[Treebase-guts] SF.net SVN: treebase:[1027] trunk/treebase-core/db/cleaning

[<sfr...@us...>]

Revision: 1027
          http://treebase.svn.sourceforge.net/treebase/?rev=1027&view=rev
Author:   sfrgpiel
Date:     2012-01-31 21:58:59 +0000 (Tue, 31 Jan 2012)
Log Message:
-----------
Script and data file for updating TB1 citations

Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/
    trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README
    trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt
    trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/update_citations.pl

Added: trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README
===================================================================
--- trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README	2012-01-31 21:58:59 UTC (rev 1027)
@@ -0,0 +1,11 @@
+This script is intended to update citation information from a UTF8-encoded tab-separated 
+export of EndNote citation metadata. The records are identified by the legacy study_id. 
+Author names are unaffected. The order of the columns in the input file is as follows:
+
+ legacyID, authors, year, title, journal, vol, num, pages, doi, url, keywords, abstract, citation_id
+
+To apply, edit the database credentials on lines 18-21, and then type:
+
+      perl update_citations.pl citationdata.txt
+
+ ... where citationdata.txt is the citation metadata file.
\ No newline at end of file

Added: trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt	2012-01-31 21:58:59 UTC (rev 1027)
@@ -0,0 +1,2284 @@
+S1847	K. Voigt;L. Olsson	2008	Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi)	Acta Biologica Hungarica	59	3					A multigene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of essentially all fifty genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae Schröter form a monophyletic group. The monotypic genus Gilbertella Hesseltine, which is classified into the monogeneric family Gilbertellaceae Benny, appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae is supported by aberrantly from low to higher ranging bootstrap proportions (67 and 98 % in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (98 and 100 %) proposing that both families can be joined into one family which leads to the elimination of the Gilbertellaceae as a separate family. In order to validate these relationships single-locus Neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the elongation factor 1 alpha (tef) and beta tubulin (btub) nucleotide sequences. The monophyly of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees. The ultrastructure of sporangia, sporangiola and sporangiospores show several morphological characters (e.g. longitudinal sutures splitting the sporangial walls, striations and polar ciliate appendages on the sporangiospores) which occur only in the Choanephoraceae-Gilbertellaceae clade. Based on these results and reanalysis of other morphological and physiological evidences from the literature, we propose to fuse the two families Choanephoraceae and Gilbertellaceae into one family, the Choanephoraceae.
+S465	J. A. Coddington	1991	Cladistics and spider classification: Araneomorph phylogeny and the monophyly of orb weavers (Araneae: Araneomorphae; Orbiculariae)	Acta Zoologica Fennica	190		75-87				Nineteen new characters pertinent to the phylogeny of the spider suborder Araneomorphae are reviewed and tested against a previous data set, using quantitative cladistic techniques. An hypothesis of cladistic structure within Araneomorphae in the form of a quantitatively analysed cladogram is presented for the first time. The analysis supports orb weaving spiders (Orbiculariae: Deinopoidea and Araneoidea) as a monophyletic group (apparently sister to Dictynoidea) and Linyphiidae as an araneoid family. Likely precursors of orbs are discussed, as are relevant fossil evidence and possible times of origin
+S11x5x95c12c16c30	L. E. Graham;C. F. Delwiche;B. D. Mishler	1991	Phylogenetic connections between the 'green algae' and the 'bryophytes'	Advances in Bryology	4		213-244				An updated cladistic analysis of charophycean green algae, focusing on divergence of the embryophyte clade, was derived by application of Wagner parsimony to a data set consisting of morphological, ultrastructural, and biochemical characters. Characters not previously used in such analyses include: sexual growth response (cell-to cell interactions between gametes or zygotes and vegetative thallus cells), post-fertilization enlargement of zygotes, polyphenolic deposition induced by zygote formation, diagonal cell divisions in spermatid ontogeny, cortical microtubule arrays, preprophase microtubule bands, bicentriolar centrosomes, and sporic meiosis. Despite the addition of these new characters, the topology of the most parsimonious tree resulting from their use was remarkably similar to a cladogram previously published by Mishler and Churchill. The present analyses suggest that future biochemical and cellular studies should be focused on the following: the pattern of occurrence of glycolate oxidase and class I aldolases in lower charophytes and putative ancestral flagellates; cell-to-cell growth interactions related to sexual reproduction; cell division and sexual reproduction in Chaetosphaeridium; patterns of involvement of callose in reproductive development; biochemical pathways leading to flavonoid synthesis and polyphenolic deposition in cell walls; cytoskeleton dynamics, phragmoplast development, and structure and rob of plasmodesmata; comparative structure of chloroplasts and pyrenoids; behavior of peroxisomes during cell division-- and the nature of the surface layer present on thalli of some species of Coleochaete. Evidence is presented to support the view that while the archegonium bearing plants may well be polyphyletic or paraphyletic, as has been effectively argued by others, the embryophytes are most likely monophyletic. The molecular, biochemical, and structural evidence suggests that embryophytes are derived from charophycean ancestors similar to Charales and Coleochaete. It is concluded that charophycean algae should be the taxa of choice for use as model experimental systems in which to study the cellular, biochemical, and molecular bases of many embryophyte features, rather than more distantly related green algae.
+S1404	D. A. Morrison	2006	Phylogenetic analyses of parasites in the new millennium	Advances in Parasitology	63						Phylogenetic analysis has changed greatly in the last decade, and the most important themes in that change are reviewed here. Sequence data have become the most common source of phylogenetic information. This means that explicit models for evolutionary processes have been developed in a likelihood context, which allow more realistic data analyses. These models are becoming increasingly complex, both for nucleotides and for amino acid sequences, and so all such models need to be quantitatively assessed for each data set, to find the most appropriate one for use in the tree-building analysis. Bayesian analysis has been developed for tree-building and is greatly increasing in popularity. This is because a good heuristic strategy exists, which allows large data sets to be analysed with complex evolutionary models in a practical time. Perhaps the most disappointing aspect of tree interpretation is the ongoing confusion between rooted and unrooted trees, the latter being of very limited practical use for most biological questions. The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted elsewhere.
