Boreotropical range expansion and long-distance dispersal explain two amphi-Pacific tropical disjunctions in Sabiaceae

Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)

Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events.

The evolutionary history of bees in time and space

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.

Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean -insights into divergence modes of pantropical flora

There are about 140 species of Callicarpa L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for Callicarpa, derived from more inclusive taxonomic samplings, and employing data on both two-nuclear and eight-chloroplast regions. To address time and patterns of diversification in Callicarpa, we conducted divergence time and biogeographic analyses, and inferred shifts in the distribution areas across the phylogenetic clades. Our phylogenetic results show that Callicarpa is monophyletic with respect to the groups considered, and eight well-supported primary clades were discerned in the combined analyses. Our estimates indicated that the crown group of Callicarpa originates around the Late-Eocene (ca. 36.23 Ma) and diversification within most clades is concentrated in the Miocene and continued to the Pleistocene. In addition, our biogeographic analyses suggested that the probable ancestor of the Callicarpa crown clade originated in East Asia and Southeast Asia. Multiple dispersal and vicariance events contributed to the current distribution of the taxa. Furthermore, this genus expanded eastward out of East and Southeast Asia to the New World by long-distance dispersal, which inspired us to better understand the amphi-Pacific disjunct distribution.

Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae)

The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.

Phylogenomic analyses of Camellia support reticulate evolution among major clades

Camellia (Theaceae) is a morphologically highly diverse genus of flowering plants and includes many famous species with high economic value, and the phylogeny of this genus is not fully resolved. We used 95 transcriptomes from 87 Camellia species and identified 1481 low-copy genes to conduct a detailed analysis of the phylogeny of this genus according to various data-screening criteria. The results show that, very different from the two existing classification systems of Camellia, 87 species are grouped into 8 main clades and two independent species, and that all 8 clades except Clade 8 were strongly supported by almost all the coalescent or concatenated trees using different gene subsets. However, the relationships among these clades were weakly supported and different from analyses using different gene subsets; furthermore, they do not agree with the phylogeny from chloroplast genomes of Camellia. Additional analyses support reticulate evolution (probably resulting from introgression or hybridization) among some major Camellia lineages, providing explanation for extensive gene tree conflicts. Furthermore, we inferred that together with the formation of East Asian subtropical evergreen broad-leaved forests, Camellia underwent a radiative divergence of major clades at 23 ∼ 19 Ma in the late Miocene then had a subsequent species burst at 10 ∼ 5 Ma. Principal component and cluster analyses provides new insights into morphological changes underlying the evolution of Camellia and a reference to further clarify subgenus and sections of this genus. The comprehensive study here including a nuclear phylogeny and other analyses reveal the rapid evolutionary history of Camellia.

Complete chloroplast genomes of 11 Sabia samples: Genomic features, comparative analysis, and phylogenetic relationship

The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate identification and refinement of taxonomic relationships in this genus. In this study, chloroplast genomes of 11 samples of the genus Sabia were assembled and analyzed. These chloroplast genomes showed a typical quadripartite structure and ranged in length from 160,956 to 162,209 bp. The structure of the genomes was found to be relatively conserved, with 130 genes annotated, including 85 coding genes, 37 tRNA genes, and eight rRNA genes. A total of 78-98 simple sequence repeats and 52-61 interspersed repeats were detected. Sequence alignment revealed 11 highly variable loci in chloroplast genomes. Among these loci, ndhF-ndhD achieved a remarkably higher resolution than the other regions. In addition, phylogenetic analysis indicated that Sect. Pachydiscus and Sect. Sabia of Sabia did not form two separate monophyletic groups. The divergence time calculated based on the Reltime method indicated that the evolutionary branches of Sabia and Meliosma started to form approximately 85.95 million years ago (Mya), and the species within Sabia began to diverge approximately 7.65 Mya. In conclusion, our study provides a basis for comprehensively exploring the phylogenetic relationships of Sabia. It also provides a methodological basis and data support for establishing a standardized and scientific identification system for this genus.

