Table of Contents
  • Volume 58 Issue 6

    Special issue: Collections-Based Systematics and Biogeography in the 21st Century: A Tribute to Dr. Vicki Funk

    Cover illustration: Vicki Funk images (left to right, top to bottom): Collecting below the Cerro de la Neblina in South America in 1984 (photo by Roy McDiarmid); Collecting Compositae in Tibet, China, in 2006 (photo by Deborah Bell); Collecting Espeletia hartwegiana Cuatrec. ex Herzog. in the Valle de los Frailejones, Puracé National Park, Cauca, Colombia (photo by Mauricio Diazgranados); Collecting Bidens orofenensis M. L. Grant in Society Islands, Tahiti, Orohena, in 2012 (photo by Jean-Yves Meye [Detail] ...
      
    Issue Information
    2020, 58 (6): 1-4.
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    Editorial
    Jun Wen and Warren L. Wagner
    2020, 58 (6): 743-750.
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    This special issue honors Dr. Vicki Ann Funk (26 November 1947 – 22 October 2019), who passed away after a battle with an aggressive cancer (Fig. 1). Dr. Funk was a Botanist at the Smithsonian Institution in 1981–2019.

    Review
    Tod F. Stuessy
    2020, 58 (6): 751-766.
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    Oceanic islands and archipelagos are natural laboratories for investigating patterns and processes of evolution. Islands change with the course of time, resulting in a dynamic ontogeny over millions of years. The combined forces of tectonic plate subsidence and erosion from waves, wind, and rainwater bring about substantial geomorphological change over millions of years, until islands eventually disappear under the sea. Added to these long‐term natural changes to the environment of the islands are the changes caused by human activities in recent centuries. After humans reach a previously unpopulated island, they utilize the natural resources for their own survival, cutting forests for making houses, boats, and firewood. The size of the human population and the length of time on the island determine the degree of environmental impact. Evolutionary processes in plants of oceanic islands take place during ontogeny of the islands, resulting in population divergence, speciation, and hybridization. Due to the dramatic alterations suffered by many islands over millions of years, the present patterns of distribution and ecology of species within endemic groups may have little to do with the patterns when the species originated. Understanding these environmental changes is fundamental to infer a founder effect, reasons for levels of genetic variation within and among populations, and modes of speciation. Special caution must be exercised while making comparisons between groups located on islands of different geological ages and that have endured differing environmental modifications from humans. Examples are provided from the Juan Fernández Archipelago and Lord Howe Island.

    Research Articles
    Susy Echeverría‐Londoño, Tiina Särkinen, Isabel S. Fenton, Andy Purvis, and Sandra Knapp
    2020, 58 (6): 767-782.

    Explosive radiations—substantial increases in net species diversification—have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement, and extinction of the constituent lineages make radiations hard to discern or understand as geological time passes. We used the megadiverse angiosperm genus Solanum L. (Solanaceae), with ca. 1200 currently accepted species distributed worldwide in a wide array of habitats, to explore these patterns on a global scale. We synthesized phylogenetic and distributional data for this ongoing radiation to show how dispersal events and past climatic changes have interacted to shape diversification. We find that, despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent increase in diversification coincides with a long‐distance dispersal event from the Neotropics to regions where major climatic changes were taking place. Two separate groups of Solanum have migrated and established in Australia, but only the arid‐adapted lineages underwent significant increases in diversification rate, as they were able to adapt to the continent's long‐term climatic trend towards seasonally dry and arid biomes (a pattern observed in the diversification of other arid‐adapted groups). Our findings provide a clear example of how successful colonization of new areas and niches can—but does not always—drive explosive diversifications.

