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Bayesian tree obtained from the 3-gene data set for basal Santalales. Posterior probabilities are given to the right of each node. Circled letters identify clades of Olacaceae s. lat. (see discussion in text). Taxon abbreviations are as in Fig. 1. Scale at bottom gives the number of substitutions per site.
Source publication
As traditionally circumscribed, the family Olacaceae contains a morphologically diverse assemblage of genera that has historically caused much confusion regarding their classification. For example, Olacaceae contain parasites and nonparasites, climbing lianas and trees, and members with dichlamydous and monochlamydous perianths. This family is basa...
Contexts in source publication
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... in topology and generally differed only in the degree of reso- lution, the partitions were concatenated and analyzed to- gether. MP analysis of the 3-gene matrix yielded ten most parsimonious trees of 5,691 steps, the strict consensus of which is shown in Fig. 2. Of the 52 total clades, 30 received BS support of 90% or greater. The BI tree (Fig. 3) recovered many of the same clades as the MP tree, thus the two will be dis- cussed together, focusing upon clades of particular relevance (labeled A-J on Figs. 2, 3). Both MP and BI resolved a mono- phyletic Santalales (clade A) with 100% BS support ( Fig. 2) and a PP of 1.0 ( Fig. 3). Moderate (BS = 71) to high (PP = 1.0) support was ...
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... clades, 30 received BS support of 90% or greater. The BI tree (Fig. 3) recovered many of the same clades as the MP tree, thus the two will be dis- cussed together, focusing upon clades of particular relevance (labeled A-J on Figs. 2, 3). Both MP and BI resolved a mono- phyletic Santalales (clade A) with 100% BS support ( Fig. 2) and a PP of 1.0 ( Fig. 3). Moderate (BS = 71) to high (PP = 1.0) support was obtained for a sister-group relationship between Santalales and the asterid ...
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... D received only poor MP BS support (i.e. 66%) but was resolved with high posterior probability (1.0) on the BI tree (Fig. 3). This clade contains the remainder of taxa clas- sified in Olacaceae as well as Misodendraceae, Schoepfiaceae, Loranthaceae, and ...
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... E and F are unresolved with BI ( Fig. 3) but do occur as sister (but not supported) with MP (Fig. 2). Clade E (BS = 100, PP = 1.0) contains Ochanostachys, Coula, and Minquartia, a group of arborescent taxa that have traditionally been clas- sified in tribe Couleae. For clade F (BS = 100, PP = 1.0), the pantropical Ximenia is sister to Curupira from South America and this ...
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... and Tetrastylidium). The exact rela- tionships among these tribes differed between the two analy- ses; however, support for these nodes on the morphological tree was low. In the following section we will integrate rel- evant morphological data that characterize the clades. Al- though the most parsimonious MP tree ( Fig. 2) and BI tree ( Fig. 3) give some indication of the general progression from the basalmost to more advanced clades, the presence of polytomies precludes fully discussing relationships among all seven olacaceous clades; this must be left to future ...
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... the BI tree shows S. grandifolia as sister to S. philippinensis. The clade of four paucispecific genera, Diogoa, Engomegoma, Tet- rastylidium, and Strombosiopsis, was well supported with mo- lecular (94% BS) and morphological (85% BS in ) data. These taxa have the synapomorphy of apiculate anther connectives ( ). Both molecular (BI tree, Fig. 3) and morphological data support a sister relation- ship between Strombosiopsis and Tetrastylidium, whereas these different analyses gave conflicting topologies for the other two ...
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... The genera Aptandra and Ongokea are clearly closely related as evidenced by a number of synapomorphies such as fused staminal fila- ments, glandular tissue between the stamens and petals, and a concave apocolpium on the pollen. Moreover, the branches leading to these genera are comparatively longer than those of other taxa on the BI tree (Fig. 3), thus indicating their higher rates of molecular ...