Plastome phylogenomics and biogeography of the subfam. Polygonoideae (Polygonaceae)

Polygonaceae has a complex taxonomic history, although a few studies using plastid or nuclear DNA fragments have explored relationships within this family, intrafamilial relationships remain controversial. Here, we newly sequenced and annotated 17 plastomes representing 12 genera within Polygonaceae. Combined with previously published data, a total of 49 plastomes representing 22/46 Polygonaceae genera and 16/20 Polygonoideae genera were collected to infer the phylogeny of Polygonaceae, with an emphasis on Polygonoideae. Plastome comparisons revealed high conservation within Polygonoideae in structure and gene order. Phylogenetic analyses using both Maximum Likelihood and Bayesian methods revealed two major clades and seven tribes within Polygonoideae. BEAST and S-DIVA analyses suggested a Paleocene origin of Polygonoideae in Asia. While most genera of Polygonoideae originated and further diversified in Asia, a few genera experienced multiple long-distance dispersal events from Eurasia to North America after the Miocene, with a few dispersal events to the Southern Hemisphere also being detected. Both ancient vicariance and long-distance events have played important roles in shaping the current distribution pattern of Polygonoideae.

Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

BACKGROUND

The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae).

RESULTS

Our plastid tree topologies were robust to analyses based on different plastid regions and different strategies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae comprised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversification rates of tribe Perseeae accelerated twice in the late Miocene.

CONCLUSIONS

Our findings suggest that the intensified precipitation in East Asia in the early Miocene may have facilitated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late Miocene, species assembly and diversification within the EBLFs had become rapid.

Fossil Leaves of Meliosma (Sabiaceae) With Associated Pollen and a Eupodid Mite From the Eocene of Maoming Basin, South China

A first occurrence of the genus Meliosma (Sabiaceae) is reported from the upper Eocene of the Maoming Basin of South China. This fossil is one of the oldest reliable records of the genus within its modern center of diversity. Fossil leaves are assigned to a new species, Meliosma eosinica sp. nov. based on leaf morphology and epidermal characters. The leaf epidermal anatomy of fossil Meliosma is illustrated for the first time. We also provide the first SEM observation of pollen grains associated with Meliosma. This study also documents an occurrence of mites within the leaf domatia previously unknown from the fossil record. We presume that the studied mite belongs to the superfamily Eupodoidea (Arthropoda), and probably the family Eupodidae, which comprises very small soft-bodied cosmopolitan mites occupying a wide range of terrestrial habitats. Additionally, we analyze the damage types on the fossil leaves of Meliosma. They exhibit exclusively external foliage feeding damage caused by arthropods and traces of probable fungal infection. A review of currently known fossil occurrences of leaves, fruits, and wood of Meliosma provides evidence for the geological and geographical distribution of the genus.

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)

Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong support for a Boreotropical origin of the family with contrasting evolutionary trajectories between the temperate subfamily Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae rapidly evolved frost tolerance when the global climate shifted to ice-house conditions from the Oligocene, with diversification at high latitudes especially in Europe and Asia during the Miocene. Subsequent range contraction at high latitudes and high levels of extinction in Europe driven by global cooling led to the current regional disparity in species diversity. Engelhardioideae showed temperature conservatism while adapting to increased humidity, tracking tropical climates to low latitudes since the middle Eocene with comparatively little diversification, perhaps due to high competition in the tropical zone. The biogeographic history of Juglandaceae shows that the North Atlantic land bridge and Europe played more critical roles than previously thought in linking the floras of East Asia and North America, and showcases the complex interplay among climate change, niche evolution, dispersal, and extinction that shaped the modern disjunct pattern of species richness in temperate woody plants. [Boreotropical origin; climatic niche evolution; disjunct distribution; dispersal; diversity anomaly; extinction; Juglandaceae.].

A dated phylogeny of Lardizabalaceae reveals an unusual long-distance dispersal across the Pacific Ocean and the rapid rise of East Asian subtropical evergreen broadleaved forests in the late Miocene

Temperate South American-Asian disjunct distributions are the most unusual in organisms, and challenging to explain. Here, we address the origin of this unusual disjunction in Lardizabalaceae using explicit models and molecular data. The family (c.40 species distributed in ten genera) also provides an opportunity to explore the historical assembly of East Asian subtropical evergreen broadleaved forests, a typical and luxuriant vegetation in East Asia. DNA sequences of five plastid loci of 42 accessions representing 23 species of Lardizabalaceae (c. 57.5% of estimated species diversity), and 19 species from the six other families of Ranunculales, were used to perform phylogenetic analyses. By dating the branching events and reconstructing ancestral ranges, we infer that extant Lardizabalaceae dated to the Upper Cretaceous of East Asia and that the temperate South American lineage might have split from its East Asian sister group at c. 24.4 Ma. A trans-Pacific dispersal possibly by birds from East Asia to South America is plausible to explain the establishment of the temperate South American-East Asian disjunction in Lardizabalaceae. Diversification rate analyses indicate that net diversification rates of Lardizabalaceae experienced a significant increase around c. 7.5 Ma. Our findings suggest that the rapid rise of East Asian subtropical evergreen broadleaved forests occurred in the late Miocene, associated with the uplift of the Tibetan Plateau and the intensified East Asian monsoon, as well as the higher winter temperature and atmospheric CO₂ levels.

