American Journal of Botany

Published by Botanical Society of America
Online ISSN: 1537-2197
Print ISSN: 0002-9122
Classification of tribes and genera under Monsteroideae sensu Mayo et al. (1997). 
The chloroplast trnL-F region was used as an independent data set for phylogenetic analysis of 118 aroid taxa. We investigated the intergeneric relationships of subfamily Monsteroideae (Araceae) and used this as a basis for an interspecific phylogenetic study of Rhaphidophora Hassk., the largest genus of the Monsteroideae. Results of the molecular tree were useful for inferring subfamilial and tribal circumscription and evolution in Araceae. Our results show that family Araceae consists of five clades that correspond to the subfamilies traditionally recognized. Starting from the most basal clade, these correspond to subfamilies Gymnostachydoideae and Orontioideae (proto aroids), with Lemna sp. (Lemnaceae) embedded in the Araceae and sister to the true aroids consisting of Pothoideae sister to Monsteroideae, immediately sister to Lasioideae and Aroideae. There is less agreement with existing tribal classifications. Complex relationships exist between members of the Monsteroideae. Our results show that Rhaphidophora and Epipremnum are paraphyletic with species of Rhaphidophora sampled, forming three informal groups with other genera of the Monstereae. Phylogenetic results may be used to suggest taxonomic changes to the current systematics of the monsteroids.
Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution.
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.
Frequency of number of seedlings found within 5 m of Stage 2 and 3 individuals (N 324).  
Estimates of densities (no. individuals/ha) of Ancistrocladus korupensis by stage class based on mean distances from nearest neighbor within same stage class and from nearest neighbor of any stage class. Empty cells indicate insufficient sample size to estimate density.
Correlogram of Wright's coefficient of coancestry ( ij ) vs. 10-m interplant distances. Dotted line indicates 99% confidence intervals around null hypothesis of no spatial autocorrelation ( ij 0).  
Mean michellamine B dry mass concentrations by (a) leaf type, (b) stage class, and (c) site (1 SE). Mean values with the same letter are not significantly different ( 0.05, Tukey post hoc test). Leaf types defined as follows: 1 old, fallen, brown; 2 old, senescent, mottled green/yellow/brown; 3 old leaf on vine, dark green with many epiphyllae; 4 mature dark green leaf; 5 young, fully expanded leaf, pale green; 6 very young leaf, not fully expanded, pale green–(/-) red. Stage classes: 1 free-standing 2 m; 2 subcanopy climber; 3 canopy climber.  
(a) Frequencies of stage classes across all sites, and (b) frequencies of stem diameters for all individuals (excluding Nursery sample ) grouped by stage class. Stage 1 free-standing 2 m, 2 subcanopy climber, 3 canopy climber.  
Ancistrocladus korupensis D. W. Thomas & Gereau (Ancistrocladaceae) is a recently described liana from Cameroon. Its leaves yield the alkaloid michellamine B, which shows in vitro activity against HIV. The only known population is limited to ~15,000 ha within Korup National Park and its immediate surroundings. This study: (1) describes ecological patterns (geographic range, population density, stage and size class distributions, host tree characteristics, and seed dispersal patterns) of A. korupensis ; (2) quantifies patterns of genetic variation on species and subpopulation levels and fine-scale genetic structure; (3) describes variation in michellamine B content; and (4) makes conservation recommendations based on ecological and genetic data. Ecological data from 457 individuals from seven sites indicate that the A. korupensis population is dominated by canopy-climbing individuals. Population densities are low with values ranging from 2.5 to 12.9 individuals/ha. Reproduction data suggest limited seed dispersal, episodic fruiting, and no vegetative reproduction. Allozyme data indicate low genetic diversity with only 7.1% of the 14 loci polymorphic. Values for Hobs and He were 0.022 (_ 0.000 SE) and 0.041 (_ 0.000 SE), respectively. Wright's F statistics analysis suggests that A. korupensis is highly inbred (FIS = 0.455) with moderate levels of subpopulation differentiation (FST = 0.1153). Michellamine B content was best predicted by leaf type but also showed a significant relationship for stage class. The occurrence of rare, private alleles in most of the sites, low overall population size and density, and low availability of individuals for recruitment into the adult stage class are important considerations for the rational management of A. korupensis.
Unlabelled: • Premise of the study: In Chinese bayberry (Myrica rubra), the available simple sequence repeat (SSR) markers are insufficient to meet the developing demand for genetic and molecular breeding research. This study was aimed at developing a large number of polymorphic expressed sequence tag (EST)-SSRs from the transcriptome of Chinese bayberry. • Methods and results: Five hundred ninety-four compound EST-SSRs and 5557 noncompound ones were identified from 41239 unigene sequences generated from the transcriptome of M. rubra cv. Biqi. Using 10 Chinese bayberry cultivars, 109 polymorphic EST-SSRs were screened from 412 selected. In total, they generated 389 alleles, with a polymorphism ratio of 93.8%. In addition, it was observed that the polymorphism levels of compound EST-SSRs were somewhat lower than those of noncompound ones. • Conclusions: The 109 polymorphic EST-SSRs developed from the Chinese bayberry transcriptome should greatly promote the development of genetic and molecular breeding studies in this as well as other Myricaceae species.
Unlabelled: Premise of the study: Simple sequence repeat (SSR) markers were developed for faba bean using expressed sequence tags (ESTs) from the NCBI database to study for genetic diversity. • Methods and results: A total of 11 novel EST-SSR loci were generated and characterized when tested on four populations of 29 faba bean individuals from China and Europe. The number of alleles (A) ranged from 1 to 3 in each population, and observed heterozygosity (H(O)) and expected heterozygosity (H(E)) ranged from 0 to 0.5000 and 0.6400, respectively. Furthermore, transferable analysis revealed that eight of these loci (72.73%) amplified in Pisum sativum L., six of which (75.00%) detected polymorphism. • Conclusions: The developed markers in this study will provide valuable tools for genetic diversity, resource conservation, genetic mapping, and marker-assisted breeding of faba bean in the future.
