Rpl16 Intron Research Articles

Towards a Phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences.

The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling. Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL-F intron, trnL-F intergenic spacer (IGS), rpl16 intron and accD-psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5.8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics. Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea.

PHYLOGENY AND SYSTEMATICS OF THE RAUVOLFIOIDEAE (APOCYNACEAE) BASED ON MOLECULAR AND MORPHOLOGICAL EVIDENCE1

Abstract To elucidate deeper relationships within Rauvolfioideae (Apocynaceae), a phylogenetic analysis was conducted using sequences from five DNA regions of the chloroplast genome (matK, rbcL, rpl16 intron, rps16 intron, and 3′ trnK intron), as well as morphology. Bayesian and parsimony analyses were performed on sequences from 50 taxa of Rauvolfioideae and 16 taxa from Apocynoideae. Neither subfamily is monophyletic, Rauvolfioideae because it is a grade and Apocynoideae because the subfamilies Periplocoideae, Secamonoideae, and Asclepiadoideae nest within it. In addition, three of the nine currently recognized tribes of Rauvolfioideae (Alstonieae, Melodineae, and Vinceae) are polyphyletic. We discuss morphological characters and identify pervasive homoplasy, particularly among fruit and seed characters previously used to delimit tribes in Rauvolfioideae, as the major source of incongruence between traditional classifications and our phylogenetic results. Based on our phylogeny, simple style-heads, sync...

PHYLOGENY OF APOCYNOIDEAE AND THE APSA CLADE (APOCYNACEAE S.L.)1

Phylogenetic relationships were reconstructed among 59 of 77 genera of subfamily Apocynoideae and exemplars of Periplocoideae, Secamonoideae, and Asclepiadoideae (collectively the APSA clade) using sequences from four regions of the chloroplast genome (trnL intron and trnL-trnF spacer, rpl16 intron, rps16 intron, matK and 3′ half of trnK intron) and 16 morphological characters. Apocynoideae are resolved as paraphyletic. The five tribes recognized within this subfamily in the classification of Endress and Bruyns are all paraphyletic or polyphyletic. Seven major clades of Apocynoideae are identified. The first three include genera classified predominantly in tribes Wrightieae and Malouetieae sensu Endress and Bruyns and form a paraphyletic grade to a crown clade. The crown clade includes four clades of Apocynoideae genera classified in tribes Apocyneae, Mesechiteae, and Echiteae together with Periplocoideae, Secamonoideae, and Asclepiadoideae; the latter three constitute the traditional Asclepiadaceae. Asclepiadaceae are resolved as polyphyletic, although the node that precludes a paraphyletic Asclepiadaceae does not have bootstrap support. The clade of Secamonoideae–Asclepiadoideae is well supported as sister to a clade of three African Apocynoideae genera (Baissea A. DC., Motandra A. DC., and Oncinotis Benth.). There is a strong correlation between geographic distribution and phylogeny among crown clade Apocynoideae. A New World clade is composed of American genera plus the predominantly Australasian Parsonsia R. Br. and Artia Guillaumin. An Asian clade is composed of Asian, Malesian, and Australasian genera plus the north temperate Apocynum L. Trachelospermum Lem. is polyphyletic with American and Asian species nested in the New World and Asian clades, respectively. The implications of this phylogeny for the evolution of pollen aggregation and mass transfer, the traits that were used to separate Asclepiadaceae from Apocynaceae s. str., are discussed.

Chloroplast DNA phylogeography of Pedicularis ser. Gloriosae (Orobanchaceae) in Japan

Phylogeographic analyses using chloroplast DNA (cpDNA) variation were performed for Pedicularis ser. Gloriosae (Orobanchaceae). Eighty-one plants of 18 populations of 6 species (P. gloriosa, P. iwatensis, P. nipponica, P. ochiaiana, P. sceptrum-carolinum and P. grandiflora) were analyzed. Fifteen distinct haplotypes were identified based on six cpDNA regions: the intergenic spacer between the trnT and trnL 3'exon, trnL 3'exon-trnF, atpB-rbcL, accD-psaI, the rpl16 intron and the trnK region (including the matK gene). Via phylogenetic analyses of the haplotypes, two continental species, P. sceptrum-carolinum and P. grandiflora, were placed at the most ancestral position in the trees. The former species is widely distributed in the Eurasian continent, and the latter is distributed in Far East Asia. Two robust major cpDNA clades (clades I and II) were revealed in the Japanese archipelago, although the statistical values of monophyly of these clades were weak. Clade I included the haplotypes (A-1, A-2, B-1, B-2 and J) of three species (P. gloriosa, P. iwatensis and P. ochiaiana), and Clade II included seven haplotypes (C-D, E-1, E-2 and F-H) of P. nipponica. These results suggest that this series originated on the Eurasian continent and that subsequently populations at the eastern edge of the continent differentiated into the two Japanese lineages.

