Generic Circumscription Research Articles

The classification of the fern family Gleicheniaceae, with the description of a new genus, segregated from Sticherus

Abstract Gleicheniaceae is an early diverging lineage of leptosporangiate ferns. Although the family can be readily recognized by the pseudodichotomous branching pattern of its fronds, generic circumscription has long been debated. Phylogenetic analyses based on genomic data supported the monophyly of six genera (Dicranopteris, Diplopterygium, Gleichenella, Gleichenia, Rouxopteris, and Stromatopteris) but indicate the paraphyly of Sticherus. To accommodate this latter result, we describe a new genus, Sticheropsis, gen. nov., segregated from Sticherus. We provide a new taxonomic treatment of Gleicheniaceae, including an identification key to all eight genera, descriptions of the genera with comments and notes concerning geographic distributions and phylogenetic affinities, as well as an overview of the morphology of the family with a revised and unified terminology for the fronds. We recognize 149 species plus two hybrids for the family, distributed into eight genera, and propose six new combinations.

Taxonomic revision of the genus Punjuba (Leguminosae, Caesalpinioideae)

Punjuba is a Neotropical genus of the mimosoid clade (Leguminosae). The genus was recently restablished and is recognized by presenting shrubs and trees, with lax racemes or spiciform racemes, leaves with 1–3 pairs of pinnae and 2–7 pairs of leaflets in each pinna, thin and lateraly compressed legumes, curved to spiral, and seeds lacking pleurogram. Recent advances on legumes systematics have been producing great challenges on the circumscription of genera, especially on the mimosoid clade. Molecular phylogenetic studies confirm that Punjuba is monophyletic, and a revision of the genus and species circumscriptions are needed. Here we present a taxonomic revision of Punjuba, providing an identification key for all species currently recognized in the genus, morphological descriptions, and distribution maps. We recognize six species in the genus: P. callejasii, P. centiflora, P. killipii, P. lehmannii, P. racemiflora and P. foreroana, being the last one described here as a new species. Abarema josephi is proposed as a new synonym of P. lehmannii. Morphological characters including the inflorescence, indumentum, leaves and leaflets, besides quantitative characters, were applied as diagnostic to recognize the species.

Piecing together the taxonomic puzzle: Generic delimitation in the Stoebe clade of Cape daisies (Asteraceae: Gnaphalieae) and a synopsis of the species

The Stoebe clade is a Cape-centred lineage comprising ca. 70 species, currently in eight genera. Despite recent generic taxonomic changes, many generic characters are ambiguous, and generic circumscription is likely to remain unstable in the absence of a robust species-level phylogeny. Here, we present a hypothesis of species relationships in the clade, based on parsimony and Bayesian analyses of DNA sequence and morphological characters, in order to assess generic monophyly. The trees based on morphology alone and plastid sequences alone are poorly resolved, with few well-supported nodes, while those based on nuclear sequences alone are better resolved. There is no evidence of phylogenetic conflict, and concatenation of all three data sources produces a well-resolved tree with many highly-supported nodes. We show that none of the currently-accepted genera are monophyletic, with the exception of Muscosomorphe, which is supported as monospecific. Amphiglossa species are recovered in two separate clades, requiring the resurrection of the genus Pterothrix to house ten of the twelve species. All the characters used to circumscribe the remaining genera, such as the possession of ray florets, are shown to be homoplasious. As a result, these remaining genera (Dicerothamnus, Disparago, Elytropappus, Myrovernix, Seriphium, and Stoebe) are here synonymised with Stoebe. The main morphological synapomorphy for this enlarged concept of Stoebe is the aggregation of the tiny capitula into conflorescences with varying degrees of complexity and congestion. The proposed taxonomy for the Stoebe clade comprises just four genera: Amphiglossa, Muscosomorphe, Pterothrix, and Stoebe. We present the new combinations, keys and generic descriptions, as well as keys to the species.

Coniocybe Ach. Revisited.

