Disparate molecular results

James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Wed May 7 09:24:55 CDT 1997


On Wed, 7 May 1997, Gregory Zolnerowich wrote:

> Much attention has been given to problems when morphological and molecular
> data produce conflicting results when used to infer phylogenies. Has anyone
> encountered or examined cases where different molecular datasets produced
> disparate results for a taxonomic group?
>

Greg,

Yes.  In fact, conflicting evolutionary trees are the norm for different
molecules, and interpretations include (1) one tree is wrong, (2) both
trees are wrong, and if differential lineage sorting is in principle
possible (i.e., between nuclear loci and haploid genomes such as
choroplasts or mitochondria, or between different nuclear loci).

Try the following examples:

Patton and Smith (1994) Syst Biol 43            Pocket Gophers
Kim and Jansen (1994) Pl. Syst. Evol 190        Krigia (dwarf dandelions)
Bakker et al. (1995)                            Cladophora
Clark et al. (1994)  MBE                        Drosophila
Mason-Gamer and Kellogg 1996 Syst Biol          Triticaceae


more examples can be found in table 1 of
Chippendale and Weins, Syst Biol 43:278-287

And for readings on whether to analyze data separately or combined, see


CONSENSUS

Adams, E. N., III.  1972.  Consensus techniques and the comparison of
taxonomic trees.  Systematic Zoology 21:390-397.

Adams, E. N., III.  1986.  N-trees as nestings:complexity, similarity, and
consensus.Journal of Classification 3:29

Barrett, M., M.J. Donoghue, and E. Sober. 1991. Against consensus.
Systematic Zoology 40:486-493.

Bremer, K.  1990.  Combinable component consensus. Cladistics 6:369-372.

Bledsoe, A.H. Raikow, R.J.A . 1990. Quantitative Assement of Congruence
between Molecular and Nonmolecular Estimates of Phylogeny. Journal of
Molecular Evolution. 30:247-259.

Critchlow, D.E., D.K. Pearl, and C. Qian. 1996. The triples distance for
rooted bifurcating phylogenetic trees. Systematic Biology 45:323-335.

De Queiroz, Alan. 1993. For consensus (sometimes). Systematic Biology
42:368-372.

Hendy, M. D., M. A. Steel, D. Penny, and I. M. Henderson.  1988.  Families
of trees and consensus. Pages 355-362 in H. H. Bock (ed.),Classification
and Related Methods of Data Analysis (Elsevier: Amsterdam).

Miyamoto, M. M.  1985.  Consensus cladograms and general classifications.
Cladistics 1:186- 189.

Margush, T. and F.R. McMorris. 1981. Consensus n-trees. Bulletin of
Mathematical Biology 43:239-244.

Nelson, G.J. 1993. Why crusade against consensus? a reply to Barrett,
Donoghue, and Sober. Systematic Biology 42:215-216.

Rohlf, F. J.  1982.  Consensus indices for comparing classifications.
Mathematical Biosciences 59: 131-144.


CONGRUENCE

Bousquet, J , S.H. Strauss and L. Peng. 1992. Complete Congruence between
Morphological and rbcL based Molecular Phylogenies in Birches and Related
Species (Betulaceae). Molecular Biology and Evolution. 9:1076-1088.

Bremer, B. and L. Struwe. 1992. Phylogeny of the Rubiaceae and the
Loganiaceae: congruence or conflict between morphological and molecular
data? American Journal of Botany. 79 :1171-1184

Brown, J.M. O.Pellmyr and J.N. Thomspon.  1994. Phylogeny of Greya
(Lepidoptera: Prodoxidae), Based on Nucleotide Sequence Variation in
Mitochondrial Cytochrome Oxidase I and II: Congruence with Morphological
Data. Molecular Biology and Evolution.11:128-141.

Bull, J.J. J.P. Huelsenbeck, C.W. Cunningham, D.L. Swofford, and P.J.
Waddell. 1993. Partitioning and combining data in phylogenetic analysis.
Systematic Biology 42:384-397.

Campbell, C.S., M.J. Donoghue, and M.F. Wojciechowski. 1995. Phylogenetic
relationships in Maloideae (Rosaceae): evidence from sequences of the
internal transcribed spaces of nuclear ribosomal DNA and its congruence
with morphology.  American Journal of Botany 82:903-918.

Chippendale, P.T.  and J.J. Weins. 1994. Weighting, partitioning, and
combining characters in phylogenetic analysis. Systematic Biology
43:278-287.

Wiens, J. J. and P. T. Chippindale.  1994.  Combining and weighting
characters and the prior agreement approach revisited.Systematic Biology
43: 564-566.

Critchlow, D.E., D.K. Pearl, and C. Qian. 1996. The triples distance for
rooted bifurcating phylogenetic trees. Systematic Biology 45:323-335.

Doyle,  J.L. and  A.H.D. Brown. 1990. A Chloroplast DNA Phylogeny of the
Wild Perennial Relatives of Soybean (Glycine subgenus Glycine): Congruence
with Morphological and Crossing Groups. Evolution 44 :371-389.

