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The causes of heterogeneity in evolutionary rates are a key question in macroevolution. Origination and extinction rates are closely related to abiotic factors, such as climate 1,2 and geography, 3,4 as well as biotic factors such as taxonomic richness 5,6 and morphology, 7 which are influenced by phylogeny. 8,9 Studies on the relationship between morphology and macroevolution have focused on morphological traits, including body size, 6,7,9 shape, 10 color, 11,12 and complexity, 13,14,15 and have proposed biological laws, such as the zero-force evolutionary law 16 and Cope's rule. 17 However, the relationship between morphological complexity and turnover rates remains poorly defined because of the lack of suitable measures for various subjects. 18,19 Here, we establish a quantitative method, the two-dimensional ornamentation index (2D-OI), which allows the description of the ornamental complexity of ammonoids. Ammonoids are one of the most abundant and well-studied fossil groups, with complex conch structures. 20 Ammonoids display some similarities with trilobites and mammals 21,22 in terms of their high evolutionary rates; however, the underlying mechanisms remain elusive. Moreover, ammonoids exhibit marked heterogeneity in turnover rates across spatiotemporal scales 23 and clades, 23,24 making them key clades for investigating the relationship between turnover rates and morphological complexity. The results show that morphologically complex genera and species often have higher origination and extinction rates than morphologically simple taxa. Diversity fluctuations of taxa with complex ornamentation generally overimprint and control the overall net diversification rates of ammonoids. This double-edged sword of rapid evolution and increased extinction risk driven by complex morphologies has significant implications for our understanding of how species survive over geological timescales. • New method ("2D-OI") to estimate the ornamentation complexity in shelled animals • Complex morphologic ammonoids generally exhibit shorter longevity than simple taxa • Complex morphologic taxa have higher origination and extinction rates than simple taxa • Complex taxa dominate overall fluctuations in ammonoid diversification rates Miao et al. show that morphologically complex ammonoid genera and species generally have shorter longevity and faster rates of turnover than morphologically simple taxa. The diversification rate of taxa with complex morphology controls the apparent overall diversification fluctuations of ammonoids. [ABSTRACT FROM AUTHOR]

Aim Location Methods Results Main Conclusions Rapid loss in global insect diversity has generated substantial public worry due to their critical ecological roles. However, there is controversy about the effectiveness of the global‐scale hotspots in guiding the conservation of diversity at the regional scale. Even worse, little is known about the knowledge of insect distributional dynamics in many understudied regions, such as East and Southeast Asia. Here, to guide for setting regional‐scale conservation priorities for insect diversity, we explore hawkmoths (Lepidoptera: Sphingidae) for their distributional dynamics and identify regional hotspots requiring protection.South China (including Guangdong, Guangxi, Hainan, Hong Kong and Macau) and northern Vietnam (17°~26.5° N, 102°~117.5° E).Species distribution models were generated for 194 hawkmoth species based on 3597 occurrence records to predict their distributions. We calculated the spatial patterns of taxonomic and phylogenetic diversity and identified regional hotspots. Furthermore, the potential assembly mechanisms underlying insect diversity were explored by analysing the rates of speciation, extinction and dispersal between phyloregions.(a) The coastal regions of South China and northern Vietnam represent a regional hotspot of hawkmoths in East and Southeast Asia, with significantly higher α‐diversity than that in inland regions. (b) Dispersal played a more important role than local speciation and extinction in the formation of regional hawkmoth hotspots.In this study, the ‘Out‐of‐the‐tropics model’ can explain the formation of the hawkmoth regional hotspots and the enhanced version of the ‘Pure dispersal model’ can explain the formation of the hotspots in Hainan Island. Compared with the local speciation and extinction, dispersal is the main driving factor that promoted the formation of the regional biodiversity hotspot of hawkmoths in South China. The case of Hainan Island suggests that protection within hotspots needs to account for specific regional macro‐evolutionary dynamics rather than indiscriminate coverage of identified hotspots. [ABSTRACT FROM AUTHOR]