Calicioids form a research field that has encompassed ascomycetous fungi with stalked ascomata similar to those of the lichen genus Calicium. Early generic circumscriptions of calicioid lichens and fungi were mainly based on morphological and secondary chemistry information. After the introduction of molecular data, taxonomy in the group has been reconsidered. Here, based on a broad geographical sampling, Coniocybe Ach. was revised using molecular and morphological features. Three loci (ITS, LSU and rpb1) were compared to infer its phylogenetic position, and a total of 52 new sequences (14 ITS, 24 LSU and 14 rpb1) were produced. Apart from its type C. furfuracea, Coniocybe was revised and emended to also include C. brachypoda and C. confusa. In addition, a new species, Coniocybe eufuracea, was described, and a key to the species of Coniocybe was provided.

Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae)

The genus Andropogon sensu lato is known to be polyphyletic. Accordingly, we here adjust part of the classification of the genus to reflect its evolutionary history and morphological diversity. A plastome phylogeny including 20 new plastome sequences confirms a well-supported clade of species broadly corresponding to Andropogon section Leptopogon. Morphological diversity was assessed across Andropogon sensu lato using specimens held at the K, MO, and A/GH herbaria, GrassBase, and photographs of spikelet pairs, with an emphasis on identifying members of this clade and their distinguishing features. The genus Anatherum is here reestablished, expanded to incorporate 45 of the 131 of Andropogon sensu lato species worldwide, and described and illustrated. Five species names in Anatherum are reinstated and new combinations are made for 40 species and one subspecies. Anatherum is most common and diverse in the Americas but also commonly found across Africa. Few species occur in Europe or Asia. Anatherum inflorescences generally have 2 branches, linear and slender internodes and pedicels with long trichomes, small elliptic to lanceolate spikelets, and flat to concave 2-keeled lower glumes with no intercarinal veins visible. Generic circumscription in this group is complicated by its polyploid history and limited understanding of the relationship between genomic composition and key morphological characters. Five species of doubtful generic affiliation are listed for future analysis.

Paraphyly and cryptic diversity unveils unexpected challenges in the “naked lichens” (Calvitimela, Lecanoromycetes, Ascomycota)

Molecular phylogenetics has revolutionized the taxonomy of crustose lichens and revealed an extensive amount of cryptic diversity. Resolving the relationships between genera in the crustose lichen family Tephromelataceae has proven difficult and the taxon limits within the genus Calvitimela are only partly understood. In this study, we tested the monophyly of Calvitimela and investigated phylogenetic relationships at different taxonomic levels using an integrative taxonomic approach. We performed a global sampling of all species currently assigned to Calvitimela and conducted additional sampling of C. melaleuca sensu lato across Norway. We included 108 specimens and produced more than 300 sequences from five different loci (ITS, LSU, MCM7, mtSSU, TEF1-α). We inferred phylogenetic relationships and estimated divergence times in Calvitimela. Moreover, we analyzed chemical and morphological characters to test their diagnostic values in the genus. Our molecular phylogenetic results show evolutionarily old and deeply divergent lineages in Calvitimela. The morphological characters are overlapping between divergent subgenera within this genus. Chemical characters, however, are largely informative at the level of subgenera, but are often homoplastic at the species level. The subgenus Calvitimela is found to include four distinct genetic lineages. Detailed morphological examinations of C. melaleuca s. lat. reveal differences between taxa previously assumed to be morphologically cryptic. Furthermore, young evolutionary ages and signs of gene tree discordance indicate a recent divergence and possibly incomplete lineage sorting in the subgenus Calvitimela. Phylogenetic analysis and morphological observations revealed that C. austrochilensis and C. uniseptata are extraneous to Calvitimela (Tephromelataceae). We also found molecular evidence supporting C. septentrionalis being sister to C. cuprea. In the subgenus Severidea, one new grouping is recovered as a highly supported sister to C. aglaea. Lastly, two fertile specimens were found to be phylogenetically nested within the sorediate species C. cuprea. We discuss the need for an updated classification of Calvitimela and the evolution of cryptic species. Through generic circumscription and species delimitation we propose a practical taxonomy of Calvitimela.

