Phylogeny and biogeography of Pachygoneae (Menispermaceae), with consideration of the boreotropical flora hypothesis and resurrection of the genera Cebatha and Nephroia
Lian LianRosa Del C. OrtizFlorian JabbourCaifei ZhangXiaoguo XiangAndrey S. ErstTian‐Gang GaoZhiduan ChenWei Wang
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NdhF
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Molecular Phylogenetics
Testing the monophyly of Simaba (Simaroubaceae): Evidence from five molecular regions and morphology
Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic. To test the monophyly of Simaba and its infrageneric classification, we used a molecular approach based on DNA sequence data from two nuclear ribosomal spacer regions (ITS and ETS) and three plastid regions (rps16 intron, and intergenic spacers psbA-trnH and trnL-trnF), including a comprehensive sampling of species from Simaba and closely related genera. We also performed ancestral character reconstructions to identify morphological characters that could serve as synapomorphies for major clades and to explore patterns of homoplasy in the morphological dataset. Our results show Simaba as traditionally circumscribed is not monophyletic, with taxa segregated into two strongly supported but distinct clades, one of which is more closely related to Simarouba. The three main clades that emerged in the phylogeny include a mostly Amazonian Simaba clade (which includes the type species of Simaba and the remaining species of S. sect. Tenuiflorae, here proposed to be recognized as Simaba sensu stricto), a mostly extra-Amazonian Simaba clade (a distinct lineage that will be recognized as Homalolepis, a genus currently treated in synonymy and equivalent to Simaba sections Grandiflorae and Floribundae), and the Simarouba clade (including all of its current species). These three clades are characterized by a combination of morphological characters, described in detail herein, some of which are novel features for Simaba not previously reported in the literature. Mapping character-states on the phylogenetic tree provides tests for evolutionary hypotheses. For example, our reconstruction of habit and geographic distribution suggests that the diversification of several shrubby species within the extra-Amazonian lineage in the South American cerrados probably occurred from ancestors inhabiting tropical forests, involving transitions in morphological and ecological traits.
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The genus Setaria is the largest genus in the so‐called bristle clade, a monophyletic group of panicoid grasses distinguished by the presence of sterile branches, or bristles, in their inflorescences. The clade includes both foxtail millet and pearl millet, the latter an important cereal crop in dry parts of the world. Other members of the clade are weeds that are widespread agricultural pests. Previous molecular phylogenetic studies have suggested that Setaria might not be monophyletic but did not have a large enough sample of species to test this rigorously. In addition, taxonomic studies have suggested a close relationship between Setaria and Paspalidium, with some authors combining them into a single genus, but molecular studies included too few Paspalidium accessions for a meaningful conclusion. Accordingly, we have produced 77 new sequences of the chloroplast gene ndhF for 52 species not in previous analyses. These were added to available sequences for 35 species in 10 genera of the bristle clade and four outgroup taxa. We find that Setaria species fall into several moderately to strongly supported clades that correlate with geography but not with the existing subgeneric classification. Relationships among these clades and among other genera within the bristle clade are unclear. Constraint experiments using the approximately unbiased test reject the monophyly of Pennisetum, Setaria, and Setaria plus Paspalidium, as well as several other groupings, although the test may be overly sensitive and prone to Type I error. The more conservative Shimodaira‐Hasegawa test fails to reject monophyly of any of the tested clades.
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Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in
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Recent molecular phylogenetic studies have shown that most traditional families of zooxanthellate shallow‐water scleractinians are polyphyletic, whereas most families mainly composed of deep‐sea and azooxanthellate species are monophyletic. In this context, the family Dendrophylliidae (Cnidaria, Scleractinia) has unique features. It shows a remarkable variation of morphological and ecological traits by including species that are either colonial or solitary, zooxanthellate or azooxanthellate, and inhabiting shallow or deep water. Despite this morphological heterogeneity, recent molecular works have confirmed that this family is monophyletic. Nevertheless, what so far is known about the evolutionary relationships within this family, is predominantly based on skeleton macromorphology, while most of its species have remained unstudied from a molecular point of view. Therefore, we analysed 11 dendrophylliid genera, four of which were investigated for the first time, and 30 species at molecular, micromorphological and microstructural levels. We present a robust molecular phylogeny reconstruction based on two mitochondrial markers ( COI and the intergenic spacer between COI and 16S) and one nuclear ( rDNA ), which is used as basis to compare micromorphogical and microstructural character states within the family. The monophyly of the Dendrophylliidae is well supported by molecular data and also by the presence of rapid accretion deposits, which are ca . 5 μ m in diameter and arranged in irregular clusters, and fibres that thicken the skeleton organized in small patches of a few micrometres in diameter. However, all genera represented by at least two species are not monophyletic, Tubastraea excluded. They were defined by traditional macromorphological characters that appear affected by convergence, homoplasy and intraspecific variation. Micromorphogical and microstructural analyses do not support the distinction of clades, with the exception of the organization of thickening deposits for the Tubastraea clade.
