Jose L. Panero

The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed

The largest family of flowering plants Asteraceae (Compositae) is found to contain 12 major lineages rather than five as previously suggested. Five of these lineages heretofore had been circumscribed in tribe Mutisieae (Cichorioideae), a taxon shown by earlier molecular studies to be paraphyletic and to include some of the deepest divergences of the family. Combined analyses of 10 chloroplast DNA loci by different phylogenetic methods yielded highly congruent well-resolved trees with 95% of the branches receiving moderate to strong statistical support. Our strategy of sampling genera identified by morphological studies as anomalous, supported by broader character sampling than previous studies, resulted in identification of several novel clades. The generic compositions of subfamilies Carduoideae, Gochnatioideae, Hecastocleidoideae, Mutisioideae, Pertyoideae, Stifftioideae, and Wunderlichioideae are novel in Asteraceae systematics and the taxonomy of the family has been revised to reflect only monophyletic groups. Our results contradict earlier hypotheses that early divergences in the family took place on and spread from the Guayana Highlands (Pantepui Province of northern South America) and raise new hypotheses about how Asteraceae dispersed out of the continent of their origin. Several nodes of this new phylogeny illustrate the vast differential in success of sister lineages suggesting focal points for future study of species diversification. Our results also provide a backbone exemplar of Asteraceae for supertree construction.

Nuclear rDNA Evidence for Major Lineages of Helenioid Heliantheae (Compositae)

Abstract Results of phylogenetic analyses of nuclear 18S–26S rDNA internal transcribed spacer (ITS) region sequences for representatives of most genera of helenioid Heliantheae and various members of Heliantheae s.s. (sensu stricto) and Eupatorieae help to clarify major lineages and relationships in the clade corresponding to Heliantheae s.l. (sensu lato) and Eupatorieae. Most subtribes of helenioid Heliantheae as circumscribed by Robinson (1981) correspond closely with ITS clades. Polygeneric subtribes of helenioid Heliantheae that appear to be monophyletic based on ITS data include Flaveriinae sensu Turner and Powell (1977), Madiinae sensu Carlquist (1959), and Peritylinae sensu Robinson (1981). Chaenactidinae sensu Robinson (1981) is polyphyletic, but most members of the group are encompassed within only four ITS clades. Based on the ITS data and results of combined analyses of ITS variation plus previously published morphological and chloroplast DNA data, we conclude that Heliantheae s.s. and Eupatorieae represent nested clades within helenioid Heliantheae, as previously suggested. Loss of paleae appears to have been a rare occurrence during radiation of Heliantheae s.s.; only one epaleate taxon that we sampled (Trichocoryne) was placed within an ITS clade of otherwise paleate taxa, referable to Heliantheae s.s. We conclude that expression of paleae in Heliantheae s.s., Madiinae, and Marshallia is homoplasious. We also conclude that pappi of bristles or bristle-like subulate scales have arisen in various lineages of Heliantheae s.l. and in general have received too much weight in previous circumscriptions of suprageneric taxa. Multiple examples of extreme dysploidy from high (putatively polyploid) ancestral chromosome numbers in helenioid Heliantheae are evident from the phylogenetic data. Bidirectional ecological shifts between annual and perennial habits and repeated origins of woodiness from herbaceous ancestors also can be concluded for helenioid Heliantheae. Based on modern distributions of taxa and evident phylogenetic patterns, Baeriinae, Madiinae, and the x = 19 “arnicoid” taxa probably share a common Californian ancestry. To produce a tribal taxonomy for Heliantheae s.l. that better reflects phylogenetic relationships, Eupatorieae and (provisionally) Heliantheae s.s. are retained in essentially the traditional senses, Helenieae is recognized in a restricted sense, Madieae and Tageteae are expanded, and three new tribes (Bahieae, Chaenactideae, and Perityleae) are erected. In Madieae, three new subtribes (Arnicinae, Hulseinae, and Venegasiinae) are recognized, in addition to Baeriinae and Madiinae. In Peritylinae, a new combination, Perityle montana, is proposed for Correllia montana. Communicating Editor: Richard Jensen

Phylogenetic analysis of Silphium and subtribe Engelmanniinae (Asteraceae: Heliantheae) based on ITS and ETS sequence data