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution.

The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

A generic monograph of the Hyacinthaceae subfamily Urgineoideae

Taxonomy and systematics and specifically the generic circumscription of the Hyacinthaceae subfamily Urgineoideae have been a matter of controversy in recent decades. Widely contrasting taxonomic treatments have been proposed, ranging from systems comprising only two genera (including a morphologically very variable Drimia covering nearly the whole subfamily) to about 20 genera based mainly on preliminary phylogenetic studies supporting recognition of traditionally accepted and morphologically distinct genera such as Litanthus, Schizobasis, Tenicroa, and Thuranthos. All previous studies covered only a limited diversity and distribution of the subfamily, precluding comprehensive insight into the evolution of the diversity within the subfamily. Based on detailed morphological, phylogenetic, and biogeographic studies in Urgineoideae, covering its whole distribution range and most of the currently known species, we present a new taxomic treatment of the subfamily focusing on the circumscription of genera. Our analyses revealed 31 phylogenetic lineages corroborating unique syndromes of morphological characters linked to well-defined biogeographic patterns. These lineages are interpreted as well-defined genera. An identification key to the genera is provided to facilitate further taxonomic work in Urgineoideae and morphological descriptions of the accepted genera are presented. Two new genera, Spirophyllos gen. nov. and Zulusia gen. nov., are described to accommodate newly revealed phylogenetic lineages from northwestern and southeastern Africa, respectively. Further, a complete list of taxa included in the accepted genera is presented, providing details on typification, and the 50 new combinations, and one new name required to appropriately accomodate taxa in the new taxonomic treatment.

New species of Notocupes (Coleoptera: Archostemata) from the Middle Jurassic Daohugou beds, with discussion on the generic circumscription

Exquisitely preserved fossils from the Middle Jurassic Haifanggou Formation (the Daohugou beds; ~165 Ma) and mid-Cretaceous Burmese amber (~99 Ma) are studied to clarify the external morphology of Notocupes. Three new species from Daohugou are described as N. spinosus sp. nov., N. robustus sp. nov., and N. daohugouensis sp. nov. Our examination of specimens from Burmese amber does not support the division of Notocupes into Notocupes s.s. and Echinocups. Therefore we treat Echinocups syn. nov. as a junior synonym of Notocupes, and N. ohmkuhnlei comb. rev., N. neli comb. rev. and N. denticollis comb. rev. are returned to Notocupes from Echinocups.

Systematics and biogeography of Oleaceae subtribe Schreberinae, with recircumscription and revision of the Malagasy members

Abstract Clarifying generic circumscriptions in Oleaceae improves its complicated infrafamilial classification. Focusing on the small and disjunctly distributed subtribe Schreberinae, we use phylogenomic data from plastid and nuclear DNA from an extensive sampling to assess its phylogenetic patterns and biogeographic history. Results show paraphyly in the subtribe, with Comoranthus nested in Schrebera, leading us to synonymize these genera. Schrebera s.l. occurs in four major regions of the world, but its centre of origin remains uncertain, with three possible ancestral ranges identified. However, the diversification of this genus is estimated to have started in the Early Oligocene (c. 34 Mya), and its current distribution pattern is best explained by dispersal between landmasses rather than continental vicariance. Madagascar is the centre of diversity of Schrebera s.l., where ten endemic species, of which five are new, were recovered from analyses of morphological, molecular and ecoclimatic data. Therefore, a taxonomic treatment of the species from Madagascar and the Comoro Islands is presented. As currently circumscribed, Schrebera s.l., and thus the monogeneric subtribe, includes 16 species (one in South America, two in Southeast Asia, three in Africa, of which one is shared with Madagascar, and 11 in Madagascar and the Comoro Islands).