+S1098	A. L. Hipp;P. E. Rothrock;A. A. Reznicek;P. E. Berry	2004	Chromosome number changes associated with speciation in sedges: A phylogenetic study in Carex section Ovales (Cyperaceae) using AFLP data	Aliso	23		193-203				AFLP data recover a tree that is topologically congruent with previous phylogenetic estimates based on nrDNA sequences and provide support for four species groups within ENA Clade I. A maximum likelihood method designed for analysis of restriction site data is used to evaluate the strength of support for alternative topologies. While there is little support for the precise placement of the root, likelihood of topologies in which any of the four clades identified within ENA Clade I is forced to be paraphyletic is much lower than likelihood of the optimal tree. Chromosome counts for a sampling of species from throughout section Ovales are mapped onto the tree as well as counts for all species in ENA Clade I. Parsimony reconstruction of ancestral character states suggest that (1) Heilborn's hypothesis that more highly derived species in Carex have higher chromosome counts does not apply within section Ovales, (2) the migration to Eastern North America involved a decrease in average chromosome count within section Ovales, and (3) intermediate chromosome counts are ancestral within ENA Clade I. A more precise understanding of chromosomal evolution in Carex should be possible using likelihood analyses that take into account the intraspecific polymorphism and wide range of chromosome counts that characterize the genus.
+S1890	J. T. Columbus;R. Cerros-Tlatilpa;M. S. Kinney;M. E. Siqueiros-Delgado;H. L. Bell;M. P. Griffith;N. F. Refulio-Rodriguez	2007	Phylogenetics of Chloridoideae (Gramineae): a preliminary study based on nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences	Aliso	23		587-601				The phylogeny of Chloridoideae (Gramineae) was inferred from parsimony analyses of DNA sequences from two genomes˜the chloroplast trnL intron, trnL 3? exon, and trnLˆF intergenic spacer, and the nuclear ribosomal internal transcribed spacer region (ITS1 + 5.8S + ITS2). Eighty species representing 66 chloridoid genera were sampled, including all but four of the native New World genera. Analyses of the individual and combined data sets were performed. The phylogenies were found to be highly congruent. Of the four tribes and seven subtribes of Chloridoideae sensu Clayton and Renvoize (1986) whose phylogenetic status could be tested with our taxon sample, only Orcuttieae and Uniolinae were monophyletic. The phylogenies suggested significant homoplasy in morphological traits, including inflorescence type, number of florets per spikelet, and number of lemma nerves. We propose a new classification based on the three main clades in the phylogenies˜tribes Cynodonteae, Eragrostideae, and Zoysieae. The Eragrostideae clade is well resolved and supported and is further divided into three subtribes, Cotteinae, Eragrostidinae, and Uniolinae. Cynodonteae include most of the genera in our study, but the clade is poorly resolved. However, a clade formed of Muhlenbergia and nine other genera is present in both phylogenies and is well resolved and supported. A number of interesting, well-supported relationships are evident in the phylogenies, including PappophorumˆTridens flavus, TragusˆWillkommia, and GouiniaˆTridens muticusˆTriplasisˆVaseyochloa. Except for Bouteloua, no genus represented by multiple species proved to be monophyletic in the phylogenies.
+S1141	J. R. Starr;G. Gravel;A. Bruneau;A. M. Muasya	2007	Phylogenetic Implications of a Unique 5.8S nrDNA Insertion in Cyperaceae. Monocots III/Grasses IV	Aliso	23		84-98				The purpose of this study was to assess the phylogenetic utility of a large insertion (3 bp) in the 5.8S gene of nuclear ribosomal DNA (rDNA) in the Cyperaceae and selected Juncaceae. This was done by reconstructing the character evolution of the insertion on a phylogeny derived from rbcL sequences. Results suggest that the insertion was gained once at the base of the Cyperaceae followed by multiple losses in its most derived taxa. Despite several homoplastic loses (CI = 0.20), the pattern of insertion loss (RI = 0.88) and base pair variation within the insertion were useful for defining sedge clades at various taxonomic levels. For example, whereas an indel loss appeared to characterise a major terminal clade within the Cyperaceae, both insertion losses and sequence variation were consistent with infrageneric clades previously discovered in an ITS phylogeny of the genus Eleocharis. The presence/absence of the insertion also supported previous conclusions based on morphological and molecular data that the tribe Scirpeae and the genus Scirpus s.l. are polyphyletic. In the context of our current understanding of Cyperaceae relationships, evolutionary patterns related to this insertion provide additional support for groups defined in prior phylogenetic analyses. Differences between maximum likelihood and parsimony analyses indicated that the paraphyly of Juncaceae and Cyperaceae, as detected in previous molecular analyses, is based upon a chimeric rbcL sequence for the controversial genus Oxychloe (Juncaceae). When the Cyperaceae portion of the molecule is removed, Juncaceae and Cyperaceae are monophyletic, with Oxychloe positioned within a Southern Hemisphere clade of single-flowered genera in the Juncaceae. Keywords: Cyperaceae, 5.8S insertion, ITS region, Juncaceae, Oxychloe, rDNA.
+S249	R. K. Jansen;J. D. Palmer	1988	Phylogenetic implications of chloroplast DNA restriction site variation in the Mutisieae (Asteraceae)	American Journal of Botany	75		753-766				Phylogenetic relationships among 13 species in the tribe Mutisieae and a single species from each of three other tribes in the Asteraceae were assessed by chloroplast DNA restriction site mapping Initially, 211 restriction site mutations were detected among 16 species using 10 restriction enzymes. Examination of 12 of these species using nine more enzymes revealed 179 additional restriction site mutations. Phylogenetic analyses of restriction site mutations were performed using both Dollo and Wagner parsimony, and the resulting monophyletic groups were statistically tested by the bootstrap method. The phylogenetic trees confirm an ancient evolutionary split in the Asteraceae that was previously suggested by the distribution of a chloroplast DNA inversion. The subtribe Barnadesiinae of the tribe Mutisieae is shown to be the ancestral group within the Asteraceae. The molecular phylogenies also confirm the paraphyly of the Mutisieae and provide statistical support for the monophyly of three of its four currently recognized subtribes (Barnadesiinae, Mutisiinae, and Nassauviinae). The fourth subtribe, Gochnatiinae, is shown to be paraphyletic. Within the subtribes, several closely related generic pairs are identified. Chloroplast DNA sequence divergence among genera of the Asteraceae ranges between 0.7 and 5.4%, which is relatively low in comparison to other angiosperm groups. This suggests that the Asteraceae is either a relatively young family or that its chloroplast DNA has evolved at a slower rate than in other families.
