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The rapid diversification and high species richness of flowering plants is regarded as ‘Darwin’s second abominable mystery’. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous–Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.

Floristic regions reflect the geographic organization of floras and provide essential tools for biological studies. Previous global floristic regions are generally based on floristic endemism, lacking a phylogenetic consideration that captures floristic evolution. Moreover, the contribution of tectonic dynamics and historical and current climate to the division of floristic regions remains unknown. Here, by integrating global distributions and a phylogeny of 12,664 angiosperm genera, we update global floristic regions and explore their temporal changes. Eight floristic realms and 16 nested sub-realms are identified. The previously-defined Holarctic, Neotropical and Australian realms are recognized, but Paleotropical, Antarctic and Cape realms are not. Most realms have formed since Paleogene. Geographic isolation induced by plate tectonics dominates the formation of floristic realms, while current/historical climate has little contribution. Our study demonstrates the necessity of integrating distributions and phylogenies in regionalizing floristic realms and the interplay of macroevolutionary and paleogeographic processes in shaping regional floras.

Floristic regions reflect the geographic organization of floras and provide essential tools for biological studies. Previous global floristic regions are generally based on floristic endemism, lacking a phylogenetic consideration that captures floristic evolution. Moreover, the contribution of tectonic dynamics and historical and current climate to the division of floristic regions remains unknown. Here, by integrating global distributions and a phylogeny of 12,664 angiosperm genera, we update global floristic regions and explore their temporal changes. Eight floristic realms and 16 nested sub-realms are identified. The previously-defined Holarctic, Neotropical and Australian realms are recognized, but Paleotropical, Antarctic and Cape realms are not. Most realms have formed since Paleogene. Geographic isolation induced by plate tectonics dominates the formation of floristic realms, while current/historical climate has little contribution. Our study demonstrates the necessity of integrating distributions and phylogenies in regionalizing floristic realms and the interplay of macroevolutionary and paleogeographic processes in shaping regional floras.

The rapid diversification and high species richness of flowering plants is regarded as ‘Darwin’s second abominable mystery’. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous–Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.

The rapid diversification and high species richness of flowering plants is regarded as ‘Darwin’s second abominable mystery’. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification dynamics of angiosperms through space and time. Our analyses show that diversification rates increased throughout the early Cretaceous and then slightly decreased or remained mostly stable until the end of the Cretaceous–Paleogene mass extinction event 66 million years ago. After that, diversification rates increased again towards the present. Younger genera with high diversification rates dominate temperate and dryland regions, whereas old genera with low diversification dominate the tropics. This leads to a negative correlation between spatial patterns of diversification and genus diversity. Our findings suggest that global changes since the Cenozoic shaped the patterns of flowering plant diversity and support an emerging consensus that diversification rates are higher outside the tropics.

The increasing prevalence of marine pollution during the past few decades motivated recent research to help ease the situation. Typical water quality assessment requires continuous monitoring of water and sediments at remote locations with labour intensive laboratory tests to determine the degree of pollution. We propose an automated framework where we formalise a predictive model using Machine Learning to infer the water quality and level of pollution using collected water and sediments samples. One commonly encountered difficulty performing statistical analysis with water and sediment is the limited amount of data samples and incomplete dataset due to the sparsity of sample collection location. To this end, we performed extensive investigation on various data imputation methods' performance in water and sediment datasets with various data missing rates. Empirically, we show that our best model archives an accuracy of 75% after accounting for 57% of missing data. Experimentally, we show that our model would assist in assessing water quality screening based on possibly incomplete real-world data.

Aim Biodiversity hotspots are widely used as conservation priorities to preserve the tree of life. However, many conservation practices identify biodiversity hotspots without considering phylogenetic diversity (PD), which reflects total evolutionary history and feature diversity of a region. Moreover, conservation planning rarely distinguishes between neo- and palaeo-biodiversity hotspots despite their differences. Here, we (a) estimated large-scale patterns in PD of woody plants, (b) identified neo- and palaeo-biodiversity hotspots and (c) demonstrated their implication in conservation planning, with special focus on Hengduan Mountains and southern China.Location China.Methods Distributions of 11,405 woody species from the Atlas of Woody Plants in China were updated and were transformed into a grid of 50 x 50 km(2). By integrating distribution maps with a genus-level phylogeny of angiosperms, we estimated Faith's PD of each grid cell and evaluated the contribution of species relatedness to PD at given levels of species diversity (i.e. standardized PD, sPD) using regressions and three null models. Then, we identified areas with significantly lower or higher sPD than expected as neo- and palaeo-hotspots and estimated the coverage of protected areas in these regions.Results Species diversity and PD decreased towards the north. Southern China had high species diversity, PD and sPD, while Hengduan Mountains had high species diversity and PD but low sPD. The coverage of protected areas in southern China was less than half of that in Hengduan Mountains and entire China.Main conclusions Our results identified Hengduan Mountains as a neo-hotspot and southern China as a palaeo-hotspot, highlighting their importance for biodiversity conservation. Compared to Hengduan Mountains, southern China has low coverage of protected areas, which calls for more conservation attention. Our study demonstrates a way of incorporating the phylogenetic component

