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

Comparative diversification analyses of Hydrangeaceae and Loasaceae reveal complex evolutionary history as species disperse out of Mesoamerica

PREMISE

The movement of lineages into novel areas can promote ecological opportunity and adaptive radiation, leading to significant species diversity. Not all studies, however, have identified support for ecological opportunity associated with novel intercontinental colonizations. To gain key insights into the drivers of ecological opportunity, we tested whether intercontinental dispersals resulted in ecological opportunity using the Hydrangeaceae-Loasaceae clade, which has numerous centers of diversity across the globe.

METHODS

A time-calibrated phylogeny was reconstructed from four molecular markers. We tested for bursts of speciation rates followed by a decrease as expected phylogenetic patterns under an ecological opportunity model. Ancestral ranges were estimated using historical biogeographic analyses to examine the relationships of ancestral distributions and habitats with speciation and extinction rates.

RESULTS

Hydrangeaceae and Loasaceae originated in arid Mesoamerica, then dispersed into South America, Eurasia, and eastern North America. Six clades experienced increased diversification rates, but those increases were not associated with transitions into new continental areas. Mentzelia section Bartonia was the only clade that exhibited a burst of speciation followed by a decrease. Both families originated in arid environments and experienced multiple transitions into mesic and tropical environments, but Loasaceae experienced a higher speciation-to-extinction ratio than Hydrangeaceae in the western Nearctic.

CONCLUSIONS

Dispersal between continents did not trigger speciation rate shifts in Loasaceae and Hydrangeaceae. Instead, shifts occurred in regions inhabited by intrafamilial relatives and were likely driven by climate change in the Miocene, where species in drier microhabitats diversified into newly created habitats.

Out of and in East Asia: phylogeny, biogeography and diversification of Thalictroideae (Ranunculaceae) in the Northern Hemisphere

BACKGROUND AND AIMS

Understanding the biogeographical patterns and processes underlying the distribution of diversity within the Northern Hemisphere has fascinated botanists and biogeographers for over a century. However, as a well-known centre of species diversity in the Northern Hemisphere, whether East Asia acted as a source and/or a sink of plant diversity of the Northern Hemisphere remains unclear. Here, we used Thalictroideae, a subfamily widely distributed in the Northern Hemisphere with the majority of species in East Asia, to investigate the role of East Asia in shaping the biogeographical patterns of the Northern Hemisphere and to test whether East Asia acted as a museum or a cradle for herbaceous taxa.

METHODS

Based on six plastid and one nuclear DNA regions, we generated the most comprehensive phylogeny for Thalictroideae, including 217 taxa (~66 % species) from all ten of the currently recognized genera. Within this phylogenetic framework, we then estimated divergence times, ancestral ranges and diversification rates.

KEY RESULTS

The monophyletic Thalictroideae contains three major clades. All genera with more than one species are strongly supported as monophyletic except for Isopyrum, which is nested in Enemion. The most recent common ancestor of Thalictroideae occurred in East Asia in the late Eocene (~36 Mya). From the Miocene onwards, ≥46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ~10 Mya.

CONCLUSIONS

The biogeographical patterns of Thalictroideae support the 'out of and in East Asia' hypothesis, i.e. East Asia is both a source and a sink of biodiversity of the Northern Hemisphere. The global cooling after the middle Miocene Climatic Optimum, combined with the exposed land bridges owing to sea-level decline, might jointly have caused the bidirectional plant exchanges between East Asia and other Northern Hemisphere regions. East Asia serves as evolutionary museums and cradles for the diversity of Thalictroideae and probably for other herbaceous lineages.