+S2x2x96c16c32c09	E. A. Kellogg	1989	Comments on genomic genera in the Triticeae (Poaceae)	American Journal of Botany	76		796-805				Generic delimitation in the Triticeae has long been problematical because the extensive hybridization in the group is not readily accomodated in a hierarchical classification. The genomic genera of Love (1984) are one solution, but fully one-third of them are polyphyletic, incorporating 2 or more genomes. The suggestion that the tribe be considered a single genus (Stebbins, 1956) is theoretically defensible—the genus would be strictly monophyletic—but probably impractical. This paper presents a cladistic analysis of the tribe that differs from previous analyses in that it uses only strictly monophyletic (monogenomic) groups as terminal taxa; hybrids (heterogenomic groups) are shown as reticulations. Monophyletic groups can then be delimited to minimize the number of polyphyletic genera. A classification incorporating genomic information is derived from the phylogeny.
+S11x6x95c09c31c53	R. J. Soreng	1990	Chloroplast-DNA phylogenetics and biogeography in a reticulating group: Study in Poa (Poaceae)	American Journal of Botany	77		1383-1400				Cladistic analysis of Poa chloroplast DNA (cpDNA) restriction sites tested previously hypothesized relationships within the genus. Forty-six taxa representing 19 sections or groups and three subgenera of Poa and two out-group genera, Puccinellia and Bellardiochloa, are analyzed. Five major and several minor cpDNA groups are identified. The cpDNA cladogram is generally congruent with the subgeneric taxonomy of Poa. Exceptions are reclassified or are discussed in terms of character incompatibilities and possible reticulation events. The cpDNA tree detected relationships among sections that were unresolved using traditional character sets and provides a basis for polarization of morphological character states. An assessment of biogeographic events based on the cpDNA tree suggests: 1 ) Poa originated in Eurasia; 2) at least six groups of species independently colonized North America; and 3) two of the latter groups colonized South America, and one closely related group colonized New Zealand and Australia. The cpDNA tree provided a conservative estimate of the number of amphi-neotropical disjunctions when compared to the known number of species disjunctions.
+S2x4x96c13c37c50	P. G. Wolf;D. E. Soltis;P. S. Soltis	1990	Chloroplast-DNA and allozymic variation in diploid and autotetraploid Heuchera Grossulariifolia (Saxifragaceae)	American Journal of Botany	77		232-244				Diploid and autotetraploid populations of Heuchera grossulariifolia occur throughout mountainous regions of the Pacific Northwest. Controlled greenhouse crosses indicated that the two cytotypes are largely reproductively isolated. Fourteen diploid and 11 tetraploid populations were analyzed electrophoretically. Individual tetraploid plants expressed up to four alleles per isozyme locus, and tetraploid populations had significantly higher levels of heterozygosity than diploids. Mean observed heterozygosity was 0.159 for tetraploid populations and 0.058 for diploid populations. The patterns of allelic distribution betwecn cytotypes suggested multiple origins of autotetraploids. This hypothesis was supported by restriction-site analysis of chloroplast-DNA (cpDNA) variation which indicated that there had been at least three independent origins of tetraploids. Electrophoretic data, in conjunction with a cpDNA-based phylogeny and geographic distribution of populations, suggest that autopolyploid populations evolved several times as migration of diploids occurred down river systems. This study further supports the contention that autopolyploidy can be a common and successful speciation process in some groups of plants.
+S11x5x95c20c33c35	B. Bremer;R. K. Jansen	1991	Comparative restriction site mapping of chloroplast DNA implies new phylogenetic relationships within Rubiaceae	American Journal of Botany	78		198-213				Phylogenetic analyses of 33 species of Rubiaceae were performed using chloroplast DNA restriction site mutations. Complete cleavage maps of eight enzymes were constructed for Psychotria bacteriophila and used as a reference in comparisons among other species. The species examined represent 33 genera from 18 tribes and four subfamilies of the Rubiaceae. A total of 268 restriction site mutations was detected, 161 of which were phylogenetically informative. Wagner and Dollo parsimony trees were compared to the classifications of Verdcourt, Bremekamp, and Robbrecht. The Wagner analysis resulted in six equally parsimonious trees with 348 steps and 54% homoplasy. Dollo analysis resulted in a single most parsimonious tree. Most clades were identical in the two analyses. The subfamily Cinchonoideae is paraphyletic. The subfamilies Antirheoideae, Ixoroideae, and Rubioideae are monophyletic, although their circumscriptions differ from previous classifications. Several new phylogenetic relationships are indicated: the tribe Chiococceae (Ixoroideae) groups with Exostema and Coutarea (Cinchonoideae); the subfamily Ixoroideae including tribe Vanguerieae is closely related to Pogonopus, Pinckneya, Calycophyllum, and Mussaenda (Cinchonoideae); and tribe Hamelieae forms a monophyletic group outside the subfamily Rubioideae.
+S279	K. J. Curry;L. M. McDowell;W. S. Judd;W. L. Stern	1991	Osmophores, floral features, and systematics of Stanhopea (Orchidaceae)	American Journal of Botany	78		610-623				The floral fragrance glands (osmophores) of 18 species of Stanhopea and Sievekingia were examined through a series of developmental studies at light and electron microscope levels including late bud stages through postanthesis. Various characters were identified to be of potential systematic value and were recorded for each species. These characters included: texture of the osmophore surface, number of distinct cell layers comprising the osmophore, nature of lipid inclusions in osmophore cells, and presence or absence of plastoglobuli in osmophore amyloplasts. These characters were combined with traditional features of floral lip morphology for cladistic analysis. Sievekingia was the postulated outgroup. Stanhopea ecornuta showed the largest number of plesiomorphic characters. Stanhopea pulla, S. annulata, and S. candida were only slightly more derived. Stanhopea anfracta, S. gibbosa, S. martiana, S. oculata, S. radiosa, S. ruckeri, S. saccata, S. shuttleworthii, S. tigrina, S. vasquezii, and S. wardii form a monophyletic group that can be recognized by a labellum with an articulated epichile and a bicornuate mesochile (or hypochile). Stanhopea tricornis may be a hybrid between a species of Sievekingia and Stanhopea.
+S2x3x96c13c09c47	M. Lavin;S. Mathews;C. Hughes	1991	Cholorplast DNA variation in Gliricidia sepium (Leguminosae): Intraspecific phylogeny and tokogeny	American Journal of Botany	78		1576-1585				An analysis of chloroplast DNA restriction site variation in Gliricidia sepium reveals two geographically distinct chloroplast lineages, one in the Yucatan Peninsula and the other along the Pacific Coast in Mexico and Central America. Geographical, morphological, biochemical, and habitat distinctions suggest that these two chloroplast lineages reflect organismal lineages. Within the Pacific coastal chloroplast lineage, there exist sublineages that most likely reflect tokogenetic systems of relationship rather than organismal phylogeny, a hypothesis supported by the co-occurrence of more than one of these chloroplast sublineages in a single population. The genetic distance between any two of these chloroplast lineages ranges from 0.0001 to 0.0024 nucleotide substitutions per site and reveals relatively high levels of intraspecific divergence. We suggest that assessing intraspecific chloroplast DNA variation is important generally in higher level phylogenetic analysis because it enables one to obtain truer estimates of homoplasy, detect potentially cryptic species, and distinguish among molecular markers that reflect phylogenetic vs. tokogenetic relationships. This is in addition to determining the extent of potential complicating factors such as introgression and lineage sorting from polymorphic ancestry.
