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9. Members of Compositae, subfamilies Barnadesioideae through Cichorioideae. A Schlechtendalia luzulaefolia Less.
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... Most nodes in the phylogenetic trees displayed high support values and were similar. The phylogenetic relationships of five subfamilies were consistent with earlier investigations (Funk et al., 2009;Fu et al., 2016;Panero and Crozier, 2016;Mandel et al., 2017). Previous studies have indicated the phylogenetic position and demographic histories of the tribe Pertyeae utilizing short DNA fragments (e.g., ndhF, rbcL, and matK) or the complete cp genomes data. ...
The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae.
... McCann et al. [14] applied statistical methods to determine the ancestral chromosome number in the genus Melampodium (Tribe Millerieae) using an ITS/matK sequence-based phylogeny, which included multiple polytomies, and hypothesized that both decreasing and increasing dysploidy had occurred in the genus with x 2 = 11 and dysploidy changes down to x 2 = 9 and up to x 2 = 14 all listed as x in their paper. Statistical methods were also used to determine chromosome base numbers for branches of the phylogenetic supertree of the Asteraceae provided by a 757 taxa phylogeny [17] in an analysis of the entire family [15] and concluded that x = 9 was most likely (high statistical probability) for all tribes in the family, even in the Heliantheae alliance. A base number of x = 10 was supported for the Vernonieae clade [22] . ...
A brief overview to the Index to Chromosome Numbers in Asteraceae database is provided. The database contains karyological information on Asteraceae and has been repeatedly improved and updated and is now hosted at the National Bioscience Database center. Also, we take the opportunity to revisit the evolution of base chromosome numbers in Asteraceae, emphasizing the phenomena of polyploidy, descending dysploidy, and hybridization, common in the family. Chromosome numbers for species included in one of the most recent phylogenetic treatments of the Asteraceae were obtained from the Index to Chromosome Numbers in Asteraceae database were mapped on to the modified phylogeny diagram, and base chromosome numbers were determined for each branch of the phylogeny. Results for tribal base numbers were the same as those hypothesized in our previous work with additional base numbers added for tribes not previously recognized but supported by newer phylogenetic methods. The Asteraceae show an ancestral base chromosome number of x = 9 and originated in the Antarctica (Gondowanaland) in Cretaceous (80 Mys ago). The x = 9 number has been retained through successive South American lineages of the Barnadesieeae, Gochnatieae, Stiffieae, Wunderlichieae, Astereae, and Senecioneae following northward migration. Northward migration to Africa was accompanied with x = 10 becoming the dominant base chromosome number as the family evolved multiple additional tribes. Northward migration to Australasia with x = 9 was in Astereae and the families Goodeneaseae, Menyanthaceae, and Stylydiaceae. The evolution of the North American Heliantheae alliance began with the appearance of x2 = 19 which persisted in multiple additional new tribes. Frequent dysploidy decreases, polyploidy and hybridization occurred throughout the history of the family.
... The sunflower family (Asteraceae or Compositae) is probably the most diversified of plants, with about 25,000-35,000 species, being distributed worldwide and accounting for ca. 10% of angiosperms [1,2]. The family contains many important crops (such as lettuce, sunflower or artichoke) and many ornamentals (such as marigolds or dahlias) but also many weeds (such as dandelion or some thistles) [1]. ...
... 10% of angiosperms [1,2]. The family contains many important crops (such as lettuce, sunflower or artichoke) and many ornamentals (such as marigolds or dahlias) but also many weeds (such as dandelion or some thistles) [1]. Two of the defining morphological traits of the family have been crucial for the evolutionary and ecological success of Asteraceae: the characteristic inflorescence in the capitulum, in which many tiny flowers (florets) are packed in a receptacle, and the cypsela, an indehiscent dry fruit derived from a compound inferior ovary, which usually has adaptations for an effective dispersal and to herbivory [3,4]. ...