Comparative case study of evolutionary insights and floral complexity in key early-diverging eudicot Ranunculales models

Famously referred to as "Darwin's abominable mystery," the rapid diversification of angiosperms over the last ~140 million years presents a fascinating enigma. This diversification is underpinned by complex genetic pathways that evolve and rewire to produce diverse and sometimes novel floral forms. Morphological innovations in flowers are shaped not only by genetics but also by evolutionary constraints and ecological dynamics. The importance of model organisms in addressing the long-standing scientific questions related to diverse floral forms cannot be overstated. In plant biology, Arabidopsis thaliana, a core eudicot, has emerged as a premier model system, with its genome being the first plant genome to be fully sequenced. Similarly, model systems derived from crop plants such as Oryza sativa (rice) and Zea mays (maize) have been invaluable, particularly for crop improvement. However, despite their substantial utility, these model systems have limitations, especially when it comes to exploring the evolution of diverse and novel floral forms. The order Ranunculales is the earliest-diverging lineage of eudicots, situated phylogenetically between core eudicots and monocots. This group is characterized by its exceptional floral diversity, showcasing a wide range of floral morphologies and adaptations that offer valuable insights into the evolutionary processes of flowering plants. Over the past two decades, the development of at least five model systems including, Aquilegia, Thalictrum, Nigella, Delphinium and Eschscholzia within the Ranunculales order has significantly advanced our understanding of floral evolution. This review highlights the conservation and divergence of floral organ identity programs observed among these models and discusses their importance in advancing research within the field. The review also delves into elaborate petal morphology observed in Aquilegia, Nigella, and Delphinium genera, and further discusses the contributions, limitations, and future research directions for Ranunculales model systems. Integrating these diverse models from the early-diverging eudicot order has enhanced our understanding of the complex evolutionary pathways that shape floral diversity in angiosperms, bridging the knowledge gaps essential for a comprehensive understanding of floral evolution.

Papaver recircumscribed: A review of neighbouring Papaveraceae genera, including Afropapaver nom. et stat. nov. and Oreomecon, a large, Arctic-Alpine genus

Papaveraceae tribus Papavereae includes an American and a mainly Eurasian group of genera. The latter is proposed here to include eight genera. Amongst these, the recently described genus Oreomecon is phylogenetically a sister group to Meconopsis, a genus from Himalaya and central China, which is reviewed here as including 95 species and 21 subspecies. By contrast, Oreomecon has a circumpolar northern alpine and Arctic distribution, including incompletely understood taxa, many threatened by climatic warming. Based on a review of literature and phylogenies, it is proposed here that Oreomecon includes 68 species and 29 subspecies. Oreomeconaurantiaca, O.cornwallisensis, O.keelei, O.ochotensis and O.uschakovii, 29 subspecies and four varieties are placed in Oreomecon here, 29 of these as recombinations, the remaining ones as nomenclatural novelties. A total of 21 existing Oreomecon names are placed into synonymy. The taxonomically challenging O.alpina group from Central Europe is treated as comprising three species, with the remaining entities positioned at the subspecies level pending further studies. The much-studied Nordic species O.radicata is treated with eight subspecies here, based on morphometric studies, whereas four accepted entities are provisionally recombined at the variety level. The name Papavertenellum and the basionyms of Oreomeconalborosea, O.alpinasubsp.corona-sancti-stephani, O.alpinasubsp.degenii, O.anomala, O.lapeyrouseanasubsp.endressii, O.lapponicasubsp.laestadiana and O.nivalis are lectotypified here. Two replacement names, Oreomeconalpinasubsp.markgrafiana and O.radicatasubsp.knabeniana, are introduced. Papaver, as currently understood, is recircumscribed here to represent four genera. The isolated sectionHorrida, from southern Africa, is raised to genus level with the new name Afropapaver and its only species is recombined as Afropapaveraculeatum. Papaversect.Californica from California and adjacent Mexico is treated as the genus Stylomecon. The name has been applied to one of the two species of this group and we now recombine the other one as S.crassifolia, based on an older basionym replacing Papavercalifornicum. Papavercambricum is accepted in its alternative position as the monotypic genus Parameconopsis. As reviewed here, Papaver comprises 59 species and 14 subspecies and is only the third-largest genus in the group. Based on the distribution of its closest relatives and oldest sections, it is hypothesised here that Papaver arose in the western Mediterranean. Its poricidal capsule dehiscence serves as an excellent adaptation to seed dispersal in open, arid environments, possibly explaining its later success in the Türkiye-Caucasus-Middle East area, where its diversity both at species and section level is highest.

