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Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere
Abstract
The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.
... (Kadereit & al., 2019), Eranthis Salisb. (Xiang & al., 2021), and Actaea L. (Ling & al., 2023). Among the genera with more than 10 species in Ranunculaceae, only one genus, i.e., Adonis L., lacks a molecular phylogeny. ...
... On the basis of the assumed evolutionary patterns of morphological characters in Adonis, W.T. Wang (1994a) hypothesized that Adonis originated in the QTP and then migrated out of the QTP through three routes: (1) from the western Himalaya to southwestern Europe; (2) from the mountainous areas of southwestern China to eastern Siberia and Japan along the Southwest-Northeast Corridor in China; (3) from the southwestern mountainous regions to northern Asia. Currently, model-based ancestral range reconstructions (Ronquist & Sanmartín, 2011;Matzke, 2013) in combination with divergence time estimation (Drummond & Rambaut, 2007) have been widely applied to infer the spatio-temporal patterns of evolution of organisms (e.g., Ling & al., 2023;Peng & al., 2023a). Adonis provides an opportunity to study the biogeography of the Eurasian flora using explicit models and the absolute divergence ages estimated by molecular data. ...
The genus Adonis (Ranunculaceae) contains about 30 species and is widespread in Eurasia. This genus contains some species of pharmaceutical and ornamental interest, yet a phylogenetic framework for understanding its evolution is still lacking. It has been hypothesized that Adonis originated in the Qinghai‐Tibet Plateau (QTP) and migrated out of the QTP through three dispersal routes. This biogeographical hypothesis has never been tested using molecular data. Using nine plastid and nuclear DNA regions, we first reconstructed a robust phylogenetic framework for Adonis with its currently recognized 31 species. We then inferred evolutionary patterns of morphological characters, estimated divergence times, and reconstructed ancestral ranges. Our results show that Adonis and its two subgenera A. subg. Adonis and subg. Adonanthe are monophyletic with strong support. Among the four non‐monotypic sections, only A. sect. Adonanthe is recognized as monophyletic. Habit, basal leaf, pollen, and carpel carry a strong phylogenetic signal in Adonis , while achene, beak shape, and beak length exhibit relatively higher levels of evolutionary flexibility. Adonis originated in the QTP in the Oligocene (ca. 30 Ma) and subsequently dispersed into the Irano‐Turanian region in the early Miocene (ca. 20 Ma). In Adonis , four out‐of‐QTP dispersal routes were recognized from the late Miocene to the Pliocene. This study provides the first comprehensive phylogeny for Adonis and highlights the indispensable role of the QTP uplift and associated climatic events in shaping the current distribution and endemism of Adonis , hence contributing to the knowledge on the historical biogeography of plants in Eurasia.
... During the late Eocene-early Oligocene, global temperature dropped sharply (Westerhold et al., 2020), and aridification in Central Asia began to occur (Bosboom et al., 2014). These events probably caused the southward retreat of evergreen forests and facilitated the development of temperate deciduous forests in Asia (Ling et al., 2023), which might create many new ecological niches for the early diversification of Thalictroideae. A few plant lineages in East Asian deciduous forests, such as Fagus (Fagaceae; Hai et al., 2022) and Actaea (Ranunculaceae; Ling et al., 2023), also diversified rapidly during the same period. ...
... These events probably caused the southward retreat of evergreen forests and facilitated the development of temperate deciduous forests in Asia (Ling et al., 2023), which might create many new ecological niches for the early diversification of Thalictroideae. A few plant lineages in East Asian deciduous forests, such as Fagus (Fagaceae; Hai et al., 2022) and Actaea (Ranunculaceae; Ling et al., 2023), also diversified rapidly during the same period. ...
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 (ca. 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 (ca. 36 Ma). From the Miocene onwards, at least 46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ca. 10 Ma.
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 due to sea-level decline, might have jointly 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 likely for other herbaceous lineages.
... (14 species), and Beesia Balf. f. & W.W. Sm. (two species), which have a circumboreal distribution (Compton and Culham 2002;Ling et al. 2023). Two genera are endemic to some regions, e.g., Anemonopsis grows only in Japan, and Beesia occurs only in China and N. Myanmar. ...
A comparative karyomorphological analysis was performed on Actaea acuminata, A. asiatica, and A. erythrocarpa. The karyotype of A. acuminata was re-examind; its formula proved to be 2n = 16 = 10m + 2sm + 2st + 2t. This species' karyotype was found to differ from that of A. spicata (2n = 16 = 10m + 4sm + 2t), thus allowing us to propose a species status of A. acuminata in contrast to the subspecies status (previously suggested by Compton): A. spicata var. acuminata. Karyotype structure of the analyzed A. asiatica from Shandong Province matches previously obtained data for Yunnan Province in China and corresponds to 2n = 16 = 10m + 4sm + 2t. The chromosome set of A. erythrocarpa was investigated in five regions of Russia; its structure proved to be similar among all the analyzed populations and is described by formula 2n = 16 = 10m + 4sm + 2t, consistently with previous findings about this species in Western Siberia. There are differences among the populations in the number and localization of secondary constrictions. A conclusion was made about conservatism of karyotype structure within the genus Actaea.
... This finding is consistent with a previous study based on more comprehensive sampling of subspecies in H. rhamnoides that suggested this species started to diverge in the QTP during the middle Miocene and dispersed out of the QTP in the late Miocene (Jia and Bartish, 2018). The dispersal into Europe and mainland East Asia of multiple plants groups that originated in the QTP and previously thrived in alpine environments (e.g., Rhodiola L., see Zhang et al., 2014; Physochlaina G. Don, see Lei et al., 2021; Actaea L., see Ling et al., 2023; Pleione D. Don, see Wu et al., 2023; and Lilium Tourn. ex L., see Zhou et al., 2024) coincides with a substantial decrease in global temperatures that began in the middle Miocene (Zachos et al., 2001). ...
The angiosperm family Elaeagnaceae comprises three genera and ca. 100 species distributed mainly in Eurasia and North America. Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted, limiting the application and preservation of natural genetic resources. Here, we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand inter- and intrageneric relationships, as well as the origin and biogeographical history of the family. For this purpose, we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and, along with current distributional data, infer historical biogeographical processes. Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera. Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia. The intrageneric relationships of Elaeagnus and Hippophae were also well resolved. High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus, and our analyses suggest putative ancient and recent hybridization. We inferred that Elaeagnaceae originated at ca. 90.48 Ma (95% CI = 89.91–91.05 Ma), and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution. This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date, offers new insights into previously unresolved relationships in Elaeagnus, and provides a foundation for further studies on classification, evolution, biogeography, and conservation of Elaeagnaceae.
