Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

Cretaceous and Paleocene fossils reveal an extinct higher clade within Cornales, the dogwood order

PREMISE

Characterization and phylogenetic integration of fossil angiosperms with uncertain affinities is relatively limited, which may obscure the diversity of extinct higher taxa in the flowering plant tree of life. The order Cornales contains a diversity of extinct taxa with uncertain familial affinities that make it an ideal group for studying turnover in angiosperms. Here, we describe a new extinct genus of Cornales unassignable to an extant family and conduct a series of phylogenetic analyses to reconstruct relationships of fossils across the order.

METHODS

Two permineralized endocarps were collected from the Cedar District Formation (Campanian, 82-80 Ma) of Sucia Island, State of Washington, United States. Fossils were sectioned with the cellulose acetate peel technique and incorporated into a morphological dataset. To assess the utility of this dataset to accurately place taxa in their respective clades, we used a series of phylogenetic pseudofossilization analyses. We then conducted a total-evidence analysis and a scaffold-based approach to determine relationships of fossils.

RESULTS

Based on their unique combination of characters, the fossils represent a new genus, Fenestracarpa washingtonensis gen. nov. et sp. nov. Pseudofossilization analyses indicate that our morphological dataset can be used to accurately recover taxa at the major clade to family level, generally with moderate to high support. The total-evidence and scaffold-based analyses recovered Fenestracarpa and other fossil genera in an entirely extinct clade within Cornales.

CONCLUSIONS

Our findings increase the reported diversity of extinct Cornales and indicate that the order's initial radiation likely included the divergence of an extinct higher clade that endured the end-Cretaceous Mass extinction but perished during the Cenozoic.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Cornus hongkongensis Hemsl. 1888 (Cornaceae)

Cornus hongkongensis Hemsl. 1888, native to Hong Kong, belongs to the subgenus Syncarpea within the Cornus genus of the Cornaceae family. The complete chloroplast genome of C. hongkongensis spans 156,954 bp, comprising four subregions: a large single-copy region (86,290 bp), a small single-copy region (18,394 bp), and a pair of inverted repeats (26,135 bp). Within the chloroplast genome of C. hongkongensis, we identified 113 unique genes, including 80 protein-encoding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome of 30 related taxa of the Cornus genus indicates that C. hongkongensis has not formed a monophyletic lineage. Analyses of sequence divergence found three intergenic regions including rps19-rpl22, ccsA-ndhD, and atpH-atpI, exhibiting a high degree of variations. The first chloroplast genome of C. hongkongensis was reported in this work contributes to the enrichment of genomic data for the genus Cornus.

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Plastid phylogenomics of the tribe potentilleae (Rosaceae)

The tribe Potentilleae comprises approximately 1700 species in 13 genera, making it one of the largest of the 16 tribes in Rosaceae. Our understanding of the composition and relationships among members of Potentilleae has advanced dramatically with the application of molecular markers in the last two decades. Yet there is still much work remaining toward a robust phylogenetic framework for the entire Potentilleae and a comprehensive genus-level dating framework for the tribe. The goals of the present study were to establish a phylogenetic framework for Potentilleae, infer the origin and diversification of the tribe using a temporal framework, and explore the taxonomic implications in light of the updated phylogenetic framework. We used the plastome sequences from 158 accessions representing 139 taxa covering all 13 recognized genera of the tribe to reconstruct the Potentilleae phylogeny. High phylogenetic resolution was recovered along the Potentilleae backbone. Two major clades were recovered within Potentilleae, corresponding to the two subtribes Fragariinae and Potentillinae. Within Fragariinae, two subclades were recovered. In one subclade, Sibbaldia sensu stricto is sister to a clade containing Sibbaldianthe, Comarum, Farinopsis, and Alchemilla sensu lato. In the other subclade, Fragaria is sister to a clade comprising Chamaerhodos, Chamaecallis, Drymocallis, Dasiphora, and Potaninia. Within Potentillinae, Argentina is sister to Potentilla sensu stricto. Within Potentilla sensu stricto, clade Himalaya is sister to Alba, and the Himalaya-Alba clade together is sister to a clade comprising Reptans, Potentilla ancistrifolia Bunge, Fragarioides, Ivesioid, and Argentea. Divergence time estimates indicated that tribe Potentilleae originated during the middle Eocene, and subtribes Fragariinae and Potentillinae diverged around the Eocene-Oligocene transition, and divergence times dated for Potentilleae genera ranged from the early Miocene to the late Pleistocene.