+S2x3x96c16c45c53	L. H. Rieseberg	1991	Homoploid reticulate evolution in Helianthus (Asteraceae): Evidence from ribosomal genes	American Journal of Botany	78		1218-1237				Phylogenetic relationships among the 21 taxa comprising Helianthus sect. Helianthus and three outgroup species were assessed by restriction site mapping of the 1 8S-25S nuclear ribosomal RNA gene family. Wagner parsimony analysis of the 41 restriction site or length mutations observed produced a single 59-step most parsimonious tree. This tree was then compared to a cytoplasmic-based plastid phylogeny for this group. Several major discrepancies were observed between the two phylogenies suggesting both recent and ancient introgression. Furthermore, three cases of diploid hybrid speciation are unambiguously documented and a fourth case is suggested. These data are interpreted to suggest that evolution in Heliathus is reticulate rather than exclusively dichotomous and branching.
+S11x6x95c09c42c30	L. E. Talbert;G. M. Magyar;M. Lavin;T. K. Blake;S. L. Moylan	1991	Molecular evidence for the origin of the S-derived genomes of polyploid Triticum species	American Journal of Botany	78		340-349				The genus Triticum includes several polyploid species that arose due to hybridization between two or more diploid species. Section Sitopsis is comprised of five diploid species given the genome designation S. Four polyploid species are recognized that contain an S or S-derived genome. We have used two repetitive DNA sequences found primarily in the S genomes of Triticum to determine the likely diploid progenitors of the polyploid species. Comparison of restriction fragments that hybridize to probes for these sequences suggests that T. speltoides is distinct from other members of section Sitopsis (i.e., T. longissimum, T. bicorne, T. searsii, and T. sharonense). The S-derived genome of T. aestivum is more closely related to T. speltoides than to the other Sitopsis diploids. The restriction fragment pattern of T. timopheevii is 98% identical to that of T. speltoides, while those of T. kotschyi and T. syriacum are identical to the group of diploids represented by T. longissimum, T. bicorne, T. searsii, and T. sharonense. Our results are compatible with previous molecular and biochemical data regarding relationships among Triticum species containing an S or S-derived genome.
+S2x7x96c15c33c46	D. A. Waters;M. A. Buchheim;R. A. Dewey;R. L. Chapman	1992	Preliminary inferences of the phylogeny of bryophytes from nuclear-encoded ribosomal RNA sequences	American Journal of Botany	79		459-466				Ribosomal RNA sequences and cladistic analysis were used to infer a phylogeny for eight bryophyte taxa. Portions of the cytoplasmic large (26S-like) and small (18S-like) subunit ribosomal RNA genes were sequenced for three marchantioid liverworts (Asterella, Conocephalum, and Riccia), three mosses (Atrichum, Fissidens, and Plagiomnium), and two hornworts (Phaeoceros and Notothylas). Cladistic analysis of these data suggests that the hornworts are the sister group to the mosses, the mosses and hornworts form a clade that is sister to the tracheophytes, and the liverworts form a clade sister to the other land plants. These results differ from previous cladistic analyses based on morphology, ultrastructure, and biochemistry, wherein the mosses alone are sister group to the tracheophytes. We conclude that cladistic analysis of molecular data can provide an independent data set for the study of bryophyte phylogeny, but the differences between the molecular and morphological results are a topic for further investigation.
+S11x6x95c09c20c33	D. E. Soltis;D. R. Morgan;A. Grable;P. S. Soltis;R. Kuzoff	1993	Molecular systematics of Saxifragaceae sensu stricto	American Journal of Botany	80		1056-1081				To circumscribe Saxifragaceae sensu stricto better, as well as to elucidate generic relationships within this group, we sequenced the chloroplast gene rbcL and its 3' flanking region (yielding 1,471 bp) from 19 genera considered to represent core members of Saxifragaceae. In addition, we conducted a restriction site analysis of chloroplast DNA (cpDNA) for 21 core genera using 23 restriction endonucleases. Phylogenetic analyses using both data sets corroborate the results obtained from surveying the distribution of the loss of the intron in the chloroplast gene rpl2 in delimiting a well-defined Saxifragaceae sensu stricto. Within the Saxifragaceae s.s. clade, a number of poorly resolved, basal phylogenetic branches supports the hypothesis that Saxifragaceae s.s. radiated rapidly very early in its evolutionary history. Molecular data also indicate the presence of several strongly supported groups of genera, such as the Boykinia group (Boykinia, Suksdorfia, Bolandra, Sullivantia, Jepsonia, and Telesonix), the Heuchera group (Heuchera, Bensoniella, Conimitella, Elmera, Lithophragma, Mitella, Tellima, Tiarella, and Tolmiea) the Leptarrhena/Tanakaea group, and the Darmera group (Darmera, Astilboides, Mukdenia, Bergenia, and Rodgersia). Significantly, molecular data suggest that the very large, taxonomically complex genus Saxifraga may not be monophyletic. DNA data have also helped to resolve the generic relationships of problematic taxa, indicating, for example, that Telesonix and the enigmatic Jepsonia are sister taxa. In addition to its phylogenetic implications, this study provides insight into basic trends in morphological, chemical, and cytological evolution within Saxifragaceae s.s. The molecular-based phylogenies suggest multiple origins and/or losses of several classes of flavonoid compounds, as well as several independent instances of reduction in stamen and petal number, hypanthium-ovary fusion, and aneuploidy. This study also illustrates the ability of rbcL sequence data to resolve generic-level relationships in some taxonomic groups.