(2942) Proposal to conserve the name Dicksonia bipinnata (Dennstaedtia bipinnata, Mucura bipinnata) (Dennstaedtiaceae) with a conserved type

(2942) Proposal to conserve the name <i>Dicksonia bipinnata</i> (<i>Dennstaedtia bipinnata</i>, <i>Mucura bipinnata</i>) (<i>Dennstaedtiaceae</i>) with a conserved type

Rubiacearum Americanarum Magna Hama Pars L: New Species, Combinations, and Notes for Some South American Genera of Dialypetalantheae (Former Condamineeae)

Review of Dialypetalantheae (formerly called Condamineeae; Rubiaceae) with capsular fruits in western South America has clarified the identities of several names in our current circumscriptions of these genera, discovered some new species, and found new specimens that shed light on some poorly known species. Here, updated generic circumscriptions and characterizations are outlined for Bathysa C. Presl, Elaeagia Wedd., Holtonia Standl., and Warszewiczia Klotzsch, with several species reclassified among them. Five new combinations are published here: B. grandis (Rusby) C. M. Taylor &amp; Maldonado is based on Malanea grandis Rusby; B. mollis (Rusby) C. M. Taylor &amp; Maldonado is based on E. mollis Rusby; B. subspicata (Standl.) C. M. Taylor is based on E. subspicata Standl.; E. ambigua (Standl.) Maldonado &amp; C. M. Taylor is based on W. ambigua Standl.; and H. microcarpa (Ruiz &amp; Pav.) C. M. Taylor is based on Macrocnemum microcarpum Ruiz &amp; Pav. Seven new species are described here: B. schunkei C. M. Taylor, from central Peru; E. homeieri C. M. Taylor, from Ecuador; Rustia delpreteana C. M. Taylor, from northern Colombia; R. ucayalina C. M. Taylor, from central Peru; Schizocalyx ecuadorensis C. M. Taylor, from northwestern Ecuador; S. magdalenae C. M. Taylor, from northern Colombia; and S. magnorum C. M. Taylor, from Bolivia. The typification of several names is clarified here: the types of E. utilis (Goudot) Wedd. and W. peltata Wedd. have been located, and lectotypes are designated here for Exostema (Pers.) Bonpl. sect. Pseudostemma DC., Elaeagia mariae Wedd., Elaeagia mollis Rusby, Elaeagia obovata Rusby, Malanea grandis Rusby, and W. cordata Spruce ex K. Schum. The identities of some additional names are clarified here: Chimarrhis goudotii Baill. and Sickingia myriantha Standl. are synonyms of H. microcarpa; Elaeagia glomiflora Standl. is a synonym of B. mollis; Ferdinandusa leucantha Standl. is a synonym of Agouticarpa isernii (Standl.) C. H. Perss.; and W. peltata Wedd. and W. cordata Spruce ex K. Schum. are separate species from W. coccinea (Vahl) Klotzsch.

Testing and using complete plastomes for authentication of medicinal Polygonatum species (Asparagaceae)

Polygonati Rhizoma, a traditional Chinese medicine important to the pharmaceutical and food industries, is frequently adulterated with morphologically similar congeneric species, posing quality and effectiveness issues for the products. Accordingly, the accurate and sensitive authentication of medicinal Polygonatum species is vital to the standardization of Polygonati Rhizoma products. In view of the difficulties in morphological analysis and the use of standard DNA barcodes for authentication of medicinal Polygonatum species, an alternative authentication method is needed. Based on inter- and intraspecies sampling, phylogenetic and genetic distance analyses were performed to evaluate the discriminative power of complete plastomes for the identification of Polygonatum species. The results indicate that the genetic criteria of complete plastomes are in good correspondence with species boundaries and therefore can be used for unambiguous identification of medicinal Polygonatum species and morphologically similar congeners, which verifies the theoretical prediction that the application of genome skimming to generate complete plastomes as molecular tags can serve as an effective and accurate method to detect whether Polygonati Rhizoma is adulterated with congeneric species. Additionally, in this study, a taxonomically well-curated and high-resolution reference plastome superbarcode library for Polygonatum was developed for the first time, providing a valuable genetic resource for the application of genome skimming to monitor and control the production and trade of Polygonati Rhizoma to guarantee the effectiveness of downstream products. The findings also provide new insights to clarify the taxonomic ambiguities of the generic circumscription of Polygonatum and Heteropolygonatum, as well as the species delimitation of Polygonatum cyrtonema, Polygonatum nodosum, and Polygonatum punctatum, which will contribute to proper exploitation and conservation of Polygonatum species.