Marshall, C.R. 1992. Character Analysis and the Integration of Molecular
and Morphological Data in an Understanding of Sand Dollar Phylogeny.
Molecular Biology and Evolution. 9:309-322.

Mickevich, M. F.  1978. Taxonomic congruence.  Systematic Zoology 27:
143-158.

Mickevich, M. F.  1980.  Taxonomic congruence: Rohlf and Sokal's
misunderstanding.  Systematic Zoology 29: 162-176.


Olmstead, R.G.  and J.A. Sweere. 1994. Combining data in phylogenetic
systematics: an empirical approach to using three molecular data sets in
the Solanaceae. Systematic Biology 43:467-481.

Page, R. D. M.  1989.  Comments on component-compatibility in historical
biogeography. Cladistics 5:167-182.

Penny, D. and M. D. Hendy.  1985.  The use of tree comparison metrics.
Systematic Zoology 34: 75-82.

Purvis, A.  1995.  A modification to Baum and Ragan's method for combining
phylogenetic trees.  Systematic Biology 44: 251-255.

Swofford, D. L. When are phylogeny estimates from molecular and
morphological data incongruent? In: M. M. Miyamoto and J. Cracraft [eds.],
Phylogenetic Analysis of DNA Sequences,295-333.  Oxford University Press,
New York.

Vane-Wright, R. I., S. Schulz, and M. Boppre.  1992.  The cladistics of
Amauris Butterflies: Congruence, consensus and total evidence.  Cladistics
8: 125-138.


TOTAL EVIDENCE

Eernisse, D. J. A.G. Kluge. 1993. Taxonomic Congruence versus Total
Evidence, and Amniote Phylogeny Inferred from Fossils, Molecules, and
Morphology. Molecular Biology and Evolution. 10:1170-1195.

Kluge, A.G. 1989.  A concern for evidence and a phylogenetic hypothesis of
relationships among Epicrates(Boideae, Serpentes). Systematic Zoology
38-7-25.




And for gene tree/species tree issues, see

Avise, J.C. 1994. Moelcular markers, natural history and evolution.
Chapman and Hall, New York.

Avise, J.C. and R.M. Ball. 1990. Principles of genealogical concordance in
species concepts and biological taxonomy.  pp. 45-67 in Futuyma, D. and J.
Antonovics, eds. Oxford Surveys in Evolutionary Biology, Volume 7. Oxford
University Press.

Doyle, J.J. 1992. Gene trees and species trees: molecular systematics as
one-character taxonomy. Systematic  Botany 17:144-163.

Guigo, R., I. Muchnik, and T.F. Smith. 1996. Reconstruction of ancient
phylogenies. Mol. Phylo. Evol. 6:189-213.

Hoelzer, G.A., and D.J. Melnick. 1994. Patterns of speciation and limits
to phylogenetic resolution. Trends Ecol. Evol. 9:104-107.

Hudson, R. 1990. Gene genealogies and the coalescent process.  pp 1-44 in:
Futuyma, D. and J. Antonovics, eds. Oxford Surveys in Evolutionary
Biology, Volume 7. Oxford University Press.

Hudson, R.R. and N. L. Kaplan, 1994.  Gene trees with background
selection. pp. 140-153 in Golding, B. (ed.). Non-neutral evolution:
theories and molecular data. Chapman and Hall, N.Y.

Huelsenbeck, J.P. and D.M. Hillis. 1993.  Success of phylogenetic methods
in the four-taxon case. T., Systematic Biology 42:247-264.

Kaplan, N.L., T. Darden, and R.R. Hudson. 1988. The coalescent process in
models with selection. Genetics 120: 819-829.

Kingman 1982. The coalescent. Stochast. Proc. Appl 13:235-248.
Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press,
New York.

Nei, M. and N. Takahata. 1993.  Effective population size, genetic
diversity, and coalescence time in subdivided populations.  J. Mol. Evol.
37:240-244.

Pamilo, P. and M. Nei, 1988. Relationships between gene trees and species
trees. Mol. Biol. Evol. 5:568-583.

Rogers, J. 1994. Levels of geneaological hierarchy and the problem of
hominoid phylogeny.  Am. J. Phys. Anthr. 94:81-88.

Ruvolo, M.E. 1994. Molecular evolutionary processes and conflicting gene
trees: the hominoid case.  Am. J. Phys. Anthr. 94:89-113.

Slatkin ,M. and W.P. Maddison. 1989. A cladistic measure of gene flow from
phylogenies of alleles. Genetics 123:603-613.


Finally, there is a review in the latest Annual Rev Ecol Syst by Borwer,
DeSalle and Vogler.


There is a preponderance of opinion based on theoretical results that it
may take many loci to approximate a species phylogeny (with some
dissention, such as Brower et al.)  but it is my opinion that averaging
disparate signal will result in less resolved trees.

James Lyons-Weiler




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