The study of adaptive radiations has shed light on our current understanding of evolution. However, previous studies examining the mode in which species diversified, how diversification rates varied, and how ecological specialisation affected these processes have found few different results across different taxa and geographic and ecological systems, showing how complex this process is. To gain a more complete picture of how species evolve, additional model systems that encompass alternative ecological requirements are needed. Here, we present the results of a study aimed at unravelling the diversification mode and evolutionary drivers of the spider genus Dysdera, the red devil spiders, endemic to the Canary Islands. These species exhibit remarkable phenotypic variability in their mouthparts, which has been related to different levels of specialisation in the predation of isopods. We explored patterns of lineage diversification and assessed the role of trophic specialisation as a driver of species diversification. Additionally, we used climatic variables, occurrence data and morphological information to unravel the underlying mode of speciation by means of joint species distribution models and age‐range correlation methods. Our results reveal that red devil spiders underwent an early burst of diversification, followed by a slowdown of diversification rates, which is a hallmark of adaptive radiation. We also found evidence that the trophic morphology shaped diversification, with specialist species exhibiting higher rates of diversification. Finally, our analyses suggest that speciation occurred mostly in allopatry, with subsequent secondary sympatry following range expansion. [ABSTRACT FROM AUTHOR]

Why and how organismal lineages radiate is commonly studied through either assessing abiotic factors (biogeography, geomorphological processes, and climate) or biotic factors (traits and interactions). Despite increasing awareness that both abiotic and biotic processes may have important joint effects on diversification dynamics, few attempts have been made to quantify the relative importance and timing of these factors, and their potentially interlinked direct and indirect effects, on lineage diversification. We here combine assessments of historical biogeography, geomorphology, climatic niche, vegetative, and floral trait evolution to test whether these factors jointly, or in isolation, explain diversification dynamics of a Neotropical plant clade (Merianieae, Melastomataceae). After estimating ancestral areas and the changes in niche and trait disparity over time, we employ Phylogenetic Path Analyses as a synthesis tool to test eleven hypotheses on the individual direct and indirect effects of these factors on diversification rates. We find strongest support for interlinked effects of colonization of the uplifting Andes during the mid-Miocene and rapid abiotic climatic niche evolution in explaining a burst in diversification rate in Merianieae. Within Andean habitats, later increases in floral disparity allowed for the exploitation of wider pollination niches (i.e. shifts from bee to vertebrate pollinators), but did not affect diversification rates. Our approach of including both vegetative and floral trait evolution, rare in assessments of plant diversification in general, highlights that the evolution of woody habit and larger flowers preceded the colonization of the Andes, but was likely critical in enabling the rapid radiation in montane environments. Overall, and in concert with the idea that ecological opportunity is a key element of evolutionary radiations, our results suggest that a combination of rapid niche evolution and trait shifts was critical for the exploitation of newly available niche space in the Andes in the mid-Miocene. Further, our results emphasize the importance of incorporating both abiotic and biotic factors into the same analytical framework if we aim to quantify the relative and interlinked effects of these processes on diversification. [ABSTRACT FROM AUTHOR]

Technological and methodological advances in biogeography, phylogenetics, and bioinformatics during the past couple of decades provide greatly enhanced insights into the evolutionary history of birds in space and time. Molecular data, especially next-generation DNA sequencing, have produced a revolution in reconstructing the phylogenetic history of lineages. These advances shed a new light on the mode, tempo, and spatial context of differentiation processes that shaped the composition and structure of extant forest bird communities of temperate forests of the Northern Hemisphere. This paper offers a framework for understanding this history based on analytical tools that allow us to decipher the imprint of changes in the geographic configuration of land masses and in climates since the Mesozoic, with a focus on the temperate-tropical flyways that connect the massive forest blocks of the Northern to those of the Southern Hemispheres. Differentiation of most extant bird lineages and species has been shown to have begun in a deeper past than formerly thought, although recent analyses from molecular phylogenies also support the much-debated Late Pleistocene model of speciation. Geographical connections between tropical and temperate realms make north-south flyways important drivers of differentiation for many lineages. The histories of differentiation and colonisation of clades, including both resident and long-distance migrants, are discussed in relation to two alternative theories, the ‘southern home theory’ and the ‘northern home theory’. The region-specific characters of the bird faunas and differences between the main temperate forest blocks of the Northern Hemisphere are discussed in light of the hypotheses concerning dispersal processes related with geographical configuration of land masses. Differential dispersal-colonisation rates from tropical regions and subsequent diversification in temperate regions (and vice versa) are also considered. The causes of the observed decline in diversification rates during the Pleistocene are examined from phylogenetic reconstructions of various clades.