... According to morphological and molecular phylogenetic data, Anemonopsis and Beesia form a separate clade that is sister to the Eranthis + Actaea clade. [8]. A morphological analysis of Loconte et al. ...
Anemonopsis Siebold et Zucc. is an unstudied single-species genus belonging to the tribe Cimicifugeae (Ranunculaceae). The only species of this genus—Anemonopsis macrophylla Siebold and Zucc.—is endemic to Japan. There are no data on its chemical composition. This work is the first to determine (with liquid chromatography–high-resolution mass spectrometry, LC-HRMS) the chemical composition of methanol extracts of leaves and flowers of A. macrophylla. More than 100 compounds were identified. In this plant, the classes of substances are coumarins (13 compounds), furocoumarins (3), furochromones (2), phenolic acids (21), flavonoids (27), and fatty acids and their derivatives (15 compounds). Isoferulic acid (detected in extracts from this plant) brings this species closer to plants of the genus Cimicifuga, one of the few genera containing this acid and ferulic acid at the same time. Isoferulic acid is regarded as a reference component of a quality indicator of Cimicifuga raw materials. The determined profiles of substances are identical between the leaf and flower methanol extracts. Differences in levels of some identified substances were revealed between the leaf and flower extracts of A. macrophylla; these differences may have a substantial impact on the manifestation of the biological and pharmacological effects of the extracts in question.
... and includes four recognized genera and ~49 species: Actaea L. ( [1][2][3]. Most of these species occur mainly in the northern hemisphere and are perennial herbs [4]. The taxonomic position of the genera Eranthis and Beesia has been a matter of systematic uncertainty within the tribal rank in the Ranunculaceae family. ...
This review summarizes information about the chemical composition and beneficial properties of species of the genus Eranthis Salisb. from the world’s flora. To date, seven out of ~14 species found in Asia and parts of Europe have been studied to various degrees. Here, data are presented on the diversity of sets of chromones, furochromones, triterpene saponins, coumarins, and other classes of secondary metabolites of Eranthis species according to the literature. For new compounds—isolated from Eranthis for the first time—structural formulas are also provided. Among the new compounds, chromones and coumarins predominate, as do triterpene saponins of the olean and cycloartane series and lectin. The results of pharmacological studies are presented showing anti-inflammatory, antioxidant, antiviral, and other types of biological activities found in extracts, in their fractions, and in individual compounds of the aboveground and underground organs and parts of Eranthis species. Despite the limited geographic range of Eranthis plants, it is possible to search for active substances, develop methods for biological and chemical synthesis of the isolated substances, and create a finished therapeutic substance based on them. In addition, it is feasible to obtain the desired standardized pure materials from Eranthis species grown in vitro.
This manuscript outlines the current growing sites of the endemic medicinal plant of Central Asia, E. longistipitata. Today, this plant garners significant interest from the global scientific community due to its remarkable anti-tumor, antioxidant, and anti-inflammatory properties. No analysis of herbarium collections had been performed before, so we took the first step to analyze the herbarium of the Botanical Institute in Uzbekistan and the GBIF. More than 100 herbarium labels were studied from 1916 to 2020. Based on the herbarium materials, 37 actual locations of E.longistipitata populations with GPS data were identified. As a result populations were found in the five states – Kazakhstan, Uzbekistan, Kyrgyzstan, Turkmenistan, and Tajikistan. In Kazakhstan E.longistipitata was found in the three growing points located in the western Tien Shan, Pamir-Alay, and Karatau mountain ranges. The research allowed for the refinement and supplementation of information on the distribution range of E.longistipitata in Central Asia.
Examining the pollination biology of plant species is not only crucial for enhancing our understanding of their reproductive biology, but also essential for elucidating their adaptation and evolutionary history. Here, we investigated the breeding system and pollination biology of two closely related species in Actaea. The flower of A. purpurea is unique in the genus with purple and chartaceous (paper-like) sepals, fewer stamens with yellow anthers and purple filaments. Through three seasons of field observation and exclusion experiments, we determined that A. purpurea was primarily pollinated by a hornet species, Vespa bicolor, which also served as the most efficient pollinator. In contrast, A. japonica was primarily pollinated by large flies. A. purpurea exhibited a significantly higher cumulative nectar volume than A. japonica, which could be a crucial factor attracting V. bicolor. A control experiment further demonstrated that removing the nectar leaf (petal) significantly decreased the visiting frequency of V. bicolor. Breeding system studies revealed that both species were self-compatible, yet they primarily underwent outcrossing in natural habitats. Our study presents a compelling case of possible pollinator shift in A. purpurea accompanied by morphological divergence. A more in-depth investigation of this system would offer crucial insights into the extent to which pollinators are involved in the plant speciation process and whether they contribute to reproductive isolation between closely related species.
Plant fossils play an important role in understanding landscape evolution across the Tibetan Region, as well as plant diversity across wider eastern Asia. Within the last decade or so, paleobotanical investigations within the Tibet Region have led to a paradigm shift in our understanding of how the present plateau formed and how this affected the regional climate and biota This is because: (1) Numerous new taxa have been reported. Of all the Cenozoic records of new plant fossil species reported from the Tibet (Xizang) Autonomous Region 45 out of 63 (70%) were documented after 2010. Among these, many represent the earliest records from Asia, or in some cases worldwide, at the genus or family level. (2) These fossils show that during the Paleogene, the region now occupied by the Tibetan Plateau was a globally significant floristic exchange hub. Based on paleobiogeographic studies, grounded by fossil evidence, there are four models of regional floristic migration and exchange, i.e., into Tibet, out of Tibet, out of India and into/out of Africa. (3) Plant fossils evidence the asynchronous formation histories for different parts of the Tibetan Plateau. During most of the Paleogene, there was a wide east-west trending valley with a subtropical climate in central Tibet bounded by high (>4 km) mountain systems, but that by the early Oligocene the modern high plateau had begun to form by the rise of the valley floor. Paleoelevation reconstructions using radiometrically-dated plant fossil assemblages in southeastern Tibet show that by the earliest Oligocene southeastern Tibet (including the Hengduan Mountains) had reached its present elevation. (4) The coevolution between vegetation, landform and paleoenvironment is evidenced by fossil records from what is now the central Tibetan Plateau. From the Paleocene to Pliocene, plant diversity transformed from that of tropical, to subtropical forests, through warm to cool temperate woodland and eventually to deciduous shrubland in response to landscape evolution from a seasonally humid lowland valley, to a high and dry plateau. (5) Advanced multidisciplinary technologies and novel ideas applied to paleobotanical material and paleoenvironmental reconstructions, e.g., fluorescence microscopy and paleoclimatic models, have been essential for interpreting Cenozoic floras on the Tibetan Region. However, despite significant progress investigating Cenozoic floras of the Tibetan Region, fossil records across this large region remain sparse, and for a better understanding of regional ecosystem dynamics and management more paleobotanical discoveries and multidisciplinary studies are required.