The complete chloroplast genome sequence of Hypecoum erectum L. (Papaveraceae)

Hypecoum erectum L., a widespread species in northern Eurasia, is a valuable medicinal plant, but its chloroplast genome has not previously been reported. We determined its complete chloroplast genome using a high-throughput sequencing technique. Its total length was 169,241 bp, consisting of a large single-copy region of 93,301 bp and a small single-copy region of 17,316 bp, separated by a pair of inverted repeat regions of 29,312 bp. A total of 140 genes were annotated, including 91 protein coding genes, 41 tRNA genes, and eight rRNA genes. The phylogenetic analysis shows that H. erectum and H. zhukanum of the subfamily Hypecoideae are monophyletic with the highest support.

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.

Traditional multilocus phylogeny fails to fully resolve Palearctic ground squirrels (Spermophilus) relationships but reveals a new species endemic to West Siberia

Previous efforts to reconstruct evolutionary history of Palearctic ground squirrels within the genus Spermophilus have primarily relied on a single mitochondrial marker for phylogenetic data. In this study, we present the first phylogeny with comprehensive taxon sampling of Spermophilus via a conventional multilocus approach utilizing five mitochondrial and five nuclear markers. Through application of the multispecies coalescent model, we constructed a species tree revealing four distinct clades that diverged during the Late Miocene. These clades are 1) S. alaschanicus and S. dauricus from East Asia; 2) S. musicus and S. pygmaeus from East Europe and northwestern Central Asia; 3) the subgenus Colobotis found across Central Asia and its adjacent regions and encompassing S. brevicauda, S. erythrogenys, S. fulvus, S. major, S. pallidicauda, S. ralli, S. relictus, S. selevini, and S. vorontsovi sp. nov.; and 4) a Central/Eastern Europe and Asia Minor clade comprising S. citellus, S. taurensis, S. xanthoprymnus, S. suslicus, and S. odessanus. The latter clade lacked strong support owing to uncertainty of taxonomic placement of S. odessanus and S. suslicus. Resolving relationships within the subgenus Colobotis, which radiated rapidly, remains challenging likely because of incomplete lineage sorting and introgressive hybridization. Most of modern Spermophilus species diversified during the Early-Middle Pleistocene (2.2-1.0 million years ago). We propose a revised taxonomic classification for the genus Spermophilus by recognizing 18 species including a newly identified one (S. vorontsovi sp. nov.), which is found only in a limited area in the southeast of West Siberia. Employing genome-wide single-nucleotide polymorphism genotyping, we substantiated the role of the Ob River as a major barrier ensuring robust isolation of this taxon from S. erythrogenys. Despite its inherent limitations, the traditional multilocus approach remains a valuable tool for resolving relationships and can provide important insights into otherwise poorly understood groups. It is imperative to recognize that additional efforts are needed to definitively determine phylogenetic relationships between certain species of Palearctic ground squirrels.

Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya-Hengduan Mountains and adjacent regions