    William A. DiMichele and Richard M. Bateman
    2020, 58 (6): 783-804.
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    Paralycopodites Morey & Morey, a Carboniferous‐age arboreous lycopsid that grew in the tropical wetlands of Pangea, is the phylogenetically basalmost member of the Carboniferous stigmarian lycopsids to be conceptually reconstructed. We update its description through reciprocal illumination between anatomy (coal‐balls) and gross morphology (adpressions). Revised assessment of its architecture and development shows that the determinate, columnar main trunk eventually underwent several isotomous divisions to form a crown. Two opposite rows of closely‐spaced, compact lateral branches were initiated anisotomously throughout the trunk and crown, each branch further undergoing multiple anisotomous divisions to form an apparently planar scaffold for numerous bisporangiate cones. We infer that branches were initially emitted near‐vertically, but rapidly moved to a more horizontal position; they were abscised after the cones had matured but before the continuous phellogen had produced a centripetal periderm. Leaves were not abscised, though anatomy and morphology both suggest a photosynthetic economy that was localized within the plant body. Character content and clarity of interpretation make Paralycopodites the preferred name for the reconstructed plant rather than Anabathra, Ulodendron, or Bergeria. Phylogenetic analysis of rhizomorphic lycopsids based on a reduced spectrum of features observable in adpression returns the same topology as that based on a full matrix combining both anatomical and externally visible traits, permitting adpression fossils to be assigned to anatomically‐circumscribed genera rather than perpetuating an unnecessary parallel taxonomy.

    Matthew L. Knope, Vicki A. Funk, Melissa A. Johnson, Warren L. Wagner, Erin M. Datlof, Gabriel Johnson, Daniel J. Crawford, J. Mauricio Bonifacino, Clifford W. Morden, David H. Lorence, Kenneth R. Wood, Jean‐Yves Meyer, and Sherwin Carlquist
    2020, 58 (6): 805-822.

    The genus Bidens (Compositae) comprises c. 230 species distributed across five continents, with the 41 Polynesian species displaying the greatest ecomorphological variation in the group. However, the genus has had a long and complicated taxonomic history, and its phylogenetic and biogeographic history are poorly understood. To resolve the evolutionary history of the Polynesian Bidens, 152 individuals representing 91 species were included in this study, including 39 of the 41 described species from Polynesia. Four chloroplast and two nuclear DNA markers were utilized to estimate phylogenetic relationships, divergence times, and biogeographic history. Bidens was found to be polyphyletic within Coreopsis, consistent with previous assessments. The Polynesian radiation was resolved as monophyletic, with the initial dispersal into the Pacific possibly from South America to either the Hawaiian or Marquesas Islands. From the Marquesas, Bidens dispersed to the Society Islands, and ultimately to the Austral Islands. The initial diversification of the crown group in the Pacific is estimated to have occurred ~1.63 mya (0.74–2.72, 95% HPD), making Polynesian Bidens among the youngest and most rapid plant diversification events documented in the Pacific. Our findings suggest that relatively rare long‐distance dispersal and founder‐event speciation, coupled with subsequent loss of dispersal potential and within‐island speciation, can explain the repeated and explosive adaptive radiation of Bidens throughout the archipelagoes of Polynesia.

    Marc S. Appelhans, Claudia Paetzold, Kenneth R. Wood, and Warren L. Wagner
    2020, 58 (6): 823-840.

    The Hawaiian radiation of Myrsine (primrose family, Primulaceae) is the only one among the ten most species‐rich Hawaiian plant lineages that has never been included in a phylogenetic analysis. Our study is based on a RADseq dataset of nearly all Hawaiian Myrsine species and a Sanger sequencing dataset based on a worldwide sampling of Myrsine and related genera. Myrsine as a whole might be paraphyletic with respect to the monotypic Macaronesian genera Heberdenia and Pleiomeris, whereas Hawaiian Myrsine is resolved as monophyletic. The Sanger sequencing proved to be insufficient to resolve the Hawaiian lineage, whereas RADseq fully resolved the relationships with high support. Hawaiian Myrsine consists of three main lineages, of which one contains the majority of species and is mainly confined to Kauaʻi, and the other two lineages primarily consist of few widespread species. Although phylogenetic reconstructions delivered fully resolved and supported tree topologies, Quartet Sampling and HyDe analyses reveal phylogenetic incongruence throughout the phylogeny and provide the first molecular evidence of extensive hybridization in the lineage.

    Linda E. Watson, Carolina M. Siniscalchi, and Jennifer Mandel
    2020, 58 (6): 841-852.

    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 data sets 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 concordance and conflicting support in both data sets 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.

    Isaac H. Lichter‐Marck, William A. Freyman, Carolina M. Siniscalchi, Jennifer R. Mandel, Arturo Castro‐Castro, Gabriel Johnson, and Bruce G. Baldwin
    2020, 58 (6): 853-880.