The dominant species of a biome can be regarded as its genuine indicator. Evergreen broadleaved forests (EBLFs) in subtropical East Asia harbor high levels of species biodiversity and endemism and are vital to regional carbon storage and cycling. However, the historical assembly of this unique biome is still controversial. Fagaceae is the most essential family in East Asian subtropical EBLFs and its dominant species are vital for the existence of this biome. Here, we used the dominant Fagaceae species to shed light on the dynamic process of East Asian subtropical EBLFs over time. Our results indicate high precipitation in summer and low temperature in winter are the most influential climatic factors for the distribution of East Asian subtropical EBLFs. Modern East Asian subtropical EBLFs did not begin to appear until 23 Ma, subsequently experienced a long‐lasting development in the Miocene and markedly deteriorated at about 4 Ma, driven jointly by orogenesis and paleoclimate. We also document that there is a lag time between when one clade invaded the region and when its members become dominant species within the region. This study may improve our ability to predict and mitigate the threats to biodiversity of East Asian subtropical EBLFs and points to a new path for future studies involving multidisciplinary methods to explore the assembly of regional biomes.
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
Temperate Deciduous Forests occur almost exclusively in the northern hemisphere and thrive under temperate climate with cold winter and warm-humid summer. They covered a continuous belt during most of the Tertiary across the continent Laurasia occupying a large area in higher latitudes. With the cooling of the Earth's climate and the appearance of the subtropical aridity areas, in combination with the separation of North America from Eurasia, this continuous area split into the three mainly existing now: Eastern North America, Western Eurasia and Eastern Asia. The tree flora reveals the common origin of the three current areas and the events causing more or less severe extinctions during the cold periods of the Pleistocene, in combination with the mountain uplift did happen since the Miocene affected differently to them. The basic features of the deciduous trait and its likely origin are discussed, as well as the ecologic implications of such a trait. For further research, the current possibilities provided by available vegetation datasets (EVA, sPlot) opens the possibility of using a large mass of vegetation plots data involving most of the vascular flora of these forests to find out insights about their origin and evolution over time as well as their links with current or past environmental conditions.
Background: The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. How‑
ever, 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 diferent plastid regions and diferent strate‑
gies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae com‑
prised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversifca‑
tion rates of tribe Perseeae accelerated twice in the late Miocene.
Conclusions: Our fndings suggest that the intensifed precipitation in East Asia in the early Miocene may have facili‑
tated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late
Miocene, species assembly and diversifcation within the EBLFs had become rapid.
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
The evolutionary history of organisms with poor dispersal abilities usually parallels geological events. Collisions of the Indian and Arabian plates with Eurasia greatly changed Asian topography and affected regional and global climates as well as biotic evolution. However, the geological evolution of Asia related to these two collisions remains debated. Here, we used Eranthis , an angiosperm genus with poor seed dispersal ability and a discontinuous distribution across Eurasia, to shed light on the orogenesis of the Qinghai–Tibetan, Iranian and Mongolian Plateaus. Our phylogenetic analyses show that Eranthis comprises four major geographical clades: east Qinghai–Tibetan Plateau clade (I-1), North Asian clade (I-2), west Qinghai–Tibetan Plateau clade (II-1) and Mediterranean clade (II-2). Our molecular dating and biogeographic analyses indicate that within Eranthis , four vicariance events correlate well with the two early uplifts of the Qinghai–Tibetan Plateau during the Late Eocene and the Oligocene–Miocene boundary and the two uplifts of the Iranian Plateau during the Middle and Late Miocene. The origin and divergence of the Mongolian Plateau taxa are related to the two uplifts of the Mongolian Plateau during the Middle and Late Miocene. Additionally, our results are in agreement with the hypothesis that the central part of Tibet only reached an altitude of less than 2.3 km at approximately 40 Ma. This study highlights that organismal evolution could be related to the formation of the three great Asian plateaus, hence contributing to the knowledge on the timing of the key tectonic events in Asia.
Ulmaceae are a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio‐temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera comprising the family are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera, ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses shows that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages.
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Knowledge of the topographic evolution of the Tibetan Plateau is essential for understanding its construction and its influences on climate, environment, and biodiversity. Previous elevations estimated from stable isotope records from the Lunpola Basin in central Tibet, which indicate a high plateau since at least 35 Ma, are challenged by recent discoveries of low-elevation tropical fossils apparently deposited at 25.5 Ma. Here, we use magnetostratigraphic and radiochronologic dating to revise the chronology of elevation estimates from the Lunpola Basin. The updated ages reconcile previous results and indicate that the elevations of central Tibet were generally low (<2.3 km) at 39.5 Ma and high (3.5 to 4.5 km) at ~26 Ma. This supports the existence in the Eocene of low-elevation longitudinally oriented narrow regions until their uplift in the early Miocene, with potential implications for the growth mechanisms of the Tibetan Plateau, Asian atmospheric circulation, surface processes, and biotic evolution.
Significance
The ancient topography of the Tibetan Plateau and its role in biotic evolution are still poorly understood, mostly due to a lack of fossil evidence. Our discovery of ∼47-Mya plant fossils from a present elevation of 4,850 m in central Tibet, diminishes, significantly, that lack of knowledge. The fossils represent a humid subtropical vegetation and some of the 70 different plant forms show affinity to Early-Middle Eocene floras in both North America and Europe. Using leaf architecture, we calculate that the forest grew at ∼1,500-m elevation within an east–west trending valley under a monsoonal climate. Our findings highlight the complexity of Tibet’s ancient landscape and emphasize the importance of Tibet in the history of global biodiversity.
