Cássio van den Berg

A DNA barcode for land plants

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) widespread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications.

AN EXPANDED PLASTID DNA PHYLOGENY OF ORCHIDACEAE AND ANALYSIS OF JACKKNIFE BRANCH SUPPORT STRATEGY

An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.

An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae).

Phylogenetic relationships within the epidendroid orchids with emphasis on tribes Epidendreae and Arethuseae were assessed with parsimony and model-based analyses of individual and combined DNA sequence data from ITS nuclear ribosomal DNA and plastid trnL intron, the trnL-F spacer, matK (gene and spacers), and rbcL regions. Despite the absence of boostrap support for some of the relationships, a well-resolved and supported consensus was found, for which most clades were present in more than one individual analysis. Most clades of this consensus attained high posterior probabilities with a Bayesian approach. Circumscription of Arethuseae and Epidendreae are different from most orchid systems based on morphology, but they correspond to a combination of patterns from several less comprehensive orchid phylogenetic analyses previously published. A new circumscription of Epidendreae includes only Neotropical subtribes (Bletiinae, Chysiinae, Laeliinae, Ponerinae, and Pleurothallidinae), whereas Arethuseae include Coelogyninae (all Old World) and Arethusinae (pantropical). Many previously included genera will need to be moved to other tribes. Taxa previously assigned to be Old World Epidendreae are related to different groups of Old World orchids, and this study can serve as a guide for sampling strategies in future studies to resolve troublesome epidendroid orchid clades.

A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences

BACKGROUND AND AIMS Laeliinae are a neotropical orchid subtribe with approx. 1500 species in 50 genera. In this study, an attempt is made to assess generic alliances based on molecular phylogenetic analysis of DNA sequence data. METHODS Six DNA datasets were gathered: plastid trnL intron, trnL-F spacer, matK gene and trnK introns upstream and dowstream from matK and nuclear ITS rDNA. Data were analysed with maximum parsimony (MP) and Bayesian analysis with mixed models (BA). KEY RESULTS Although relationships between Laeliinae and outgroups are well supported, within the subtribe sequence variation is low considering the broad taxonomic range covered. Localized incongruence between the ITS and plastid trees was found. A combined tree followed the ITS trees more closely, but the levels of support obtained with MP were low. The Bayesian analysis recovered more well-supported nodes. The trees from combined MP and BA allowed eight generic alliances to be recognized within Laeliinae, all of which show trends in morphological characters but lack unambiguous synapomorphies. CONCLUSIONS By using combined plastid and nuclear DNA data in conjunction with mixed-models Bayesian inference, it is possible to delimit smaller groups within Laeliinae and discuss general patterns of pollination and hybridization compatibility. Furthermore, these small groups can now be used for further detailed studies to explain morphological evolution and diversification patterns within the subtribe.

DIVERSIFICATION OF ASCLEPIADOIDEAE (APOCYNACEAE) IN THE NEW WORLD1

Abstract Plastid sequences of trnL-F are used to estimate the age of biogeographical events in New World Asclepiadoideae. These data suggest that the subfamily arose somewhere in the Old World in the Late Eocene (40 million years ago (Ma)) and that there were at least four independent episodes of dispersal to the New World. The MOG clade, comprising Metastelmatinae, Oxypetalinae, and Gonolobinae, probably colonized South America through transoceanic dispersal from Africa at 32 Ma. The three subtribes emerged at 24 Ma, radiating 15–16 Ma. Cynanchum L. subg. Mellichampia (A. Gray) Woodson (Cynanchinae) only arrived in the New World at 24 Ma and has since diversified gradually. Asclepias L. (Asclepiadinae) probably arrived in the New World through the Bering Strait at 20 Ma, dispersing to South America before the emergence of the Isthmus of Panama. More recently, tropical Marsdenia R. Br. (Marsdenineae) probably arrived in the New World by long-distance dispersal at 16 Ma. Most diversification in New World Asclepiadoideae is estimated to have occurred during the Miocene. The synchrony of events suggests an environmental influence on the diversification of the lineages. Nevertheless, individual rates of diversification point out the importance of intrinsic factors.

Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and possible hybrid speciation.