    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 United States 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 an 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 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 of next‐generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae.

    Jennifer R. Ackerfield, David J. Keil, Wendy C. Hodgson, Mark P. Simmons, Shannon D. Fehlberg, and Vicki A. Funk
    2020, 58 (6): 881-912.

    Cirsium (i.e., “thistles”) are one of the most taxonomically challenging groups of Compositae in North America. This study represents the first attempt to infer a broadly sampled phylogeny of Cirsium in North America. The two main objectives are to: (i) test whether currently hypothesized species variety complexes (C. arizonicum, C. clavatum, C. eatonii, and C. scariosum) constitute monophyletic lineages, and (ii) recircumscribe any taxa that are identified as problematic. Phylogeny reconstructions based on DNA sequence data from two nuclear ribosomal regions and four plastid markers were used to infer evolutionary lineages and test species’ delimitations. Eight species varietal complexes were resolved as polyphyletic. We recircumscribed these complexes and in doing so found evidence to support the recognition of six new taxa. We hypothesize that the extensive taxonomic difficulty within Cirsium is the result of several factors: (i) previously undescribed taxa, (ii) inadequate representation of taxa from herbarium specimens, (iii) phenotypic convergence, (iv) hybridization, and (v) incipient speciation. While we can provide evidence to support the recircumscription of some taxa, others remain unresolved. Therefore, we are working on a phylogenomic study of North American Cirsium to answer remaining taxonomic questions as well as provide a robust framework for biogeographic studies.

    Jun‐Nan Wan, Yan‐Ping Guo, and Guang‐Yuan Rao
    2020, 58 (6): 913-924.

    Allopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species could lead to the origin of different taxa has received little attention. Here we used a new progenitor‐specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, Achillea alpina L. and Achillea wilsoniana Heimerl ex Hand.‐Mazz., through allotetraploidy from the same diploid progenitor species pair, Achillea acuminata (Ledeb.) Sch. Bip. and Achillea asiatica Serg. Based on the sequences of 17 nuclear genes from 21 wild populations of the four Achillea species investigated, a clear view of genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, A. acuminata, and ancestors belonging to those two groups contributed to the two tetraploid species. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study indicates that independent allopolyploidization events between the same Achillea parental species have generated two genetically and ecologically distinct taxa.

    Yue‐Ping Ma, Liang Zhao, Wen‐Jie Zhang, Ying‐Hua Zhang, Xia Xing, Xia‐Xia Duan, Jing Hu, AJ Harris, Pei‐Liang Liu, Si‐Lan Dai, and Jun Wen
    2020, 58 (6): 925-944.

    The origins of cultivated chrysanthemums have attracted considerable attention, but they remain poorly known. Here, we reconstructed the phylogeny of representative well‐known cultivars and wild species of the genus Chrysanthemum using chloroplast genomes and the nuclear LEAFY gene. Our results suggest that geographic and ecological factors may determine the opportunities for wild species to be involved in the origin of the cultivars. The wild species C. indicum, C. zawadskii, C. dichrum, C. nankingense, C. argyrophyllum, and C. vestitum were likely directly or indirectly involved as paternal species of most of the chrysanthemum cultivars examined in this study. Yet, the maternal species is supported to be a lineage of an extinct wild Chrysanthemum species and its subsequent cultivars, as all accessions of chrysanthemum cultivars sampled formed a strongly supported clade, distinct from all other species of Chrysanthemum in the plastome tree. Thus, the cultivated chrysanthemums originated from multiple hybridizations involving several paternal species rather than only two or a few wild species, with an extinct species and its subsequent cultivars serving as the maternal parents. This finding is consistent with Chrysanthemum having high rates of hybridization and gene flow, which has been demonstrated within previous studies; nevertheless, it is important to unravel the role of an extinct wild Chrysanthemum species as the ultimate maternal parent species for all the chrysanthemum cultivars. Our results also suggest that C. vestitum from Tianzhu and Funiu Mountains in Anhui and Henan Provinces of China represent two distinct cryptic species.

    Yi‐Xuan Zhu, Feng‐Wei Lei, Ling Tong, Xian‐Yun Mu, Jun Wen, and Zhi‐Xiang Zhang
    2020, 58 (6): 945-957.