Introduction: The phenomenal expansion of angiosperms has prompted many investigations into the factors driving their diversification, but there remain significant gaps in our understanding of flowering plant species diversity. Methods: Using the crown age of families from five studies, we used a maximum likelihood approach to classify families as having poor, predicted or high species richness (SR) using strict consensus criteria. Using these categories, we looked for associations between family SR and i) the presence of an inferred familial ancestral polyploidization event, ii) 23 life history and floral traits compiled from previously published datasets and papers, and iii) sexual system (dioecy) or genetically determined self-incompatibility (SI) mating system using an updated version of our own database and iv) geographic distribution using a new database describing the global distribution of plant species/families across realms and biomes and inferred range. Results: We find that more than a third of angiosperm families (65%) had predicted SR, a large proportion (30.2%) were species poor, while few (4.8%) had high SR. Families with poor SR were less likely to have undergone an ancestral polyploidization event, exhibited deficits in diverse traits, and were more likely to have unknown breeding systems and to be found in only one or few biomes and realms, especially the Afrotropics or Australasia. On the other hand, families with high SR were more likely to have animal mediated pollination or dispersal, are enriched for epiphytes and taxa with an annual life history, and were more likely to harbour sporophytic SI systems. Mapping the global distribution of georeferenced taxa by their family DR, we find evidence of regions dominated by taxa from lineages with high vs low SR. Discussion: These results are discussed within the context of the literature describing "depauperons" and the factors contributing to low and high biodiversity in angiosperm clades. [ABSTRACT FROM AUTHOR]

Aim: Contemporary environmental, historical and evolutionary factors are increasingly used to decipher the drivers of spatial patterns of species richness. Evidence of such correlations for Chinese reptiles is scarce and poorly understood. We therefore explored the validity of the environmental capacity, historical climatic stability and diversification rates hypotheses on Chinese lizard richness. Location: Mainland China. Taxon: Squamata: Sauria. Methods: We mapped the distribution ranges of all 237 lizards in mainland China using a combination of different datasets. We used current environmental conditions (ambient energy, environmental productivity, and habitat heterogeneity), historical climate stability indices (long term: since ~3.3 Ma and short term: since the last glacial maximum) and mean tip diversification rates, to test whether current environmental conditions, historical climate change and diversification rates drive contemporary richness patterns of lizards in China. We applied piecewise structural equation models (pSEM) to jointly evaluate our hypotheses, considering direct and indirect effects. Results: Chinese lizards showed strong latitudinal diversity gradients. We found consistent support for contemporary climatic and environmental factors relationships with richness. Richness was also positively correlated with short‐term climatic stability, but less so with long‐term stability. Diversification rates were seldom found to be positively correlated with lizard richness. Main Conclusions: Our results support the environmental capacity and historical climate hypotheses, which link high richness to highly productive warm and stable regions (and low richness to cold and unstable regions). We conclude that post‐speciation dispersal and short‐term climatic oscillations quickly swamp the long‐term signal of diversification rates and climatic fluctuations, creating strong current climate–richness associations. [ABSTRACT FROM AUTHOR]

Introduction: The phenomenal expansion of angiosperms has prompted many investigations into the factors driving their diversification, but there remain significant gaps in our understanding of flowering plant species diversity. Methods: Using the crown age of families from five studies, we used a maximum likelihood approach to classify families as having poor, predicted or high species richness (SR) using strict consensus criteria. Using these categories, we looked for associations between family SR and i) the presence of an inferred familial ancestral polyploidization event, ii) 23 life history and floral traits compiled from previously published datasets and papers, and iii) sexual system (dioecy) or genetically determined self-incompatibility (SI) mating system using an updated version of our own database and iv) geographic distribution using a new database describing the global distribution of plant species/families across realms and biomes and inferred range. Results: We find that more than a third of angiosperm families (65%) had predicted SR, a large proportion (30.2%) were species poor, while few (4.8%) had high SR. Families with poor SR were less likely to have undergone an ancestral polyploidization event, exhibited deficits in diverse traits, and were more likely to have unknown breeding systems and to be found in only one or few biomes and realms, especially the Afrotropics or Australasia. On the other hand, families with high SR were more likely to have animal mediated pollination or dispersal, are enriched for epiphytes and taxa with an annual life history, and were more likely to harbour sporophytic SI systems. Mapping the global distribution of georeferenced taxa by their family DR, we find evidence of regions dominated by taxa from lineages with high vs low SR. Discussion: These results are discussed within the context of the literature describing "depauperons" and the factors contributing to low and high biodiversity in angiosperm clades. [ABSTRACT FROM AUTHOR]

