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PREMISE The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. METHODS Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%⁠) and 2333 genera (17%⁠). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.], This work was supported by grants from the Calleva Foundation and the Sackler Trust to the Plant and Fungal Trees of Life project at the Royal Botanic Gardens, Kew. Additional support was received from the Garfield Weston Foundation, as part of the Global Tree Seed Bank Programme.

Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothesis for Abildgaardieae using targeted sequencing data obtained with the Angiosperms353 enrichment panel for 50 species. We test whether recent taxonomic decisions made based on Sanger sequencing data are validated by our targeted sequencing data. Our results support subsuming the small African genus Nemum into the large genus Bulbostylis and subsuming the monotypic genus Crosslandia into the diverse genus Fimbristylis. Also, our results support the recent publication of the new genus Zulustylis for two African species previously placed in Fimbristylis. Furthermore, we investigate the phylogenetic placement of recently described tropical Australian endemic species of Actinoschoenus, which are recognized here as the new morphologically cryptic genus Scleroschoenus. Based on our phylogenetic hypothesis and supported by morphological data, we recognize the genus Abildgaardia. The placement in Abildgaardieae of two monotypic genera Nelmesia and Trichoschoenus, only known from the type collections from the Democratic Republic of Congo and Madagascar, respectively, are also discussed. New combinations and lectotypifications are made in Abildgaardia, Actinoschoenus, Arthrostylis and Scleroschoenus.

We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.

International audience; Premise To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. Methods We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. Conclusions High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

PREMISE: The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra-familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework. METHODS: Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using coalescence-based and concatenated methods. The clades recovered are discussed in light of both benchmark studies to identify synapomorphies and distributional evidence to underpin an updated infra-familial classification. KEY RESULTS: Coalescence-based and concatenated phylogenetic trees had identical topologies and node support, except for the placement of Melicoccus bijugatus Jacq. Twenty-one clades were recovered, which serve as the basis for a revised infra-familial classification. CONCLUSIONS: Twenty tribes are recognized in four subfamilies: two tribes in Hippocastanoideae, two in Dodonaeoideae, and 16 in Sapindoideae (no tribes are recognized in the monotypic subfamily Xanthoceratoideae). Within Sapindoideae, six new tribes are described: Blomieae Buerki & Callm.; Guindilieae Buerki, Callm. & Acev.-Rodr.; Haplocoeleae Buerki & Callm.; Stadmanieae Buerki & Callm.; Tristiropsideae Buerki & Callm.; and Ungnadieae Buerki & Callm. This updated classification provides a backbone for further research and conservation efforts on this family.

International audience; Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur’s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower and embryo characters plus anatomical and other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family‐wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. Additionally, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes and 10 subtribes and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae and Oreobolinae. This article is protected by copyright. All rights reserved.

Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations concordant with evolutionary history, we use increased taxonomic and genomic sampling to investigate phylogenetic relationships among Urera and associated genera. A cost-effective two-tier genome-sampling approach provides good phylogenetic resolution by using (i) a taxon-dense sample of Sanger sequence data from two barcoding regions to recover clades of putative generic rank, and (ii) a genome-dense sample of target-enrichment data for a subset of representative species from each well-supported clade to resolve relationships among them. The results confirm the polyphyly of Urera s.l. with respect to the morphologically distinct genera Obetia, Poikilospermum and Touchardia. Afrotropic members of Urera s.l. are recovered in a clade sister to the xerophytic African shrubs Obetia; and Hawaiian ones with Touchardia, also from Hawaii. Combined with distinctive morphological differences between Neotropical and African members of Urera s.l., these results lead us to resurrect the previously synonymised name Scepocarpus Wedd. for the latter. The new species epiphet Touchardia oahuensis T.Wells & A.K. Monro is offered as a replacement name for Touchardia glabra non H.St.John, and subgenera are created within Urera s.s. to account for the two morphologically distinct Neotropical clades. This new classification minimises taxonomic and nomenclatural disruption, while more accurately reflecting evolutionary relationships within the group.

Premise Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. Methods We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. Results For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. Conclusions The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.