Aim Biodiversity hotspots are widely used as conservation priorities to preserve the tree of life. However, many conservation practices identify biodiversity hotspots without considering phylogenetic diversity (PD), which reflects total evolutionary history and feature diversity of a region. Moreover, conservation planning rarely distinguishes between neo- and palaeo-biodiversity hotspots despite their differences. Here, we (a) estimated large-scale patterns in PD of woody plants, (b) identified neo- and palaeo-biodiversity hotspots and (c) demonstrated their implication in conservation planning, with special focus on Hengduan Mountains and southern China.Location China.Methods Distributions of 11,405 woody species from the Atlas of Woody Plants in China were updated and were transformed into a grid of 50 x 50 km(2). By integrating distribution maps with a genus-level phylogeny of angiosperms, we estimated Faith's PD of each grid cell and evaluated the contribution of species relatedness to PD at given levels of species diversity (i.e. standardized PD, sPD) using regressions and three null models. Then, we identified areas with significantly lower or higher sPD than expected as neo- and palaeo-hotspots and estimated the coverage of protected areas in these regions.Results Species diversity and PD decreased towards the north. Southern China had high species diversity, PD and sPD, while Hengduan Mountains had high species diversity and PD but low sPD. The coverage of protected areas in southern China was less than half of that in Hengduan Mountains and entire China.Main conclusions Our results identified Hengduan Mountains as a neo-hotspot and southern China as a palaeo-hotspot, highlighting their importance for biodiversity conservation. Compared to Hengduan Mountains, southern China has low coverage of protected areas, which calls for more conservation attention. Our study demonstrates a way of incorporating the phylogenetic component

Mechanisms underlying species richness patterns remain a central yet controversial issue in biology. Climate has been regarded as a major determinant of species richness. However, the relative influences of different evolutionary processes, (i.e. niche conservatism, diversification rate and time for speciation) on species richness-climate relationships remain to be tested. Here, using newly compiled distribution maps for 11 422 woody plant species in eastern Eurasia, we estimated species richness patterns for all species and for families with tropical and temperate affinities separately, and explored the phylogenetic signals in species richness patterns of different families and their relationships with contemporary climate and climate change since the Last Glacial Maximum (LGM). We further compared the effects of niche conservatism (represented by contemporary-ancestral climatic niches differences), diversification rate and time for speciation (represented by family age) on variation in the slopes of species richness-climate relationships. We found that winter coldness was the best predictor for species richness patterns of most tropical families while Quaternary climate change was the best predictor for those of most temperate families. Species richness patterns of closely-related families were more similar than those of distantly-related families within eudicots, and significant phylogenetic signals characterized the slopes of species richness-climate relationships across all angiosperm families. Contemporary-ancestral climatic niche differences dominated variation in the relationships between family-level species richness and most climate variables. Our results indicate significant phylogenetic conservatism in family-level species richness patterns and their relationships with contemporary climate within eudicots. These findings shed light on the mechanisms underlying large-scale species richness patterns and suggest that ancestral climatic niche may influenc