Abstract Relaxed clock Bayesian evolutionary inference (BEI) enables the co‐estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. However, there is limited availability of bioinformatic tools to pre‐ and postprocess data from BEI, such as identifying morphological data partitions, or statistically testing and creating publication quality plots of evolutionary hypotheses. Here, we introduce EvoPhylo, an r package to perform automated morphological character partitioning and analyse macroevolutionary parameter from relaxed clock (time‐calibrated) BEI outputted by the programs Mr.Bayes and BEAST2. These include rates of evolution and mode of selection for each character partition, diversification rate parameters, and handling fossil‐only posterior trees. We present the theoretical background behind EvoPhylo's functions and analytical tools for evolutionary hypothesis testing, its potential uses, and interpretation of its results with a series of vignettes and links to a step‐by‐step tutorial using examples from two empirical datasets. EvoPhylo will facilitate the use of Bayesian relaxed clocks as a tool for macroevolutionary inference across a wide range of users and fields of research, especially those that make usage of morphological datasets, from paleontological to total evidence dating analyses.

IntroductionThe phenomenal expansion of angiosperms has prompted many investigations into the factors driving their diversification, but there remain significant gaps in our understanding of flowering plant species diversity.MethodsUsing the crown age of families from five studies, we used a maximum likelihood approach to classify families as having poor, predicted or high species richness (SR) using strict consensus criteria. Using these categories, we looked for associations between family SR and i) the presence of an inferred familial ancestral polyploidization event, ii) 23 life history and floral traits compiled from previously published datasets and papers, and iii) sexual system (dioecy) or genetically determined self-incompatibility (SI) mating system using an updated version of our own database and iv) geographic distribution using a new database describing the global distribution of plant species/families across realms and biomes and inferred range.ResultsWe find that more than a third of angiosperm families (65%) had predicted SR, a large proportion (30.2%) were species poor, while few (4.8%) had high SR. Families with poor SR were less likely to have undergone an ancestral polyploidization event, exhibited deficits in diverse traits, and were more likely to have unknown breeding systems and to be found in only one or few biomes and realms, especially the Afrotropics or Australasia. On the other hand, families with high SR were more likely to have animal mediated pollination or dispersal, are enriched for epiphytes and taxa with an annual life history, and were more likely to harbour sporophytic SI systems. Mapping the global distribution of georeferenced taxa by their family DR, we find evidence of regions dominated by taxa from lineages with high vs low SR.DiscussionThese results are discussed within the context of the literature describing “depauperons” and the factors contributing to low and high biodiversity in angiosperm clades.

Given the diverse nature of traits involved in territorial defence, they may respond to different selective pressures and then exhibit distinct patterns of evolution. These selective pressures also may cause territorial behaviour to be associated with environmental and morphological variables. Such associations, however, have mostly been studied at the intraspecific level, being phylogenetic analyses of territoriality in a broad taxonomic framework rare in the literature. We used the anuran subfamily Hylinae to test (1) whether two territorial‐behaviour traits with different levels of aggression—territorial call and physical combat—are evolutionarily more labile than a morphological trait used in physical combat—the spine‐shaped prepollex; (2) whether reproduction in lentic waters and phytotelmata, as well as resource scarcity, might favour the occurrence of territoriality; (3) if physical combat is more important than territorial call for the evolution of body size and sexual size dimorphism and (4) the relationships between territorial‐behaviour traits and lineage diversification. We mainly used the literature to build two datasets with different levels of certainty. Territorial‐behaviour traits exhibited intermediate levels of phylogenetic signal in Hylinae, whereas the phylogenetic signal for the presence of the spine‐shaped prepollex was strong. We found support for the hypothesis that reproduction in lentic water favours the occurrence of territorial behaviour, because the expression of territorial‐behaviour traits was more associated with reproduction in lentic than in lotic waters. Territorial‐behaviour traits were not correlated with annual precipitation nor with habitat complexity. Body size and sexual size dimorphism were not correlated with the presence of territorial call nor with physical combat. We identified negative correlations between diversification rates and physical combat. Relationships of territorial call and physical combat with diversification rates suggest that these territorial behaviours influence evolutionary processes in different ways. [ABSTRACT FROM AUTHOR]