+S2x6x96c17c48c00	M. F. Wojciechowski;M. J. Sanderson;B. G. Baldwin;M. J. Donoghue	1993	Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequences	American Journal of Botany	80		711-722				Evolutionary relationships within Astragalus L. (Fabaceae) were inferred from nucleotide sequence variation in nuclear ribosomal DNA of both New World and Old World species. The internal transcribed spacer regions (ITS) of 18S-26S nuclear ribosomal DNA from representatives of 26 species of Astragalus, three species of Oxytropis DC., and two outgroup taxa were analyzed by polymerase chain reaction amplification and direct DNA sequencing. The length of the ITS I region within these taxa varied from 221 to 231 bp, while ITS 2 varied in length from 207 to 217 bp. Of the aligned, unambiguous positions, approximately 34% were variable in each spacer region. In pairwise comparisons among Astragalus species and outgroup taxa, sequence divergence at these sites ranged from 0 to 1 8.8% in ITS I and from 0 to 21.7% in ITS 2. Parsimony analyses of these sequences resulted in a well-resolved phylogeny that is highly concordant with previous cytogenetic and chloroplast DNA evidence for a major phylogenetic division in the genus. These data suggest that the New World aneuploid species of Astragalus form a monophyletic but morphologically cryptic group derived from euploid species of Old World (Eurasian) origin, which are consequently paraphyletic.
+S2x4x96c14c20c12	J. V. Freudenstein	1994	Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). II. Morphological variation and phylogenetic analysis	American Journal of Botany	81		1458-1467				Morphological and anatomical study of Corallorhiza. a genus of primarily New World leafless mycoparasitic orchids, was undertaken in order to produce a hypothesis of relationships among the species and to gain some understanding of character transformations. Cladistic analysis of the resulting data set gave two most parsimonious trees. Analysis of combined plastid DNA and morphological data yielded a single topology, identical to one of the two from the analysis of morphological data alone. Molecular data do not conflict with the morphological data set, and provide more resolution within the C. maculata complex. The combined data indicate that C. striata is the sister group to the remainder of the genus; the circumboreal C. trifida also occupies a basal position. Corallorhiza wisteriana and C. odontorhiza comprise the sister group to the C. maculata+ C. mertensiana + C. bulbosa clade. Only two synapomorphies, presence of the coralloid rhizome and loss of leaves, unite the species of Corallorhiza. The coralloid rhizome appears to be a paedomorphic development, due to its similarity to a protocorm; if so, it too is a loss character and may be considered only weak support for monophyly of the genus. Predominant autogamy, seen in C. trifida and cleistogamous C. odontorhiza, has probably arisen independently in these taxa.
+S228	J. V. Freudenstein;J. J. Doyle	1994	Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). I. Plastid DNA	American Journal of Botany	81		1449-1457				As part of a phylogenetic study of Corallorhiza. a genus of ten species of leafless mycoparasitic orchids, the large single copy region (LSC) and inverted repeat of plastid DNA were examined with restriction fragment analysis to obtain information on relationships among the species, as well as to determine whether structural changes had occurred in the plastome, Deletion areas of between 1.3 and 6.0 kb were detected in the LSC of the C. maculata complex and C. striata. but most of the genome was not significantly affected. Cladistic analysis of restriction site characters produced one most parsimonious tree; additional accessions screened were shown to be most closely related to the primary accession for each species. No synapomorphy was found to unite Corallorhiza. The same topology resulted when deletion characters were added and indicates that deletions in the region of rpo and psa genes have occurred independently in the C. maculata and C striata groups. Because of the coarse level of resolution in the probing, it is not clear to what extent the genes themselves have been affected. Only one species, the undeleted C. trifida, has been examined physiologically, and it was found to be photosynthetic. This fact, and the deletion pattern, suggest that species of Corallorhiza may show a range of levels of autotrophy.
+S2x7x96c17c37c03	T. Mione;R. C. Olmstead;R. K. Jansen;G. J. Anderson	1994	Systematic implications of chloroplast DNA variation in Jaltomata and selected Physaloid genera (Solanaceae)	American Journal of Botany	81		912-918				Chloroplast DNA restriction site data were used to assess relationships among the solanaceous genera Jaltomata, Hebecladus, Old and New World Physalis, Chamaesaracha, Leucophysalis, Margaranthus, Nicandra, and Saracha, and to assess interspecific relationships within Jaltomata. Cladograms rooted with Nicotiana tabacum were constructed with Wagner and Dollo parsimony. Strict consensus trees indicate that Hebecladus onginated from within Jaltomata; together these genera are monophyletic and constitute the recently circumscribed genus Jaltomata. There are two primary clades in Jaltomata: one a morphologically diverse group confined to western (largely Andean) South America, the Greater Antilles, and the Galapagos Islands; and the othcr a morphologically homogeneous group widely distributed from the southwestern United States to Bolivia. The controversial Leucophysalis viscosa, formerly treated as Jaltomata viscosa, is related to Leucophysalis, Physalis, Chamaesaracha, and Margaranthus; it does not group with any of the sampled species of Jaltomata. Physalis appears to be polyphyletic since P. alkekengi of the Old World branches off prior to a clade including Chamaesaracha, Margaranthus, and the two New World Physalis species sampled.
+S2x4x96c12c57c00	G. A. Verboom;H. P. Linder;N. P. Barker	1994	Haustorial synergids: An important character in the systematics of Danthonioid grasses (Arundinoideae: Poaceae)	American Journal of Botany	81		1601-1610				The mature ovule and megagametophyte of 42 grass species (23 genera), mostly from the taxonomically troublesome subfamily Arundinoideae, was investigated. Haustorial synergids, first described from the Arundineae, are reported for a further 26 species (ten genera) of danthonioid grasses, a group for which they appear to be synapomorphic. The evolution of this character and a suite of associated integument and nucellar characters is discussed. The danthonioid clade, as defined by haustorial synergids, includes Cortaderia (often treated as nondanthonioid) but excludes a number of taxa currently contained in the Arundineae. The full extent of the group remains undetermined, however, since several of its potential members remain unstudied. The data provide some indication of phylogenetic structure within the clade. At least two of the species of Merxmuellera studied appear to occupy a basal position, while three do not, suggesting that this genus may be paraphyletic, or even polyphyletic. Also, the reduction or absence of synergid haustoria in Prionanthium, Pentaschistis, and Pentameris is considered to be secondarily derived and weakly corroborates the monophyly of this generic cluster as indicated by spikelet morphology.