Mechanisms underlying species richness patterns remain a central yet controversial issue in biology. Climate has been regarded as a major determinant of species richness. However, the relative influences of different evolutionary processes, (i.e. niche conservatism, diversification rate and time for speciation) on species richness-climate relationships remain to be tested. Here, using newly compiled distribution maps for 11 422 woody plant species in eastern Eurasia, we estimated species richness patterns for all species and for families with tropical and temperate affinities separately, and explored the phylogenetic signals in species richness patterns of different families and their relationships with contemporary climate and climate change since the Last Glacial Maximum (LGM). We further compared the effects of niche conservatism (represented by contemporary-ancestral climatic niches differences), diversification rate and time for speciation (represented by family age) on variation in the slopes of species richness-climate relationships. We found that winter coldness was the best predictor for species richness patterns of most tropical families while Quaternary climate change was the best predictor for those of most temperate families. Species richness patterns of closely-related families were more similar than those of distantly-related families within eudicots, and significant phylogenetic signals characterized the slopes of species richness-climate relationships across all angiosperm families. Contemporary-ancestral climatic niche differences dominated variation in the relationships between family-level species richness and most climate variables. Our results indicate significant phylogenetic conservatism in family-level species richness patterns and their relationships with contemporary climate within eudicots. These findings shed light on the mechanisms underlying large-scale species richness patterns and suggest that ancestral climatic niche may influenc

A key challenge in ecology is to understand the relationships between organismal traits and ecosystem processes. Here, with a novel dataset of leaf length and width for 10 480 woody dicots in China and 2374 in North America, we show that the variation in community mean leaf size is highly correlated with the variation in climate and ecosystem primary productivity, independent of plant life form. These relationships likely reflect how natural selection modifies leaf size across varying climates in conjunction with how climate influences canopy total leaf area. We find that the leaf size‒primary productivity functions based on the Chinese dataset can predict productivity in North America and vice‐versa. In addition to advancing understanding of the relationship between a climate‐driven trait and ecosystem functioning, our findings suggest that leaf size can also be a promising tool in palaeoecology for scaling from fossil leaves to palaeo‐primary productivity of woody ecosystems.

GenBank is the leading public genetic resources database and currently contains over 1012 base pairs from about 300,000 formally described species. It offers valuable resources for studies on the evolution of species, genes, and genomes. However, difficulties in GenBank data mining hinder the potential wide application of this tool for big data collection. To address this issue, we introduce new bioinformatics software —NCBIminer. NCBIminer is a freely available, cross-platform, and user-friendly software for mining nucleotide sequences from GenBank. The main purpose of NCBIminer is to download sequences for user required genes and taxonomic groups based on gene names, types, and one or several reference sequences. The program algorithms have been described elsewhere and here, we focus on introducing the details in the usage of the program including how to install, run, and set parameters.

Cupressaceae fossil tree stumps from the early Oligocene Lühe coal mine in southwestern China contain abundant quartz-petrified damage traces. The wood fossils were assigned to Taxodioxylon (very similar to extant Taxodium) based on wood anatomy analysis. Within the woods, three types of arthropods- and one fungus-mediated ichnofossils LHIF 1–4 (Lühe wood ichnofossils 1–4) were observed. The boring wood types for LHIF 1–3 are comparable to extant longicorn beetles (Cerambycidae), snout beetles (Curculionidae), and wood wasps (Siricidae). The polyporous structured traces of LHIF 4 were attributed to the invasion of stem canker fungus (Polyporaceae). This first-ever report of Taxodium-like fossil from the Oligocene of southwestern China points to Yunnan serving as a refugium for some lineage of gymnosperms at that time. Furthermore, the extensive traces of arthropods and fungus discovered from the fossil wood have filled a gap in fossil records for insect herbivory in this region. The wood stumps and decomposers suggest a swamp-like environment. The disappearance of Taxodium after the Oligocene supports incremental aridification and changes in winter season temperature conditions, which shifted the late Paleogene mixed deciduous broad-leaved and needle-leaved forest into the present evergreen broad-leaved forest.

Spinescence is an important functional trait possessed by many plant species for physical defence against mammalian herbivores. The development of spinescence must have been closely associated with both biotic and abiotic factors in the geological past, but knowledge of spinescence evolution suffers from a dearth of fossil records, with most studies focusing on spatial patterns and spinescence-herbivore interactions in modern ecosystems. Numerous well-preserved Eocene (~39 Ma) plant fossils exhibiting seven different spine morphologies discovered recently in the central Tibetan Plateau, combined with molecular phylogenetic character reconstruction, point not only to the presence of a diversity of spiny plants in Eocene central Tibet but a rapid diversification of spiny plants in Eurasia around that time. These spiny plants occupied an open woodland landscape, indicated by numerous megafossils and grass phytoliths found in the same deposits, as well as numerical climate and vegetation modelling. Our study shows that regional aridification and expansion of herbivorous mammals may have driven the diversification of functional spinescence in central Tibetan woodlands, ~24 million years earlier than similar transformations in Africa. [Abstract copyright: © 2022. The Author(s).]