Searching for the relatives of Coffea (Rubiaceae, Ixoroideae): the circumscription and phylogeny of Coffeeae based on plastid sequence data and morphology

The circumscription of Coffeeae (Rubiaceae) and phylogenetic relationships within the tribe were evaluated using sequence data from four plastid regions (trnL-F intron, trnL-F intergenic spacer [IGS], rpl16 intron, and accD-psa1 IGS) and a morphological data set. Eleven candidates for inclusion in Coffeeae were examined using plastid data, and a further three were investigated using morphology alone. Based on previous phylogenetic analysis of the subfamily Ixoroideae, nine genera representing five tribes were used as outgroups. Our results support an enlarged circumscription for Coffeeae, containing 11 genera, viz. Argocoffeopsis, Belonophora, Calycosiphonia, Coffea, Diplospora, Discospermum, Nostolachma, Psilanthus, Tricalysia, Sericanthe, and Xantonnea. The inclusion of Diplospora and Tricalysia within Coffeeae, based on published molecular data, and the inclusion of Argocoffeopsis, Belonophora, Calycosiphonia, Discospermum, and Sericanthe, based on morphological evidence, are well supported. Nostolachma is newly transferred from Gardenieae subtribe Diplosporinae to Coffeeae, and Xantonnea from Octotropideae to Coffeeae. The exclusion of Bertiera from Coffeeae and placement in tribe Bertiereae is supported on the basis of molecular and morphological data. The removal of Diplospora and all other genera from Gardenieae subtribe Diplosporinae to Coffeeae and Octotropideae renders Diplosporinae superfluous. It is proposed that Xantonneopsis be transferred to Octotropideae; Petitiocodon is tentatively placed in Gardenieae. The monophyly of seven genera is supported, but Coffea is identified as paraphyletic in relation to Psilanthus on the basis of molecular and combined molecular and morphological data.

Phylogenetic Relationships Within the Centothecoideae + Panicoideae Clade (Poaceae) Based on ndhF and rpl16 Intron Sequences and Structural Data

The PACCAD clade (Panicoideae, Arundinoideae, Chloridoideae, Centothecoideae, Aristidoideae, Danthonioideae) is well supported in all recent studies of Poaceae. However, phylogenetic relationships within the clade are still unresolved, although several branches are strongly supported. In this study, we focus on the phylogeny of the Centothecoideae + Panicoideae clade, one of the major lineages within the PACCAD clade, and one of the most diverse in the family. Two previously unsampled tribes, Isachneae and Steyermarkochloeae, are included, as are additional taxa of Centothecoideae. Phylogenetic analyses of plastid genome sequences (ndhF gene and rpl16 intron) and structural data show increased support of the centothecoid–panicoid clade, but phylogenetic relationships between the two putative subfamilies remain unresolved. Centothecoideae may be sister to Panicoideae or they may be paraphyletic with respect to Panicoideae, as monophyly of Centothecoideae is weakly supported at best. Polyphyly of Panicoideae is demonstrated as Isachneae and Steyermarkochloeae (only with ndhF) form well-supported clades with Micraira–Eriachne and Chasmanthium, respectively. Polyphyly of Arundinelleae is also confirmed as Danthoniopsis and related genera resolve elsewhere. Centothecoideae, as recently circumscribed, resolve as three strongly supported clades including Danthoniopsis and related genera. Cyperochloa (previously incertae sedis) and arundinoid Spartochloa are sister and fall within the centothecoids with strong support. Centotheceae are polyphyletic and segregate into three major groups. One centothecoid genus, Zeugites, is demonstrably paraphyletic.