First record of the genus Camptotheca (Nyssaceae) in Vietnam and the lectotypification of C.acuminata

As a primary source of anticancer camptothecin, Camptotheca (Nyssaceae) is an economically valuable genus and has long been recorded as endemic to China. Here, Camptotheca is reported as a new record to the flora of Vietnam with the discovery of a wild population of C.acuminata from Lai Chau Province of northern Vietnam. Based on the consultation of relevant literature and type specimens of C.acuminata, a lectotype of the species is designated. Photographic illustrations, morphological description and a distribution map of C.acuminata is provided, and a key to all known species of Nyssaceae in Vietnam is presented, too.

Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships

The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.

Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification

Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation probably accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.

A complete genus-level phylogeny reveals the Cretaceous biogeographic diversification of the poppy family

Angiosperms, a trigger for the Cretaceous Terrestrial Revolution (KTR), underwent a rapid expansion and occupied all the environments during the Mid-Upper Cretaceous. Yet, Cretaceous biogeographic patterns and processes underlying the distribution of angiosperm diversity in the Northern Hemisphere are still poorly known. Here, we elucidated the biogeographic diversification of the angiosperm family Papaveraceae, an ancient Northern Hemisphere clade characterized by poor dispersal ability and high level of regional endemism. Based on both plastome and multi-locus datasets, we reconstructed a robust time-calibrated phylogeny that includes all currently recognized 45 genera of this family. Within the time-calibrated phylogenetic framework, we conducted 72 biogeographic analyses by testing the sensitivity of uncertainties of area delimitation, maxarea constraints, and the parameters of the model, i.e., j (describing jump-dispersal events) and w (modifying dispersal multiplier matrices), to ancestral range estimations. We also inferred ancestral habitat and ecological niches. Phylogenetic analyses strongly support Papaveraceae as monophyletic. Pteridophylloideae is strongly supported as sister to Hypecoideae-Fumarioideae. Our results indicate that the j parameter and number of predefined areas strongly affect ancestral range estimates, generating questionable ancestral ranges, whereas maxarea constraint and w parameter have no effect and improve model fit. After accounting for these uncertainties, our results indicate that Papaveraceae differentiated in Asian wet forests during the Lower Cretaceous and subsequently occupied the Asian and western North American arid and open areas. Three dispersals from Asia to western North America via the Bering land bridge occurred in the Mid-Upper Cretaceous, largely in agreement with the KTR. Habitat shift and ecological niche divergence resulted in the subsequent disjunctions between Asia and western North America. These findings suggest that the interplay of range expansion and niche divergence-driven vicariance might have shaped Cretaceous biogeographic patterns of angiosperms with Papaveraceae-like ecological requirements and dispersal abilities in the Northern Hemisphere, hence contributing to the knowledge on the geographic expansion of angiosperms during the KTR.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data

PREMISE

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group.

METHODS

We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis.

RESULTS

A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode.

CONCLUSIONS

Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.

Phylogenomics and the flowering plant tree of life

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

Comparative chloroplast genomics provides insights into the genealogical relationships of endangered Tetraena mongolica and the chloroplast genome evolution of related Zygophyllaceae species

A comprehensive understanding of genetic background for rare species will provide an important theoretical basis for the future species management, monitoring and conservation. Tetraena mongolica is restrictedly distributed in the western Ordos plateau of China and has been listed as a national protected plant. We generated 13 chloroplast (cp) genomes of T. mongolica (size range of 106,062-106,230 bp) and conducted a series of comparative analyses of six Zygophyllaceae cp genomes. T. mongolica cp genome exhibited a quadripartite structure with drastically reduced inverted repeats (IRs, 4,315 bp) and undergone the loss of a suit of ndh genes and a copy of rRNAs. Furthermore, all the T. mongolica populations were divided into two genetic groups based on complete cp phylogenomics. In addition, notably variable genome size, gene order and structural changes had been observed among the six Zygophyllaceae cp genomes. Overall, our findings provide insights into the cp genome evolution mode and intraspecific relationships of T. mongolica, and provide a molecular basis for scientific conservation of this endangered plant.

The Phylogenetic Significance of Fruit Structures in the Family Cornaceae of China and Related Taxa

The fruit morphological structures of the Cornaceae of China and related taxa were studied using the wax GMA semi-thin section method and other methods to identify characters useful in delimiting clades circumscribed in previous molecular phylogenetic studies. Maximum parsimony analyses of 27 fruit structural characters resulted in a generally poorly resolved strict consensus tree, yet one whose major clades matched those revealed previously. Cornaceae of China and related taxa are recognized in four significant clades with the following fruit structural features: (1) Helwingia, fruits lack trichome, the abdominal vascular bundles are close to the endocarp, and the endocarp sclereid is elongated; (2) Aucuba, single-cell lanceolate trichomes, pericarp without secretory structure; (3) Torricellia, polygon and elongated sclereids in the endocarp, pericarp without crystal and tannin; and (4) Cornus sensu lato, the trichome is T-shaped, the abdominal ventral bundle is absent, and the endocarp sclereid is nearly round. In Cornus sensu lato, this document supported that the cornelian cherries (CC, subg. Cornus) and the big-bracted dogwoods (BB, subg. Syncarpea) are sister groups. The dwarf dogwoods (DW, subg. Arctocrania) are sister to them, and the blue- or white-fruited dogwoods (BW, subg. Kraniopsis, subg. Yinquania, and subg. Mesomora) are the base of the Cornus sensu lato clade. The number of cell layers of endocarps and the types of crystals afford sound evidence for identifying their relationship. This study indicated that the fruit structures of Cornaceae might provide morphological and anatomical evidence for molecular phylogeny.