Biogeography is the study of where, when, and how modern species evolved and diversified. Acer L. (maple) is one of the most diverse and widespread genera in the Northern Hemisphere. It comprises 124–156 species in the world, approximately 80% species of Acer are native in Asia. The current diversity center of Acer is not congruent with the distribution of the oldest fossils of the genus. Therefore, we herein used 84 species and subspecies to reconstruct the phylogeny and investigate the biogeographic history of Acer using nuclear ITS and three cpDNA fragments (psbA-trnH spacer, rpl16 intron, and trnL-trnF spacer) with maximum likelihood, maximum parsimony, and Bayesian inference methods. The analyses showed that the current diversity center and the origin center of Acer is Asia. Additionally, the North American and Euro-Mediterranean species originated from multiple sources from Asia via the North Atlantic Land Bridge and the Bering Land Bridge, and intercontinental migration has mainly occurred since the Miocene. This study not only provides a novel insight of the origin and dispersal routes of Acer but also exemplifies how past climatic changes affect the diversification-rates of Northern Hemisphere forest trees.
Much of our understanding of Earth's past climate comes from the measurement of oxygen and carbon isotope variations in deep-sea benthic foraminifera. Yet, long intervals in existing records lack the temporal resolution and age control needed to thoroughly categorize climate states of the Cenozoic era and to study their dynamics. Here, we present a new, highly resolved, astronomically dated, continuous composite of benthic foraminifer isotope records developed in our laboratories. Four climate states-Hothouse, Warmhouse, Coolhouse, Icehouse-are identified on the basis of their distinctive response to astronomical forcing depending on greenhouse gas concentrations and polar ice sheet volume. Statistical analysis of the nonlinear behavior encoded in our record reveals the key role that polar ice volume plays in the predictability of Cenozoic climate dynamics.
Using Pacific benthic foraminiferal δ ¹⁸ O and Mg/Ca records, we derive a Cenozoic (66 Ma) global mean sea level (GMSL) estimate that records evolution from an ice-free Early Eocene to Quaternary bipolar ice sheets. These GMSL estimates are statistically similar to “backstripped” estimates from continental margins accounting for compaction, loading, and thermal subsidence. Peak warmth, elevated GMSL, high CO 2 , and ice-free “Hothouse” conditions (56 to 48 Ma) were followed by “Cool Greenhouse” (48 to 34 Ma) ice sheets (10 to 30 m changes). Continental-scale ice sheets (“Icehouse”) began ~34 Ma (>50 m changes), permanent East Antarctic ice sheets at 12.8 Ma, and bipolar glaciation at 2.5 Ma. The largest GMSL fall (27 to 20 ka; ~130 m) was followed by a >40 mm/yr rise (19 to 10 ka), a slowing (10 to 2 ka), and a stillstand until ~1900 CE, when rates began to rise. High long-term CO 2 caused warm climates and high sea levels, with sea-level variability dominated by periodic Milankovitch cycles.
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.
Floristic similarities between European and Asian mountain ranges have long been recognized, and the hypothesis that European mountain plant taxa immigrated from Asian mountain areas has been confirmed by several molecular phylogenetic analyses. Callianthemum contains ca. 14 species, of which ca. 11 are distributed in Asia and three in Europe. A molecular phylogenetic analysis of the genus using ITS and four plastid DNA sequences (matK, rpL32–trnL intergenic spacer, trnL–trnF intergenic spacer, trnV–ndhC intergenic spacer) revealed that the genus reached Europe twice, with C. coriandrifolium representing one, and C. anemonoides and C. kernerianum a second lineage. Support for C. anemonoides and C. kernerianum as sister species is weak. The crown group ages of the C. coriandrifolium lineage (median 2.2 million years) and of the C. anemonoides/C. kernerianum lineage (median 1.62 million years) are similar and place their immigration to Europe in the Quaternary. Analysis of climatic data shows that C. coriandrifolium grows in colder climate than C. anemonoides/C. kernerianum and that the climatic niches of the three European species are different considering all climatic variables analyzed.
Today East Asia harbors many “relict” plant species whose ranges were much larger during the Paleogene-Neogene and earlier. The ecological and climatic conditions suitable for these relict species have not been identified. Here, we map the abundance and distribution patterns of relict species, showing high abundance in the humid subtropical/warm-temperate forest regions. We further use Ecological Niche Modeling to show that these patterns align with maps of climate refugia, and we predict species’ chances of persistence given the future climatic changes expected for East Asia. By 2070, potentially suitable areas with high richness of relict species will decrease, although the areas as a whole will probably expand. We identify areas in southwestern China and northern Vietnam as long-term climatically stable refugia likely to preserve ancient lineages, highlighting areas that could be prioritized for conservation of such species.
Background
Drylands cover nearly 41% of Earth’s land surface and face a high risk of degradation worldwide. However, the actual timeframe during which dryland floras rose on a global scale remains unknown. Zygophyllaceae, an important characteristic component of dryland floras worldwide, offers an ideal model group to investigate the diversification of dryland floras. Here, we used an integration of the phylogenetic, molecular dating, biogeographic, and diversification methods to investigate the timing and patterns of lineage accumulation for Zygophyllaceae overall and regionally. We then incorporated the data from other dominant components of dryland floras in different continents to investigate the historical construction of dryland floras on a global scale.
Results
We provide the most comprehensive phylogenetic tree for Zygophyllaceae so far based on four plastid and nuclear markers. Detailed analyses indicate that Zygophyllaceae colonized Africa, Asia, Australia, and the New World at different periods, sometimes multiple times, but Zygophyllaceae lineages in the four regions all experienced a rapid accumulation beginning at the mid-late Miocene (~ 15–10 Ma). Other eleven essential elements of dryland floras become differentiated at the same time.
Conclusions
Our results suggest that the rise of global dryland floras is near-synchronous and began at the mid-late Miocene, possibly resulting from the mid-Miocene global cooling and regional orogenetic and climate changes. The mid-late Miocene is an essential period for the assembly and evolution of global dryland floras.
Electronic supplementary material
The online version of this article (10.1186/s12862-018-1277-z) contains supplementary material, which is available to authorized users.
