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McMahon, M. M. and L. Hufford.  2005. Evolution and development in the amorphoid clade (Amorpheae: Papilionoideae: Leguminosae): petal loss and dedifferentiation.  International Journal of Plant Sciences 166: 383-396.  pdf.
We used comparative developmental morphology to study the evolution of nonpapilionaceous corollas in the amorphoid clade of the tribe Amorpheae (Papilionoideae). This clade consists of five genera in which there are no papilionaceous corollas (five petals differentiated into one banner, two wing, and two keel petals). We studied the ontogenies of three nonpapilionaceous forms: corollas consisting of one petal (exemplified by Amorpha canescens), no petals (Parryella filifolia), and five petals in two types (Errazurizia megacarpa). We compared these to the ontogeny of a papilionaceous corolla (exemplified by the closely related Psorothamnus scoparius). In A. canescens, all petals initiated, but four did not grow beyond the primordial stage. In P. filifolia, no distinct petal primordia were visible. The corolla of E. megacarpa, which has only two types of petals, exhibits nonpapilionaceous characteristics at an early ontogenetic stage. Aside from the earliest primordial mounds, the petals of Psorothamnus and Errazurizia do not resemble each other, indicating that paedomorphosis is not responsible for the nonpapilionaceousness of Errazurizia. Comparing the morphological results to a phylogeny,we infer a single origin of the characteristics that differentiate Errazurizia petals from Psorothamnus petals, and we infer at least two evolutionary events leading to the reduced corolla in Parryella, Amorpha, and Errazurizia rotundata. When considered in the context of the remaining Amorpheae, in which additional floral diversification has occurred, and in the context of the entire papilionoid group, in which floral form is relatively conserved, our results indicate a relaxation of selective or developmental constraint within the clade Amorpheae.

Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson.  2005.  Covarion structure in plastid genome evolution: a new statistical test.  Molecular Biology and Evolution 22: 914-924. access.
Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.

Hufford, L., M. M. McMahon, R. O’Quinn, M. S. Poston.  2005. A phylogenetic analysis of Loasaceae subfamily Loasoideae based on plastid DNA sequences.  International Journal of Plant Sciences 166: 289-300.  pdf.
Questions of tribal and generic circumscriptions and relationships in Loasaceae subfamily Loasoideae are addressed in phylogenetic analyses that apply four plastid regions in parsimony and maximum likelihood analyses. As circumscribed in the influential monograph of Urban and Gilg, Loaseae are paraphyletic to the sister clades Klaprothieae (Klaprothia, Plakothira, and Xylopodia) and Kissenieae (Kissenia). This problem centers on the paraphyly of Huidobria: Huidobria chilensis is sister to Klaprothieae + Kissenieae, and Huidobria fruticosa is sister to all other Loasoideae. Parametric bootstrapping finds topologies that force the monophyly of Huidobria to be significantly different from the optimal topologies in which the genus is paraphyletic; however, Templeton and Shimodaira-Hasegawa tests did not distinguish between these phylogenetic alternatives. We recognize a strongly supported Loaseae sensu stricto (s.str.) as a clade consisting of Nasa, Aosa, Chichicaste, Presliophytum, Blumenbachia, Cajophora, Loasa sect. Loasa, and Scyphanthus. In Loaseae s.str., the monophyly of each of the following has strong support: (1) Nasa, (2) Aosa + Chichicaste, (3) Presliophytum + Loasa malesherbioides, and (4) a higher Loaseae clade that consists of Blumenbachia, Cajophora, Scyphanthus, and the Loasa complex (=sect. Loasa, excluding L. malesherbioides). Blumenbachia, Cajophora (including exemplars from sections Bialatae and Bicallosae), and Scyphanthus are independently monophyletic, and clades of the Loasa complex are mixed among them. The paraphyletic Loasa complex includes the following clades: (1) ser. Pinnatae, (2) ser. Acaules + Volubile, (3) ser. Macrospermae, placed as the sister of Blumenbachia, and (4) ser. Acanthifolia + Floribundae + Deserticolae, which includes the type for Loasa and is the group we recommend as the basis for a revised circumscription of Loasa.

Driskell, A. C., C. Ané, J. G. Burleigh, M. M. McMahon, B. C. O’Meara, and M. J. Sanderson.  2004.  Prospects for building the tree of life from large sequence databases.  Science 306: 1172-1174.  pdf (paper), pdf (supp).
We assess the phylogenetic potential of ~300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two ‘‘supermatrices’’ suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.