    The mechanisms underlying the origin, evolution, and distributional patterns of organisms are a major focus of biogeography. Vicariance and long‐distance dispersal (LDD) are two important explanations for disjunctive distribution patterns among lineages. In‐depth biogeographic studies of taxa that exhibit wide‐ranging disjunctions can provide valuable information for addressing the relative importance of these biogeographic mechanisms. The genus Celastrus contains ca. 30 species that are disjunctly distributed in five continents of both the Northern and Southern Hemispheres, providing an excellent system for historical biogeographic analyses. Here, we used sequence data from five markers (nuclear external transcribed spacer and internal transcribed spacer, and plastid psbA‐trnH, rpl16, and trnL‐F) to reconstruct the phylogeny of Celastrus and investigate its phylogenetic relationships with Tripterygium, estimate clade divergence times using the fossil‐calibrated method, and infer its ancestral distribution range. Celastrus and Tripterygium were each supported as monophyletic. The morphology‐based classification systems were not supported by the phylogenetic results. The divergence time between Celastrus and Tripterygium was estimated to be 26.22 Ma (95% highest posterior density: 24.46–28.17 Ma), and the diversification of Celastrus were suggested to be linked to global warming events during the Miocene. Celastrus was suggested to have a tropical Asian origin, and dispersed to Central and South America, North America, Oceania, and Madagascar at different periods, most probably through LDD. Birds may have facilitated transoceanic migrations of Celastrus because of its bicolored fruits, which contain red and fleshy arils. Our results highlight the importance of key morphological innovations and animal‐mediated dispersals for the rapid diversification of plant lineages across vast distributional ranges.

    Meng‐Hua Zhang, Chao‐Yong Wang, Cheng Zhang, Dai‐Gui Zhang, Ke‐Gang Li, Ze‐Long Nie, and Ying Meng
    2020, 58 (6): 958-971.
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    Saxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.

    Hong‐Xin Wang, Michael J. Moore, Russell L. Barrett, Sven Landrein, Shota Sakaguchi, Masayuki Maki, Jun Wen, and Hua‐Feng Wang
    2020, 58 (6): 972-987.

    Understanding the causes of the Sino‐Japanese disjunctions in plant taxa has been a central question in eastern Asian biogeography, with vicariance or long‐distance dispersal often invoked to explain such patterns. Diabelia Landrein (Caprifoliaceae; Linnaeoideae) comprises four shrubby species with a Sino‐Japanese disjunct distribution. The species diversification time within Diabelia, covering a long geological history of the formation process of the Sino‐Japanese flora, dated back to the middle Oligocene, therefore, Diabelia would be an ideal model to elucidate the biogeographic patterns of Sino‐Japanese disjunctions with climate fluctuation. In this study, we analyzed complete plastome sequence data for 28 individuals representing all four species of Diabelia. These 28 plastomes were found to be highly similar in overall size (156 243–157 578 bp), structure, gene order, and content. Our phylogenomic analysis of the plastomes supported a close relationship between Diabelia ionostachya (Nakai) Landrein & R.L. Barrett var. wenzhouensis (S.L. Zhou ex Landrein) Landrein from eastern China and Diabelia spathulata (Siebold & Zucc.) Landrein var. spathulata from Japan. Diabelia serrata (Siebold & Zucc.) Landrein was identified as sister to a population of Diabelia sanguinea (Makino) Landrein from Tochigi in central Japan and D. spathulata Landrein, from Toyama, central Japan. Most Diabelia lineages were estimated to have differentiated 8–28 Mya. Our results indicate that two independent vicariance events could explain the disjunction between Japan and Korea in the mid to late Miocene, and between Zhejiang and Japan in the early Miocene.

    Hong‐Mei Liu, Eric Schuettpelz, and Harald Schneider
    2020, 58 (6): 988-1002.