Relaxed clock Bayesian evolutionary inference (BEI) enables the co‐estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. However, there is limited availability of bioinformatic tools to pre‐ and postprocess data from BEI, such as identifying morphological data partitions, or statistically testing and creating publication quality plots of evolutionary hypotheses.Here, we introduce EvoPhylo, an r package to perform automated morphological character partitioning and analyse macroevolutionary parameter from relaxed clock (time‐calibrated) BEI outputted by the programs Mr.Bayes and BEAST2. These include rates of evolution and mode of selection for each character partition, diversification rate parameters, and handling fossil‐only posterior trees.We present the theoretical background behind EvoPhylo's functions and analytical tools for evolutionary hypothesis testing, its potential uses, and interpretation of its results with a series of vignettes and links to a step‐by‐step tutorial using examples from two empirical datasets.EvoPhylo will facilitate the use of Bayesian relaxed clocks as a tool for macroevolutionary inference across a wide range of users and fields of research, especially those that make usage of morphological datasets, from paleontological to total evidence dating analyses. [ABSTRACT FROM AUTHOR]

Abstract Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

Chameleons are charismatic and common lizards across Madagascar, Africa, and some surrounding regions. Little is known about their diversification dynamics and how this relates to their ecology, so we estimated diversification rate variation and consider this in the context of three hypotheses previously proposed in the literature. First, that the transoceanic dispersal from Africa to Madagascar on two separate occasions has resulted in fast radiation of Malagasy chameleons. Second, that the substantial floral turnover in their distributions within South Africa has resulted in rapid radiations of the endemic dwarf chameleons (Bradypodion). Finally, that the evolution of distinct ecomorphs of chameleon has fuelled fast diversification via adaptive radiations. We use the most recent and complete phylogeny of chameleons to estimate the diversification dynamics of the group using three methods: BAMM (which estimates constant or gradually changing diversification regimes and tests for shifts in these), MEDUSA (which tests for rate shifts in particular clades), and ClaDS (which estimates branch‐specific diversification rates). Our results from all analyses estimate a diversification rate increase in a clade containing most of the genus Bradypodion, a group containing the South African dwarf chameleons which occur in recognized biodiversity hotspots in diverse habitats. We find no evidence for shifts resulting from dispersal events to Madagascar or related to the strong ecomorphological divergence of short‐tailed chameleon lineages (Brookesia, Palleon, Rhampholeon, and Rieppeleon). The single burst of diversification within chameleons was in a clade which was associated with geographic areas which have experienced rapid habitat turnover and vicariance over the last ~10 million years. This suggests that 'habitat vicariance' resulting from ecological changes in vegetation has contributed to the diversity of species in this area by increasing diversification rates. [ABSTRACT FROM AUTHOR]

Diversification rates inferred from phylogenies are not identifiable if the rates are allowed to vary freely over time. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known.Prior hypotheses typically render diversification rates identifiable, but the results then depend on these a priori hypotheses and assumptions. To test the robustness of diversification results to these a priori hypotheses, we use two different approaches to explore congruence classes: (i) constructing congruent models under alternative hypotheses and (ii) sampling alternative rate function within the congruence class.Our methods are implemented in the open‐source R package CRABS (https://github.com/afmagee/CRABS). CRABS provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, that is, increasing, flat or decreasing rates.Although there are infinitely many equally likely diversification rate functions, these can share common features. CRABS can be used to assess if diversification rate patterns are robust despite the non‐identifiability of the birth–death model. In our example, we clearly identify three phases of diversification rate changes that are common among all models which we sampled from the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies. [ABSTRACT FROM AUTHOR]

Abstract Background The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae). Results Our plastid tree topologies were robust to analyses based on different plastid regions and different strategies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae comprised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversification rates of tribe Perseeae accelerated twice in the late Miocene. Conclusions Our findings suggest that the intensified precipitation in East Asia in the early Miocene may have facilitated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late Miocene, species assembly and diversification within the EBLFs had become rapid.