McMahon, M. and L. Hufford. 2004.  Phylogeny of Amorpheae (Fabaceae: Papilionoideae).  American Journal of Botany 91: 1217-1228.  pdf.
The legume tribe Amorpheae comprises eight genera and 240 species with variable floral form.  In this study, we inferred a phylogeny for Amorpheae using DNA sequence data from the plastid trnK intron, including matK, and the nuclear ribosomal ITS1, 5.8S, and ITS2.  Our data resulted in a well-resolved phylogeny in which the tribe is divided into the daleoids (Dalea, Marina, and Psorothamnus), characterized by generally papilionaceous corollas, and the amorphoids (Amorpha, Apoplanesia, Errazurizia, Eysenhardtia, and Parryella), characterized by non-papilionaceous flowers.  We found evidence for the paraphyly of Psorothamnus and for the monophyly of Dalea once D. filiciformis is transferred to monophyletic MarinaErrazurizia rotundata is more closely related to Amorpha than to the other errazurizias, and Eysenhardtia is supported to be monophyletic.  The monotypic Parryella and Apoplanesia are placed within the amorphoids.  Among Papilionoideae, trnK/matK sequence data provide strong evidence for the monophyly of Amorpheae and place Amorpheae as sister to the recently discovered dalbergioid clade.
Supplemental LINKS coming soon.

Hufford, L. and M. McMahon.  2004.  Morphological evolution and systematics of Synthyris and Besseya (Veroniceae): A phylogenetic analysis.  Systematic Botany 29:716-736.  pdf.
Phylogenetic analyses are used to examine the morphological diversity and systematics of Synthyris and Besseya. The placement of Synthyris and Besseya in Veronicaceae is strongly supported in parsimony analyses of nuclear ribosomal ITS DNA sequences. Parsimony and maximum likelihood (ML) criteria provide consistent hypotheses of clades of Synthyris and Besseya based on the ITS data. The combination of morphological characters and ITS data resolve additional clades of Synthyris and Besseya. The results show that Synthyris is paraphyletic to Besseya. In the monophyletic Synthyris clade, Besseya forms part of a Northwest clade that also includes the alpine S. canbyi, S. dissecta, and S. lanuginosa and mesic forest S. cordata, S. reniformis, S. platycarpa, and S. schizantha. The Northwest clade is the sister of S. borealis. An Intermountain clade, comprising S. ranunculina, S. laciniata, S. pinnatifida, and S. missurica, is the sister to the rest of the Synthyris clade. Constraint topologies are used to test prior hypotheses of relationships and morphological similarities. Parametric bootstrapping is used to compare the likelihood values of the best trees obtained in searches under constraints to that of the best tree found without constraints. These results indicate that topologies in which a monophyletic Synthyris is the sister of Besseya are significantly worse than the best ML tree in which Synthyris is paraphyletic to Besseya. Similarly, forcing either the monophyly of all taxa that have deeply incised leaf margins or those that have reniform laminas and broadly rounded apices results in trees that are significantly worse than the best ML tree, in which leaf margin incision and reniform laminas are homoplastic. We propose a new classification for Synthyris that emphasizes monophyletic groups. The new combination Synthyris oblongifolia is proposed.

Hufford, L. and M. McMahon, 2003. Beyond morphoclines and trends: the elements of diversity and the phylogenetic patterning of morphology. In T. F. Stuessy, V. Mayer & E. Hörandl (eds.). Deep Morphology: Toward a Renaissance of Morphology in Plant Systematics. Koeltz, Königstein.
"Trend" is a prevailing descriptor for evolutionary diversity in the botanical literature, but workers seldom explain the particular morphological pattern or how they are using the term.  Trends too often have been described using a priori assessments of character state transformations in morphoclines, rather than inferred a posteriori through robust phylogenetic analyses.  A better understanding of morphological diversity can be achieved by attention to the variety of patterns that result from evolution, and we provide a general system to characterize these patterns.  The approach emphasizes mapping cladograms into character space (morphospace) to infer patterns of morphological diversity, which can be characterized in terms of the following five parameters:  boundedness, disparity, continuity, divergence, and reversibility.  The proposed system will facilitate comparisons of diversity patterns among clades. 