+S2x4x96c13c48c42	A. D. Wolfe;W. J. Elisens	1994	Nuclear ribosomal DNA restriction-site variation in Penstemon section Peltanthera (Scrophulariaceae): An evaluation of diploid hybrid speciation and evidence for introgression	American Journal of Botany	81		1627-1635				Penstemon spectabilis is a putative stabilized diploid hybrid of P. centranthifolius and P. grinnellii. It is morphologically intermediate, and all three species have different pollinators. Penstemon centranthifolius and P. spectabilis have been proposed as parents of P. clevelandii, which is purportedly isolated by ecological factors. Although hybridization between the proposed parental species has been reported, hybrid swarm formation has not been observed and introgression is purported to be minimal. We tested hypotheses of diploid hybrid speciation and introgression among these species based on rDNA restriction-site and length variation for 56 populations within and outside of the hybrid complex. Unambiguous molecular markers clearly differentiated P. centranthifolius, P. grinnellii, and P. spectabilis, whereas P. spectabilis and P. clevelandii had the same rDNA type. The P. centranthifolius rDNA type was found in some populations of P. spectabilis and P. clevelandii, but there was no evidence of the additive profile documented for other recent diploid hybrid species. In contrast, the rDNA profile of P. x parishii had a completely additive profile of its proposed parental species P. centranthifolius and P. spectabilis. Ribosomal DNA markers for P. gnnnellii were restricted to populations within the species and were not found in any population of P. spectabilis. Our data did not support hybrid-speciation hypotheses, but were in accord with allozyme data that provided evidence for introgression between P. centranthifolius and P. grinnellii, P. spectabilis and P. clevelandii. These results were used to propose criteria to differentiate ancient diploid hybrid speciation from patterns of introgression.
+S1x29x96c17c45c48	M. H. G. Gustafsson;K. Bremer	1995	Morphology and phylogenetic interrelationships of the Asteraceae, Calyceraceae, Campanulaceae, Goodeniaceae, and related families (Asterales)	American Journal of Botany	82	2	250-265		http://www.jstor.org/stable/2445532		In search for the sister group of the Asteraceae, morphological evidence was assembled for investigating the relationship between the Asteraceae and those families most frequently considered to be their closest relatives, in particular the Calyceraceae, Campanulaceae (along with the frequently included Lobeliaceae, Cyphiaceae, Cyphocarpaceae, and Nemacladaceae), and Goodeniaceae (and the sometimes included Brunoniaceae). Several other families that have been associated with this group of families, the Asterales-Campanulales-complex, were also considered: Pentaphragmataceae, Sphenocleaceae, Stylidiaceae, Donatiaceae, Menyanthaceae, and Argophyllaceae. In order to delineate the complex more precisely, another eight putatively related families were also included in the analysis. Cladistic parsimony analysis of 46 morphological and chemical characters for the 23 families was undertaken. Stability of the branches was estimated by the number of extra steps necessary to lose the group, as well as by the number of reweighted extra steps (using rescaled consistency indices) necessary to lose the group (a new approach). The results indicate that there is a monophyletic group of 14 families comprising those of the Asterales-Campanulales-complex as well as Pentaphragmataceae, Sphenocleaceae, Stylidiaceae, Donatiaceae, and Menyanthaceae; this group is recognized as the order Asterales. Within the order, the Asteraceae, Calyceraceae, Brunoniaceae, and Goodeniaceae form one comparatively well-supported clade and the five families of the Campanulaceae sensu lato form another well-supported clade.
+S2x3x96c13c29c27	R. T. Pennington	1995	Cladistic analysis of chloroplast DNA restriction site characters in Andira (Leguminosae: Dalbergieae)	American Journal of Botany	82	4	526-534		http://www.jstor.org/stable/2445701		Chloroplast DNA (cpDNA) restriction site variation was examined in 29 accessions, representing 29 populations of 17 species of Andira (Leguminosae, Papilionoideae, tribe Dalbergieae). This sample spans the morphological and geographical diversity of this poorly known, woody genus of approximately 30 species, which occurs throughout the neotropics, with one species in Africa. Cladistic analysis of 38 restriction site characters generated 182 equally most-parsimonious trees. The strict consensus tree preserved four well-supported clades, which are incongruent with previous infrageneric classifications of Andira. None of these clades has been recognized by previous workers, and three are not marked by any major morphological innovations. There were few restriction site differences between closely related species, but two (possibly three) species showed intraspecific cpDNA polymorphism, which probably reflects processes of hybridization with subsequent introgression, or lineage sorting.
+S2x3x96c13c46c17	M. Pillay;K. W. Hilu	1995	Chloroplast-DNA restriction site analysis in the genus Bromus (Poaceae)	American Journal of Botany	82	2	239-249		http://www.jstor.org/stable/2445531		Chloroplast DNA (cpDNA) restriction site variation was examined in 32 species, representing five subgenera, of Bromus (Poaceae). Thirty-seven phylogenetically informative restriction sites were detected. Cladistic analysis of the restriction site data produced a single most-parsimonious tree of 50 steps. The cladogram indicated two major clades within the genus. One clade included B. trinii of subgenus Neobromus and species of subgenus Ceratochloa. The other was composed of subgenera Festucaria, Stenobromus, and Bromus. Within the second clade, species of subgenus Festucaria appeared in three lineages. The second clade also contained an assemblage of species belonging to subgenera Stenobromus and Bromus in a separate lineage. There was very little resolution of relationships in this assemblage since several species appeared individually in separate lineages. The cpDNA phylogenetic hypothesis did not separate species of subgenera Stenobromus and Bromus into well-defined clades as circumscribed by morphology and cytogenetics. The cpDNA tree is in agreement with the phylogenetic scheme based on traditional data in that: 1) subgenera Neobromus and Ceratochloa were the first to diverge, while Bromus and Stenobromus diverged later; 2) within the genus Bromus species with small chromosomes are ancestral; and 3) subgenera Bromus and Stenobromus probably originated from similar ancestors as Festucaria. The tree based on cpDNA data does not support that: 1) subgenera Neobromus and Ceratochloa did not have a common origin; 2) subgenus Festucaria is monophyletic; and 3) subgenera Stenobromus and Bromus are distinct entities. The mean nucleotide sequence divergence values between pairs of subgenera ranged from p = 0.0 to 0.9. These values suggest that cpDNA evolution in Bromus is slow.
+S447	D. J. Bogler;B. B. Simpson	1996	Phylogeny of Agavaceae based on ITS rDNA sequence variation	American Journal of Botany	83	9	1225-1235		http://www.jstor.org/stable/2446206	Agavaceae; Convallariaceae; Dracaenaceae; internal transcribed spacer; molecular systematics; Nolinaceae	Several systems of classification have been proposed for the family Agavaceae. A distinctive bimodal karyotype and similarities of fruits and seeds strongly support close relationships among Yucca, Hesperaloe, Beschorneria, Furcraea, Agave, Manfreda, Polianthes, Prochnyanthes, and perhaps Hosta. However, Dasylirion, Beaucarnea, Nolina, Calibanus, Dracaena, and Sansevieria differ in so many cytological and morphological features that many have concluded they should be excluded from Agavaceae and separated into two families, Nolinaceae and Dracaenaceae Chloroplast DNA restriction site data support these separations and indicate that Nolinaceae and Dracaenaceae are very close to Convallariaceae (Maianthemum, Convallaria, Aspidistra, Liriope, etc.) In this paper we report the results of an ITS rDNA sequencing study of 40 taxa in Agavaceae sensu lato and related groups in the order Asparagales. Sequence alignments were optimized using the Consistency Index, Retention Index, and Rescaled Consistency Index to find the alignment that exhibited the least amount of homoplasy. The results of our study are congruent with the conclusions drawn from cytological, immunological, cpDNA, and rbcL studies, which support a narrow interpretation of Agavaceae and a close relationship among Convallariaceae, Dracaenaceae, and Nolinaceae. In addition, the ITS sequence data provide evidence for some interesting relationships within these families.
