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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 Marina. Errazurizia 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.
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