The Himalaya-Hengduan Mountains (HHM), a renowned biodiversity hotspot of the world, harbors the most extensive habitats for alpine plants with extraordinary high levels of endemism. Although the general evolution pattern has been elucidated, the underlying processes driving spectacular radiations in many species-rich groups remain elusive. Corydalis DC. is widely distributed throughout the Northern Hemisphere containing more than 500 species, with high diversity in HHM and adjacent regions. Using 95 plastid genes, 3,258,640 nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs) generated from genome skimming data, we reconstructed a robust time-calibrated phylogeny of Corydalis comprising more than 100 species that represented all subgenera and most sections. Molecular dating indicated that all main clades of Corydalis began to diverge in the Eocene, with the majority of extant species in HHM emerged from a diversification burst after the middle Miocene. Global pattern of mean divergence times indicated that species distributed in HHM were considerably younger than those in other regions, particularly for the two most species-rich clades (V and VI) of Corydalis. The early divergence and the recent diversification of Corydalis were most likely promoted by the continuous orogenesis and climate change associated with the uplift of the Qinghai-Tibetan Plateau (QTP). Our study demonstrates the effectivity of phylogenomic analyses with genome skimming data on the phylogeny of species-rich taxa, and sheds lights on how the uplift of QTP has triggered the evolutionary radiations of large plant genera in HHM and adjacent regions.

The RanOmics group, Becker A, Bachelier JB, Carrive L, Conde e Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage

The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike.

The evolution of ephemeral flora in Xinjiang, China: insights from plastid phylogenomic analyses of Brassicaceae

BACKGROUND

The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, the evolutionary history of this flora remains unclear. To gain new insights into its origin and evolutionary dynamics, we comprehensively sampled ephemeral plants of Brassicaceae, one of the essential plant groups of the ephemeral flora.

RESULTS

We reconstructed a phylogenetic tree using plastid genomes and estimated their divergence times. Our results indicate that ephemeral species began to colonize the arid areas in north Xinjiang during the Early Miocene and there was a greater dispersal of ephemeral species from the surrounding areas into the ephemeral community of north Xinjiang during the Middle and Late Miocene, in contrast to the Early Miocene or Pliocene periods.

CONCLUSIONS

Our findings, together with previous studies, suggest that the ephemeral flora originated in the Early Miocene, and species assembly became rapid from the Middle Miocene onwards, possibly attributable to global climate changes and regional geological events.

Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.

The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic

Rapid diversification of a group is often associated with exploiting an ecological opportunity and/or the evolution of a key innovation. However, how the interplay of such abiotic and biotic factors correlates with organismal diversification has been rarely documented in empirical studies, especially for organisms inhabiting drylands. Fumarioideae is the largest subfamily in Papaveraceae and is mainly distributed in temperate regions of the Northern Hemisphere. Here, we used one nuclear (ITS) and six plastid (rbcL, atpB, matK, rps16, trnL-F, and trnG) DNA sequences to investigate the spatio-temporal patterns of diversification and potential related factors of this subfamily. We first present the most comprehensive phylogenetic analysis of Fumarioideae to date. The results of our integrated molecular dating and biogeographic analyses indicate that the most recent common ancestor of Fumarioideae started to diversify in Asia during the Upper Cretaceous, and then dispersed multiple times out of Asia in the Cenozoic. In particular, we discover two independent dispersal events from Eurasia to East Africa in the late Miocene, suggesting that the Arabian Peninsula might be an important exchange corridor between Eurasia and East Africa in the late Miocene. Within the Fumarioideae, increased speciation rates were detected in two groups, Corydalis and Fumariinae. Corydalis first experienced a burst of diversification in its crown group at ∼42 Ma, and further accelerated diversification from the mid-Miocene onwards. During these two periods, Corydalis had evolved diverse life history types, which could have facilitated the colonization of diverse habitats originating from extensive orogenesis in the Northern Hemisphere as well as Asian interior desertification. Fumariinae underwent a burst of diversification at ∼15 Ma, which temporally coincides with the increasing aridification in central Eurasia, but is markedly posterior to the shifts in habitat (from moist to arid) and in life history (from perennial to annual) and to range expansion from Asia to Europe, suggesting that Fumariinae species may have been pre-adapted to invade European arid habitats by the acquisition of annual life history. Our study provides an empirical case that documents the importance of pre-adaptation on organismal diversification in drylands and highlights the significant roles of the synergy of abiotic and biotic factors in promoting plant diversification.