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... In subsequent works the family often included the genus Okoubaka (Louis and Léo- nard 1948; Takhtajan 1997) which was transferred to Santa- laceae by Stauffer (1957) -a placement supported by molecu- lar data (Nickrent and Malécot 2001). The MP tree (Fig. 2) includes this taxon in an unsupported sister group position with clades I and J. With BI (Fig. 3), Octoknema is sister to clade J but with essentially no support. This position stands in contrast to the morphological cladistic analysis of where the genus was placed with taxa equivalent to our clades B, C, and E. Morphological features are either unusual for Santalales (e.g. dioecy, stellate pubescence, ex- panded stigmatic ...
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... composed of Dulacia, Olax, and Ptychopetalum, was recognized as Olacaceae s. str. by van Tieghem (1896). This group of three genera share several anatomical, morphological, and palynological char- acters ( ). Although the 3-gene MP tree (Fig. 2) gives a polytomy for the two species of Olax and Dulacia, greater resolution is obtained with BI (Fig. 3). In this case, the New World taxon Dulacia is embedded within the Old World genus Olax, a position maintained with increased sampling within the genus (Malécot 2002). Thus, to maintain mono- phyly, we recommend including the 13 species of Dulacia in Olax. This genus was originally regarded as a section of Olax (Valeton 1886) based on ...
Citations
... Importantly, certain taxonomic groups such as the Olacaceae s.l. plant family are paraphyletic (Chase et al., 2016), and thus randomizing PUTs at any point below the crown node of this family (i.e., setting "use.paraphyletic" to FALSE) may result in an excessively conservative parameter space that would encompass almost the entire Santalales order (Malécot & Nickrent, 2008). ...
Aim
The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non‐molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms.
Innovation
Here, we present a completely generalized and flexible framework to expand incomplete phylogenies. The framework is implemented in the R package “randtip”, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip can generate fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the “blind” expansion of phylogenies using “quick‐and‐dirty” approaches often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step‐by‐step tutorial that was designed to provide guidelines to non‐specialist users.
Main Conclusions
Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.
... [27] Phylogenetically it is reported to be paraphyletic. [28] Leaves: 5.9 by 2.5-3.8 cm, simple alternate, elliptic or oblong elliptic, usually obtuse, glabrous above, glabrous or pubescent beneath, entire, base rounded or subacute (cuneate), petioles are 3 to 6 mm long, pubescent. ...
... Results of the evaluation variable sites indicated that among all individual markers, matK possessed the highest proportion of variable sites (16.5%), followed by trnLF (8.37%), LSU rDNA (5.67%), rbcL (4.35%), SSU rDNA (3.52%) this result was also seen in Malécot and Nickrent [20]. Manzanilla et al. [21] and Linh et al. [22] suggested that the numbers of variable sites and pairwise distances are proportional to the species divergence, though a previous study suggested that the proportion of variable sites may not affect a marker's classification ability. ...
Exploring the phylogenetic relationships between taxa provides
important information for science. The phylogenetic study of
Macrosolen was conducted based on molecular data sets of 27 taxa
with five DNA regions including chloroplast rbcL, matK, and trnL-F
and nuclear ribosomal (small subunit rDNA and large subunit rDNA)
regions to reconstruct the phylogenetic relationship of Macrosolen.
The Maximum likelihood (ML) and Bayesian inference (BI) methods
were used to build the phylogenetic trees. The results of molecular
analyses strongly supported the non-monophyly of Macrosolen with
two major clades within the genus. The nest of the three genera
Elytranthe, Lepidaria, and Macrosolen in the phylogenetic tree was
recognized to be congruent in their morphology, molecules and
distribution, but further study is necessary to resolve generic
boundaries for stable classification for the three genera. The endemic
species of Vietnam M. bidoupensis well supported as closely related
to M. tricolor by molecular data. Macrosolen from Vietnam is
genetically congruent with its individuals of the same species from
other countries.
