb02497.x. PMID 28563878. S2CID 13647124.
Brower AV, Garzón-Orduña IJ (April 2018). "Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined". Cladistics. 34 (2): 151–66. Bibcode:2018Cladi..34..151B. doi:10.1111/cla.12198. PMID 34645081.
Day WH (1987). "Computational complexity of inferring phylogenies from dissimilarity matrices". Bulletin of Mathematical Biology. 49 (4): 461–7. doi:10.1007/BF02458863. PMID 3664032.
Puttick, Mark N.; O'Reilly, Joseph E.; Tanner, Alastair R.; Fleming, James F.; Clark, James; Holloway, Lucy; Lozano-Fernandez, Jesus; Parry, Luke A.; Tarver, James E.; Pisani, Davide; Donoghue, Philip C. J. (2017). "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data". Proceedings of the Royal Society B: Biological Sciences. 284 (1846): 20162290. doi:10.1098/rspb.2016.2290. ISSN 0962-8452. PMC 5247500. PMID 28077778.
O'Reilly, Joseph E.; Puttick, Mark N.; Parry, Luke; Tanner, Alastair R.; Tarver, James E.; Fleming, James; Pisani, Davide; Donoghue, Philip C. J. (2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. ISSN 1744-9561. PMC 4881353. PMID 27095266.
Goloboff, Pablo A.; Torres, Ambrosio; Arias, J. Salvador (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Garwood, Russell J; Knight, Christopher G; Sutton, Mark D; Sansom, Robert S; Keating, Joseph N (2020). "Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. ISSN 1063-5157. PMC 7440746. PMID 32073641.
Goloboff, Pablo A.; Pittman, Michael; Pol, Diego; Xu, Xing (2019). "Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model". Systematic Biology. 68 (3): 494–504. doi:10.1093/sysbio/syy077. ISSN 1076-836X. PMID 30445627. S2CID 53567539.
Rindal E, Brower AV (2011). "Do model-based phylogenetic analyses outperform parsimony? A test with empirical data". Cladistics. 27 (3): 331–4. doi:10.1111/j.1096-0031.2010.00342.x. PMID 34875779. S2CID 84907350.
Kolaczkowski B, Thornton JW (October 2004). "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous". Nature. 431 (7011): 980–4. Bibcode:2004Natur.431..980K. doi:10.1038/nature02917. PMID 15496922. S2CID 4385277.
Desper R, Gascuel O (March 2004). "Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting". Molecular Biology and Evolution. 21 (3): 587–98. doi:10.1093/molbev/msh049. PMID 14694080.

ncbi.nlm.nih.gov

Puttick, Mark N.; O'Reilly, Joseph E.; Tanner, Alastair R.; Fleming, James F.; Clark, James; Holloway, Lucy; Lozano-Fernandez, Jesus; Parry, Luke A.; Tarver, James E.; Pisani, Davide; Donoghue, Philip C. J. (2017). "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data". Proceedings of the Royal Society B: Biological Sciences. 284 (1846): 20162290. doi:10.1098/rspb.2016.2290. ISSN 0962-8452. PMC 5247500. PMID 28077778.
O'Reilly, Joseph E.; Puttick, Mark N.; Parry, Luke; Tanner, Alastair R.; Tarver, James E.; Fleming, James; Pisani, Davide; Donoghue, Philip C. J. (2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. ISSN 1744-9561. PMC 4881353. PMID 27095266.
Garwood, Russell J; Knight, Christopher G; Sutton, Mark D; Sansom, Robert S; Keating, Joseph N (2020). "Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. ISSN 1063-5157. PMC 7440746. PMID 32073641.