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Diospyros
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Abstract Phylogenetic relationships among Vaccinium sections Macropelma, Myrtillus, and Hemimyrtillus have been the subject of much debate. These taxa have been proposed as close relatives and they share, along with sect. Oxycoccoides, the character of buds covered by two partially fused prophylls. However, the monophyly of these sections has not been assessed and hypotheses about evolutionary relationships have not been tested using a cladistic framework. While most investigators agree that the Hawaiian taxa from sect. Macropelma represent a monophyletic group, the phylogenetic position of the Polynesian V. cereum has been the subject of much discussion. Molecular data from the nrITS and the chloroplast genes matK and ndhF for 52 species of Vaccinieae were used in a phylogenetic analysis to assess the monophyly of these sections and to determine their phylogenetic position in tribe Vaccinieae. Hawaiian representatives from sect. Macropelma form a monophyletic group that is derived from within sect. Myrti...
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Trichostema (Lamiaceae) is a North American genus comprising five sections and 18 species. Phylogenetic relationships were inferred using DNA sequences (ITS, ndhF) and morphology (63 characters). The monophyly of Trichostema is well supported in four analyses (ITS, ndhF, ITS + ndhF, ITS + ndhF + morphology), but not in the analysis based on morphological data alone. In all analyses, the monophyly of sections Chromocephalum and Trichostema is well supported. The monophyly of section Paniculatum is moderately supported, and there is conflicting evidence regarding the monophyly of section Orthopodium. Although DNA data alone suggest that T. brachiatum is not a member of section Orthopodium, its retention in section Orthopodium is equivocal in the combined DNA-morphology analyses. The submerging of the monotypic section Rhodanthum into Paniculatum by Lewis and Rzedowski is not adopted because the monophyly of this grouping is poorly supported. Biogeographic history and character evolution (life history and chromosome number) are explored in the context of the phylogeny based on the combined ITS and ndhF sequence data.
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Relationships among Halimolobos, Mancoa, Pennellia ,a ndSphaerocardamum have been controversial. Higher level studies, using cpDNA data from the chloroplast encoded ndhF and trnL intron, suggested that some species of these genera represent a monophyletic group: the halimolobine clade. The research presented here focuses on the halimolobine clade with denser intra and inter-specific sampling. The primary aims of the project were: (1) to further test the monophyly of the halimolobine clade; (2) to test the monophyly Halimolobos, Mancoa, Pennellia ,a ndSphaerocardamum; and (3) to study the evolution of morphological characters in the clade. Data were generated from the trnL-F region, nrDNA ITS, pistillata intron one, and 17 non-molecular characters. The difficulties associated with incorporating these data into simultaneous analyses are discussed and a strategy is presented. Separate and simultaneous analysis confirmed a monophyletic core group of halimolobine species. The strict consensus tree contained five well-supported halimolobine subclades: Sphaerocardamum, Pennellia plus Arabis tricornuta, Mancoa bracteata plus M. foliosa, a narrowly defined Halimolobos, and a clade consisting of a subset of Halimolobos and Mancoa species. Individual morphological characters vary in their utility for classification of the group. However, the majority of the characters provide some grouping information within the halimolobine clade.
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Abstract Cleomaceae is a small pantropical family that is emerging as a promising system to investigate C 4 photosynthesis, floral evolution, and comparative genomics. However, our understanding of these phenomena is hindered by a lack of a strong phylogenetic hypothesis, despite a number of previous studies. We reconstructed the phylogeny of the family using data from all three genomes, including three cpDNA ( ndhF, matK, ycf1 ), one mtDNA ( rps3 ), and one nrDNA (ITS) regions. Analyses strongly supported 15 clades: (1) Clade 1, which includes two Old World species, Cleome khorassanica and C. turkmena ; (2) Cleome s.str., which includes the type C. ornithopodioides and Old World species; (3) Droserifolia, corresponding to three Old World species, C. droserifolia, C. fimbriata, C. quinquenervia ; (4) Polanisia , equivalent to this New World genus; (5) Angustifolia, which includes four Old World species; (6) North American cleomoids, which includes four genera, Cleomella, Peritoma, Oxystylis , and Wislizenia ; (7) Australian, which includes Old world species and worldwide weed Arivela viscosa ; (8) Gynandropsis , equivalent to this monotypic genus; (9) Clade 6, which includes Old World species of Cleome and Dipterygium ; (10) Dactylaena , corresponding to this genus and Physostemon ; (11) African, which includes species distributed in Old World; (12) Andean, which includes Podandrogyne and tropical New World species of Cleome ; (13) Melidiscus , which includes New World tropical species; (14) Cleoserrata , which includes New World tropical species; and (15) Tarenaya , a large New World clade. Major relationships amongst the clades are strongly supported for the first time, including North American cleomoids sister to all remaining Cleomaceae. While five genera are confirmed or newly identified here to be non‐monophyletic ( Cleome, Cleomella, Hemiscola, Peritoma, Tarenaya ), six are supported ( Cleoserrata, Dactylaena, Melidiscus, Physostemon, Podandrogyne, Polanisia ). Thus, there are many taxonomic and evolutionary implications to our revised phylogenetic hypothesis.
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