Migrations from the Qinghai-Tibetan Plateau (QTP) to other temperate regions represent one of the main biogeographical patterns for the Northern Hemisphere. However, the ages and routes of these migrations are largely not known. We aimed to reconstruct a well-resolved and dated phylogeny of Hippophae L. (Elaeagnaceae) and test hypothesis of a westward migration of this plant out of the QTP across Eurasian mountains in the Miocene. We produced two data matrices of five chloroplast DNA (cpDNA) and five nuclear DNA markers for all distinct taxa of Hippophae. These matrices were used to reconstruct phylogenetic relationships in the genus. In dating analyses, we first estimated the stem node age of Elaeagnaceae using five fossil records evenly distributed across a tree of Rosales. We used this estimate and two fossil records to calibrate the cpDNA and nDNA phylogenies of Hippophae. The same phylogenies were used to reconstruct ancestral areas within the genus. The monophyly of Hippophae, all five species, and most of subspecies was strongly supported by both plastid and nuclear data sets. Diversification of Hippophae likely started in central Himalayas/southern Tibet in the early Miocene and all extant distinct species had probably originated by the middle Miocene. Diversification of Hippophae rhamnoides likely started in the late Miocene east of the QTP from where this species rapidly expanded to central and western Eurasia. Our findings highlight the impact of different stages in uplift of the QTP and Eurasian mountains and climatic changes in the Neogene on diversification and range shifts in the highland flora on the continent. The results provide support to the idea of an immigration route for some European highland plants from their ancestral areas on the QTP across central and western mountain ranges of Eurasia in the late Miocene.
Background
Numerous studies have favored dispersal (colonization) over vicariance (past fragmentation) events to explain eastern Asian-North American distribution patterns. In plants, however the disjunction between eastern Asia and western North America has been rarely examined using the integration of phylogenetic, molecular dating, and biogeographical methods. Meanwhile, the biogeographic patterns within eastern Asia remain poorly understood. The goldthread genus Coptis Salisb. includes 15 species disjunctly distributed in North America, Japan, mainland China, and Taiwan. We present a dated phylogeny for Coptis under the optimal clock model and infer its historical biogeography by comparing different biogeographic models.
Results
The split of Coptis and Xanthorhiza Marshall occurred in the middle Miocene (ca. 15.47 Ma). Coptis started their diversification in the early late Miocene (ca. 9.55 Ma). A late Miocene vicariance event resulted in the eastern Asian and western North American disjunction in the genus. Within eastern Asia, dispersals from mainland Asia to Japan and from Japan to Taiwan occurred at ca. 4.85 Ma and at ca. 1.34 Ma, respectively.
Conclusions
Our analyses provide evidence that both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.
Electronic supplementary material
The online version of this article (10.1186/s12862-018-1195-0) contains supplementary material, which is available to authorized users.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
As the terrestrial human footprint continues to expand, the amount of native forest that is free from significant damaging human activities is in precipitous decline. There is emerging evidence that the remaining intact forest supports an exceptional confluence of globally significant environmental values relative to degraded forests, including imperilled biodiversity, carbon sequestration and storage, water provision, indigenous culture and the maintenance of human health. Here we argue that maintaining and, where possible, restoring the integrity of dwindling intact forests is an urgent priority for current global efforts to halt the ongoing biodiversity crisis, slow rapid climate change and achieve sustainability goals. Retaining the integrity of intact forest ecosystems should be a central component of proactive global and national environmental strategies, alongside current efforts aimed at halting deforestation and promoting reforestation.
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
In 2008, the Ministry of Environmental Protec-tion (MEP) in co-operation with Chinese Academy of Sciences (CAS) initiated work on a comprehensive new edition of the Red List of the Chinese flora. The project, named China Biodiversity Red List—Higher Plants, extended to 2013. We assessed the threatened status of all known species of higher plants in China to produce the Red List of China Higher Plants (RLCHP). In September 2013, the RLCHP was officially released in the form of a joint announcement by MEP and CAS (http://www.zhb.gov.cn/gkml/hbb/bgg/ 201309/t20130912_260061.htm/).
In the present paper, we report on the revised 2013 Red List through the use of new literature and data (Dong et al, 2017; He & Jia, 2017; Qin et al, 2017; Yang et al, 2017). Due to space limitations, we list only 3,879 threatened species, i.e. species categorized as Critically Endagnered (CR), Endangered (EN) and Vulnerable (VU). The data include the scientific name of each species, the Chinese name, endemism, red list category and criterion for assigning the designation.
We invited more than 300 experts to contribute survival information of species and/or to review the assessments. The RLCHP covers 35,784 species, in-cluding 30,068 species of angiosperms, 251 species of gymnosperms, 2,244 species of lycophytes and ferns, and 3,221 species of bryophytes. This is the first Red List that covers the entire Chinese flora, and the number of experts involved and data used are much more than in previous analyses.
Two documents were used as a standard in this assessment: IUCN Red List Categories and Criteria (Version 3.1, Second edition) (IUCN, 2012a) and Guideline for Application of IUCN Red List Criteria at Regional and National Levels (Version 4.0) (IUCN, 2012b). Nine IUCN Red List categories were applied to the RLCHP: Extinct (EX), Extinct in the Wild (EW), Regionally Extinct (RE), Critically Endangered (CR), Endangered (EN), Vulnerable (VU), Near Threatened (NT), Least Concern (LC), and Data Deficient (DD).
Four steps were applied in the assessment: setting up a baseline checklist, collecting data, species as-sessment and review. For instance, during the review of the angiosperms assessments, eight expert meetings were held in six cities (Guangzhou, Guilin, Kunming, Wuhan, Nanjing and Beijing), and 87 experts took part in one-on-one interviews with staff members of the program. To guarantee professional results of the as-sessment, we invited 19 leading experts from institu-tions of CAS and universities to join the red list steering committee. The committee was responsible for examining and approving the assessment methodology, examining the annual report and reviewing the results of the assessments. Four steering committee meetings were held in Beijing between 2008 and 2012.
Of the 35,784 assessed species of China higher plants, 21 species are Extinct (EX), 9 species are Ex-tinct in the Wild (EW), 10 species are Regionally Ex-tinct (RE), 614 species are Critically Endangered (CR), 1,313 speices are Endangered (EN), 1,952 species are Vulnerable (VU), 2,818 species are Near Threatened (NT), 24,243 species are of Least Concern (LC), and 4,804 species are Data Deficient (DD). The results show that 3,879 species, representing 10.84% of the evaluated species, have been identified as threatened categories (CR, EN and VU).
The references cited in this paper can be found at the website http://www.biodiversity-science.net/fileup/ PDF/ 2017-144-1.pdf/.