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.

Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae)

Inferring accurate biogeographic history of plant taxa with an East Asia (EA)-North America (NA) is usually hindered by conflicting phylogenies and a poor fossil record. The current distribution of Chamaecyparis (false cypress; Cupressaceae) with four species in EA, and one each in western and eastern NA, and its relatively rich fossil record, make it an excellent model for studying the EA-NA disjunction. Here we reconstruct phylogenomic relationships within Chamaecyparis using > 1400 homologous nuclear and 61 plastid genes. Our phylogenomic analyses using concatenated and coalescent approaches revealed strong cytonuclear discordance and conflicting topologies between nuclear gene trees. Incomplete lineage sorting (ILS) and hybridization are possible explanations of conflict; however, our coalescent analyses and simulations suggest that ILS is the major contributor to the observed phylogenetic discrepancies. Based on a well-resolved species tree and four fossil calibrations, the crown lineage of Chamaecyparis is estimated to have originated in the upper Cretaceous, followed by diversification events in the early and middle Paleogene. Ancestral area reconstructions suggest that Chamaecyparis had an ancestral range spanning both EA and NA. Fossil records further indicate that this genus is a relict of the "boreotropical" flora, and that local extinctions of European species were caused by global cooling. Overall, our results unravel a complex evolutionary history of a Paleogene relict conifer genus, which may have involved ILS, hybridization and the extinction of local species.

Plastid phylogenomic insights into relationships of all flowering plant families

BACKGROUND

Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.

RESULTS

Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.

CONCLUSIONS

We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography

Alismataceae, an ancient lineage of monocots, has attracted attention due to its complex evolutionary history, ornamental value, and ecological role. However, the phylogenetic relationships and evolutionary history of the family have not been conclusively resolved. Here, we constructed the first complete genus-level plastid phylogeny of Alismataceae by using 78 genes and updated the historical biogeography based on the phylogenomic tree. Our results divide the Alismataceae into three major clades with robust support values; one clade comprises the former Limnocharitaceae, and the second clade includes the mainly temperate genera Alisma, Baldellia, Damasonium and Luronium, and the monotypic African genus Burnatia as a sister of the temperate genera. The remaining genera are either tropical or have some temperate species in addition to tropical ones, and they constitute the third major clade. Molecular dating and biogeographic analyses suggest that Alismataceae arose in Neotropical, West Palearctic, and Afrotropical regions during the Cretaceous, followed by the split into three main clades due to a combination of vicariance and dispersal events. Unlike earlier studies, we inferred that the mainly temperate clade likely originated from Afrotropical and West Palearctic regions during the Eocene. The most recent common ancestor of the other two clades lived in the Neotropical area during the Late Cretaceous. Long-distance dispersal and vicariance together seem to contribute to the transoceanic distribution of this family.

Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set

PREMISE

Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales.

METHODS

Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae.

RESULTS

We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL-III, a method statistically consistent with the multispecies coalescent model.

CONCLUSIONS

The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae-Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.

A New Pipeline for Removing Paralogs in Target Enrichment Data

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]

Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas

Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.

Genetic insights into the evolution of genera with the eastern Asia-eastern North America floristic disjunction: a transcriptomics analysis

PREMISE

Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia-eastern North America (EA-ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly.

METHODS

To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus.

RESULTS

No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species-rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions.

CONCLUSIONS

Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.

Hydrostachys flabellifera (Hydrostachyaceae), a new species from Madagascar

Hydrostachys flabellifera, a new species of Hydrostachyaceae found in a stream in Manandriana, Madagascar, is described and illustrated herein. It is similar to H. verruculosa and H. laciniata in morphology, but can be distinguished from them by its leaves with sparsely arranged, flabelliform and palmately parted emergences, obvious rachis and the pattern of segments arranged on the male bracts. Molecular phylogenetic analysis of the nuclear ribosomal internal transcribed spacer (ITS) dataset provides a robust support for it as a new species as well.

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

PREMISE

Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome.

METHODS

We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group.

RESULTS

We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications.

CONCLUSIONS

Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.