+S753	M. Lavin;E. Eshbaugh;J. M. Hu;S. Mathews;R. A. Sharrock	1998	Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data	American Journal of Botany	85	3	412-433		http://www.amjbot.org/cgi/content/abstract/85/3/412	Leguminosae; phylogeny; phytochrome genes	Phylogenetic analysis of phytochrome (PHY) genes reveals the identity and relationships of four PHY loci among papilionoid Leguminosae. A phylogenetic analysis of loci combined according to species suggests that most of the tribe Millettieae belongs to one of two monophyletic clades: the Derris-Lonchocarpus or the Tephrosia clade. Together these two form a monophyletic group that is sister to a lineage represented by Millettia grandis of Millettia sect. Compresso-gemmatae. Collectively, this large monophyletic group is referred to as the Millettieae-core groups, which based on our sampling, includes species of Millettieae that do not accumulate the nonprotein amino acid canavanine and that mostly have pseudoracemose or pseudopaniculate inflorescences. This new phylogenetic framework assists in targeting additional taxa for future sampling. For example, the American Derris (Deguelia), which accumulate canavanine, might not be members of the Millettieae core group. Afgekia is also predicted not to be a member because it accumulates canavanine and has an inflorescence of terminal racemes. PHY gene analysis specifically reveals that certain genera traditionally classified in Millettieae are actually distantly related to the Millettieae core groups, such as Austrosteenisia, Callerya, Craibia, Cyclolobium, Fordia, Platycyamus, Poecilanthe, and Wisteria.
+S506	J. E. Rodman;P. S. Soltis;D. E. Soltis;K. J. Sytsma;K. G. Karol	1998	Parallel evolution of glucosinolate biosynthesis inferred from congruent nuclear and plastid gene phylogenies	American Journal of Botany	85	7	997-1006		http://www.amjbot.org/cgi/content/abstract/85/7/997	Capparales s.l.; DNA sequencing; glucosinolates; phylogeny; rDNA (18S)	The phytochemical system of mustard-oil glucosides (glucosinolates) accompanied by the hydrolytic enzyme myrosinase (beta-thioglucosidase), the latter usually compartmented in special myrosin cells, characterizes plants in 16 families of angiosperms. Traditional classifications place these taxa in many separate orders, and thus imply multiple convergences in the origin of this chemical defense system. DNA sequencing of the chloroplast rbcL gene for representatives of all 16 families and several putative relatives, with phylogenetic analyses by parsimony and maximum likelihood methods, demonstrated instead a single major clade of mustard-oil plants and one phylogenetic outlier. In a further independent test, DNA sequencing of the nuclear 18S ribosomal RNA gene for all these exemplars has yielded the same result, a major mustard-oil clade of 15 families (Akaniaceae, Bataceae, Brassicaceae, Bretschneideraceae, Capparaceae, Caricaceae, Gyrostemonaceae, Koeberliniaceae, Limnanthaceae, Moringaceae, Pentadiplandraceae, Resedaceae, Salvadoraceae, Tovariaceae, and Tropaeolaceae) and one outlier, the genus Drypetes, traditionally placed in Euphorbiaceae. Concatenating the two gene sequences (for a total of 3254 nucleotides) in a data set for 33 taxa, we obtain robust support for this finding of parallel origins of glucosinolate biosynthesis. From likely cyanogenic ancestors, the mustard oil bomb was invented twice.
+S227	D. A. Steane;R. W. Scotland;D. J. Mabberly;R. G. Olmstead	1998	Molecular systematics of Clerodendrum (Lamiaceae): ITS sequencesces and total evidence	American Journal of Botany	86	1	98–107		http://www.amjbot.org/cgi/content/abstract/86/1/98	chloroplast DNA; Clerodendrum; Cyclonema; internal transcribed spacer; Lamiaceae	Thirty-three species of Clerodendrum s.l. and five outgroup genera were included in a sequence analysis of internal transcribed spacers of the nuclear ribosomal DNA. The results of the cladistic analysis were compared to and combined with cpDNA restriction site data from a previous study. All molecular data identified four major clades within Clerodendrum s.l. and showed the genus to be polyphyletic. Clerodendrum s.s., minus Konocalyx and Cyclonema, is monophyletic and the genus should be restricted to this group. Cyclonema and Konocalyx form a clade distinct from Clerodendrum s.s. which has been recognized as Rotheca Raf. (Steane and Mabberley, 1998).