Reproductive traits of tropical tree species vary predictably in relation to successional stage, but this variation may be due to the species' phylogenetic histories rather than selective pressures imposed by regeneration requirements. Reproductive phenology, tree size at the onset of reproduction, and fecundity of 11 sympatric, closely related Macaranga species were studied to investigate within-species variation in reproductive traits in relation to resource availability, and among-species variation in relation to other life-history traits (shade tolerance, seed size and maximum tree size, H(max)) and consequently the requirements for forest-gap colonization. Nine species reproduced in synchronous episodes, and two species reproduced continuously over 32 mo. Episodic reproduction was most intense in 1992 following a severe drought. For several species, reproductive trees had greater light availability, lower fecundity in lower light levels, and lower growth rates than nonreproductive trees, reflecting resource-limited reproduction. Among species, H(max) was negatively correlated with shade tolerance and seed size. Tree size at the onset of reproduction and fecundity was strongly linked to this axis of life-history variation, but phenological pattern was not. Absolute tree size at the onset of reproduction was positively correlated with H(max) and negatively correlated with shade tolerance. Relative size at reproductive onset was not correlated with shade tolerance or H(max). Fecundity ranged four orders of magnitude among species and was correlated positively with H(max) and negatively with seed size and shade tolerance. The interrelationships among these reproductive and other life-history traits are strongly correlated with the species' requirements for gap colonization.
Unlabelled: • Premise of the study: Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers were developed in Dendrobium officinale by screening a cDNA library. The loci were verified by sequencing and explored for polymorphism among 19 genotypes and transferability among 30 other distantly related Dendrobium species. • Methods and results: One hundred ten EST-SSRs were developed, and a set of 20 amplified two to six nucleotide repeats with a mean number of 2.5 alleles per locus and with an observed heterozygosity and polymorphism information content per locus ranging from 0.3463 to 0.9003 and 0.0997 to 0.6537 in 19 D. officinale genotypes, respectively. Furthermore, 92 of these markers have cross-taxa transferability, ranging from 6.45% to 100% among 30 other distantly related Dendrobium species. • Conclusions: The developed markers have potential for application in germplasm appraisal, genetic diversity study, genetic mapping, and molecular breeding in D. officinale and other congeneric species.
Characteristics of novel 112 TUGMS markers identifi ed in the current study. 
Tea Unigene-derived MicroSatellite (TUGMS) markers were identified from the publicly available EST data in Camellia sinensis for characterization and future genome mapping studies in tea. One hundred twelve novel TUGMS markers were identified from 4356 unigenes derived by clustering of 12788 random ESTs in C. sinensis. Amplification-based validation of the TUGMS loci proved them to be highly polymorphic [an average (av.) of 5.24 alleles], heterozygous (H(E), av. 0.746; H(o), av. 0.566) and informative (PIC, av. 0.392). TUGMS loci were 100% transferable in cultivated C. assamica and C. assamica subsp. lasiocalyx and highly cross-transferrable to the related species C. japonica, C. rosiflora, and C. sasanqua. These 112 novel highly polymorphic TUGMS markers with proven cross-species transferability will facilitate the future genetic diversity and genome mapping studies in tea.
Strict consensus tree of nine equally most parsimonious trees obtained from sequences of psbA–trnH intergenic spacer of chloroplast DNA. Tree length 38, CI 0.921 (0.875 excluding autapomorphies), RI 0.971. Above branches, bold numbers represent nucleotide substitutions , numbers in parentheses represent number of indels; numbers below branches represent bootstrap values.  
Mutations in trnL-trnF intergenic spacer.
Comparisons of sequence divergence and phylogenetic information from variable sites among two intergenic spacers and matK coding region.
The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information. The mat K coding region, evolving more rapidly than the trnL-trn F spacer and more slowly than the psb A-trn H spacer, produced the best resolved phylogenetic tree. The mat K phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.
After 120 yr of burial in moist, well-aerated sand, 23 seeds of Verbascum blattaria and two seeds of a Verbascum sp. germinated and produced normal plants (50% germination for Verbascum). After a 6-wk cold treatment, a single seed of Malva rotundifolia germinated also, producing a normal plant (2% germination). Plants were grown to maturity in a greenhouse, and flowering was induced by exposure to a 6-wk cold treatment. Flowers were artificially pollinated to produce seed of both Verbascum blattaria and Malva rotundifolia. The Verbascum sp. failed to set seed. Collected seeds were subsequently germinated, producing normal plants. F(1) seeds of V. blattaria had a germination of 64%. Seeds (6%) of M. rotundifolia germinated after a cold treatment.
Seed germination constitutes an important event in the life cycle of plants. Two related seed traits affect fitness: seed size and the timing of seed germination. In three sets of experiments, we (1) partition the sources of seed-size variance in Lobelia inflata into components attributable to fruit size, relative fruit position, and parental identity; (2) examine the influence of pregermination conditions and seed size on time to germination; and (3) assess the fitness consequences of seed size and germination timing under seminatural, harsh conditions. Seed-size variance is attributable to both parental identity and fruit position within an individual. Distal fruits produce larger but fewer seeds. No significant correlation exists between fruit size and seed size, but a trade-off is found between the number and size of seeds contained in a fruit after correcting for fruit size. The timing of germination is influenced by seed size, light conditions before winter, and winter duration. Germination timing influences survival, and despite small seed size in this species (2 × 10 g/seed), seed size has a persistent and significant association with both final plant size and the probability of survival to autumn.
Eleven flavonol glycosides and two anthocyanins, only one of which was previously identified, were isolated from the flower petals of okra, Hibiscus esculentus L. On the basis of chromatographic, spectral, and degradative evidence, the following structural assignments were made: quercetin 4′-glucoside, quercetin 7-glucoside, quercetin 5-glucoside, quercetin 3-diglucoside, quercetin 4′-diglucoside, quercetin 3-triglucoside, quercetin 5-rhamnoglucoside, gossypetin 8-glucoside, gossypetin 8-rhamnoglucoside, gossypetin 3-glucosido-8-rhamnoglucoside, cyanidin 4′-glucoside, and cyanidin 3-glucosido-4′ glucoside. Some evidence was obtained of a pentahy-droxy, monomethoxy-flavone glycoside. The total flavonoid content in the red portion of the petal was 0.48% of fresh weight; that in the white portion was 2.51%. The two anthocyanins comprised 28.5% of the flavonoid content of the red flower but only a trace of the content of the white.
Primer sequences and characteristics of 43 microsatellite markers in Pinus koraiensis . 
Unlabelled: • Premise of the study: Thirteen polymorphic microsatellite markers were developed to investigate the genetic diversity and population structure of Pinus koraiensis. • Methods and results: Using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) method with three specific PCR primers for screening the positive clones, 13 loci were found to be polymorphic in 78 individuals of P. koraiensis. Across all of the P. koraiensis samples, the number of alleles per locus ranged from two to 11. • Conclusions: These polymorphic markers will be useful for conservation genetics studies of this species and to inform the development of effective P. koraiensis conservation programs.