Phylogenetic Relationships Among the One-Flowered, Determinate Genera of Bambuseae (Poaceae: Bambusoideae)

Bambuseae (woody bamboos), one of two tribes recognized within Bambusoideae (true bamboos), comprise over 90% of the diversity of the subfamily, yet monophyly of the tribe is generally only moderately supported, and phylogenetic relationships within the tribe are poorly understood. In addition, there appears to be some level of conflict between morphological and molecular data within the tribe. We conducted a parsimony analysis of 43 species of Bambuseae, three of Olyreae (herbaceous bamboos), and two outgroup taxa using morphological and plastid rpl16 intron sequence data to (1) further test the monophyly of Bambuseae, (2) test the monophyly of Chusqueinae and Hickelinae (the two one-flowered, determinate subtribes), and (3) examine the apparent conflict between molecular and morphological data sets in the determinate, one-flowered genera of Bambuseae. We recovered a monophyletic Bambusoideae, Bambuseae, Olyreae, and Chusqueinae, although support for Bambuseae remained moderate. Our results suggest that the morphological similarities between Chusqueinae and Hickelinae are homoplasious, but robust resolution of relationships among the major lineages of woody bamboos is still wanting.

IS MANDEVILLA (APOCYNACEAE, MESECHITEAE) MONOPHYLETIC? EVIDENCE FROM FIVE PLASTID DNA LOCI AND MORPHOLOGY1

In order to test the monophyly of Mandevilla Lindl., the largest genus in tribe Mesechiteae (Apocynaceae, Apocynoideae), and its affinities to other genera in the tribe, maximum parsimony analysis was conducted on a data set comprising DNA sequences from five plastid loci (rpl16, rps16, and trnK introns; trnSGCU-trnGUUC intergenic spacer; and matK gene), as well as morphological data for 65 taxa of Mesechiteae (48, Mandevilla) and nine taxa from other tribes of the subfamily. Mandevilla, as circumscribed by Pichon, was found to be monophyletic, whereas Woodson's circumscription proved to be polyphyletic. Thus defined, Mandevilla forms a strongly supported clade that can be divided into six clades of species groups. Most of the infrageneric taxa of Mandevilla proposed by Woodson and Pichon are polyphyletic. Many of the diagnostic characters previously used to define taxonomic groups are shown to have arisen multiple times, rendering them unsuitable for classificatory purposes. The similar growth form and tubular flowers of Macrosiphonia Müll. Arg. and Telosiphonia (Woodson) Henr., two geographically disjunct segregates, represent the most extreme case of parallel evolution within Mandevilla, with their striking similarities most likely correlated to colonization of open, dry habitats and pollination by hawkmoths.

Molecular Authentication of the Traditional Tibetan Medicinal Plant Swertia mussotii

Swertia mussotii is an important species in Tibetan folk medicine. However, it is quite expensive and frequently adulterated, so reliable methods for authentication of putative specimens and preparations of the species are needed to protect consumers and to support conservation measures. We show here that the chloroplast (cp) DNA RPL16 intron has limited utility for differentiating S. mussotii from closely related species, since the cpDNA RPL16 sequences are identical in S. mussotii and two other species of Swertia. However, the rDNA internal transcribed spacer (ITS) sequences differ significantly between S. mussotii and all of 13 tested potential adulterants. Thus, the ITS region provides a robust molecular marker for differentiating the medicinal S. mussotii from related adulterants. Therefore, a pair of allele-specific diagnostic primers based on the divergent ITS region was designed to distinguish S. mussotii from the other species. Authentication by allele-specific diagnostic PCR using these primers is convenient, effective and both simpler and less time-consuming than sequencing the ITS region.