Abstract Background Understanding drivers of animal biodiversity has been a longstanding aim in evolutionary biology. Insects and fishes represent the largest lineages of invertebrates and vertebrates respectively, and consequently many ideas have been proposed to explain this diversity. Natural enemy interactions are often important in diversification dynamics, and key traits that mediate such interactions may therefore have an important role in explaining organismal diversity. Venom is one such trait which is intricately bound in antagonistic coevolution and has recently been shown to be associated with increased diversification rates in tetrapods. Despite ~ 10% of fish families and ~ 16% of insect families containing venomous species, the role that venom may play in these two superradiations remains unknown. Results In this paper we take a broad family-level phylogenetic perspective and show that variation in diversification rates are the main cause of variations in species richness in both insects and fishes, and that venomous families have diversification rates twice as high as non-venomous families. Furthermore, we estimate that venom was present in ~ 10% and ~ 14% of the evolutionary history of fishes and insects respectively. Conclusions Consequently, we provide evidence that venom has played a role in generating the remarkable diversity in the largest vertebrate and invertebrate radiations.

Explaining global variation in geographic and taxonomic diversity gradients represents a central focus of macroecology and macroevolution. Ultimately, these diversity gradients have been generated over deep timescales as a consequence of historical variation in rates of dispersal, diversification, and the capacity of different geographic areas to preserve taxa through time. Here, I assess the relationships among these processes, to elucidate the causes of geographic and taxonomic variation in species richness among the most speciose order of birds: the Passeriformes (c. 6,500 species). To achieve this, I comparatively analyze phylogenetic, distributional and eco-morphological trait data collated at broad taxonomic and spatial scales. The results of my analyses strongly support the prevalence of historical dispersal events across large geographic scales, in addition to spatiotemporal variation in diversification rates. These findings reflect that some lineages and some geographic regions (notably tropical mountain regions and island archipelagoes) generate and maintain a much larger amount of species diversity than others. In addition, the evolution of particular life-history and eco-morphological traits, specifically pair breeding systems, and higher wing aspect-ratios, increased rates of range expansion and diversification. In summary, geographic variation in historical diversification combined with differences in the capacity of lineages to colonize new areas, determines spatial and taxonomic differences in passerine species richness.

Evolutionary and ecological processes that influenced the assembly of the New World flora are best understood through investigation of spatio-temporal processes of specific lineages, but some groups still lack a historical overview. Here, we produced a well-sampled dated tree, reconstructed ancestral ranges and performed diversification analyses for Sisyrinchium (Iridaceae) to elucidate its evolution in the Americas. Eight molecular markers and samples representing its full geographical range and morphological diversity were used to estimate divergence times with a Bayesian relaxed clock with secondary calibrations. Ancestral range reconstruction under likelihood methods and diversification analyses were performed. Sisyrinchium originated in a broad range including the Andes and Mesoamerica in the Mid-Miocene. Diversification at high elevations occurred in the early diverging lineages, which feature the highest extinction rates. Increase in diversification rate was detected during the Pliocene/Pleistocene after the colonization of lower elevations. Later sympatric speciation in south-eastern Brazil was followed by movements to other regions, including a long-dispersal event to North America. Higher extinction rates were followed by movements to lower elevations, with periods of accelerated Andean orogeny and global temperature decrease. Our results indicate that palaeoclimate and changes in elevational range influenced diversification in Sisyrinchium. [ABSTRACT FROM AUTHOR]

Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host‐type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee‐parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state‐dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic‐taxonomic approach based on birth‐death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee‐parasitoid, and that transitions towards a phoretic bee‐parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee‐parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee‐and grasshopper‐parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics. [ABSTRACT FROM AUTHOR]

Background: The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the assembly of this biome, we generated a molecular phylogeny of one of its essential plant groups, the tribe Perseeae (Lauraceae). Results: Our plastid tree topologies were robust to analyses based on different plastid regions and different strategies for data partitioning, nucleotide substitution saturation, and gap handling. We found that tribe Perseeae comprised six major clades and began to colonize the subtropical EBLFs of East Asia in the early Miocene. The diversification rates of tribe Perseeae accelerated twice in the late Miocene. Conclusions: Our findings suggest that the intensified precipitation in East Asia in the early Miocene may have facilitated range expansions of the subtropical EBLFs and establishment of tribe Perseeae within this biome. By the late Miocene, species assembly and diversification within the EBLFs had become rapid. [ABSTRACT FROM AUTHOR]