... S. borneensis has remained the only member of this genus and recognized as such by many taxonomists (Valeton 1886, Boerlage 1890, King 1895, Ridley 1900, Sleumer 1980, Sleumer 1984. Scorodocarpus is a member of Strombosiaceae, which is not well-defined and there is no agreement as to whether to treat it as an independent family (Nickrent et al. 2010, Su et al. 2015 or to consider it within Olacaceae sensu lato (Malécot et al. 2004, Malécot & Nickrent 2008, Kuijt 2015. In recent systematics studies on the Santalales and updated classification in the Angiosperm Phylogeny Website, the familial status of Strombosiaceae was recognized wherein S. borneensis is sister to the remaining genera (Stevens 2001-onwards, Malécot & Nickrent 2008, Su et al. 2015, Nickrent et al. 2019, Nickrent 2020. ...
Scorodocarpus borneensis (Baill.) Becc., a tree that exudes garlic or onion smell, was discovered growing in a secondary lowland forest of Balabac Island in the Palawan Biogeographic Region. The tropical tree species also occurs in Borneo, the Malay Peninsula, and Sumatra. Our finding represents the first record of this monotypic genus from the Philippines. Here we provide information on the taxonomy, morphology, vernacular name, ecology, geographical distribution, conservation status, and local utilization of S. borneensis.
... With climate change, ecophysiological stress is increasing, potentially making trees more susceptible to mistletoe infection, which in turn leads to higher forest mortality rates [2][3][4][5]. Recent phylogenetic studies confirm that families: Misodendronaceae, Eremolepidaceae, Santalaceae, Viscaceae and Loranthaceae [6][7][8]. The largest family of this mistletoe is Loranthaceae which has 75 genera and over 900 species [1]. ...
... Based on molecular data, the phylogenetic relationship among the genera of Olacaceae s.l. has been changed (Malécot & Nickrent 2008). In APG III (2009), Schoepfia Schreb, traditionally placed in Olacaceae, was recognized as a separate family, Schoepfiaceae, also included in the order Santalales. ...
This study provides descriptions, identification key and illustrations of diagnostic characters, as well as comments on the distribution and habitat of species of Olacaceae and Schoepficeae occurring in the eastern portion of northeastern Brazil, this area includes the states of Alagoas, Ceará, Paraíba, Pernambuco and Rio Grande do Norte. The morphological descriptions are based on samples collected during field expeditions (2017-2019) and analysis of herbarium specimens. Were recorded five species in four genera belonging to the family Olacaceae (Cathedra rubricaulis, Dulacia gardneriana, Heisteria ovata, H. perianthomega and Ximenia americana) and one of Schoepfiaceae (Schoepfia brasiliensis), these species occur mainly in Atlantic Forest domain (Lowland and Montane Forests) are also registered in Caatinga and Cerrado domains. The distribution of D. gardneriana and H. perianthomega was expanded, to the states of Rio Grande do Norte and Paraíba, respectively. The main vegetative characters useful for specific delimitation are presence/absence of armed branches, petiole dorso-ventrally flattened or cylindrical and nerves impressed or flat on the adaxial surface. The presence/absence of staminodes, of a pubescent ovary and hypogynous disc, as well as floral pedicel size and diameter of accrescent calyx in fruits, are the most important reproductive characters for species determination.
... In Santalales, we confront a difficult question about how best to represent the phylogenetic results obtained by Mal ecot & Nickrent (2008) and Der & Nickrent (2008), as summarized in Nickrent et al. (2010), Su et al. (2015) and J.W. Byng (unpubl. data). ...
... data). APG III (2009) reported the results of the two phylogenetic papers (Der & Nickrent, 2008;Mal ecot & Nickrent, 2008; as summarized in Nickrent et al., 2010), but refrained from making any changes to the classification. Mal ecot & Nickrent (2008;as summarized in Nickrent et al., 2010) split 'Olacaceae' into eight families: Aptandraceae, Coulaceae, Erythropalaceae, Octoknemaceae, Olacaceae s.s., Schoepfiaceae, Strombosiaceae and Ximeniaceae. ...