    Hybridization has long been recognized as common in ferns, but the products of this arguably evolutionary important process have often been ignored in classifications. For example, the recently published Pteridophyte Phylogeny Group classification (PPG I) covered all hierarchical ranks from class to genus but did not include intergeneric hybrids (nothogenera). Here, we provide for the first time a comprehensive evaluation of previously proposed nothogenera in the context of a current phylogeny‐based pteridophyte classification (i.e., PPG I). We find that several nothogenera nested in the orders Osmundales and Polypodiales are supported in the framework of PPG I, but others are superfluous. Five new nothogenera are introduced here for the first time. We also explore the distribution of nothospecies across the pteridophyte phylogeny for the first time. We are unable to reject the hypothesis that species richness and nothospecies diversity are correlated, despite the finding that some temperate lineages contribute more nothospecies than expected whereas several tropical lineages lack them. This pattern could be the consequence of either fundamental differences in modes of speciation in temperate and tropical zones or unequal efforts to record nothospecies. In general, we emphasize the need to take nothogenera into account when proposing generic classifications, but the information provided by the existence of such hybrids needs to be carefully evaluated. Our results underscore the need to report and study hybrids in ferns and lycophytes, especially in biodiversity rich areas.

    Cassiano A. D. Welker, Michael R. McKain, Matt C. Estep, Rémy S. Pasquet, Gilson Chipabika, Beatrice Pallangyo, and Elizabeth A. Kellogg
    2020, 58 (6): 1003-1030.

    The grass tribe Andropogoneae (Poaceae—Panicoideae) includes several important crops such as maize, sugarcane, and sorghum, and dominates the tropical grasslands of the world. We present here a plastome phylogeny of the tribe with the largest sample of genera to date (about 73%), including 65 newly assembled plastomes, together with a broad biogeographic analysis of Andropogoneae. Major relationships found in previous phylogenetic studies were confirmed here, with most nodes having higher resolution and support, including those of the backbone of the tree, which had been a major problem in previous phylogenies of the tribe. Our dated tree suggests that Andropogoneae diverged from Arundinelleae in the Early Miocene, while the “core Andropogoneae” clade originated in the Late Miocene. The tribe originated in East Asia, but intercontinental dispersal has been common, with many independent dispersal events to Africa and the New World. Based on the plastome phylogeny, we propose here a new classification of Andropogoneae as most of its previously accepted subtribes are not monophyletic. Our classification comprises 14 subtribes, 92 genera, and ∼1224 species. About 90% of the Andropogoneae species could be assigned to a subtribe, which represents a major step toward clarification of the taxonomy of the tribe. The remaining taxa were placed incertae sedis pending additional molecular data. The new subtribes Chrysopogoninae and Rhytachninae are described herein. Our plastome trees also indicate that several Andropogoneae genera are para‐ or polyphyletic and require additional studies to define their circumscriptions.

    Robert J. Soreng, Marina V. Olonova, Nina S. Probatova, and Lynn J. Gillespie
    2020, 58 (6): 1031-1058.

    Poa sect. Poa subsect. Nivicolae (Prob.) Tzvelev was circumscribed to include four species of the Soviet Union: Poa shumushuensis, Poa caucasica, Poa irkutica, and Poa veresczaginii. Bayesian phylogenetic analyses of plastid and nuclear‐ribosomal DNA revealed that it is polyphyletic, none of these species are closely related. Poa shumushuensis, type of sect. Nivicolae, or its ancestor, likely displayed the nrDNA genotype characteristic of the higher polyploid P. sect. Malacanthae. Genotype codes are designated for each species: Hx, C c, Php, and Shp. Poa sect. Nivicolae s.s. is restricted to P. shumushuensis; P. sect. Irkuticae is restricted to P. irkutica; P. caucasica is moved to P. subg. & sect. Caucasicae nov.; and P. sect. Dschungaricae is resurrected for P. veresczaginii and two other species. Although diclinous breeding systems are known in many western hemisphere species of Poa, dicliny is infrequent and little studied in Asian Poa. Poa shumushuensis is judged to be either sequentially gynomonoecious or gynodioecious. A ratio of 2 perfect‐, to 2 mixed‐, to 1 pistillate‐flowered inflorescences from different plants in P. shumushuensis is suggestive of a recessive allele for stamen suppression, and this is associated with subtle sexual‐dimorphism. Poa irkutica is diclinous with a breeding system between simple gynomonoecy and sequential gynomonoecy; P. caucasica is perfectly flowered; and P. veresczaginii has infrequent abortive anthers, indicative of limited dicliny, or sterility for other reasons possibly related to its reticulate origin. In total, 23 Asian species are here reported to be diclinous and their breeding systems are characterized. A lectotype is designated for P. fauriei.