... Resolving the systematic relationships within Asteraceae has been, however, a more challenging task. Since the first molecular-based approaches [13,14] to the major compilation and meta-tree analyses by [1], plastid DNA has been a preferred target of researchers interested in Asteraceae evolution. The combination of slowly evolving genic regions and the fast evolutionary rate of intergenic spacers has made plastid markers classical candidates for phylogenetic reconstruction at different taxonomic levels within the family [15]. ...
Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.
... Asteraceae Bercht. & J. Presl are the second largest genera in the world with about 1623 genera and 24.700 spesies (Funk, et al., 2009;Shi, et al., 2011;Christenhusz & Byng, 2016). The family could be found abundantly with high number of diversity, start from tropical, subtropical, semi-arid, to mediteranian area. ...
Asteraceae is the second largest plant family in the world. The family member has reached 227 species in Java. However, there is no current record of wild Asteraceae around local village within Gunung Halimun-Salak National Park. This study is to provide current Asteraceae species data and the threat for the conservation area. Explorative method has been conducted in 6 sites. The result shows that there are 20 species found with the tribes composition are 8 Heliantheae, 6 Eupatorieae, 3 Senecioneae, 1 Astereae, 1 Cichorieae, and 1 new record Vernonieae in Java. Key identification for species are provided and the new record has been described. Most species categorized as introduced with several other categorized as invasive alien species. In conclusion, numbers of Asteraceae family has been recorded with some potential ivansive threat in Gunung Halimun-Salak National Park. Regular population control and treatment are recommended in order to protect native species in the conservation area.
... Asteraceae nuclear phylogeny reveals highly supported relationships among subfamilies To reconstruct a tribal-level Asteraceae phylogeny, 243 Asteraceae species were sampled, representing all 13 subfamilies and 41 of the 45 recognized tribes (Panero and Funk, 2008;Funk et al., 2009b;Panero et al., 2014;Fu et al., 2016;Huang et al., 2016b) (149 species in Asteroideae, e.g., sunflowers, daisies, and chrysanthemums; 27 in Cichorioideae, e.g., lettuce and dandelion; 33 in Carduoideae, e.g., artichoke and thistles; and five outgroup taxa). We newly generated transcriptome and genome sequences from 121 (for one species, RNAs from two samples were sequenced) and 16 species, respectively (see Supporting Information; Tables S1, S2), plus 67 previous datasets from our lab (Zeng et al., 2014;Liu et al., 2015;Huang et al., 2016b) and 44 publicly available datasets (Tables S1, S2). ...
... On the other hand, most members of the large subfamilies Asteroideae and Cichorioideae (s.l.) and the tribe Cardueae are herbaceous, although habit transitions have also occurred later in Asteraceae history, even among closely related species (e.g., Panero et al., 1999), with woody members in these groups likely derived secondarily from herbs. Asteraceae are characterized by a head inflorescence (capitulum) with sessile florets surrounded by bract-like organs in a compact structure (Funk et al., 2009b), which can be solitary or part of a higher order inflorescence (capitulescence) ( Figure S37). The florets in a capitulum can be uniformly bisexual (homogamous) or exhibit sexual differentiation between the outermost and inner florets (heterogamous) ( Figure S38). ...
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole‐genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous–Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower‐like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
... Characters such as corolla color and type, patterns of seed-coat thickening, receptacular bract (or chaff) occurrence, types of pappus elements, pollen ornamentation, and the structure of anthers and style branches have often been emphasized in Compositae systematics. At the same time, the evolutionary lability of floral and fruit traits in composites is perceived to have been an important factor in the widespread ecological success of the family (Stuessy & Garver, 1994;Funk et al., 2009b;Panero & Crozier, 2016;Mandel et al., 2019). Pappus elements are particularly multi-functional, aiding in dispersal, as well as protecting against herbivores and desiccation (Robinson, 1981;Mandel et al., 2019), with rapid loss or reduction of the pappus commonly associated with isolation on islands or island-like habitats. ...
Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera and ca. 84 minimum‐rank taxa that mostly occur as narrow endemics on sheer rock‐cliffs throughout the southwest U.S. and northern Mexico. Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics. To test taxonomic hypotheses and utility of characters emphasized in past treatments, we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution. We inferred phylogenetic trees from whole chloroplast genomes, nuclear ribosomal cistrons, and hundreds of low‐copy nuclear genes using genome skimming and target‐capture. Discordance between sources of molecular data suggests a underappreciated history of hybridization in Perityleae. Phylogenies support the monophyly of subtribe Peritylinae, a distinctive group possessing a four‐lobed disc corolla; however, all of the phylogenetic trees generated in this study reject the monophyly of the most species‐rich genus, Perityle, as well as its sections: Perityle sect. Perityle, Perityle sect. Laphamia, and Perityle sect. Pappothrix. Using reversible jump MCMC, our results suggest that morphological characters traditionally used to classify members of Perityleae have evolved multiple times within the group. A base chromosome number of x=9 gave rise to higher base numbers in subtribe Peritylinae (x=12, 13, 16, 17, 18 and 19) through polyploidization followed by ascending or descending dysploidy. Most taxa constitute a monophyletic lineage with a base chromosome number of x=17, with multiple neo‐polyploidization events. These results demonstrate the advantages and obstacles to next‐generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.
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... & J. Presl. experienced explosive diversifications that ultimately gave rise to 95% of the family's extant species and the majority of its modern tribes (Funk et al., 2005(Funk et al., , 2009Mandel et al., 2019). Among these hyperdiverse lineages are five tribes that together form one (of two) enormous clade in Subfamily Asteroideae (Cass.) ...
Asteraceae account for 10% of all flowering plant species, and 35‐40% of these are in five closely‐related tribes that total over 10,000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and nearly 1000 nuclear loci, known as Conserved Orthologous Sequences. We tested for conflicting support in both datasets and used network analyses to assess patterns of reticulation to explain the early evolutionary history of this lineage which has experienced whole genome duplications and rapid radiations. We found both concordance and conflicting support in both datasets and documented four ancient hybridization events. Due to the timing of the early radiation of this five‐tribe lineage, shortly before the Eocene‐Oligocene extinction event (34 MYA), early lineages were likely lost, obscuring some details of their early evolutionary history.
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... Globally, Asteraceae is one of the most diverse angiosperm families, including ca. 23 600 species (Stevens, 2001;Panero & Crozier, 2016). Its species display a great diversity of growth forms, vegetative morphology and anatomy, chromosome numbers, floral structure, and pollen form and structure (Anderberg et al., 2007;Funk et al., 2009). The family is recognized as a monophyletic group due to various synapomorphies, including the flowers arranged in an inflorescence called "capitulum," the modification of the calyx on a pappus, the syngenesious stamens in which the pollen is exposed by the bifid style, the ovaries with a single basal egg, and the production of sesquiterpene lactones (Bremer, 1994;Anderberg et al., 2007;Funk et al., 2009;Mandel et al., 2017). ...
... Its species display a great diversity of growth forms, vegetative morphology and anatomy, chromosome numbers, floral structure, and pollen form and structure (Anderberg et al., 2007;Funk et al., 2009). The family is recognized as a monophyletic group due to various synapomorphies, including the flowers arranged in an inflorescence called "capitulum," the modification of the calyx on a pappus, the syngenesious stamens in which the pollen is exposed by the bifid style, the ovaries with a single basal egg, and the production of sesquiterpene lactones (Bremer, 1994;Anderberg et al., 2007;Funk et al., 2009;Mandel et al., 2017). It is cosmopolitan and represented in a variety of ecosystems (Mandel et al., 2017(Mandel et al., , 2019. ...
... Processes as whole-genome duplication and hybridization are common in Asteraceae (Ellstrand et al., 1996;Barker et al., 2008;Symonds et al., 2010;Soto-Trejo et al., 2013;Huang et al., 2016) and can obscure evolutionary patterns and hinder the recognition and delimitation of clades. Currently, 12-13 subfamilies and between 35 and 45 tribes are recognized (Anderberg et al., 2007;Funk et al., 2009;Panero et al., 2014;Fu et al., 2016;Panero & Crozier, 2016). The efforts to resolve relationships within the family have resulted in robust phylogenetic hypothesis (Funk et al., 2009;Panero et al., 2014;Huang et al., 2016;Panero & Crozier, 2016;Mandel et al., 2017Mandel et al., , 2019. ...