The rise of angiosperms has been regarded as a trigger for the Cretaceous revolution of terrestrial ecosystems. However, the timeframe of the rise angiosperm-dominated herbaceous floras (ADHFs) is lacking. Here, we used the buttercup family (Ranunculaceae) as a proxy to provide insights into the rise of ADHFs. An integration of phylogenetic, molecular dating, ancestral state inferring, and diversification analytical methods was used to infer the early evolutionary history of Ranunculaceae. We found that Ranunculaceae became differentiated in forests between about 108–90 Ma. Diversification rates markedly elevated during the Campanian, mainly resulted from the rapid divergence of the non-forest lineages, but did not change across the Cretaceous-Paleogene boundary. Our data for Ranunculaceae indicate that forest-dwelling ADHFs may have appeared almost simultaneously with angiosperm-dominated forests during the mid-Cretaceous, whereas non-forest ADHFs arose later, by the end of the Cretaceous terrestrial revolution. Furthermore, ADHFs were relatively unaffected by the Cretaceous-Paleogene mass extinction.
Background
The evolutionary origin and historical demography of extant Arcto-Tertiary forest species in East Asia is still poorly understood. Here, we reconstructed the evolutionary and population demographic history of the two extant Euptelea species in China (E. pleiosperma) and Japan (E. polyandra). Chloroplast/nuclear DNA sequences and microsatellite loci were obtained from 36 Euptelea populations to explore molecular structure and diversity in relation to past and present distributions based on ecological niche modelling (ENM). Time-calibrated phylogenetic/phylogeographic inferences and niche-identity tests were used to infer the historical process of lineage formation.
Results
Euptelea pleiosperma diverged from E. polyandra around the Late Miocene and experienced significant ecological differentiation. A near-simultaneous diversification of six phylogroups occurred during the mid-to-late Pliocene, in response to the abrupt uplift of the eastern Tibetan Plateau and an increasingly cooler and drier climate. Populations of E. pleiosperma seem to have been mostly stationary through the last glacial cycles, while those of E. polyandra reflect more recent climate-induced cycles of range contraction and expansion.
Conclusions
Our results illustrate how Late Neogene climatic/tectonic changes promoted speciation and lineage diversification in East Asia’s Tertiary relict flora. They also demonstrate for the first time a greater variation in such species’ responses to glacial cycles in Japan when compared to congeners in China.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-016-0636-x) contains supplementary material, which is available to authorized users.
Cimicifuga nanchuanensis P. K. Hsiao (Ranunculaceae) has been regarded as an imperfectly known species. Based on critical examination of herbarium specimens and living plants we have determined that it is a morphologically distinctive species and that its geographical range is much wider than believed before, far from locally endemic to its type locality. Our cytological examination reveals the species to be a diploid (2n = 16). Our molecular phylogenetic analyses using nrDNA and cpDNA datasets confirm our morphological observations. As the generic concept and delimitation of Actaea L., in which Cimicifuga Wernisch. and Souliea Franch. are included, have also been strongly corroborated by our molecular phylogenetic analyses, here we adopt a broad Actaea and make a new combination for the species in question, i.e. Actaea nanchuanensis (P. K. Hsiao) J. P. Luo, Q. Yuan & Q. E. Yang.
Study on Late Cenozoic propagation of uplift in the southeast margin of the Tibetan Plateau is critical to link with development of intra-continental deformation in the periphery of the Tibetan Plateau. The apatite fission track analysis in Chayu area of the southeast Tibetan Plateau reveals that the Late Cenozoic differential uplift-exhumation of Demula, Arza Gongla and Chayu batholiths, which arrayed from north to south and controlled by faults, is a proxy of propagation of uplift. The time series of uplift-exhumation are ca. 15.1 ∼ 13.7Ma, 6.3 ∼ 4.3Ma, 3.5 ∼ 3.3Ma, 1.9 ∼ 1.7Ma and 1.1 ∼ 1.0Ma and the overall activities show southward propagation and migration. It is in Late Miocene (ca. 6 ∼ 5Ma) that uplift-exhumation rate turns speedup with a regional response in southeast Tibet and northwest Yunnan and may establish the development pattern of modern terrain for the southeast margin of the Tibetan Plateau. From the southeast to northeast of the Tibetan Plateau, the outward propagation and growth of late Cenozoic deformation is characterized by multistage, coeval and disequilibrium developments.
Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot.com/biogeobears.
Traditional models for tropical species richness contrast rainforests as 'museums' of old species or 'cradles' of recent speciation. High plant species diversity in rainforests may be more likely to reflect high episodic evolutionary turnover of species-a scenario implicating high rates of both speciation and extinction through geological time.
Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS, which implements several models in a common framework, allowing models to be compared with standard likelihood‐based methods of statistical model comparison. Ree and Sanmartín (Journal of Biogeography, 45, 741–749, 2018) critiqued the comparison of Dispersal–Extinction–Cladogenesis (DEC) and a modification of it, DEC+J, which adds the process of jump dispersal at speciation. DEC+J provides highly significant improvements in model fit on most (although not all) datasets. They claim that the comparison is statistically invalid for a variety of reasons. I analyse the key claims made by the critique. Simulated data. Simulated data. Likelihood calculations are checked by comparison between programs and by‐hand calculations, and by summing likelihoods across all possible datasets. Model adequacy of DEC versus DEC+J is checked by a simulation/inference experiment. Mistakes in the critique's example likelihood calculations are demonstrated. DEC+J fits better on datasets because the DEC model is statistically inadequate in the common situation when most species have geographical ranges of single areas; the DEC model requires long residence times of multi‐area ranges, and when these are not observed, a model that does produce such data patterns, such as DEC+J, prevails. More fundamentally, statistical comparison of DEC and DEC+J produces identical log‐likelihood differences to statistical comparison of two submodels of ClaSSE where extinction rates are fixed to 0. DEC fails a basic model adequacy check for understandable reasons, while DEC+J does not. As Ree and Sanmartín recommend ClaSSE models as valid for comparison, the comparison of DEC and DEC+J is statistically valid according to their own criteria.