The phylogenetic relationships of Silphium and subtribe Engelmanniinae were examined using DNA sequence data. The internal transcribed spacer (ITS) region and the external transcribed spacer (ETS) region were sequenced for 39 specimens representing the six genera of subtribe Engelmanniinae (Berlandiera, Chrysogonum, Dugesia, Engelmannia, Lindheimera, and Silphium), plus five additional genera identified as closely related to the Engelmanniinae by chloroplast DNA restriction site analysis, and three outgroups. Phylogenetic analysis supported the monophyly of Silphium with Lindheimera as sister. Silphium can be divided into two sections based upon two well-supported clades that correspond to root type and growth form. These results also supported the expansion of subtribe Engelmanniinae to include Balsamorhiza, Borrichia, Rojasianthe, Vigethia, and Wyethia. We hypothesize that subtribe Engelmanniinae originated in Mesoamerica and later radiated to the United States. We suggest that the cypsela complex, which is present in Berlandiera, Chrysogonum, Engelmannia, and Lindheimera, arose only once and was subsequently lost in Silphium.

Phylogenetic reticulation in subtribe Helianthinae

Incongruence between phylogenetic estimates based on nuclear and chloroplast DNA (cpDNA) markers was used to infer that there have been at least two instances of chloroplast transfer, presumably through wide hybridization, in subtribe Helianthinae. One instance involved Simsia dombeyana, which exhibited a cpDNA restriction site phenotype that was markedly divergent from all of the other species of the genus that were surveyed but that matched the restriction site pattern previously reported for South American species of Viguiera. In contrast, analysis of sequence data from the nuclear ribosomal DNA internal transcribed spacer (ITS) region showed Simsia to be entirely monophyletic and placed samples of S. dombeyana as the sister group to the relatively derived S. foetida, a result concordant with morphological information. A sample of a South American species of Viguiera was placed by ITS sequence data as the sister group to a member of V. subg. Amphilepis, which was consistent with cpDNA restriction site data. Samples of Tithonia formed a single monophyletic clade based on ITS sequence data, whereas they were split between two divergent clades based on cpDNA restriction site analysis. The results suggested that cpDNA transfer has occurred between taxa diverged to the level of morphologically distinct genera, and highlight the need for careful and complete assessment of molecular data as a source of phylogenetic information.

Phylogenetic relationships of subtribe Ecliptinae (Asteraceae: Heliantheae) based on chloroplast DNA restriction site data

Phylogenetic analysis of chloroplast DNA restriction site data for 76 of the 302 genera of Heliantheae sensu lato using 16 restriction endonucleases reveals that subtribe Ecliptinae is polyphyletic and that its genera are distributed in four different lineages. The ecliptinous genera Squamopappus, Podachaenium, Verbesina, and Tetrachyron (of the Neurolaeninae), along with other members of subtribe Neurolaeninae are the basalmost clades of the paleaceous Heliantheae. The mostly temperate species of subtribe Ecliptinae (exemplified by Balsamorhiza, Borrichia, Chrysogonum, Engelmannia, Silphium, Vigethia, and Wyethia) are strongly nested in a clade with the Mesoamerican monotypic genus Rojasianthe as basal. The genera characterized by marcescent ray corollas traditionally classified in subtribe Zinniinae constitute a strongly supported group sister to Acmella, Spilanthes, and Salmea. The largest clade of ecliptinous genera is the most recently derived group within Heliantheae sampled. This large group of mostly Neotropical lowland genera (variously characterized by their winged cypselae, foliaceous phyllaries, and opposite phyllotaxy and exemplified by Perymenium, Wedelia, and Zexmenia) has been and continues to be the most challenging group from a taxonomic standpoint. The study provides new insights as to their relationships that will have a positive impact in future monographic studies of the group. The genera of the Espeletiinae form a monophyletic clade and are sister to members of the Milleriinae and Melampodiinae. This result is consistent with their traditional taxonomic placement with genera such as Smallanthus with which they share a tendency for functionally staminate disc flowers. The phylogenetically enigmatic genus Montanoa is sister to Melampodium. Members of subtribe Galinsoginae are clustered in two main lineages that correspond to the traditional division of the subtribe based on pappus characteristics. There is no support for the monophyly of subtribe Galinsoginae, and the same results indicate some of its genera are paraphyletic.

Evidence from chloroplast DNA restriction site analysis on the relationships of Scalesia (Asteraceae: Heliantheae)

Helianthus and later assigned to Helianthopsis. Two other groups considered as potential sister groups based on their geographic distribution in South America were not placed near Scalesia in the most parsimonious tree. Viguiera sect. Diplostichis appears to be relatively basal within subtribe Helianthinae, and the South American species of Viguiera, although previously classified in more than one subgenus, appear to form a single, monophyletic group that is not the sister group to Scalesia. The minimum of ten restriction site differences between Scalesia and Pappobolus of approximately 525 sites surveyed yielded an estimated sequence divergence of 0.19%, and an estimated time of divergence of approximately 1.96.2 million years.