Asteraceae is the largest plant family in México with about 417 genera and 3,113 species, more than 60% of them endemic. Phylogenetic relationships at subfamily and tribal levels have been previously resolved employing both nuclear and plastid molecular markers. However, Asteraceae species native to Mexico have been underrepresented in such phylogenies. To tackle this issue, the taxon sampling of this study included 90 Asteraceae species native to México, four species from the Caribbean, 119 previously sequenced species, and six outgroups. With this sampling, all the Asteraceae subfamilies and all of the tribes recognized to date are represented. The analyzed data set consisted of eleven chloroplast markers (atpB, matK, ndhC, ndhD, ndhF, ndhI, ndhJ, ndhK, rbcL, trnL‐trnF, 23S‐trnA). We present two phylogenetic reconstructions obtained by maximum likelihood and pseudocoalescent methods. Besides, we present a time‐calibrated phylogeny, used to infer the best configuration of diversification rate shifts. Our results show that Mexican species are distributed mainly in the subfamily Asteroideae (80 species), followed by Cichorioideae (6 species), Carduoideae (2 species), and Mutisioideae (2 species). Four net diversification rate shifts were found: One near the base of the tree and four within Asteroideae subfamily. Our extended sampling of the family with the representation of native species to Mexico allowed us to identify important events in the evolutionary history of the family.
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... A generalized phylogenetic tree of the Asteroideae-Helianthodae (based onFunk et al. 2009c) onto which the different style types are plotted. Assignments of stylar types only on the basis of own investigations, apart from the presumed Madia type in Marshallia (Helenieae). ...
The monospecific genus Pelucha (endemic to the Mexican islands in the Gulf of California and the
nearby coast of Baja California) has been assigned to Inuleae (Inulinae or Plucheinae) or, more
recently, to Heliantheae/Helenieae. Both affiliations were justified by style characters (“inuloid” versus
“asteroid” arrangement of stigmatic papillae, i.e. marginal stigmatic bands confluent apically or
separate throughout), although the style were never imaged in a paper. To eliminate these inconsistencies
concerning in particular the arrangement of the stigmatic papillae, this paper deals with the style
morphology of Pelucha in detail, studied by SEM and histological sections.
The style of Pelucha trifida is assigned to the Mutisia-style type (acute stylar branches covered by
stylar hairs extending halfway down their length and stigmatic tissue arranged in two marginal bands
that become confluent apically).
This style type of Pelucha that otherwise is not found within the “Heliantheae alliance” is in agreement
with other features (pollen grains, absence of phytomelanin deposition) and supports an intermediate
position between Inuleae and the phytomelanic fruit clade (PF clade sensu Panero & Croizat
2016) within the “Heliantheae alliance”.
... Recent studies have estimated family-level phylogenies for Asteraceae: Fu et al. (2016) and Panero and Crozier (2016) used multi-locus plastid data, and Huang et al. (2016) used HTS to obtain 175 orthologous nuclear markers from transcriptome data. Following Funk et al. 's (2009) Asteraceae family-wide supertree approach and phylogenetic studies for different tribes (see parts 2-4 within Funk et al., 2009), the Asteraceae community needed a set of loci that could be used for phylogenetic analyses across the family and, if possible, for multiple taxonomic levels (i.e., family, tribe, genus, species). Therefore, Mandel et al. (2014) published a probe set designed for hybrid capture in combination with genome skimming, using HTS (hereafter Hyb-Seq; Weitemier et al., 2014), that targets 1061 nuclear loci that are potentially low-copy and orthologous across the Asteraceae family, based on conserved markers (hereafter referred to as the conserved orthologous set [COS]; Mandel et al., 2014). ...
Premise:
Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here.
Methods:
Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.
Results:
Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches.
Discussion:
The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