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

We report a new set of nine primer pairs specifically developed for amplification of Brassica plastid SSR markers. The wide utility of these markers is demonstrated for haplotype identification and detection of polymorphism in B. napus, B. nigra, B. oleracea, B. rapa and in related genera Arabidopsis, Camelina, Raphanus and Sinapis. Eleven gene regions (ndhB-rps7 spacer, rbcL-accD spacer, rpl16 intron, rps16 intron, atpB-rbcL spacer, trnE-trnT spacer, trnL intron, trnL-trnF spacer, trnM-atpE spacer, trnR-rpoC2 spacer, ycf3-psaA spacer) were sequenced from a range of Brassica and related genera for SSR detection and primer design. Other sequences were obtained from GenBank/EMBL. Eight out of nine selected SSR loci showed polymorphism when amplified using the new primers and a combined analysis detected variation within and between Brassica species, with the number of alleles detected per locus ranging from 5 (loci MF-6, MF-1) to 11 (locus MF-7). The combined SSR data were used in a neighbour-joining analysis (SMM, D (DM) distances) to group the samples based on the presence and absence of alleles. The analysis was generally able to separate plastid types into taxon-specific groups. Multi-allelic haplotypes were plotted onto the neighbour joining tree. A total number of 28 haplotypes were detected and these differentiated 22 of the 41 accessions screened from all other accessions. None of these haplotypes was shared by more than one species and some were not characteristic of their predicted type. We interpret our results with respect to taxon differentiation, hybridisation and introgression patterns relating to the 'Triangle of U'.

Phylogeny of the Schisandraceae Based on cpDNA mat‐K and rpL16 Intron Data

The chloroplast mat-K region and rpL16 intron region were sequenced for 14 species of Schisandraceae, representing both genera Kadsura Kaempf. ex Juss. and Schisandra Michx, to discuss the phylogeny of this family. Analyses were performed both in separate and combined sequence data sets (including the rbc-L sequence), with Illicium angustispealum A. C. Smith as the out-group. The results showed that the Schisandraceae are monophyletic. In all the analyses, Schisandra propinqua var. chinensis Oliva and Schisandra plena A. C. Smith were nested within Kadsura, which implies that the genera Kadsura and Schisandra are closely related. They might have originated from a common ancestor, but then evolved via different routes. The result inferred from the combined data showed a greater resolution within Schisandra than those from the two separate data sets. High bootstrap values supported the monophyly of most subgenera according to Law's system (1996). A combination of morphological, anatomical, and chemical analyses indicates that S. chinensis and S. rubriflora may be the primitive taxa in Schisandra.

Chloroplast DNA phylogeny and phylogeography of the North American plums (PrunussubgenusPrunussectionPrunocerasus, Rosaceae)

The North American plums are a closely related group that are not easily circumscribed, have overlapping morphologies, and are known to hybridize. We previously showed that the North American plums are a closely related, monophyletic group of taxa with little to no cpDNA sequence divergence between taxa. In that study, we came to the unanticipated conclusion that relationships inferred among the taxa contrast sharply with previously defined groups based on morphological characters. Here the aim was to determine if the primary cpDNA haplotypes identified in our earlier study are confined to the taxa in which they were initially observed. The cpDNA rpL16 intron was sequenced for 207 accessions of the 17 North American plum taxa plus Prunus texana. The results show that many taxa contain more than one of the three primary cpDNA haplotypes. Aside from the results found in sect. Prunocerasus, this study has broader implications for phylogenetics in general. The common practice of choosing a single exemplar to represent a taxon can be profoundly misleading in closely related groups. In hindsight, the possibility existed in our earlier study that we could have chosen a different combination of exemplars, which could have resulted in a different inferred phylogeny.

Molecular Phylogenetics of the Leafy Cactus Genus <I>Pereskia</I> (Cactaceae)

Abstract Members of Pereskia exhibit some presumably plesiomorphic characters for the Cactaceae including shrubby habit, non-succulent or partially succulent leaves, and in some species, nearly superior ovaries. In addition, the members show a transition from perigynous flowers with half-inferior ovaries to those species having true receptacular epigyny (the predominant condition in the Cactaceae). To examine interspecific relationships within Pereskia we utilized cpDNA restriction-site data and sequences from two non-coding regions of the plastid genome—the psbA-trnH intergenic spacer and the rpl16 intron. Maximum parsimony and Bayesian analyses identified three major clades: a clade containing the widespread P. aculeata and the Andean species, a clade containing six species found primarily in southeastern Brazil, Paraguay, Uruguay, Argentina, and Bolivia, and a third clade centered in southern Central America and the Caribbean. The relationship between these three clades and the rest of the Cactaceae re...

Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae

Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a significant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR amplification primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of five cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL UAA– trnF GAA intergenic spacer in this group. To these published data we added sequences of the trnS GCU– trnG UUC intergenic spacer + the trnG UUC intron region, the trnS GGA– rpS4 intergenic spacer + rpS4 gene, and the rpL16 intron. Both the trnS GCU– trnG UUC and rpL16 regions are highly variable in angiosperms and the trnS GGA– rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the five sampled regions the trnS GCU– trnG UUC spacer + trnG UUC intron region provided the strongest support for the inferred phylogeny.

An assessment of old and new DNA sequence evidence for the paraphyly of Banksia with respect to Dryandra (Proteaceae)

Banksia (80 spp.; Proteaceae) has undergone extensive speciation and adaptive radiation on the island continent of Australia. Its members range from prostrate shrubs in the dry, infertile sandplains to 25 m tall trees in the loams of river margins, and they display striking variation in their fire survival strategies and floral and foliar morphologies. We examine the weight of both previously published (most trnL intron, trnL/F spacer, and rpl16 intron data) and new (matK, atpB, and waxy data, as well as most ITS data) DNA sequence evidence for the paraphyly of Banksia with respect to a monophyletic Dryandra (93 spp.). The nuclear waxy gene appears to be at two loci in the Proteaceae, and sequences presumably from the same locus resolve Banksia as paraphyletic with respect to Dryandra. The waxy and combined chloroplast DNA (cpDNA) data reject the monophyly of Banksia at a threshold of P = 0.05 using the winning sites and Kishino–Hasegawa tests. We consider this result and the repeated placement of Dryandra in the same clade (/Cryptostomata) of Banksia with each separate analysis of the DNA datasets (cpDNA, ITS, and waxy), to be strong molecular support for the paraphyly of Banksia with respect to Dryandra. The morphological synapomorphy of beaked follicles for /Cryptostomata (including Dryandra) reinforces this conclusion. We argue that realignment of taxa to produce one or more monophyletic genera is best attained by moving the taxa of Dryandra to Banksia. This would produce an easily recognised genus Banksia with four morphological synapomorphies. It would also probably confer some of the research attention garnered by the adaptive radiation of Banksia to the under-studied taxa of Dryandra, for Dryandra makes the radiation of Banksia even more remarkable.

Phylogenetics of Mentha (Lamiaceae): Evidence from Chloroplast DNA Sequences

Phylogenetic relationships in Mentha were inferred from DNA sequences of the chloroplast (cp) rpl16 intron and trnL-trnF region. The objectives were to test monophyly of Mentha and each of its sections and assess relationships among Mentha species. Based on cpDNA data, Mentha is strongly supported as monophyletic. The suggestions that M. cervina and M. cunninghamii should be placed in other genera gain no support from this analysis. Mentha cervina is sister to M. gattefossei, and the New Zealand endemic, M. cunninghamii, is allied with species from Australia (M. australis, M. diemenica, M. satureioides). No recognized section with more than one species sampled forms a monophyletic group. Section Pulegium may be monophyletic, but the third member of this section, M. grandiflora, was not sampled. Chloroplast DNA sequences of the putative allopolyploids M. canadensis and M. spicata suggest that M. arvensis and M. longifolia, respectively, may be their maternal parents.

Tribal and intergeneric relationships of Mesechiteae (Apocynoideae, Apocynaceae): evidence from three noncoding plastid DNA regions and morphology

The Neotropical tribe Mesechiteae (Apocynaceae) is currently considered to include nine genera: Allomarkgrafia, Galactophora, Macrosiphonia, Mandevilla, Mesechites, Quiotania, Secondatia, Telosiphonia, and Tintinnabularia. Tribal and intergeneric relationships, however, are in dispute. To test the monophyly of the tribe and evaluate intratribal relationships, a maximum parsimony analysis was conducted based on DNA sequences from the plastid rpl16 intron, rps16 intron, and trnS-G intergenic spacer region as well as morphological data for 23 taxa of Mesechiteae and 11 taxa from other tribes of Apocynoideae. Mesechiteae, as currently circumscribed, was found to be polyphyletic. Only removal of Secondatia and Galactophora and inclusion of Forsteronia rendered the tribe monophyletic. Thus defined, Mesechiteae forms a strongly supported clade including seven genera in three subclades: the Mesechites subclade (comprising Tintinnabularia, Allomarkgrafia, and Mesechites), the Forsteronia subclade (containing only Forsteronia) and the Mandevilla subclade (comprising Macrosiphonia, Mandevilla, and Telosiphonia). Allomarkgrafia is nested in Mesechites. Macrosiphonia and Telosiphonia form two distinct monophyletic clades. Both, however, are nested in Mandevilla. Results suggest upholding the following genera in Mesechiteae: Allomarkgrafia, Forsteronia, Mandevilla, Mesechites, and Tintinnabularia. The status of Quiotania could not be evaluated.