semanticscholar.org

api.semanticscholar.org

Farris JS (October 2008). "Parsimony and explanatory power". Cladistics. 24 (5): 825–47. doi:10.1111/j.1096-0031.2008.00214.x. S2CID 32931349.
De Laet J (2014). "Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not Minimization of operationally defined total cost or minimization of equally weighted transformations". Cladistics. 31 (5): 550–567. doi:10.1111/cla.12098. PMID 34772278. S2CID 221582410.
Goloboff, Pablo; De Laet, Jan; Ríos-Tamayo, Duniesky; Szumik, Claudia (2021). "A reconsideration of inapplicable characters, and an approximation with step-matrix recoding". Cladistics. 37 (5): 596–629. doi:10.1111/cla.12456. PMID 34570932. S2CID 234846773.
Bremer K (July 1988). "The limits of amino acid sequence data in angiosperm phylogenetic reconstruction". Evolution; International Journal of Organic Evolution. 42 (4): 795–803. doi:10.1111/j.1558-5646.1988.tb02497.x. PMID 28563878. S2CID 13647124.
Bremer KR (September 1994). "Branch support and tree stability". Cladistics. 10 (3): 295–304. doi:10.1111/j.1096-0031.1994.tb00179.x. S2CID 84987781.
Goloboff, Pablo A.; Pittman, Michael; Pol, Diego; Xu, Xing (2019). "Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model". Systematic Biology. 68 (3): 494–504. doi:10.1093/sysbio/syy077. ISSN 1076-836X. PMID 30445627. S2CID 53567539.
Rindal E, Brower AV (2011). "Do model-based phylogenetic analyses outperform parsimony? A test with empirical data". Cladistics. 27 (3): 331–4. doi:10.1111/j.1096-0031.2010.00342.x. PMID 34875779. S2CID 84907350.
Kolaczkowski B, Thornton JW (October 2004). "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous". Nature. 431 (7011): 980–4. Bibcode:2004Natur.431..980K. doi:10.1038/nature02917. PMID 15496922. S2CID 4385277.
Catanzaro D (2009). "The minimum evolution problem: Overview and classification". Networks. 53 (2): 112–125. doi:10.1002/net.20280. S2CID 6018514.

wired.com

For one example, see the 2016 #ParsimonyGate controversy on Twitter, set off by an editorial from the journal Cladistics: Simon, Matt. "Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud". Wired.

worldcat.org

search.worldcat.org

Wiens, John J. (2001). "Character Analysis in Morphological Phylogenetics: Problems and Solutions". Systematic Biology. 50 (5): 689–699. doi:10.1080/106351501753328811. ISSN 1076-836X. PMID 12116939.
Grand, Anaïs; Corvez, Adèle; Duque Velez, Lina Maria; Laurin, Michel (2001). "Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements". Biological Journal of the Linnean Society. 110 (4): 914–930. doi:10.1111/bij.12159. ISSN 0024-4066.
Rineau, Valentin; Grand, Anaïs; Zaragüeta, René; Laurin, Michel (2015). "Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes". Contributions to Zoology. 84 (2): 129–148. doi:10.1163/18759866-08402003. ISSN 1875-9866.
Rineau, Valentin; Zaragüeta, René; Laurin, Michel (2018). "Impact of errors on cladistic inference: simulation-based comparison between parsimony and three-taxon analysis". Contributions to Zoology. 87 (1): 25–40. doi:10.1163/18759866-08701003. ISSN 1875-9866.
Puttick, Mark N.; O'Reilly, Joseph E.; Tanner, Alastair R.; Fleming, James F.; Clark, James; Holloway, Lucy; Lozano-Fernandez, Jesus; Parry, Luke A.; Tarver, James E.; Pisani, Davide; Donoghue, Philip C. J. (2017). "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data". Proceedings of the Royal Society B: Biological Sciences. 284 (1846): 20162290. doi:10.1098/rspb.2016.2290. ISSN 0962-8452. PMC 5247500. PMID 28077778.
O'Reilly, Joseph E.; Puttick, Mark N.; Parry, Luke; Tanner, Alastair R.; Tarver, James E.; Fleming, James; Pisani, Davide; Donoghue, Philip C. J. (2016). "Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data". Biology Letters. 12 (4): 20160081. doi:10.1098/rsbl.2016.0081. ISSN 1744-9561. PMC 4881353. PMID 27095266.
Goloboff, Pablo A.; Torres, Ambrosio; Arias, J. Salvador (2018). "Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology". Cladistics. 34 (4): 407–437. doi:10.1111/cla.12205. hdl:11336/57822. ISSN 0748-3007. PMID 34649370.
Garwood, Russell J; Knight, Christopher G; Sutton, Mark D; Sansom, Robert S; Keating, Joseph N (2020). "Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations". Systematic Biology. 69 (5): 897–912. doi:10.1093/sysbio/syaa012. ISSN 1063-5157. PMC 7440746. PMID 32073641.
Goloboff, Pablo A.; Pittman, Michael; Pol, Diego; Xu, Xing (2019). "Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model". Systematic Biology. 68 (3): 494–504. doi:10.1093/sysbio/syy077. ISSN 1076-836X. PMID 30445627. S2CID 53567539.