While carbon transport and partitioning is largely determined by phloem source-sink relationships, it may be constrained by vascular connections. Tomato (Lycopersicon esculentum) plants exhibit a high degree of sectoriality, with restricted movement of nutrients from particular roots to orthostichous leaves. In this experiment we investigated the manner in which sectoriality influences source-sink phloem partitioning from shoots to roots in tomatoes and whether the size of the sink (root) modifies the pattern of carbon movement outside sectored pathways. Using (13)C, we determined that shoot-to-root carbon transport in tomatoes is sectored even from upper leaves. Sink size also influenced carbon partitioning. Specifically, when a lateral root was grown in isolation (using a split-pot technique), it grew more and acquired significantly more (13)C from an orthostichous, exposed leaf than did any other single root. Vascular constraints were evident. (13)C accumulation in a large, isolated lateral root was very low when a leaf opposite the isolated lateral root was exposed. Thus sink size did not overcome vascular constraints. Because carbon assimilates are needed for nutrient acquisition and assimilation, these vascular constraints may affect the ability of sectored plants to utilize heterogeneously distributed soil resources. If so, future studies should compare species that differ in sectoriality to determine whether vascular constraints affect competitive hierarchies when soil resource availability is patchy.
Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.
Patterns of nucleotide substitution for the four genes included in the combined analysis. 
To study the inter- and infrafamilial phylogenetic relationships in the order Caryophyllales sensu lato (s.l.), ∼930 base pairs of the matK plastid gene have been sequenced and analyzed for 127 taxa. In addition, these sequences have been combined with the rbcL plastid gene for 53 taxa and with the rbcL and atpB plastid genes as well as the nuclear 18S rDNA for 26 taxa to provide increased support for deeper branches. The red pigments of Corbichonia, Lophiocarpus, and Sarcobatus have been tested and shown to belong to the betacyanin class of compounds. Most taxa of the order are clearly grouped into two main clades (i.e., "core" and "noncore" Caryophyllales) which are, in turn, divided into well-defined subunits. Phytolaccaceae and Molluginaceae are polyphyletic, and Portulacaceae are paraphyletic, whereas Agdestidaceae, Barbeuiaceae, Petiveriaceae, and Sarcobataceae should be given familial recognition. Two additional lineages are potentially appropriate to be elevated to the family level in the future: the genera Lophiocarpus and Corbichonia form a well-supported clade on the basis of molecular and chemical evidence, and Limeum appears to be separated from other Molluginaceae based on both molecular and ultrastructural data.
This study examines molecular and morphological differentiation in Phryma L., which has only one species with a well-known classic intercontinental disjunct distribution between eastern Asia (EA) and eastern North America (ENA). Phylogenetic analysis of nuclear ribosomal ITS and chloroplast rps16 and trnL-F sequences revealed two highly distinct clades corresponding to EA and ENA. The divergence time between the intercontinental populations was estimated to be 3.68 ± 2.25 to 5.23 ± 1.37 million years ago (mya) based on combined chloroplast data using Bayesian and penalized likelihood methods. Phylogeographic and dispersal-vicariance (DIVA) analysis suggest a North American origin of Phryma and its migration into EA via the Bering land bridge. Multivariate analysis based on 23 quantitative morphological characters detected no geographic groups at the intercontinental level. The intercontinental populations of Phryma thus show distinct molecular divergence with little morphological differentiation. The discordance of the molecular and morphological patterns may be explained by morphological stasis due to ecological similarity in both continents. The divergence of Phryma from its close relatives in the Phrymaceae was estimated to be at least 32.32 ± 4.46 to 49.35 ± 3.18 mya.
Flowering phenology of Narcissus cavanillesii (closed circles) and N. serotinus (open circles) in Ajuda population in 2001. 
Mean fruit set, mean number of seeds per fruit, and mean seed mass after several pollination treatments in Narcissus cavanillesii and N. serotinus. 
Correlation between number of open flowers and number of flowers visited per observation session. Spearman's correlation coefficient was q ¼ 0.086, P ¼ 0.092, for Narcissus cavanillesii (N ¼ 301; closed circles) and q ¼ 0.671, P ¼ 0.0001, for N. serotinus (N ¼ 532; open circles). Note that during some observation sessions of N. cavanillesii, the number of visited flowers was greater than the number of open flowers, indicating that flowers were sometimes visited by more than one insect per session. 
Pollinators observed in Narcissus cavanillesii and N. serotinus. 
Mean fruit set, mean number of seeds per fruit, and mean seed mass in interspecific crosses between Narcissus cavanillesii and N. serotinus made in the two directions. 
Natural hybrids between rare and common sympatric species are commonly eradicated to avoid the potential extinction of the rare species, although there is currently no clear predictive framework to quantify this risk. As hybrids can have intrinsic value as new evolutionary pathways, further knowledge on the factors controlling hybridization is needed. In this study we evaluated the role of pollination patterns in hybridization events in two sympatric populations of Narcissus cavanillesii and N. serotinus in Portugal. Narcissus cavanillesii is a rare species, while N. serotinus is widely distributed across the Mediterranean. The hybrid, N. ×perezlarae, is quite frequent in southeastern Spain but is scarce in Portugal. Reciprocal manual crossings confirmed compatibility between the two species, although hybridization was more successful when N. cavanillesii participated as female. Narcissus cavanillesii and N. serotinus only shared one pollinator, Megachile sp. (Hymenoptera), which had low visitation rates and high flower constancy. No single isolation mechanism was fully effective in preventing hybridization. Temporal displacement of flowering peaks, strong pollinator specificity, and high flower constancy in the shared pollinator all contributed to limiting hybridization in this site. In other sympatric occurrences, different phenological windows and pollination assemblages may allow greater frequency of the hybrid.
Characteristics of 14 polymorphic microsatellite loci amplifi ed in Attalea phalerata. 
Unlabelled: Premise of the study: We developed microsatellite primers for the widely distributed tropical palm Attalea phalerata for studies on the dispersal and spatial genetic structure of palm populations. • Methods and results: Fourteen di-, tri-, and tetra-nucleotide microsatellite primer pairs were identified. The number of alleles in the population tested ranged between 3 and 25, with a mean of 12.1. Ten microsatellite loci exhibited no significant deviations from Hardy-Weinberg Equilibrium or presence of null alleles, and their combined probability of exclusion was 0.998. • Conclusions: These microsatellite loci will be useful in parentage analysis and population genetics studies of Attalea phalerata.