... APG III (2009) reported the results of the two phylogenetic papers (Der & Nickrent, 2008;Mal ecot & Nickrent, 2008; as summarized in Nickrent et al., 2010), but refrained from making any changes to the classification. Mal ecot & Nickrent (2008;as summarized in Nickrent et al., 2010) split 'Olacaceae' into eight families: Aptandraceae, Coulaceae, Erythropalaceae, Octoknemaceae, Olacaceae s.s., Schoepfiaceae, Strombosiaceae and Ximeniaceae. Additionally, Der & Nickrent (2008;as summarized in Nickrent et al., 2010) proposed recognition of seven families in the group recognized as Santalaceae in APG III (2009): Amphorogynaceae, Cervantesiaceae, Comandraceae, Nanodeaceae, Santalaceae s.s., Thesiaceae and Viscaceae. ...
... Schoepfiaceae is a recently accepted family that has been segregated from the presumably non-monophyletic Olacaceae (Sleumer, 1984). It is actually more closely related to the hemiparasitic families Santalaceae and Misodendraceae (Malécot & Nickrent, 2008;APG IV, 2016). Molecular studies have shown that Schoepfiaceae comprises three genera: Arjona Cav. ...
Schoepfia clarkii is a rare species of Schoepfiaceae that to date has been known only from the single flowering specimen used in the original description from white-sand vegetation in Venezuela. Here we report new records for this species collected from the lower Negro River basin in Brazil, ca. 900 km from the type locality, but also from white-sand vegetation. We provide a more detailed description of the species, including the first observations of fruit characters, as well as illustrations, photographs, a distribution map, and discussion of its conservation status. We also provide a key for the identification of the South American species of Schoepfia.
... In the order Santalales, which is a large order including most hemiparasites, more studies on its molecular phylogeny and genomics are needed [31,32,38]. The cp genomes of hemiparasitic plants have smaller genetic changes than those of holoparasitic plants, but studies of hemiparasites are important for understanding the evolutionary transition from autotrophs to parasites. ...
... The cp genomes of hemiparasitic plants have smaller genetic changes than those of holoparasitic plants, but studies of hemiparasites are important for understanding the evolutionary transition from autotrophs to parasites. In previous molecular phylogenetic studies, the evolutionary relationships of Santalales species have been confirmed by plastid genes (accD, matK, rbcL, and trnL-F), nuclear genes (SSU rDNA, LSU rDNA, and RPB2), and a mitochondrial gene (matR) [4,31,32,36]. In this study, most protein-coding genes in the cp genomes of Santalales species were used to confirm the phylogeny of 11 Santalales species belonging to six families. ...
Santalales is a large order, with over 2200 species, most of which are root or aerial (stem) hemiparasites. In this study, we report the newly assembled chloroplast genome of Dendrotrophe varians (140,666 bp) in the family Amphorogynaceae and the cp genomes of Helixanthera parasitica (124,881 bp) and Macrosolen cochinchinensis (122,986 bp), both in the family Loranthaceae. We compared the cp genomes of 11 Santalales including eight currently available cp genomes. Santalales cp genomes are slightly or not reduced in size (119–147 kb), similar to other hemiparasitic species, when compared with typical angiosperm cp genomes (120–170 kb). In a phylogeny examining gene content, the NADH dehydrogenase gene group is the only one among eight functional gene groups that lost complete functionally in all examined Santalales. This supports the idea that the functional loss of ndh genes is the initial stage in the evolution of the plastome of parasitic plants, but the loss has occurred independently multiple times in angiosperms, while they are not found in some parasites. This suggests that the functional loss of ndh genes is not essential for the transition from autotroph to parasite. We additionally examined the correlation between gene content and type of parasitism (obligate/facultative and stem/root parasites) of all hemiparasitic species in which cp genomes have been reported to date. Correlation was not found in any types of parasitism.