Evolutionary radiations have intrigued biologists for more than a century, yet our understanding of the drivers of radiating diversification is still limited. We investigate the roles of environmental and species-intrinsic factors in driving the rapid radiation of Saussurea (Asteraceae) by deploying a number of palaeoenvironment-, diversity- and trait-dependent models, as well as ecological distribution data. We show that three main clades of Saussurea began to diversify in the Miocene almost simultaneously, with increasing diversification rates (DRs) negatively dependent on palaeotemperature but not dependent on species diversity. Our trait-dependent models detect some adaptive morphological innovations associated with DR shifts, while indicating additional unobserved traits are also likely driving diversification. Accounting for ecological niche data, we further reveal that accelerations in DRs are correlated with niche breadth and the size of species' range. Our results point out a macroevolutionary scenario where both adaptive morphological evolution and ecological opportunities provided by palaeoenvironmental fluctuations triggered an exceptionally radiating diversification. Our study highlights the importance of integrating phylogenomic, morphological, ecological and model-based approaches to illustrate evolutionary dynamics of lineages in biodiversity hotspots. [ABSTRACT FROM AUTHOR]

[Display omitted] • The last common ancestor for Ciliophora was likely a free-living organism. • Symbiotic relationships are recent in the evolution of Ciliophora phylum. • The parasitism emerged several times and independently within Ciliophora phylum. • The parasite ciliates originated from free-living and mutualists ancestral ciliates. • Ciliates associated host increase the rate of diversification in Ciliophora. Ciliophora is a phylum that is comprised of extremely diverse microorganisms with regard to their morphology and ecology. They may be found in various environments, as free-living organisms or associated with metazoans. Such associations range from relationships with low metabolic dependence such as epibiosis, to more intimate relationships such as mutualism and parasitism. We know that symbiotic relationships occur along the whole phylogeny of the group, however, little is known about their evolution. Theoretical studies show that there are two routes for the development of parasitism, yet few authors have investigated the evolution of these characteristics using molecular tools. In the present study, we inferred a wide dated molecular phylogeny, based on the 18S rDNA gene, for the entire Ciliophora phylum, mapped life habits throughout the evolutionary time, and evaluated whether symbiotic relationships were linked to the variation in diversification rates and to the mode of evolution of ciliates. Our results showed that the last common ancestor for Ciliophora was likely a free-living organism, and that parasitism is a recent adaptation in ciliates, emerging more than once and independently via two distinct routes: (i) a free-living ciliate evolved into a mutualistic organism and, later, into a parasitic organism, and (ii) a free-living ciliate evolved directly into a parasitic organism. Furthermore, we have found a significant increase in the diversification rate of parasitic and mutualistic ciliates compared with their free-living conspecifics. The evolutionary success in different lineages of symbiont ciliates may be associated with many factors including type and colonization placement on their host, as well as physical and physiological conditions made available by the hosts. [ABSTRACT FROM AUTHOR]

The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200‐million‐year history of teleosts. [ABSTRACT FROM AUTHOR]

Pteropodidae constitutes one of the most diverse bat families. These bats have evolved a phytophagous diet, likely lost laryngeal echolocation capability, and attained the largest body sizes among bats. Previous phylogenetic studies suggested that the family might have experienced an explosive diversification at its origin. Here, we readdress this hypothesis using a macroevolutionary approach based on Bayesian statistics (BAMM), a sampling of 139 pteropodid species, and divergence date estimates obtained in a comprehensive phylogenetic study of Chiroptera with multiple fossil calibration points. We evaluated the effect of missing data and of a reduced outgroup by repeating the analyses across simulated complete phylogenies and across a comprehensive Yinpterochiroptera phylogeny, respectively. Additionally, we performed an alternative analysis to detect diversification-rate shifts through time, the birth-death-shift method. In contrast with a previous study, we found strong statistical signals of rapid diversification at the origin of Pteropodidae. BAMM also detected diversification-rate shifts (increases) at the origin of Pteropus, as well as at crown Hipposideridae and Rhinolophidae. The birth-death-shift method detected a shift at approximately 25 million years ago, the estimated crown ages of both Pteropodidae and Hipposideridae. Our results point to a complex dynamics in the evolution of bat families, likely related to key innovations, demographic factors, and environmental opportunity enhanced by global-scale climatic and geographic changes. [ABSTRACT FROM AUTHOR]