Reproduction of polyploid Rubus species is described as facultatively apomictic. Pollination is needed for seed set, but most seedlings are produced asexually by pseudogamy. Although sexual processes may occur, clonal diversity can be extremely low. We performed a pollination experiment to investigate the breeding system and used allozyme and AFLP markers to analyze genetic variation among and within seed families in R. armeniacus and R. bifrons. Pollination either with self or outcross pollen was necessary to trigger seed set. Outbreeding marginally increased the number and quality of seeds compared with selfing. The enzyme PGI revealed some genetic variation within seed families. Seven other enzyme systems were monomorphic. The more detailed AFLP analyses with five primer pairs detected the same rate of genetic variation (14-17% of seedlings were genetically distinct) and confirmed the allozyme results for the same individuals. No genetic variation was found between the seed families from within a species collected in widely separated populations, but clear species-specific differences were observed. The results support the view that polyploid Rubus species are pseudogamous apomicts with low genetic diversity among and within seed families. However, sexual reproduction occasionally occurs and contributes to the maintenance of genetic variation within natural populations.
Scale maps of the 14 plastid and two nuclear regions included in this study, with approximate primer annealing sites indicated (arrows). The relative positions of the plastid regions are shown on the map of the Tortula ruralis plastome (taken from Oliver et al., 2010 ); the gray bars represent the inverted repeats that contain the plastid ribosomal DNA. The gap in the plastome represents the numeric beginning and end of the sequence. The nuclear regions (O, P) are a part of the nrDNA cistron. 
Contrasting all-plastid, all-nuclear, and all-data phylogenies found by maximum parsimony analyses (branch-and-bound search) of 25 collections of Plagiothecium and associated taxa, based on 14 plastid ( atpB-rbcL , cpITS, psbA-trnH , psbT-H , rbcL , rpl16 , rpoC1 , rps4 , rps4-trnL , trnD-T , trnG , trnK-psbA , trnL-F , and trnM-V ) and two nuclear (ITS and 26S) DNA regions. Gaps were treated as missing data; they were not coded as separate characters. The plastid matrix included 11 722 sites, of which 654 (5.6%) were parsimony-informative (p-i), 930 were variable but not p-i, and 10 138 were constant; the search returned a single most-parsimonious tree (shown in upper left; length = 2295, iCI = 0.57). The nuclear matrix included 1973 sites, of which 41 (2.1%) were p-i, 104 were variable but not p-i, and 1828 were constant; the search returned a single most-parsimonious tree (shown in lower left; length = 190, iCI = 0.72). The all-data matrix included 13 695 sites, of which 695 (5.1%) were p-i, 1034 were variable but not p-i, and 11 966 were constant; the search found two equally most-parsimonious trees, and the consensus of these is shown on the right (length = 2489, iCI = 0.58). For each analysis, bootstrap support values (2000 replicates) are given, based on a branch-and-bound search for the all-data and all-plastid phylogenies, and on a heuristic search for the all-nuclear phylogeny, which failed to recover one one branch-and-bound node, indicated with an asterisk (*). 
The 17 DNA markers sampled, primers used for amplifi cation and sequencing, and the best PCR reaction conditions tried. The thermal profi les have the pattern: initial melt/ x number of PCR cycles of [melting/annealing/extension]/fi nal extension. The ° C sign is omitted. For rpoC1 , the Kew "LP" primers gave the best results and the longest amplicon. For gpd , the primers preferentially amplifi ed bacterial DNA. For trnK-psbA , we used a touchdown protocol (cf. Wicke and Quandt, 2009 ). 
Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps. For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given. Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics. Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.
The vast majority of flowering plant seeds contain a triploid endosperm formed by fertilization of a monosporic, Polygonum-type female gametophyte. However, evolutionary transitions to six other genetic constructs of endosperm are widespread, and six of seven known patterns are found in the order Piperales. Within Piperaceae, Manekia has not been described, and we report its female gametophyte to be tetrasporic and 16-nucleate at maturity. Manekia ontogeny is generally characterized by early establishment of a bipolar or weakly bipolar body plan and a binucleate central cell at maturity (Drusa-type pattern); however, ca. 16% of early stages had distinctly tetrapolar organization, and ca. 21% of mature specimens had a tetranucleate central cell (Penaea-type pattern, not previously reported in Piperaceae). An evolutionary developmental analysis indicates heterochrony, heterotopy, novelties, and sequence deletions have each played roles in modulating variation within Piperales. Our data suggest the common ancestor of Piperaceae was tetrasporic and retained a plesiomorphic bipolar body plan, producing a "functionally bisporic" form of triploid endosperm derived from the lineal descendants of two megaspores and a sperm. Developmental modifications of this tetrasporic, bipolar ontogeny can account for the origin of all three other known "true" tetrasporic endosperm genetic constructs, formed from derivatives of all four megaspores and a sperm. These derived endosperms in turn have higher ploidy, higher potential heterozygosity, and reduced genetic conflicts.
Average genetic diversity for four species and one variety of Podocarpus using the 16 newly developed polymorphic microsatellite markers. Locus N a N e H o H e P value (HWE) 
Premise of the study: Sixteen polymorphic microsatellite markers were isolated and characterized from the endangered evergreen tree Podocarpus nakaii to evaluate the population structure for conservation efforts. Methods and results: Based on a modified amplified fragment length polymorphism and magnetic bead enrichment method, 16 polymorphic primer sets were developed for this endangered insular species. Allele numbers ranged from five to seven, with an observed heterozygosity ranging from 0.29 to 0.88. Most primers were able to amplify DNA from the endemic P. fasciculus and the widely distributed P. macrophyllus var. macrophyllus, P. macrophyllus var. maki, and P. costalis. Conclusions: The results reported here indicate the usefulness of codominant markers for future studies of the population genetics of P. nakaii. In addition, the markers are useful for further phytogeographic and speciation studies in P. fasciculus, P. macrophyllus var. macrophyllus, and P. macrophyllus var. maki, which are closely related species.
