The Never-ending Story: Multigene Approaches to the Phylogeny of Amaryllidaceae

a whole, strongly supported the mostly African tribe Amaryllideae as sister to the rest of the family, and resolved geographically-based monophyletic groups, but failed to resolve the relationships among several basal lineages in the family (the African Haemantheae and Cyrtantheae, the Australasian Calostemmateae, and the American and Eurasian sister clades). We present analysis of plastid ndhF sequences that fully resolved the major clades of the family. The baccate-fruited Haemantheae and Calostemmateae are sister tribes, and the African endemic Cyrtantheae is sister to them both. This clade is sister to an American/Eurasian clade. We also present preliminary nuclear ribosomal ITS sequence analysis of the Eurasian clade. Lycorideae are basal in the group and begin a grade that continues with Hannonia, then Pancratium, then Lapiedra. The genera Galanthus, Narcissus, and Sternhergia are resolved as monophyletic with strong support. Leucojum is paraphyletic and recognition of Acis for the mostly autumn-flowering Mediterranean species is supported. Recent phylogenetic analyses of various tribes and genera of the family are reviewed. Above the family level, Agapanthaceae, Alliaceae, and Amaryllidaceae form a well-supported monophyletic group, but exact resolution of the relationships among the three subclades varies depending on the sequence matrix utilized. The Angiosperm Phylogeny Group II has advocated combining all three into a single family, Alliaceae. We discuss this decision, which has historical precedent, but recommend that Amaryllidaceae be conserved as the name for the family in such a treatment

The age of chocolate: A diversification history of Theobroma and Malvaceae

Dated molecular phylogenies of broadly distributed lineages can help to compare patterns of diversification in different parts of the world. An explanation for greater Neotropical diversity compared to other parts of the tropics is that it was an accident of the Andean orogeny. Using dated phylogenies, of chloroplast ndhF and nuclear DNA WRKY sequence datasets, generated using BEAST we demonstrate that the diversification of the genera Theobroma and Herrania occurred from 12.7 (11.6-14.9 [95% HPD]) million years ago (Ma) and thus coincided with Andean uplift from the mid-Miocene and that this lineage had a faster diversification rate than other major clades in Malvaceae. We also demonstrate that Theobroma cacao, the source of chocolate, diverged from its most recent common ancestor 9.9 (7.7-12.9 [95% HPD]) Ma, in the mid-to late-Miocene, suggesting that this economically important species has had ample time to generate significant within-species genetic diversity that is useful information for a developing chocolate industry. In addition, we address questions related to the latitudinal gradient in species diversity within Malvaceae. A faster diversification rate is an explanation for the greater species diversity at lower latitudes. Alternatively, tropical conditions may have existed for longer and occupied greater areas than temperate ones meaning that tropical lineages have had more time and space in which to diversify. Our dated molecular phylogeny of Malvaceae demonstrated that at least one temperate lineage within the family diverged from tropical ancestors then diversified at a rate comparable with many tropical lineages in the family. These results are consistent with the hypothesis that Malvaceae are more species rich in the tropics because tropical lineages within the family have existed for longer and occupied more space than temperate ones, and not because of differences in diversification rate. © 2015 Richardson, Whitlock, Meerow and Madriñán

Resurrection and New Species of the Neotropical Genus Adelonema(Araceae: Philodendron Clade)

Previous studies have shown Homalomena as traditionally defined to be polyphyletic, with Neotropical species phylogenetically distinct from Asian species. This study of 29 accessions of 10 Neotropical taxa, and a total of 135 accessions representing 92 taxa of Homalomena, Furtadoa, and Philodendron for nuclear ITS and plastid matK regions, supports resurrection of the genus Adelonema for Neotropical species currently assigned to Homalomena. Adelonema is here delimited as a Neotropical genus of 16 species divided into two new sections: sect. Adelonema and sect. Curmeria, based on morphologically supported molecular results. The genus Adelonema is distinguished by a hypogeal rhizome, crushed vegetative tissues smelling of anise, an extensively sheathing, sometimes prickly petiole, chartaceous often variegated leaf blades, a spadix either obliquely inserted on the spathe/peduncle (sect. Adelonema), or stipitate (sect. Curmeria), ovaries with 2–4-pluriovulate locules, and anatropous ovules on an axile placenta. Four new species are described: Adelonema orientalis, A. palidinervia, A. panamensis, and A. yanamonoensis. Eleven new combinations are made: Adelo

Resurrection and New Species of the Neotropical Genus Adelonema(Araceae: Philodendron Clade)

Previous studies have shown Homalomena as traditionally defined to be polyphyletic, with Neotropical species phylogenetically distinct from Asian species. This study of 29 accessions of 10 Neotropical taxa, and a total of 135 accessions representing 92 taxa of Homalomena, Furtadoa, and Philodendron for nuclear ITS and plastid matK regions, supports resurrection of the genus Adelonema for Neotropical species currently assigned to Homalomena. Adelonema is here delimited as a Neotropical genus of 16 species divided into two new sections: sect. Adelonema and sect. Curmeria, based on morphologically supported molecular results. The genus Adelonema is distinguished by a hypogeal rhizome, crushed vegetative tissues smelling of anise, an extensively sheathing, sometimes prickly petiole, chartaceous often variegated leaf blades, a spadix either obliquely inserted on the spathe/peduncle (sect. Adelonema), or stipitate (sect. Curmeria), ovaries with 2–4-pluriovulate locules, and anatropous ovules on an axile placenta. Four new species are described: Adelonema orientalis, A. palidinervia, A. panamensis, and A. yanamonoensis. Eleven new combinations are made: Adelo

A remarkable new species of Pamianthe (Amaryllidaceae) from the Department of Cauca, Colombia

A new saxicolous species of Amaryllidaceae tentatively assigned to the tribe Clinantheae, Pamianthe ecollis Silverst., Meerow & Sánchez-Taborda, is described from the western slope of the Cordillera Occidental in the department of Cauca, Colombia. The new species differs from the two hitherto known species of Pamianthe in its yellow flowers and in its nearly obsolete perianth tube. The near loss of the perianth tube may be correlated with a change in pollinator. The new species lacks a bulb; it produces a large number of winged seeds that are wind-dispersed. A key to the species of Pamianthe is provided. This is the first record of the genus Pamianthe for Colombia. The phylogenetic position of the genus Pamianthe is discussed

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

Background During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown.Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong.Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.<br /

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales—Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P \u3c 10-9) and are each even more strongly associated with shaded habitats (P \u3c 10-10 to 10-23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the "abominable mysteries" of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. METHODOLOGY/PRINCIPAL FINDINGS:We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. CONCLUSIONS/SIGNIFICANCE:This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family

Systematics of the Amazon Lilies, Eucharis and Caliphruria (Amaryllidaceae)

Volume: 76Start Page: 136End Page: 22

Biosystematics of Tetraploid Eucharis (Amaryllidaceae)

Volume: 74Start Page: 291End Page: 30