    David M. Spooner, Holly Ruess, Shelby Ellison, Douglas Senalik, and Philipp Simon
    2020, 58 (6): 1059-1070.

    High‐throughput (next‐generation) DNA sequencing has removed barriers to data quantity and quality, and it has produced phylogenies with high statistical support. Such data are useful to address phylogenetic congruence among individual genes. Concatenated analyses of unlinked genes often produce well‐resolved phylogenetic trees with bootstrap support on major nodes at or approaching 100%, but they have been criticized for providing incorrect phylogenies for various reasons to include a history of hybridization, introgression, and incomplete lineage sorting. The present study compares next‐generation sequencing results of the same accessions of Daucus with different genomic regions, of which three have been reported before: (i) the entire plastid genome, (ii) 47 mitochondrial genes, and (iii) 94 conserved nuclear orthologs. Here, we report a fourth dataset, (iv) 564 895 nuclear SNPs. There are areas of discordance in all four results using the same accessions analyzed with maximum parsimony, maximum likelihood, and with the nuclear data species trees through a coalescent analysis. The nuclear results show significant areas of discordance that were unexpected, because these studies used the same DNA samples, the nuclear studies were generated from large and high‐quality datasets with the SNPs distributed on all nine linkage groups of Daucus carota, and the results were supported by high bootstrap values. These results raise questions concerning the best data and analytical methods to reconstruct and understand the “truth” of a phylogeny.

    Verônica A. Thode, Lúcia G. Lohmann, and Isabel Sanmartín
    2020, 58 (6): 1071-1089.

    The accurate analyses of massive amounts of data obtained through next‐generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate “supergene” approach. The effects of molecular evolutionary models and character partition strategies on plastome‐based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well‐supported conflicting topologies). We compared different datasets (e.g., non‐coding regions, exons, and codon‐aligned and translated amino acids) using concatenated approaches under site‐heterogeneous and site‐homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

    Romer Narindra Rabarijaona, Viet‐Cuong Dang, Gaurav Parmar, Bing Liu, Jun Wen, Zhi‐Duan Chen, and Li‐Min Lu
    2020, 58 (6): 1090-1107.

    The genus Cayratia Juss. in the traditional sense (i.e., Cayratia s.l.) of the grape family has been shown to be non‐monophyletic. Previous studies supported the splitting of Cayratia s.l. into three genera, that is, Cayratia s.s., Causonis Raf., and a new genus representing the African Cayratia clade. However, the morphology of the African Cayratia clade has not been studied carefully and its phylogenetic position within Vitaceae remains unclear. Our study integrates molecular, distributional, and morphological data and supports the recognition of the new genus Afrocayratia from continental Africa and Madagascar. Phylogenetic analyses strongly support the monophyly of Afrocayratia and resolve it as a sister of Cayratia s.s. based on the chloroplast data, but it is placed sister to Cyphostemma based on the internal transcribed spacer dataset. Molecular dating suggests that Afrocayratia split with Cayratia s.s. during the Paleocene, but that the extant species of Afrocayratia did not diversify until the early Miocene. Afrocayratia differs from its allied genera in having short stigmas and seeds with subcircular ventral infold cavities in cross‐section. Three clades are detected within Afrocayratia, with A. debilis (Baker) J.Wen & L.M.Lu as the first diverged lineage. The second diverged lineage includes A. delicatula (Willems) J.Wen & Z.D.Chen and A. gracilis (Guill. & Perr.) J.Wen & Z.D.Chen. The third diverged lineage includes A. imerinensis (Baker) J.Wen & L.M.Lu, A. longiflora (Desc.) J.Wen & Rabarijaona, and A. triternata (Baker) J.Wen & Rabarijaona from Madagascar, which form a monophyletic group that diverged from the second lineage in the middle Miocene. Combining the morphological and molecular evidence, we formally describe the new genus Afrocayratia, make seven new combinations, and provide a key to species of the genus.

Editors-in-Chief
Song Ge
Jun Wen
Impact Factor
2.779
JCR 2019 IF ranking: 56/234 (Plant Sciences, top 23.72%, Q1 quartile)
Journal Abbreviation: J Syst Evol
ISSN: 1674-4918 (Print)
1759-6831 (Online)
CN: 11-5779/Q
Frequency: Bi-monthly

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