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae.

Evolutionary Origins of a Bioactive Peptide Buried within Preproalbumin

A dual biosynthesis that produces seed albumin and a protease-inhibiting peptide in sunflower was found to have evolved over 18 million years ago and has spawned a family of peptides diverse in sequence and three-dimensional structure. Using the gene sequences and an understanding of the peptide biosynthesis, the biochemical steps that allowed these buried peptides to evolve de novo were proposed. The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin; however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif homologous to unrelated inhibitors from legumes, cereals, and frogs. To understand how PawS1 acquired this additional peptide with novel biochemical functionality, we cloned PawS1 genes and showed that this dual destiny is over 18 million years old. This new family of mostly backbone-cyclic peptides is structurally diverse, but the protease-inhibitory motif was restricted to peptides from sunflower and close relatives from its subtribe. We describe a widely distributed, potential evolutionary intermediate PawS-Like1 (PawL1), which is matured into storage albumin, but makes no stable peptide despite possessing residues essential for processing and cyclization from within PawS1. Using sequences we cloned, we retrodict the likely stepwise creation of PawS1’s additional destiny within a simple albumin precursor. We propose that relaxed selection enabled SFTI-1 to evolve its inhibitor function by converging upon a successful sequence and structure.

Macroevolutionary dynamics in the early diversification of Asteraceae

Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the familys evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5millionyears during the Middle Eocene.

Caribbean Island Asteraceae: Systematics, Molecules, and Conservation on a Biodiversity Hotspot

The Caribbean Islands are one of the ten insular biodiversity hotspots that are defined based on endemicity, massive habitat loss and vulnerability to extinction. Asteraceae genera endemic to islands have provided well known examples of plant radiation worldwide and illustrate the importance of these insular systems for evolutionary and conservation studies. A review of known patterns of taxonomic diversity and molecular cladistics is provided for Asteraceae genera and species endemic in the Caribbean Island biodiversity hotspot. We found that when compared with other island systems worldwide the Caribbean Islands have the highest number of endemic genera (41), have endemic genera in the highest number of tribes, and harbor the only Asteraceae tribe endemic to an island system, the Feddeeae which is restricted to Cuba. These unique patterns identify the Caribbean Islands as the most important insular area of endemism for this major plant family. Molecular cladistic studies are limited to only seven species in seven endemic genera and six endemic species in five non-endemic genera. These few studies are however relevant as: (1) they confirm the tribal status of the Feddeeae, (2) suggest colonization events from the highlands of Cuba toward low elevation and geologically recent areas of the Bahamas and South Florida, (3) provide evidence for biogeographical links to remote regions of the Pacific Basin, and (4) identify sister relationships with continental taxa, mostly from North America.ResumenLas Islas del Caribe son uno de los diez “punto calientes” insulares de biodiversidad, los cuales vienen definidos por sus niveles de endemicidad, masiva pérdida de habitat y vulnerabilidad y extinción. Asteráceas endémicas de islas han proporcionado ejemplos muy bien conocidos de radiación vegetal a nivel mundial, éstos ilustran la importancia de los sistemas insulares en estudios evolutivos y de conservación. Se presenta una revisión de las pautas de diversidad taxonómica y de cladismo molecular en Asteráceas de las Islas del Caribe. Hemos encontrado que comparadas con otros sistemas insulares, las Islas del Caribe tienen el mayor número de géneros endémicos (41), tienen géneros endémicos en el mayor número de tribus y poseen la única tribu de la familia endémica en islas, Feddeeae es endémica de Cuba. Estas pautas de diversidad exclusivas de las Islas del Caribe hacen que éstas sean el área de endemismos insulares más importante para las Asteráceas. Estudios de cladismo molecular se limitan solamente a siete especies en siete géneros endémicos y a seis especies en cinco géneros no endémicos. Este reducido número de estudios son de todas formas relevantes debido a que: (1) confirman el estatus a nivel de tribu de Feddeeae, (2) sugieren una ruta de colonización desde zonas altas de Cuba hacia áreas de baja elevación de las Bahamas y el sur de la Florida, (3) proporcionan evidencia de conexiones biogeográficas con regions remotas del Océano Pacífico, y (4) identifican relaciones de hermandad con táxones continentales, principalmente de América del Norte.