A molecular phylogeny of Calenduleae (Asteraceae) supports the transfer of Dimorphotheca polyptera DC. to Osteospermum L.

• A novel phylogeny for the daisy tribe Calenduleae is presented. • The phylogeny is based on nuclear and plastid DNA sequences, and morphology. • Dimorphotheca polyptera is not a Dimorphotheca , despite having dimorphic fruits. • D. polyptera is transferred to Osteospermum under O. polypterum . • the genus Osteospermum now has a member with dimorphic fruits. Generic circumscription in the small daisy tribe Calenduleae has been unstable, with various authors recognising between three and twelve genera. Evaluating alternative generic circumscriptions is difficult since existing phylogenetic hypotheses are poorly sampled. We assemble a preliminary phylogenetic hypothesis for the tribe based on nuclear ribosomal and plastid trn L- trn F DNA sequences. We recover a monophyletic Garuleum Cass. sister to the remaining species of Calenduleae. An expanded circumscription of Osteospermum L. is supported, including the former genera Calendula L., Chrysanthemoides Fabr., Monoculus B. Nord., and Tripteris Less., although sampling remains sparse. The genus Dimorphotheca Vaill. ex Moench is recovered in its current, enlarged circumscription including Castalis Cass. and O . sect. Blaxium (Cass.) Norl. However, our analysis identifies D. polyptera DC. as being distant from the rest of Dimorphotheca and embedded within an ‘ Osteospermum sensu amplo clade’, a finding corroborated by the inclusion of additional accessions. We explore the morphological basis for this placement, and transfer D. polyptera to Osteospermum in order to maintain monophyly of Dimorphotheca .

(2929–2931) Proposals to conserve the names Dipterocarpoxylon with a conserved type against Hippocrateoxylon, Dryobalanoxylon against Naucleoxylon, and Shoreoxylon against Bredaea and Grewioxylon (fossil Dipterocarpaceae, Magnoliophyta)

(2929–2931) Proposals to conserve the names <i>Dipterocarpoxylon</i> with a conserved type against <i>Hippocrateoxylon</i>, <i>Dryobalanoxylon</i> against <i>Naucleoxylon</i>, and <i>Shoreoxylon</i> against <i>Bredaea</i> and <i>Grewioxylon</i> (fossil <i>Dipterocarpaceae</i>, <i>Magnoliophyta</i>)