+S388	W. S. Alverson;B. A. Whitlock;R. Nyffeler;C. Bayer;D. A. Baum	1999	Phylogeny of the core Malvales: evidence from ndhF sequence data	American Journal of Botany	86	10	1474-1486		http://www.amjbot.org/cgi/content/abstract/86/10/1474	angiosperm phylogeny; Bombacaceae; Malvaceae; Malvales; ndhF; phylogenetic nomenclature; stamen evolution; Sterculiaceae; Tiliaceae	William S. Alverson, Barbara A. Whitlock, Reto Nyffeler, Clemens Bayer, and David A. Baum. In press. Phylogeny of the core Malvales: evidence from ndhF data. American Journal of Botany (12/21/98 version here). The monophyly of the group comprising the core malvalean families, Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae, was recently confirmed by molecular studies, but the internal structure of this clade is poorly understood. In this study, we examined sequences of the chloroplast ndhF gene (aligned length 2226 bp) from 70 exemplars representing 35 of the 40 putative tribes or subfamilies of core Malvales. The monophyly of one traditional family, the Malvaceae, was strongly supported in the trees resulting from these data, but the other three families, as traditionally circumscribed, are nonmonophyletic. In addition, the following relationships were well supported: (1) a clade (/Malvatheca) consisting of traditional Malvaceae and Bombacaceae (except some members of tribe Durioneae), plus Fremontodendron and Chiranthodendron, which are usually treated as Sterculiaceae; (2) a clade (/Malvadendrina) supported by a unique 21-bp (base pair) deletion and consisting of /Malvatheca, plus five additional subclades, including representatives of Sterculiaceae and Tiliaceae, plus Durio and Neesia (both Durionieae); 3) a clade (/Byttneriina) with genera traditionally assigned to several tribes of Tiliaceae, plus exemplars of tribes Byttnerieae, Hermannieae, and Lasiopetaleae of Sterculiaceae. The most striking departures from traditional classifications are the following: Durio and relatives appear to be more closely related to Helicteres and Reevesia (Sterculiaceae) than to Bombacaceae; several genera traditionally considered as Bombacaceae (Camptostemon, Matisia, Phragmotheca, and Quararibea) or Sterculiaceae (Chiranthodendron and Fremontodendron) appear as sister lineages to the traditional Malvaceae; tribe Helictereae (Sterculiaceae) is polyphyletic; and Sterculiaceae and Tiliaceae, as traditionally circumscribed, represent polyphyletic groups that cannot sensibly be maintained with their traditional limits for purposes of classification. We discuss morphological characters supporting the clades indicated by molecular data. These findings indicate extensive homoplasy of many morphological characters previously used to delineate taxonomic groups in core Malvales. The topologies here also suggest that /Malvatheca (the malvoid and bombacoid clades) do not have as a synapormophy monothecate anthers, as has been previously supposed but, instead, may be united by the dithecate, transversely septate (polysporangiate) anthers in basal members of both clades, from which monothecate anthers may have been derived at least twice. Key words: angiosperm phylogeny; phylogenetic nomenclature; rankless taxa; stamen evolution; Bombacaceae; Malvaceae; Malvales; Sterculiaceae; Tiliaceae. Baum, D. A., W. S. Alverson, and R. N. Nyffeler. 1998. A durian by any other name: taxonomy and nomenclature of the core Malvales. Harvard Papers in Botany 3: 317-332. The phylogeny of the core Malvales (including plants traditionally placed in the families Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae) has been greatly clarified by recent molecular systematic studies. In this paper we explore the options available for incorporating this phylogenetic information into a classification for the group. We first discuss a range of options within the traditional system of nomenclature with the added constraint of only recognizing monophyletic groups. These schemes differ in the ranks applied and in the degree to which currently used names continue to apply to familiar groups. We then propose an alternative set of unranked names within the framework of phylogenetic nomenclature. This phylogenetic classification shares the same names as a recently published traditional classification, except that the phylogenetic names are distinguished by a clademark. We note some advantages of phylogenetic nomenclature: monophyly of taxa can be ass med; there is no limit to the number of nested clades that can be named; classifications are stable so long as phylogenetic knowledge does not change, and; it will be easy to establish useful data base resources. The traditional and phylogenetic classifications of the core Malvales are almost identical given current knowledge of phylogeny. Therefore, this group provides a controlled experiment with which to see how the two nomenclatural codes perform in practice as phylogenetic knowledge increases.
+S759	J. M. Hu;M. Lavin;M. F. Wojciechowski;M. J. Sanderson	2000	Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae	American Journal of Botany	87	3	418-430		http://www.amjbot.org/cgi/content/abstract/87/3/418	Fabaceae;  matK; Millettieae; Papilionoideae; phylogeny; trnK	Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were recon-structed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum parsi-mony and are well resolved and supported by high bootstrap values. A well-supported "core Millettieae" clade is recognized, comprising the four large genera Millettia, Lonchocarpus, Derris, and Tephrosia. Several other small genera of Millettieae are not in the core Millettieae clade. Platycyamus is grouped with Phaseoleae (in part). Ostryocarpus, Austrosteenisia, and Dalbergiella are neither in the core Millettieae or Phaseoleae clade. These taxa, along with core Millettieae and Phaseoleae, form a monophyletic sister group to Indigofereae. Cyclolobium and Poecilanthe are close to Brongniartieae. Callerya and Wisteria belong to a large clade that includes all the legumes that lack the inverted repeat in their chloroplast genome, which confirms previous rbcL and phytochrome gene family phylogenies. The evolutionary history of four characters was examined in Millettieae and allies: the presence of canavanine, inflorescence types, the dehiscence of pods, and the presence of winged pods. trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions.
+S1974	G. D. Weiblen	2000	Phylogenetic relationships of functionally dioecious Ficus (Moraceae) based on ribosomal DNA sequences and morphology	American Journal of Botany	87	9	1342-1357		http://www.amjbot.org/cgi/content/abstract/87/9/1342	breeding system evolution; coevolution; dioecy; Ficus; Moraceae; phylogeny;  pollination	Figs (Ficus, Moraceae) are either monoecious or gynodioecious depending on the arrangement of unisexual florets within the specialized inflorescence or syconium. The gynodioecious species are functionally dioecious due to the impact of pollinating fig wasps (Hymenoptera: Agaonidae) on the maturation of fig seeds. The evolutionary relationships of functionally dioecious figs (Ficus subg. Ficus) were examined through phylogenetic analyses based on the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and morphology. Forty-six species representing each monoecious subgenus and each section of functionally dioecious subg. Ficus were included in parsimony analyses based on 180 molecular characters and 61 morphological characters that were potentially informative. Separate and combined analyses of molecular and morphological data sets suggested that functionally dioecious figs are not monophyletic and that monoecious subg. Sycomorus is derived within a dioecious clade. The combined analysis indicated one or two origins of functional dioecy in the genus and at least two reversals to monoecy within a functionally dioecious lineage. The exclusion of breeding system and related characters from the analysis also indicated two shifts from monoecy to functional dioecy and two reversals. The associations of pollinating fig wasps were congruent with host fig phylogeny and further supported a revised classification of Ficus.
+S690	L. M. Giussani;J. H. Cota-Sánchez;F. O. Zuloaga;E. A. Kellogg	2001	A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis	American Journal of Botany	88	11	1993–2012		http://www.amjbot.org/cgi/content/abstract/88/11/1993	C4 photosynthesis; ndhF; Panicoideae; Poaceae	DNA sequence data from the chloroplast gene ndhF were analyzed to estimate the phylogeny of the subfamily Panicoideae, with emphasis on the tribe Paniceae. Our data suggest that the subfamily is divided into three strongly supported clades, corresponding to groups with largely identical base chromosome numbers. Relationships among the three clades are unclear. In unweighted parsimony analyses, the two major clades with x = 10 (Andropogoneae and x = 10 Paniceae) are weakly supported as sister taxa. The third large clade corresponds to x = 9 Paniceae. In analyses under implied weight, the two clades of Paniceae are sisters, making the tribe monophyletic. Neither resolution is strongly supported.; Our molecular phylogen...
 
[truncated message content]