Unlabelled: • Premise of the study: Expressed sequence tag (ESTs)-derived microsatellite markers were developed in Lathyrus sativus by screening the National Center for Biotechnology Information (NCBI) database. The usefulness of these novel markers was validated for size polymorphism among grasspea accessions. • Methods and results: Three hundred EST-simple sequence repeat (SSR) primer pairs were identified and loci characterized for size polymorphism among 24 grasspea accessions from worldwide sources. Among them 139 SSR loci produced no PCR product, 117 SSR loci were monomorphic, and 44 SSR loci were polymorphic. The mean number of alleles per locus ranged from two to 11. The observed heterozygosity and expected heterozygosity ranged from 0.000 to 1.000 and 0.042 to 0.836, respectively. • Conclusions: These novel markers will be useful and convenient to study genetic mapping and molecular breeding in grasspea.
The number of trees of each major graft variety of avocado (Persea americana) on farms in San Jerónimo, Costa Rica, broken down into age groups. 
The response to selection under different graft introgression rates in simulations modeling avocado (Persea americana) on farms in San Jerónimo, Costa Rica. Scores are the percentage of 100 replicate simulation runs in which the rarest allele survived 400 breeding cycles. In all cases, the census population size is 1600 individuals.
Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.
Two sympatric Delphinium species, D. barbeyi and D. nuttallianum, are ecologically and morphologically similar. However, D. barbeyi has multiple, large inflorescences while D. nuttallianum has a single, small inflorescence. These differences in floral display should result in greater intraplant pollen transfer in D. barbeyi, leading to higher rates of self-pollination through geitonogamy. Reduced gene flow by pollen should in turn produce greater population differentiation among populations of D. barbeyi relative to D. nuttallianum. We tested these predictions by comparing pollinator behavior, breeding systems, outcrossing rates, and population genetic structure of sympatric populations of the two species in Colorado. Bumble bee and hummingbird pollinators visit more flowers and inflorescences per foraging bout in D. barbeyi than in D. nuttallianum. The species differed in breeding system; D. barbeyi produced more seeds by autogamy (9 vs. 2%) than D. nuttallianum and suffered no reduction in seed set in hand-self vs. outcross pollinations, in contrast to a 41% decline in D. nuttallianum. The outcrossing rate in one D. barbeyi population was 55%, but ranged from 87 to 97% in four D. nuttallianum populations. Genetic differentiation among population subdivisions estimated by hierarchical F statistics was >10 times greater in D. barbeyi ( = 0.055-0.126) than D. nuttallianum ( = 0.004-0.009) at spatial scales ranging from metres to 3.5 km. Spatial autocorrelation analysis also indicated more pronounced local genetic structure in D. barbeyi than D. nuttallianum populations. Fixation indices (F(IS)) of D. barbeyi adults were much lower than expected based on mating system equilibrium and suggest that differences in the degree of self-compatibility and/or the timing of postpollination selection/inbreeding depression between the two species further contribute to the genetic differences between them.
Mating and ecological variables used in the analysis.
Hierarchical levels of relatedness within and among Sorbus torminalis maternal pollen clouds (see Table 1 for code definitions of variables). (A) Average F S values within maternal progeny (MP), with among-fruit and within-fruit components, computed on the 14 maternal families (267 seeds) with seeds nested within fruits. The average F S value within maternal progenies is also given for the whole sample of 59 maternal families analyzed in 2000. Bars correspond to 95% confidence intervals. (B) F gh values among maternal pollen clouds computed using the 59 maternal progenies sampled in 2000 as a function of geographic distance between mothers. Dotted lines correspond to the 95% confidence intervals computed using 10000 random permutations of paternal genotypes across mother tree locations. (C) F gh values among maternal pollen clouds computed using 58 maternal progenies sampled in 2000 as a function of flowering overlap between mother trees ( O gh ), defined as the number of days when both mother trees g and h were flowering. (D) Comparison of average F S value (lozenge) within maternal progenies and within years for all 73 progenies sampled in 1999 and 2000 and average F gg 0 value (circle) corresponding to among-year level of relatedness for the 13 maternal pollen clouds sampled in both years. The average F gh value between pollen clouds in the [0–50 m] distance class is also given. Bars correspond to 95% confidence intervals. 
Understanding the role of mother plants as pollen recipients in shaping mating patterns is essential for understanding the evolution of populations and in particular to predict the consequence of habitat fragmentation. Here, we investigated variation in mating patterns due to maternal phenotypic traits, phenological variance, and landscape features in Sorbus torminalis, a hermaphroditic, insect-pollinated and low-density, European temperate forest tree. The diversity and composition of pollen clouds received by maternal trees in S. torminalis were mainly determined by their conspecific neighborhood: isolated individuals sample more diversity through more even paternal contributions, low relatedness among paternal genes, and high rates of long-distance pollen dispersal within their progenies. Maternal phenotypic traits related to pollinator attractiveness also had an effect, but only when competition was strong: in this case, larger mother trees with more flowers sampled more diversity. The floral architecture of S. torminalis, with multiple-seeded fruit, strongly shaped mating patterns, with higher levels of correlated paternity among seeds belonging to the same fruit (30% full sibs) than among seeds belonging to different fruits (14% full sibs). Finally, flowering phenology affected the distribution of diversity among maternal pollen clouds, but the earliest and latest mother trees did not receive less diversity of pollen than the others.
Perforation plates are reported in aerial and subaerial axes of Psilotum nudum and in aerial axes of Tmesipteris obliqua. In Psilotum, both perforations lacking pit membranes and perforations with pit membrane remnants were observed. Perforation plates in Psilotum may consist wholly of one type or the other. In Tmespteris, perforations have threadlike pit membranes or consist of porose pit membranes. Wide perforations alternating with narrow pits, a conformation observed in various ferns, were observed in Psilotum (subaerial axes). In Psilotum, perforations are more common in metaxylem than in protoxylem; perforations in protoxylem consist of primary wall areas containing small circular porosities or relatively large circular to oval perforations. There are no modifications in the secondary wall framework of protoxylem or metaxylem in Psilotum or Tmesipteris that would permit one to distinguish presence of perforations or perforation plates with light microscopy, and scanning electron microscopy (SEM) is required for demonstration of porose walls or perforations. The tracheary elements of the Psilotaceae studied have no features not also observed in other ferns with SEM.
The maximum likelihood majority-rule consensus from the 17-gene analysis shown as a cladogram with mtDNA data removed for Polyosma. This single large tree has been divided into a series of interconnected trees in which subclades are labeled 2a through 2l; these designations match those given in Fig. 1. Names of the orders and families follow APG III (2009) ; other names follow Cantino et al. (2007). Numbers above branches are bootstrap percentages.
Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
Map of primers used to amplify (open arrows) and sequence (all arrows) the chloroplast gene rpl2 and its intron. Primer pair 20F/25R was typically used for PCR amplification. Primers B20F and B25R were often used as alternate sequencing primers to primers 20F and 25R, respectively. The scale is relative to Nicotiana tabacum sequence (primers are not drawn to scale). 
Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.
Until recently, rigorously reconstructing the many hybrid speciation events in plants has not been practical because of the limited number of molecular markers available for plant phylogenetic reconstruction and the lack of good, biologically based methods for inferring reticulation (network) events. This situation should change rapidly with the development of multiple nuclear markers for phylogenetic reconstruction and new methods for reconstructing reticulate evolution. These developments will necessitate a much greater incorporation of population genetics into phylogenetic reconstruction than has been common. Population genetic events such as gene duplication coupled with lineage sorting and meiotic and sexual recombination have always had the potential to affect phylogenetic inference. For tree reconstruction, these problems are usually minimized by using uniparental markers and nuclear markers that undergo rapid concerted evolution. Because reconstruction of reticulate speciation events will require nuclear markers that lack these characteristics, effects of population genetics on phylogenetic inference will need to be addressed directly. Current models and methods that allow hybrid speciation to be detected and reconstructed are discussed, with a focus on how lineage sorting and meiotic and sexual recombination affect network reconstruction. Approaches that would allow inference of phylogenetic networks in their presence are suggested.
Plant nuclear genomes exhibit extensive structural variation in size, chromosome number, number and arrangement of genes, and number of genome copies per nucleus. This variation is the outcome of a set of highly active processes, including gene duplication and deletion, chromosomal duplication followed by gene loss, amplification of retrotransposons separating genes, and genome rearrangement, the latter often following hybridization and/or polyploidy. While these changes occur continuously, it is not surprising that some of them should be fixed evolutionarily and come to mark major clades. Large-scale duplications pre-date the radiation of Brassicaceae and Poaceae and correlate with the origin of many smaller clades as well. Nuclear genomes are largely colinear among closely related species, but more rearrangements are observed with increasing phylogenetic distance; however, the correlation between amount of rearrangement and time since divergence is not perfect. By changing patterns of gene expression and triggering genome rearrangements, novel combinations of genomes (hybrids) may be a driving force in evolution.
The class Sphagnopsida (Bryophyta) includes two genera: Ambuchanania and Sphagnum. Ambuchanania contains just one rare species known from two Tasmanian localities, but Sphagnum comprises a speciose clade of mosses that dominates many wetland ecosystems, especially in the boreal zone of the Northern Hemisphere. Recent phylogenetic analyses have resolved well-supported clades within Sphagnum, but polarizing Sphagnum evolution has been problematic because the genus is so isolated that it is difficult to determine homologies between morphological and/or molecular traits within Sphagnum with those of any potential outgroup. DNA sequences from 16 genomic regions representing the mitochondrial, chloroplast, and nuclear genomes (ca. 16 kilobases) were obtained from 24 species of Sphagnum plus one species each from Takakia and Andreaea in order to resolve a rooted phylogeny. Two tropical species, S. sericeum and S. lapazense, were resolved as sister to the rest of the genus and are extremely divergent from all other sphagna. The main Sphagnum lineage consists of two clades; one includes the sections Sphagnum, Rigida, and Cuspidata, and the other includes Subsecunda, Acutifolia, and Squarrosa. The placement of section Subsecunda is weakly supported, but other nodes are strongly supported by maximum parsimony, maximum likelihood, and Bayesian analyses. In addition to homogeneous Bayesian analyses, heterogeneous models were employed to account for different patterns of nucleotide substitution among genomic regions.
Extended, Continued. 
Of the 340 genera in the Brassicaceae, apomictic reproduction is found only in the North American genus Boechera. We investigated phylogenetic relationships, ability to hybridize, mating system, and ploidy levels of 92 lines sampled from 85 populations and representing 19 Boechera species. Phylogenetic analyses based on chloroplast DNA sequences identified three lineages in the genus. Reciprocal crosses of each line were made to a common sexual diploid B. stricta tester. The resulting F(1) progeny were analyzed for the inheritance of polymorphic microsatellite loci, genome size, and seed production. Intraspecific B. stricta crosses confirmed that this species is mostly diploid and sexual. Interspecific crosses revealed many other species were diploid and sexual and could be successfully hybridized with the tester. We also found obligate and facultative apomictic diploid and triploid lines. De novo F(1) polyploids (either triploids or tetraploids) were derived from the union of nonreduced (from an apomictic parent) and reduced (from the tester) gametes. However, seed production of these F(1) plants was generally low, suggesting a failure in the transmission of apomixis. The creation of a wide array of segregating genetic populations will facilitate future research on the evolution and inheritance of quantitative variation in Boechera.
Sonneratia caseolaris, a typical mangrove species, is widely distributed in the Indo-West Pacific region. EST-SSR markers were developed for this species to examine its genetic diversity. A total of 18 EST-SSR primer pairs were designed based on the transcriptome sequences of S. caseolaris. Thirteen primer pairs showed polymorphism with one to three alleles per locus when assessed in two populations from China and Australia. The observed heterozygosity and expected heterozygosity ranged from 0 to 0.5000, and 0 to 0.5217 in the Hainan population, and from 0 to 0.2500, and 0 to 0.4891 in the Queensland population, respectively. Thirteen of the 18 primer sets identified in S. caseolaris can be successfully applied to its congener S. alba, and a much lower level of polymorphisms was observed in this widespread species. These polymorphic EST-SSR markers for S. caseolaris are likely to be useful for future genetic diversity studies.
Location of four tetraploid Vaccinium oxycoccos (O4n), four diploid V. oxycoccos (O2n), and ten V. macrocarpon (M) popula- tions sampled for the study of allozyme variation. N sample size. 
Allele frequencies at 14 variable isoenzymatic loci in diploid and tetraploid populations of Vaccinium oxycoccos and V. macrocarpon (Ericaceae). Populations are numbered as in Table 1, where their locations are also provided. 
Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation. No evidence for fixed heterozygosity was found in tetraploid V. oxycoccos. In contrast, all polymorphic loci exhibited both balanced and unbalanced heterozygotes, with some individuals exhibiting a pattern consistent with the presence of three alleles. These results support an autopolyploid origin for tetraploid V. oxycoccos. However, tetraploid V. oxycoccos possessed a suite of alleles not found in diploid V. oxycoccos; half of these alleles were shared with V. macrocarpon. This suggests that autotetraploid V. oxycoccos may have undergone hybridization with V. macrocarpon or that the autotetraploid retained the genetic variation present in an ancestral diploid species. Following theoretical expectations, proportion of polymorphic loci, mean number of alleles, and observed heterozygosity were significantly higher for the autotetraploid than for the diploid. Mean inbreeding (F(IS)) was similar for diploid and tetraploid V. oxycoccos. The latter exhibited population differentiation (F(ST)) exceeding both diploid species.
Idiograms of Arachis species showing the distribution of 5S (v) and 18S–25S rDNA loci (), 4, 6-diamidino-2-phenylindole (DAPI)-enhanced heterochromatic bands (□), DAPI-pale low condensed euchromatic regions (q), and indifferent DAPI-stained normally condensed euchromatin ( h). Genes  
The 5S and the 18S-25S rRNA genes were physically mapped by fluorescent in situ hybridization (FISH) in all botanical varieties of cultivated peanut Arachis hypogaea (2n = 4x = 40), in the wild tetraploid A. monticola, and in seven wild diploid species considered as putative ancestors of the tetraploids. A detailed karyotype analysis including the FISH signals and the heterochromatic bands was carried out. Molecular cytogenetic landmarks are provided for the construction of a FISH-based karyotype in Arachis species. The size, number, and chromosome position of FISH signals and heterochromatic bands are similar in all A. hypogaea varieties and A. monticola, but vary among the diploid species. Genome constitution of the species is discussed and several chromosome homeologies are established. The bulk of the chromosome markers mapped, together with data on geographical distribution of the taxa, suggest that peanut originated upon domestication of A. monticola and evidence that the diploids A. duranensis and A. ipaensis are the most probable ancestors of both tetraploid species. Allopolyploidy could have arisen by a single event or, if by multiple events, always from the same diploid species.
Maximum parsimony analyses of the genera of Podocarpaceae were conducted using sequence data from 18S ribosomal DNA. Trees from sequence, morphological, and combined data differ in taxon arrangement, but are similar in that Podocarpus sensu lato and Dacrydium s.l. are unnatural, while Podocarpaceae (including Phyllocladus) are monophyletic. The clade Microcachrys + Microstrobos is recognized in all analyses, but its placement differs, i.e., nested among other scale-leaved taxa in the morphological analysis, but associated with Nageia and other tropical genera in the sequence analyses. Trees from combined data reflect this ambiguity. Podocarpus sensu stricto is paraphyletic according to most trees. Inferences of plesiomorphic character states within the family are largely consistent between analyses and support the view that prototypical podocarps had bifacial leaves, cones with several fertile cone scales, and large epimatia (cone scales) that covered the inverted ovules.
The ultrastructural and biochemical database used in the cla- distic analyses (see Table 1, Saunders et al. 1995). The Emiliania huxleyi is designated as the outgroup. Missing values are repre- sented by ''?''. 
The single most parsimonious tree of the Xanthophyceae taxa (Fucus outgroup) based upon complete sequences with no sites removed (length 431, consistency index 0.88, retention index 0.61). 
Some earlier studies suggested an evolutionary relationship between the Raphidophyceae (chloromonads) and Xanthophyceae (yellow-green algae), whereas other studies suggested relationships with different algal classes or the öomycete fungi. To evaluate the relationships, we determined the complete nucleotide sequences of the 18S ribosomal RNA gene from the raphidophytes Vacuolaria virescens, Chattonella subsalsa, and Heterosigma carterae, and the xanthophytes Vaucheria bursata, Botrydium stoloniferum, Botrydiopsis intercedens, and Xanthonema debile. The results showed that the Xanthophyceae were most closely related to the Phaeophyceae. A cladistic analysis of combined data sets (nucleotide sequences, ultrastructure, and pigments) suggested the Raphidophyceae are the sister taxon to the Phaeophyceae-Xanthophyceae clade, but the bootstrap value was low (40%). The raphidophyte genera were united with high (100%) bootstrap values, supporting a hypothesis based upon ultrastructural features that marine and freshwater raphidophytes form a monophyletic group. We examined the relationship between Vaucheria, a siphoneous xanthophyte alga, and the öomycetes, and we confirmed that Vaucheria is a member of the class Xanthophyceae. Partial nucleotide sequences of the 18S rRNA gene from eight xanthophytes (including Bumillariopsis filiformis, Heterococcus caespitiosus, and Mischococcus sphaerocephalus) produce a phylogeny that is not congruent with the current morphology-based classification scheme.
Strict consensus of the shortest trees obtained for Drosera using the rbcL sequence data, onto which chromosome numbers (A) and distributions (B) have been mapped using MacClade (Maddison and Maddison, 1992). (A) Operational taxonomic units (OTUs) whose chromosome numbers were not reported are excluded from the tree. The chromosome numbers are from the references listed in For those species for which more than one chromosome number has been reported, each chromosome number corresponds to a different OTU forming a clade. The chromosome number is given in parentheses after the species name. (B) The distributions are from the Carnivorous Plant Database ( Those species distributed in different geographic areas were treated as a clade, including OTUs with different distributions. Species distributed in different geographic areas were treated as a clade, including OTUs with different distributions.  
The sundew genus Drosera consists of carnivorous plants with active flypaper traps and includes nearly 150 species distributed mainly in Australia, Africa, and South America, with some Northern Hemisphere species. In addition to confused intrageneric classification of Drosera, the intergeneric relationships among the Drosera and two other genera in the Droseraceae with snap traps, Dionaea and Aldrovanda, are problematic. We conducted phylogenetic analyses of DNA sequences of the chloroplast rbcL gene for 59 species of Drosera, covering all sections except one. These analyses revealed that five of 11 sections, including three monotypic sections, are polyphyletic. Combined rbcL and 18S rDNA sequence data were used to infer phylogenetic relationships among Drosera, Dionaea, and Aldrovanda. This analysis revealed that all Drosera species form a clade sister to a clade including Dionaea and Aldrovanda, suggesting that the snap traps of Aldrovanda and Dionaea are homologous despite their morphological differences. MacClade reconstructions indicated that multiple episodes of aneuploidy occurred in a clade that includes mainly Australian species, while the chromosome numbers in the other clades are not as variable. Drosera regia, which is native to South Africa, and most species native to Australia, were clustered basally, suggesting that Drosera originated in Africa or Australia. The rbcL tree indicates that Australian species expanded their distribution to South America and then to Africa. Expansion of distribution to the Northern Hemisphere from the Southern Hemispere occurred in a few different lineages.