Studies in the vascular flora of the southeastern United States. VIII

As part of ongoing efforts to understand, document, and conserve the flora of the southeastern United States, we make new combinations to accord with our generic taxonomy, name a new hybrid, re-recognize a species relegated to synonymy in recent decades, lectotypify and generally clarify nomenclatural issues in several genera, clarify taxonomy and distributions of species, and report important new and current distribution records. In Doellingeria (Asteraceae), we clarify the taxonomy and distribution of D. sericocarpoides and D. umbellata in the region. In Trilisa (Asteraceae), we summarize and clarify the taxonomy, name a new hybrid, and present a new key to the taxa in the genus. Species delimitation in Stillingia (Euphorbiaceae) has been controversial and unsettled in the region, and we examine the confused taxonomy and nomenclature of the genus in the southeastern United States, re-recognizing a species used by J.K. Small, but with an expanded circumscription and a clarification of various nomenclatural issues. We examine typification of Desmodium dillenii (Fabaceae) and its application to our modern understanding of the circumscription of taxa, recommending it be considered a junior synonym of Desmodium glabellum. In Juncus, we assign a lectotype for Juncus anthelatus, fixing its application. In Primulaceae, we discuss the delineation of genera in Lysimachieae, and take a middle path regarding lumping/splitting, supporting the recognition of traditional and monophyletic segregates Trientalis, Steironema, Anagallis, and Centunculus, while treating Lysimachia in a moderately broad sense, including Glaux and multiple subclades; in order to implement this taxonomy in the southeastern United states, we make a single new combination in Steironema. We also discuss generic circumscription in Selaginellaceae, and argue for the recognition at genus rank of six major clades, monophyletic, ancient, and morphologically recognizable; in order to apply this taxonomy in the southeastern United States, we make five new combinations in Bryodesma, Gymnogynum, and Stachygynandrum. Finally, we report important new records of locally, regionally, or globally rare species in North Carolina: Helanthium tenellum, Chenopodium berlandieri var. macrocalycium, Carex barrattii, Carex vestita, Eleocharis compressa var. compressa, Rhynchospora compressa, Rhynchospora sulcata, and Croton michauxii.

What is in a name? Scientific name changes of potentially poisonous plants and fungi in South Africa

Changes over the past five decades in the scientific names of some potentially poisonous plants and toxigenic fungi in South Africa are briefly reviewed. Some of the reasons why taxonomists change names are highlighted. In recent years, DNA sequencing data have contributed considerably towards establishing phylogenetic relationships among plants, often resulting in changes in generic circumscription and, consequently, the names of species. Philosophical differences between the phylogenetic and the evolutionary schools of plant classification are briefly explained as these may manifest as different classifications for the same group of plants. Although choice of classification remains the prerogative of the end-user of plant names, in this review, the classifications for plants currently adopted by the South African National Biodiversity Institute (SANBI) in its online database, Plants of Southern Africa (POSA), were followed. Noteworthy generic changes include Pachystigma to Vangueria, Homeria to Moraea, and Urginia to Drimia. Following much controversy, the species native to southern Africa that were formerly treated as Acacia are now classified in either Vachellia or Senegalia, with the genus name Acacia being retained for the mainly Australian members of the group, the latter commonly known as wattles. Former southern African members of Acacia implicated in poisoning include Vachellia erioloba(camel thorn), Vachellia sieberiana var. woodii (paperbark thorn), and Senegalia caffra (common hook thorn).

Out of chaos: Phylogenomics of Asian Sonerileae

Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.

From the Mediterranean to the Pacific: re-circumscription towardsNotelaea s.l.and historical biogeography of a generic complex in Oleinae (Oleaceae)

AbstractTackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complex Nestegis, Notelaea, Osmanthus, Phillyrea and Picconia in subtribe Oleinae, we aim to elucidate their boundaries and relationships and to evaluate their biogeographic history in light of their peculiar disjunct distribution in the Macaronesian, Mediterranean and Pacific regions. On the basis of phylogenomic data from plastid and nuclear DNA of an extensive sampling, the results show six subclades in this generic complex, which are also geographical segregates found in Australia (Notelaea), Hawaiian Islands (Nestegis sandwicensis), Macaronesia (Phillyrea and Picconia), Mediterranean Region (Phillyrea), New Caledonia (Osmanthus section Notosmanthus) and New Zealand (Nestegis s.s.). Accounting for broad morphological overlaps in this clade, we recognize three genera (Phillyrea, Picconia and Notelaea s.l.), subsuming all Pacific taxa under Notelaea. Molecular dating and biogeographic analyses indicate that this clade originated in Eurasia during the Early Miocene (mean 23.2 Mya, 95% HPD: 23.8–14.7). Finally, dispersal (rather than continental vicariance) is probably the main explanation for the global, disjunct distribution of this group, with island-hopping and local extinction as the hallmarks of its evolutionary history.