In this paper, we review evidence for a major biotic turnover across the Oligocene/Miocene in the Tibetan Plateau region. Based on the recent study of six well-preserved fossil sites from the Cenozoic Lunpola and Nima basins in the central Tibetan Plateau, we report a regional changeover from tropical/subtropical ecosystems in the Late Oligocene ecosystem (26–24 Ma) to a cooler, alpine biota of the Early Miocene (23–18 Ma). The Late Oligocene fossil biota, comprising of fish (climbing perch), insects and plants (palms), shows that the hinterland of the Tibetan Plateau was a warm lowland influenced by tropical humidity from the Indian Ocean. In the Early Miocene, the regional biota became transformed, with the evolution and diversification of the endemic primitive snow carp. Early Miocene vegetation was dominated by temperate broad-leaved forest with abundant conifers and herbs under a cool climate, and mammals included the hornless rhinoceros, Plesiaceratherium, a warm temperate taxon. This dramatic ecosystem change is due to a cooling linked to the uplift of Tibetan region, from a Late Oligocene paleo-elevation of no greater than 2300 m a.s.l. in the sedimentary basin to a paleo-elevation of about 3000 m a.s.l. Another factor was the Cenozoic global climatic deterioration toward to an ice-house world.
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.
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.
The family Ranunculaceae, a member of early-diverging eudicots that is increasingly being used as a model for the study of plant developmental evolution, has been the focus of systematic studies for centuries. Recent studies showed that the family can be divided into 14 tribes, with Glaucideae, Hydrastideae, and Coptideae being the successive basal-most lineages. The relationships among the remaining 11 tribes, however, remain controversial, so that a clear picture of character evolution within the family is still lacking. In this study, by sequencing, assembling and analyzing the chloroplast (cp) genomes of 35 species representing 31 genera of the 14 tribes, we resolved the relationships among the tribes and genera of the Ranunculaceae and clarified several long-standing controversies. We found that many of the characters that were once widely used for taxonomic and systematic considerations were actually results of parallel, convergent or even reversal evolution, suggestive of unreliability. We also found that the family has likely experienced two waves of radiative evolution, through which most of the extant tribes and genera were generated. Notably, both waves of radiation were correlated with the increase in the temperature of the earth, suggesting that global warming may have been the driving force of the radiation events. Based on these observations, we hypothesize that global warming and the associated decrease in the type and number of animal pollinators may have been the main reason why taxa with highly elaborate petals as well as those without petal were generated during each of the two waves of radiation.
After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use, and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
Availability:
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=apeFurther information may be found athttp://ape-package.ird.fr/.
Taiwan is a continental island lying at the boundary between the Eurasian and the Philippine tectonic plates and possesses high biodiversity. Southern Taiwan, viz. Hengchun Peninsula, is notably floristically different from northern Taiwan. The floristic origin and relationships of the Hengchun Peninsula have been rarely investigated in a phylogenetic context. In this study, data from six plastid and nuclear sequences were used to reconstruct phylogenetic relationships within Burasaieae (Menispermaceae), which mainly inhabits tropical rainforests. The tree-based comparisons indicate that the position of Tinospora sensu stricto conflicts significantly between the cpDNA and ITS trees. However, alternative hypothesis tests from the ITS data did not reject the result of the cpDNA data, which suggests that tree-based comparisons might sometimes generate an artificial incongruence, especially when markers with high homoplasy are used. Based on the combined cpDNA and ITS data, we present an inter-generic phylogenetic framework for Burasaieae. Sampled species of Tinospora are placed in three different clades, including Tinospora dentata from southern Taiwan and T. sagittata from mainland China in an unresolved position alongside six lineages of Burasaieae. By integrating lines of evidence from molecular phylogeny, divergence times, and morphology, we recognize the three Tinospora clades as three different genera, including Tinospora sensu stricto, a new genus (Paratinospora) for T. dentata and T. sagittata, and Hyalosepalum resurrected. Tinospora dentata, now endemic to the Hengchun Peninsula, originated from the Late Eocene (ca. 39Ma), greatly predating the formation of Taiwan. Our study suggests that the flora of the Hengchun Peninsula contains some ancient components that might have migrated from mainland China.
Aim
Geologically dynamic areas often harbour remarkable levels of biodiversity. Among other factors, mountain building is assumed to be a precondition for species radiation, and yet, the potential role of immigration as a source of biodiversity prior to radiation is often neglected. Here, we studied the biogeographical history of the large genus Saxifraga to unravel the role played by the Qinghai‐Tibet Plateau ( QTP ) for the diversification of this genus and to understand factors that have led to the establishment of high biodiversity in and around this region.
Location
QTP and surrounding mountain ranges and worldwide distribution range of Saxifraga .
Methods
Using a total of 420 taxa (321 ingroup taxa) comprising more than 60% of extant Saxifraga species, we studied the evolutionary history of Saxifraga by performing phylogenetic analyses (maximum likelihood and Bayesian inference on nuclear ITS and plastid trn L– trn F, mat K sequences), divergence time estimation (using uncorrelated log‐normal clock models and four fossil constraints in beast ) and ancestral range estimation (using BioGeo BEARS ).
Results
Saxifraga originated in North America around 74 (64–83) Ma, dispersed to South America and northern Asia during its early diversification and colonized Europe and the QTP region by the Late Eocene. The QTP region was colonized several times independently, followed in some lineages by rapid radiations, temporally coinciding with recent uplifts of the Hengduan Mountains at the southeastern fringe of the QTP . Subsequently, several lineages dispersed out of Tibet.
Main conclusions
Immigration, recent rapid radiation and lineage persistence were all important processes for the establishment of a rich species stock of Saxifraga in the QTP region. Because floristic exchanges between the neighbouring areas and the QTP region were bi‐directional, the spatio‐temporal evolution of Saxifraga contrasts with the ‘out of QTP ’ pattern, which has often been assumed for northern temperate plants.
This paper attempts to synthesize vertebrate paleontological evidence and recently acquired knowledge of the geological history of terrestrial connections across the northern North Atlantic area. In 1975 I published a survey of this subject (McKenna, 1975) but it is appropriate here to bring the synthesis up to date in view of recent geophysical work and in view of further paleontological exploration in the Arctic and elsewhere. As Alfred Wegener (1929) was well aware, the world has had but one history; for that reason geological evidence and biological evidence each provide constraints on any proposed solutions to the ancient geography of an area such as the northern end of the North Atlantic. Although I hope to bring the subject up to date, I intend also to speculate on potential vertebrate paleontological field work that might yield new evidence concerning the details of timing and position of Tertiary land connections between now separated areas.