The orchid genus Calopogon R.Br. (Orchidaceae), native to eastern North America and the northern Caribbean, currently contains five species and up to three varieties. Using nuclear internal transcribed spacer (ITS) ribosomal DNA sequences, amplified fragment length polymorphisms (AFLPs), chloroplast DNA restriction fragments, and chromosome counts, we present a phylogenetic and taxonomic study of the genus. Calopogon multiflorus and C. pallidus are consistently sister species, but the relationships of C. barbatus, C. oklahomensis, and C. tuberosus are not as clear. In the ITS analysis C. oklahomensis is sister to C. barbatus, whereas it is sister to C. tuberosus in the plastid restriction fragment analysis. Furthermore, all species were found to have chromosome numbers of 2n = 38 and 40, with the exception of the putatively hybrid-derived C. oklahomensis with 2n = 114 and 120. The hexaploidy of the latter, plus the discrepancy in its position between the ITS and plastid restriction fragment trees, could suggest that it is of hybrid origin. However, the presence of unique morphological and molecular characters might indicate that it is either an ancient hybrid or not of hybrid derivation at all. Finally, using these molecular methods all taxa appear to generally be discrete groups, with the exception of C. tuberosus vars. latifolius and tuberosus, the former of which is best combined with the latter.

Molecular phylogeny, morphology and their implications for the taxonomy of Eriocaulaceae

Eriocaulaceae e uma familia pantropical com dez generos e cerca de 1.400 especies, com centro de diversidade no Novo Mundo, especialmente no Brasil. A ultima revisao da familia foi publicada ha mais de 100 anos, e ate recentemente, as relacoes genericas e infra-genericas ainda eram pouco resolvidas. Entretanto, tem havido nos ultimos 30 anos, um grande esforco por parte de pesquisadores brasileiros para preencher as lacunas existentes, utilizando caracteres morfologicos e anatomicos, complementados por dados adicionais de diferentes fontes, como palinologia, quimica, embriologia, genetica de populacoes, citologia e, mais recentemente, estudos de filogenia molecular. Tal conjunto de dados tem levado a uma re-avaliacao do relacionamento filogenetico dentro da familia. Neste trabalho sao apresentados novos dados para as regioes de ITS e trnL-F, analisadas separadamente e em combinacao, usando maxima parcimonia e inferencia Bayesiana. Os dados obtidos confirmam resultados ja publicados, e mostram que muitos caracteres tradicionalmente usados para diferenciacao e circunscricao dos generos dentro da familia sao homoplasicos. Uma nova descricao e chave generica para a familia, utilizando caracteres de varias fontes sao apresentadas, refletindo a taxonomia atual das Eriocaulaceae.

Pollen analysis of honeys from Caatinga vegetation of the state of Bahia, Brazil

Abstract Based on pollen analysis, 17 honey samples collected in the Caatinga area from Nova Soure city were classified by botanical origin to identify the most important floral sources. Most of the honey samples were obtained in August and September. A total of 73 pollen types were identified belonging to 30 families, 64 genera and 30 species. The families best represented by their number of pollen types were Mimosaceae (11), Caesalpiniaceae (9), Rubiaceae and Fabaceae (5 each). Predominant pollen types were: Mimosa arenosa in four samples, M. sensitiva and M. tenuiflora in one sample. Pollen from Mimosa ursina was registered for the first time in the pollen spectrum of the Caatinga vegetation. The correspondence analysis showed a similarity among the honey samples based on pollen composition. The high representation of pollen from native species such as Chamaecrista nictitans, C. ramosa, C. swainsonii and Copaifera martii (Caesalpiniaceae); Aeschynomene martii and Zornia sericea (Fabaceae); Herissantia tiubae (Malvaceae); Mimosa arenosa, M. quadrivalvis, M. sensitiva, M. tenuiflora, M. ursina, Piptadenia moniliformis and Plathymenia reticulata (Mimosaceae), and Ziziphus joazeiro (Rhamnaceae) supports the origin of these honeys from Caatinga vegetation.

Phylogeny of Pleione (Orchidaceae) and Parentage Analysis of its Wild Hybrids Based on Plastid and Nuclear Ribosomal ITS Sequences and Morphological Data

Abstract Phylogenetic relationships within the orchid genus Pleione were reconstructed using maximum parsimony analyses of plastid and nuclear DNA and morphology for 20 taxa to evaluate infrageneric groups, controversial species delimitations, and parentage of several putative wild hybrids. Separate analyses of each data set produced mainly congruent clades when P. × confusa and the Chinese accession of P. hookeriana were excluded. Analysis of the combined data indicated that traditional divisions of the genus into various subgenera and sections are supported when they are based on apomorphic characters. Sections found to be paraphyletic appear to be based on homoplasious and plesiomorphic characters. For an infrageneric classification of Pleione based on phylogenetic relationships three groups are suggested. Taxa within the P. bulbocodioides complex do not show much molecular divergence. Pleione maculata and P. praecox are proposed to be the paternal and maternal parent of P. × lagenaria, respectively, as their nuclear and plastid genomes were almost identical to their natural hybrid. Furthermore, DNA sequences confirm the paternal and maternal parent origin of P. × confusa from P. forrestii and P. albiflora as already suggested by morphological and karyotype data. Molecular data are not conclusive about parentages of P. × taliensis.