Hufford, L., M. M. McMahon, A. M. Sherwood, G. Reeves, and M. W. Chase.  2003.  The major clades of Loasaceae: phylogenetic analysis using the plastid matK and trnL-trnF regions.  American Journal of Botany 90:1215-1228.  pdf.
Phylogenetic analyses of Loasaceae that apply DNA sequence data from the plastid trnL-trnF region and matK gene in both maximum-parsimony and maximum-likelihood searches are presented. The results place subfamily Loasoideae as the sister of a subfamily Gronovioideae-Mentzelia clade. Schismocarpus is the sister of the Loasoideae-Gronovioideae-Mentzelia clade. The Schismocarpus-Loasoideae-Gronovioideae-Mentzelia clade is the sister of Eucnide. Several clades in Loasoideae receive strong support, providing insights on generic circumscription problems. Within Mentzelia, several major clades receive strong support, which clarifies relationships among previously circumscribed sections. Prior taxonomic and phylogenetic hypotheses are modeled using topology constraints in parsimony and likelihood analyses; tree lengths and likelihoods, respectively, are compared from constrained and unconstrained analyses to evaluate the relative support for various hypotheses. We use the Shimodaira-Hasegawa (SH) test to establish the significance of the differences between constrained and unconstrained topologies. The SH test rejects topologies based on hypotheses for (1) the placement of gronovioids as the sister of the rest of Loasaceae, (2) the monophyly of subfamily Mentzelioideae as well as Gronovioideae and Loasoideae, (3) the monophyly of Loasa sensu lato as circumscribed by Urban and Gilg, and (4) the monophyly of Mentzelia torreyi and Mentzelia sect. Bartonia.
Supplemental LINKS coming soon.

McMahon, M. and L. Hufford.  2002.  Morphology and structural homology of corolla-androecium synorganization in the tribe Amorpheae (Fabaceae: Papilionoideae).  American Journal of Botany 89(12): 1884-1898.  pdf.
Comparative developmental morphology was used to assess structural homology of flowers in Dalea, Marina, and Psorothamnus of the tribe Amorpheae (Fabaceae: Papilionoideae). Dalea, Marina, and some species of Psorothamnus have an unusual petal-stamen synorganization (stemonozone) in which free petals are inserted on a region that is continuous with fused stamen filaments. Developmental studies of these three genera demonstrated similarity during organogenesis. Zonal growth results in several synorganized regions, including the stemonozone of Dalea, Marina, and some Psorothamnus. Psorothamnus species that lack a stemonozone have fused stamens and free petals inserted on the hypanthium, as in most other papilionoid legumes. We concluded that the stemonozone is not strictly homologous to either androecium or receptacle, but that it is the product of a modified androecial developmental program. In the prairie clover daleas, petaloid structures positioned between the stamens have been variously interpreted as petals or as staminodes; we infer that they have an extreme form of the daleoid stemonozone, on which five petals (no staminodes) and five stamens are inserted. Assessing structural homology of these flowers allows us to characterize accurately daleoid morphology for evolutionary studies in the tribe Amorpheae.

Maddison, W. and M. McMahon.  2000.  Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold).  Systematic Biology 49:400-421.  pdf.
Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape, and orientation of setae on face; shape of carapace; markings of palpi and legs; motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences in male courtship behavior and body parts exposed to the female during courtship and correlations between form and courtship behavior suggest sexual selection was involved in the differentiation. Aphylogenetic analysis of the populations yields a tree that for the most part groups geographic neighbors, but the history of H. pugillis populations may not be adequately described by a tree. Geographic proximity of apparent convergences suggests that populations from at least some of the mountain ranges acquired characteristics through introgression. Lowering of the woodland habitat during the last glacial period probably brought some populations into contact, but it is not clear whether the interrange woodlands would have provided corridors for extensive mixing.

Hufford, L. and M. McMahon.  2000.  Book review: Scotland, R., Penington, R. T. (eds.): Homology and Systematics: Coding Characters for Phylogenetic Analysis. Plant Systematics and Evolution 226:122-126.  pdf.

McMahon, S. [M.], M. Fishbein, and A. Johnson.  1994.  Noteworthy collections.  Arizona.  Madroño 41:330-331.

Publications submitted or in press

McMahon, M. M.  2005.  Phylogenetic relationships and floral evolution in the papilionoid legume clade Amorpheae.  Brittonia.  (due out in the Fall issue).

Publications in preparation

Burleigh, J. G., B. C. O'Meara, and M. M. McMahon.  Efficiency of algorithms for maximum likelihood phylogenetic inference.  Molecular Phylogenetics and Evolution.
McMahon, M. M. and M. J. Sanderson.  Bias and variance in phylogenetic inference. 
McMahon, M. M. and M. J. Sanderson.  Multi-gene papilionoid phylogeny:  a supermatrix approach.