Molecular phylogenetic analysis of Eugenia L. (Myrtaceae), with emphasis on southern African taxa

With approximately 1000 species, Eugenia s.str. (excluding Syzygium) is one of the largest genera in the Myrtaceae. Morphological and anatomical studies concluded that two supraspecific groups (X and Y) exist in African members of Eugenia. A multigene approach was used to investigate phylogenetic/molecular relationships within southern African Eugenia, as well as representatives from elsewhere in the world. The cpDNA rpl16 intron data supported the distinctness of species groups X and Y. Little sequence divergence was found within the rpl16 intron of Eugenia. Nuclear sequence data were more variable than cpDNA and also supported the two groups. Combined data enhanced the resolution of closely related species. Species group X is related to Eugenia of the New World whereas the affinity of species group Y lies with Eugenia of the Old World. It is hypothesised that the origin of Eugenia in southern Africa is twofold. The presence of cryptic dioecy (structural androdioecy) in both groups of Eugenia in Africa is probably due to convergence. The suggestion that E. incerta is not native to Africa is supported by molecular evidence. The genus Monimiastrum is embedded within a clade with Mauritian Eugenia.

Phylogenetic studies of Mammillaria (Cactaceae)—insights from chloroplast sequence variation and hypothesis testing using the parametric bootstrap

The genus Mammillaria is likely the most species-rich and morphologically variable genus in the Cactaceae. There is doubt as to whether the genus is monophyletic, and past infrageneric treatments differ regarding generic circumscription. Phylogenetic questions about Mammillaria were addressed using chloroplast DNA sequence data from the rpl16 intron and the psbA-trnH intergenic spacer for 125 taxa (113 Mammillaria, 10 Coryphantha, Escobaria, Neolloydia, Pelecyphora, Ortegocactus, and two outgroup taxa from Ferocactus and Stenocactus). Parsimony analyses were conducted using various heuristic search strategies. Bayesian analyses were conducted using the F81 and F81 + I + G models of sequence evolution. Tree topologies from the parsimony and Bayesian analyses were largely congruent. Hypothesis testing was undertaken using the parametric bootstrap to test the monophyly of the genus and the taxonomic status of Mammillaria candida. Phylogenies derived from the parsimony and Bayesian analyses indicate that Mammillaria is not monophyletic and that the genus Mammilloydia (synonym Mammillaria) is embedded within a "core" group of Mammillaria species. Both these results were corroborated by the parametric bootstrap tests. The entire rpl16 intron was deleted from species in the Mammillaria crinita group.

Addressing the “hardest puzzle in American pomology:” Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions

Prunus subg. Prunus sect. Prunocerasus (Rosaceae) is a North American taxon with 17 commonly recognized taxa. To test the hypothesis of monophyly for the section we sequenced the trnG and rpL16 introns and the trnH-psbA and trnS-trnG intergenic spacers for at least two representatives of each of the five subgenera in Prunus. Additionally we sampled heavily among Prunus subg. Prunus sections Prunus and Armeniaca and Prunus subg. Amygdalus because these groups are putatively most closely related to Prunocerasus. Once monophyly of sect. Prunocerasus was shown we added the sequences of trnL and rpS16 introns and the trnL-trnF spacer in an attempt to increase resolution within the section. The species of sect. Prunocerasus showed an initial split with P. subcordata, the only species from western North America, sister to the rest of the group. The remaining species fell into three primary clades. Within each of the three primary clades there was little phylogenetic resolution. Lastly, we present evidence that P. texana, previously classified in subg. Amygdalus, may be a plum or at least contain a Prunocerasus chloroplast. This is the first phylogenetic hypothesis presented for sect. Prunocerasus, and the clades recovered contrast sharply with previously defined groups based on morphological characters.