Herbarium specimens have become a major source of information in molecular biodiversity research, framing the term "herbarium genomics". However, obtaining good DNA from old herbarium specimens is still a challenge. Currently, DNA extraction methods from old herbarium material often yield highly degraded and fragmented DNA. A number of studies have discussed such methods, especially how to avoid further DNA fragmentation. This study aims to compare different DNA extraction methods applied to old herbarium material from Veronica subg. Pseudolysimachium. One such method is a CTABbased DNA extraction followed by a clean-up with paramagnetic beads that is used in the Jodrell Laboratory, Royal Botanic Gardens Kew, UK. This method was compared to a modified NucleoSpin Plant II protocol, based on silica columns, as used at the Technical University Munich-Freising, which was already successfully used for extracting DNA from a Linnean type specimen. Further tests were conducted on the influence of incubation time on the CTAB DNA extraction protocol with a subsample of specimens. Our preliminary results suggest that CTAB DNA extraction might have some advantages in specific cases but also that silica column-based methods have fewer problems with contamination by polysaccharides and polyphenolic compounds. Regarding the incubation time, we did not observe a clear pattern, but we developed several ideas on how to proceed with tests to find an optimal DNA extraction protocol to deal with highly fragmented DNA. Taking practical considerations into account, the column-based method proves to be preferable, especially when trying to reduce the amount of leaf tissue used, but further modifications of both methods should be explored. Гербарні зразки стали важливим джерелом інформації для молекулярних досліджень біорізноманіття, і навіть виник термін "гербарна геноміка". Проте, отримання хороших зразків ДНК зі старих гербарних зразків все ще є складним завданням. На даний час методи екстракції ДНК зі старого гербарного матеріалу часто дозволяють отримати лише деградовану або фрагментовану ДНК. Такі методи обговорювалися у багатьох дослідженнях, зокрема, щодо вирішення проблеми подальшої фрагментації ДНК. Метою нашого дослідження було порівняння різних методів екстракції ДНК зі старих гербарних зразків представників Veronica subg. Pseudolysimachium. Один з цих методів – екстракція ДНК на основі CTAB (цетилтриметиламоній бромід або цетил-триметил-бромід амонію) з наступним очищенням за допомогою парамагнітних гранул, що використовується у Лабораторії Джодрелла у Королівському ботанічному саду К'ю (Велика Британія). Цей метод порівнювався з модифікованою методикою NucleoSpin Plant II на основі силікагелевих колонок, що використовувалася у Технічному університеті Мюнхен-Фрайзінг (Німеччина) і була успішно застосована для отримання ДНК з типового зразка гербарію К. Ліннея. Проводилися подальші тести з вибіркою зразків щодо впливу часу інкубації на методику виділення ДНК за допомогою CTAB. Наші попередні результати свідчать, що CTAB-метод екстракції ДНК може мати певні переваги у конкретних випадках, але також вказують на те, що методи на основі силікагелевих колонок мають менше проблем із забрудненням полісахаридами та поліфенольними сполуками. Ми не виявили певної закономірності щодо часу інкубації, але розробили декілька ідей про те, як рухатися далі з експериментами для виявлення оптимальної методики екстракції ДНК для зразків, що містять фрагментовану ДНК. З практичного погляду, метод на основі колонок виглядає кращим, особливо тоді, коли є потреба зменшити кількість тканини листків. Проте, слід розробляти подальші вдосконалені модифікації обох методів. Гербарные образцы стали важным источником информации для молекулярных исследований биоразнообразия; возник даже термин "гербарная геномика". Однако получение хороших образцов ДНК из старых гербарных образцов все еще является сложной задачей. В настоящее время методы экстракции ДНК из старого гербарного материала позволяют получить лишь деградированную или фрагментированную ДНК. Такие методы обсуждались во многих исследованиях, в частности, при решении проблемы дальнейшей фрагментации ДНК. Целью нашего исследования было сравнение различных методов экстракции ДНК из старых гербарных образцов представителей Veronica subg. Pseudolysimachium. Один из этих методов – экстракция ДНК на основе CTAB (цетилтриметиламмоний бромид или цетил-триметил-бромид аммония) с последующей очисткой с помощью парамагнитных гранул используется в Лаборатории Джодрелла в Королевском ботаническом саду Кью (Великобритания). Этот метод сравнивали с модифицированной методикой NucleoSpin Plant II на основе силикагелевих колонок, которая использовалась в Техническом университете Мюнхен-Фрайзинг (Германия) и была успешно применена для получения ДНК из типового образца гербария К. Линнея. Дальнейшие тесты проведены с выборкой образцов по влиянию времени инкубации на методику выделения ДНК с помощью CTAB. Наши предварительные результаты свидетельствуют о том, что CTAB-метод экстракции ДНК может обладать определенными преимуществами в конкретных случаях, но также указывают на то, что методы на основе силикагелевих колонок имеют меньше проблем с загрязнением полисахаридами и полифенольными соединениями. Мы не обнаружили определенной закономерности относительно времени инкубации, но разработали несколько идей о том, как двигаться дальше с экспериментами по выявлению оптимальной методики экстракции ДНК для образцов, содержащих фрагментированную ДНК. С практической точки зрения, метод на основе колонок является лучшим, особенно, когда необходимо уменьшить количество ткани листьев. Однако, следует разрабатывать дальнейшие усовершенствованные модификации обоих методов.

Buerki, S., T. Gallaher, T. Booth, G. Brewer, F. Forest, J.T. Pereira & M.W. Callmander (2016). Biogeography and evolution of the screw-pine genus Benstonea Callm & Buerki (Pandanaceae). Candollea 71: 217–229. In English, English abstract. This study investigates the biogeography, evolution and systematics of Benstonea Callm. & Buerki (Pandanaceae) based on six plastid DNA regions and 54 specimens representing 36 species (60% of species generic diversity). Our maximum likelihood and Bayesian phylogenetic inferences support the monophyly of Benstonea and its close relationship with the speciose Pandanus Parkinson. Benstonea is subdivided into three clades exhibiting contrasting species diversities. Clades I and II have seven species each, whereas most of the species diversity occurs in clade III with 21 species. None of the sections defined by Stone in Pandanus subgenus Acrostigma (Kurz) B.C. Stone (now Benstonea) are retrieved monophyletic by our analyses. Biogeographical inference supports the o...