The 18S-26S ribosomal genes in three closely related species of Leymus (Poaceae: Triticeae) were examined using fluorescence in situ hybridization (FISH) and restriction fragment length polymorphism (RFLP). Both approaches revealed a close relationship between L. arenarius (8x = 56, northern European) and L. racemosus (4x = 28, central Eurasian), whereas L. mollis (4x = 28, northern American/Pacific) was distinct. Each species had three homologous pairs of major rDNA loci: a1, a2, and a3 for L. arenarius; m1, m2, and m3 for L. mollis; and r1, r2, and r3 for L. racemosus. Leymus arenarius had in addition three minor loci, a4, a5, and a6. The major loci of L. arenarius and L. racemosus were identical, indicating that the former species could have originated from the latter, via interspecific hybridization and/or polyploidy. The rDNA-RFLPs further indicated relationships of these species to other species of Leymus (L. karellini, 8x = 56 and L. angustus, 12x = 84) and Psathyrostachys (P. fragilis, P. huashanica, P. juncea, and P. lanuginosa, which are all diploids). A phenogram constructed from 20 BamHI, EcoRI, and DraI rDNA fragments revealed closer relationship between the two genera, Leymus and Psathyrostachys, than that among species within a genus.
The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the external transcribed spacer region of the nuclear 18S-26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus.
Molecular estimates of the age of angiosperms have varied widely, and many greatly predate the Early Cretaceous appearance of angiosperms in the fossil record, but there have been few attempts to assess confidence limits on ages. Experiments with rbcL and 18S data using maximum likelihood suggest that previous angiosperm age estimates were too old because they assumed equal rates across sites-use of a gamma distribution of rates to correct for site-to-site variation gives 10-30 my (million years) younger ages-and relied on herbaceous angiosperm taxa with high rates of molecular evolution. Ages based on first and second codon positions of rbcL are markedly older than those based on third positions, which conflict with the fossil record in being too young, but all examined data partitions of rbcL and 18S depart substantially from a molecular clock. Age estimates are surprisingly insensitive to different views on seed-plant relationships. Randomization schemes were used to quantify confidence intervals due to phylogenetic uncertainty, substitutional noise, and lineage effects (deviations from a molecular clock). Estimates of the age of crown-group angiosperms range from 68 to 281 mya (million years ago), depending on data, tree, and assumptions, with most ∼140-190 mya (Early Jurassic-earliest Cretaceous). Approximate 95% confidence intervals on ages are wider for rbcL than 18S, ranging up to 160 my for phylogenetic uncertainty, 90 my for substitutional noise, and 70 my for lineage effects. These intervals overlap the oldest occurrences of angiosperms in the fossil record, as well as some estimates from previous molecular studies.
Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.
A phylogenetic analysis of DNA sequences from the internal transcribed spacer (ITS), the external transcribed spacer (ETS), and the 5.8S regions of 18S-26S nuclear rDNA from all diploid species of Stephanomeria and related genera shows that Stephanomeria does not include either Munzothamnus blairii (previously S. blairii) or Pleiacanthus spinosus (previously S. spinosa). Without these two taxa, Stephanomeria is a well-supported (100% bootstrap), monophyletic group of ten perennial and six annual species. Munzothamnus blairii and Pleiacanthus spinosus, both now considered members of monotypic genera, had been placed in Stephanomeria primarily because they have the same chromosome number as Stephanomeria and similar pollen surface features, but many disparities were ignored in previous classifications. Within Stephanomeria, an unsuspected sister relationship was detected between the montane S. lactucina and coastal S. cichoriacea. A second clade contained all the annual taxa and five of the perennial species. Among the annuals, strong bootstrap support was obtained for the previously recognized relationships between S. diegensis and S. exigua (98%) and between S. malheurensis and its progenitor, S. exigua subsp. coronaria (96%). Among the five perennial species that constitute a clade with the annuals, the recently described S. fluminea was shown to be sister to S. runcinata, and both of them were closely allied to S. tenuifolia and S. thurberi. The clade including the annuals (and five of the perennial species) was subtended by perennial lineages and pairwise divergence values among the annual taxa were much lower than among the perennial taxa as a group (though not too different than among the perennials in the same clade). The annuals probably originated recently within the genus.
• Microsatellite primers were developed for taro (Colocasia esculenta) to investigate its population genetics and evolutionary history through germplasm improvement. • Nineteen microsatellite loci were identified in three populations. The number of alleles per locus ranged from two to seven, with a mean of 4.68. The observed and expected heterozygosities ranged from 0.231 to 0.820 and from 0.126 to 0.742, respectively. • These new genetic markers will be useful for the study of taro germplasm management and population evolution in southwestern China.
This paper examines the crucial early history of the American Journal of Botany from the years following the founding of the Botanical Society of America in 1906 to the termination of the agreement for publication with the Brooklyn Botanic Garden in 1935. It examines the efforts of individuals like F. C. Newcombe, who did the most to raise support for the journal and became the first Editor-in-Chief, in the context of the growing numbers of professional botanists and plant scientists who were actively engaged in research requiring appropriate publication venues and in the process of forming an independent identity as "American botanists." It also examines the launching of the journal in the context of the Great War in Europe and the transition from German botany to American botany in the second decade of the 20th century.
This is an historical paper examining the scientific background of George Ledyard Stebbins, Jr. (b. 1906), one of the foremost botanists of this century and one of the architects of the evolutionary synthesis, the intellectual event that brought together genetics and selection theory in the interval between 1920 and 1950. It considers his scientific influence and research, beginning with his Harvard education in 1924 and ending in 1950 with the publication of his book Variation and Evolution in Plants. The paper also more broadly assesses the contributions of other botanists to the evolutionary synthesis, including discussion of the work of Edgar Anderson (1897-1967) and others. It also traces the larger historical patterns of American botany, which saw a shift from East Coast botany as exemplified by Harvard botany, to West Coast botany, as exemplified by California botany.
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Douglas E Soltis
  • University of Florida
Pamela S Soltis
  • University of Florida
Khidir Hilu
  • Virginia Polytechnic Institute and State University
Meredith Blackwell
  • Louisiana State University
Andrew Gonzalez
  • McGill University