Biogeographic diversification of Mahonia (Berberidaceae): Implications for the origin and evolution of East Asian subtropical evergreen broadleaved forests

The subtropical evergreen broadleaved forests (EBLFs) inhabit large areas of East Asia and harbor rich biodiversity and high endemism. However, the origin and evolution of biodiversity of East Asian subtropical EBLFs remain poorly understood. Here, we used Mahonia (Berberidaceae), an eastern Asian-western North American disjunct evergreen genus, to obtain new insights into the historical assembly of this biome. We present the most comprehensive phylogenetic analysis of Mahonia do date based on six nuclear and plastid loci. Using the phylogenetic framework, we estimated divergence times, reconstructed ancestral ranges, inferred evolutionary shift of habitats, and estimated diversification rates. Mahonia and each of its two groups (Orientales and Occidentales) are strongly supported as monophyletic. Mahonia originated in western North America during the late Eocene (c. 40.41 Ma) and subsequently dispersed into East Asia prior to the early Oligocene (c. 32.65 Ma). The North Atlantic Land Bridge might have played an important role in population exchanges of Mahonia between East Asia and western North America. The western North American Occidentales began to diversify in summer-dry climates and open landscapes in the early Miocene, whereas the eastern Asian Orientales began to diversify in subtropical EBLFs in the early Miocene and furthermore had a rapid lineage accumulation since the late Miocene. The net diversification rate of Mahonia in eastern Asia appeared to be higher than that in western North America, which is ascribed to lower extinction rates and ecological opportunity. Our findings suggest that western North America is a source of biodiversity of East Asian subtropical EBLFs. This biome in eastern Asia began to rise in the early Miocene and further diversified in the late Miocene, driven by the intensifying East Asian summer monsoon during these two periods.

Freezing and water availability structure the evolutionary diversity of trees across the Americas

The historical course of evolutionary diversification shapes the current distribution of biodiversity, but the main forces constraining diversification are still a subject of debate. We unveil the evolutionary structure of tree species assemblages across the Americas to assess whether an inability to move or an inability to evolve is the predominant constraint in plant diversification and biogeography. We find a fundamental divide in tree lineage composition between tropical and extratropical environments, defined by the absence versus presence of freezing temperatures. Within the Neotropics, we uncover a further evolutionary split between moist and dry forests. Our results demonstrate that American tree lineages tend to retain their ancestral environmental relationships and that phylogenetic niche conservatism is the primary force structuring the distribution of tree biodiversity. Our study establishes the pervasive importance of niche conservatism to community assembly even at intercontinental scales.

Phylogeny and biogeography of Pachygoneae (Menispermaceae), with consideration of the boreotropical flora hypothesis and resurrection of the genera Cebatha and Nephroia

The tribe Pachygoneae consists of four genera with about 40 species, primarily distributed in tropical and subtropical Asia and America, also in Australasia and Africa. This tribe presents an ideal model to investigate the origin of the tropical and subtropical amphi-Pacific disjunction pattern. More specifically, it allows us to test whether the tropical lineages diverged earlier than the subtropical ones during the fragmentation of the boreotropical flora. In this study, we reconstructed the phylogeny of Pachygoneae using five plastid (rbcL, atpB, matK, ndhF, trnL-F) and one nuclear (26S rDNA) DNA regions. Our results indicate that Pachygoneae is not monophyletic unless Cocculus pendulus and Cocculus balfourii are excluded. We resurrected the genus Cebatha to include these two species and established a new tribe for this genus. Within Pachygoneae, the species of Cocculus are distributed in three different clades, among which two are recognized as two distinct genera, Cocculus s.str. and Nephroia resurrected, and one species is transferred into Pachygone. Our molecular dating and ancestral area reconstruction analyses suggest that Pachygoneae began to diversify in tropical Asia around the early-middle Eocene boundary (c. 48 Ma) and expanded into the New World by c. 44 Ma. In the New World, tropical Hyperbaena originated in the late Eocene (c. 40 Ma), whereas the subtropical Cocculus carolinus and Cocculus diversifolius originated later, in the early Oligocene (c. 32  Ma). These two timings correspond with the two climatic cooling intervals, which suggests that the formation and breakup of the boreotropical floral may have been responsible for the amphi-Pacific disjunct distribution within Pachygoneae. One overland migration event from Asia into Australasia appears to have occurred in the early to late Miocene.

Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution

Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.