... Over the past two decades, our understanding of phylogenetic relationships within and between the early diverging superasterid orders has greatly improved through numerous molecular studies (e.g., Soltis et al., 1997Soltis et al., , 1999Soltis et al., , 2000Soltis et al., , 2002Soltis et al., , 2003Soltis et al., , 2007Soltis et al., , 2011Fan & Xiang, 2003;Fior et al., 2006;Der & Nickrent, 2008;Malécot & Nickrent, 2008;Horn, 2009;Burke et al., 2010;Gillespie & Kron, 2010;Harbaugh et al., 2010;Moore et al., 2010Moore et al., , 2011Xiang et al., 2011;summarized in APG I [1998], Stevens [2001 onwards], APG II [2003], APG III [2009], and APG IV [2016]). Amongst these studies, a consensus has emerged that the lineage leading to Santalales separated from the remaining Superasteridae first, followed by those leading to Berberidopsidales, Caryophyllales, Cornales, and Ericales. ...
... Aside from this, a few other phylogenetic relationships within the early diverging Superasteridae remain problematic, particularly the delimitation of certain paraphyletic families, such as Olacaceae s.l. and Santalaceae s.l. (Der & Nickrent, 2008;Malécot & Nickrent, 2008). ...
... 4; DML, CHB, and DHB; all trees). Although recent phylogenetic investigations have greatly improved our understanding of inter-and supra-specific relationships in this order (Nickrent & Franchina, 1990;Vidal-Russell & Nickrent, 2007Der & Nickrent, 2008;Malécot & Nickrent, 2008), the exact delimitations of its families remain only partly understood, particularly for Santalaceae s.l. and Olacaceae s.l. In recent molecular phylogenetic studies, these two families have been divided into seven (Santalaceae s. str., Amphorogynaceae, Cervantesiaceae, Comandraceae, Nanodeaceae, Thesiaceae, and Viscaceae; Der & Nickrent, 2008) and eight (Olacaceae s. str., Aptandraceae, Coulaceae, Erythropalaceae, Octoknemaceae, Strombosiaceae, Schoepfiaceae, and Ximeniaceae; Malécot & Nickrent, 2008) familylevel groups, respectively, without strong molecular or morphological support for these relationships (summarized in Nickrent et al., 2010). ...
This study, the fifth in a series investigating palynological characters in angiosperms, aims to explore the distribution of states for 19 pollen characters on five early diverging orders of Superasteridae (Berberidopsidales, Caryophyllales, Cornales, Ericales, and Santalales) plus Dilleniales. To illustrate the character states found in the pollen of this group, we examined pollen grains of 15 species exemplifying 15 families across all studied orders using light, scanning, and transmission electron microscopy. We reconstructed the phylogeny of the early diverging Superasteridae and related taxa with eight genetic markers for 172 genera, using maximum likelihood (ML) analysis. Nineteen pollen characters were coded for the genera used in this phylogeny and compiled into two morphological matrices using two coding strategies. The characters were then optimized on the newly generated ML tree plus two constrained trees differing in the position of Dilleniales, using three methods of inference. Taxa in this grade show a striking diversity of pollen morphologies, particularly in certain characters such as size, tectum sculpture, and aperture number. The plesiomorphic condition for the early diverging Superasteridae is unambiguously and consistently inferred to comprise monad-dispersed, isopolar, spheroidal, circular in outline, equatorially arranged, tricolpate pollen grains with granular aperture membranes, a smooth tectum, and endexine present. We identify diagnostic character states and synapomorphies for several monophyletic groups, and explore the palynological evidence that may shed light on some unresolved relationships. For example, the hypothesis that Dilleniales is sister to Superrosidae is better supported than alternative hypotheses, being consistent with a number of shared palynological state changes including transitions to presence of costae, reticulate tectum, and columellar infratectum structure. Across this part of the angiosperm phylogeny, most state transitions occur repeatedly, and their frequency varies among both clades and characters. We discuss the impact of optimization method, tree topology, and coding strategy upon ancestral state reconstruction.