One of the most significant research themes in plant ecology is the vegetation-climate relationship. Mean annual temperature and precipitation are frequently used to characterize stand qualities and predict vegetation distributions, while seasonalities of climate have seldom been employed to study the climate-vegetation relationship despite their long-recognized importance to the vegetation distributions. Mountain vertical vegetation zonations are often assumed to be the reduction of vegetation distribution patterns along gradient pattern. However, the seasonality of climatic conditions for a specific mountain doesn't vary with altitude as it does with latitude. According to cost-benefit analyses of leaf longevity, short leaf life spans are largely favored in habitats with intensive seasonalities. We therefore predict that deciduous broad-leaved forests are more likely to appear in high latitudinal mountains of subtropical China. We collected data on geographic locations, climatic conditions, and vertical vegetation distribution patterns for 49 subtropical Chinese mountains (23-34° N) from published literature. The coefficients of variations of monthly mean temperature and precipitation were calculated for each mountain to quantify the temperature and rainfall seasonality, respectively, and the production of the two coefficients was used to characterize climate seasonality as a whole. Then, we determined the relationship between the vertical patterns of vegetation distribution (existence or non-existence of deciduous broad-leaved forest zones) and the seasonality intensities across the mountains. The deciduous broad-leaved forest zone is not conspicuous when the mountains are located farther south than 25 ° N, whereas it is distinct when the location is farther north than 32° N. Within the latitudes ranging between 25° N and 32° N, the mountains are more likely to have the deciduous broadleaved forest in the low latitudinal areas than the high latitudinal areas. Both temperature and climate seasonalities increase with increasing latitude, whereas rainfall seasonality is insignificantly correlated with altitudes. Non- parametric correlation analyses indicate that the vertical vegetation zonations are closely correlated with the temperature and climatic seasonalities but not the rainfall seasonality. The possibility of the mountains having the deciduous forest increases with the seasonalities of temperature and climate but not rainfall. These suggest that the temperature seasonality is more important to influence the climate seasonality and the vertical vegetation zonations relative to the rainfall seasonality. However, the rainfall seasonality modifies the vegetation distribution pattern for several mountains and hence it may explain some exceptional mountains (e.g. that have apparent the deciduous forest in low latitudinal areas). The relationships among mountain latitudes, vertical forest distributions, and climatic seasonalities are consistent with the prediction of current theoretical models on cost-benefit analysis of leaf lifespan. The revealed relationship between mountain vertical vegetation patterns and climatic seasonalities indicates the importance of studying the seasonality on vegetation structure, productivity and ecosystem functioning. It also suggests that ecological restoration practices should be site-specific, particularly on mountains. The physiological mechanisms underlying the relationship deserve to be an avenue of further researches.
The Asian interior arid zone is the largest desert landform system in the Northern Hemisphere , and has high biodiversity. Little is currently known about the evolutionary history of its biota. In this study, we used Zygophyllum, an important and characteristic component of the Asian interior arid zone, to provide new insights into the evolution of this biota. By greatly enlarged taxon sampling, we present the phylogenetic analysis of Asian Zygophyllum based on two plastid and one nuclear markers. Our phylogenetic analyses indicate that Asian Zygophyllum and Sarcozygium form a clade and Sarcozygium is further embedded within the shrub subclade. An integration of phylogenetic, biogeographic, and molecular dating methods indicates that Zygophyllum successfully colonized the Asian interior from Africa in the early Oligocene, and Asian Zygophyllum became differentiated in the early Miocene and underwent a burst of diversification in the late Miocene associated with the expansion of Asian interior arid lands due to orogenetic and climatic changes. Combining diversification patterns of other important components of the Asian interior arid zone, we propose a multi-stage evolution model for this biota: the late Eocene–early Oligocene origin, the early Miocene expansion, and the middle-late Miocene rapid expansion to the whole Asian interior arid zone. This study also demonstrates that, for Zygophyllum and perhaps other arid-adapted organisms, arid biomes are evolutionary cradles of diversity.
What factors influence whether a lineage can successfully transition into a new biome, and why have some biome shifts been more frequent than others? To orient this line of research we develop a conceptual framework in which the likelihood of a biome shift is a function of (a) exposure to contrasting environments over time, (b) the evolutionary accessibility of relevant adaptations, and (c) changing biotic interactions. We evaluate the literature on biome shifts in plants in relation to a set of hypotheses on the size, connectedness, and absolute age of biomes, as well as on the adaptability of particular lineages and ecological interactions over time. We also critique the phylogenetic inference of past biomes and a "global" model-based approach to biome evolution. More robust generalizations about biome shifts will require detailed studies of well-sampled and well-resolved clades, accounting for changes in the relevant abiotic and biotic factors through time.
Deciduousness in mesic, broad-leaved plants occurred in disturbed, middle-latitude environments during the Late Cretaceous. Only in polar environments in the Late Cretaceous was the deciduous element dominant, although of low diversity. The terminal Cretaceous event resulted in wide-spread selection for plants of deciduous habit and diversification of deciduous taxa, thus leaving a lasting imprint on Northern Hemisphere vegetation. Various environmental factors have played important roles in subsequent diversification of mesic, broad-leaved deciduous taxa and in origination and decline of broad-leaved deciduous forests. Low diversity and rarity of mesic deciduous plants in the post-Cretaceous of the Southern Hemisphere indicate that the inferred 'impact winter' of the terminal Cretaceous event had little effect on Southern Hemisphere vegetation and climate. -Author
This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral character state reconstructions were compared among three methods (parsimony, maximum likelihood, and stochastic character mapping) using MESQUITE and a full Bayesian method in BayesTraits and inferences of ancestral area distribution were compared between the parsimony-based dispersal-vicariance analysis (DIVA) and a newly developed maximum likelihood (ML) method. Results indicated that among the six inflorescence and fruit characters examined, "perfect" binary characters (no homoplasy, no polymorphism within terminals, and no missing data) are little affected by choice of method, while homoplasious characters and missing data are sensitive to methods used. Ancestral areas at deep nodes of the phylogeny are substantially different between DIVA and ML and strikingly different between analyses including and excluding fossils at three deepest nodes. These results, while raising caution in making conclusions on trait evolution and historical biogeography using conventional methods, demonstrate a limitation in our current understanding of character evolution and biogeography. The biogeographic history favored by the ML analyses including fossils suggested the origin and early radiation of Cornus likely occurred in the late Cretaceous and earliest Tertiary in Europe and intercontinental disjunctions in three lineages involved movements across the North Atlantic Land Bridge (BLB) in the early and mid Tertiary. This result is congruent with the role of NALB for post-Eocene migration and in connecting tropical floras in North America and Africa, and in eastern Asia and South America. However, alternative hypotheses with an origin in eastern Asia and early Trans-Beringia migrations of the genus cannot be ruled out.