Aim: The evolutionary causes of the latitudinal diversity gradient are debated. Hypotheses have ultimately invoked either faster rates of diversification in the tropics or more time for diversification owing to the tropical origins of higher taxa. Here, we perform the first test of the diversification rate and time hypotheses in freshwater ray‐finned fishes, a group comprising nearly a quarter of all living vertebrates. Location: Global. Time period: 368–0 Ma. Major taxa studied: Extant freshwater ray‐finned fishes. Methods: Using a mega‐phylogeny of actinopterygian fishes and a global database of occurrence records, we estimated net diversification rates, the number of colonizations and regional colonization times of co‐occurring species in freshwater drainage basins. We used generalized additive models to test whether these factors were related to latitude. We then compared the influence of diversification rates, numbers of colonizations, colonization times and surface area on species richness, and how these factors are related to each other. Results: Although both diversification rates and time were related to richness, time had greater explanatory power and was more strongly related to latitude than diversification rates. Other factors (basin surface area and number of colonizations) also helped to explain richness but were unrelated to latitude. The most diverse freshwater basins of the world (Amazon and Congo rivers) were dominated by lineages having Mesozoic origins. The temperate groups dominant today arrived near the Cretaceous–Palaeogene boundary, leaving comparatively less time to build richness. Diversification rates and colonization times were inversely related: recently colonized basins had the fastest rates, whereas ancient species‐rich faunas had slower rates. Main conclusions: We concluded that time is the leading driver of latitudinal disparities in richness in freshwater fish faunas. We suggest that the most likely path to building very high species richness is through diversification over long periods of time, rather than through rapid diversification. [ABSTRACT FROM AUTHOR]

Aim: The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been tested in the Caribbean due to its geological complexity. Here, we use the conifer genus Podocarpus to explore this hypothesis. We infer the evolutionary history, biogeography, and diversification rates of this genus under a hypothesis testing framework. Location: The Caribbean archipelago (Antilles). Taxon: Podocarpus (Podocarpaceae). Methods: We present the most comprehensive sampling for Caribbean Podocarpus to date in a Bayesian dated phylogenetic tree using a genotyping by sequencing DNA matrix of 67,589 bp. We inferred ancestral ranges and inter‐island divergence patterns using several models available. We explored diversification rates associated with island colonization, and checked for diversification rate shifts in the phylogeny. Results: Caribbean Podocarpus is the result of colonization from the Andes during the Eocene to Oligocene (c. 45–31 Ma). Lesser Antillean species originated during the Oligocene from the Andes or the Greater Antilles, depending on the model of choice. Vicariance can explain the divergence of Cuban and Hispaniolan species, with subsequent dispersals into Jamaica. Despite the availability of new habitat opportunities, which might promote cladogenesis, insular Podocarpus did not show higher diversification rates than continental taxa. Main conclusions: The conditions for progression rule were not met because colonization of younger islands (Lesser Antilles) occurred from the continent, or because suitable habitat in the partially emerged younger islands was likely present at the time older islands (Greater Antilles) were colonized. An improved palaeogeographical knowledge of the Caribbean will allow testing this hypothesis in multiple lineages. Our finding that diversification rates did not increase with island colonization might be common in other Caribbean lineages. Genotyping by sequencing proved promising to reveal complex historical assembly processes of vicariance and dispersal at a fine phylogenetic scale. [ABSTRACT FROM AUTHOR]

Determining the tempo and mode of non-avian dinosaur extinction is one of the most contentious issues in palaeobiology. Extensive disagreements remain over whether their extinction was catastrophic and geologically instantaneous or the culmination of long-term evolutionary trends. These conflicts have arisen due to numerous hierarchical sampling biases in the fossil record and differences in analytical methodology, with some studies identifying long-term declines in dinosaur richness prior to the Cretaceous–Palaeogene (K-Pg) boundary and others proposing continued diversification. Here, we use Bayesian phylogenetic generalized linear mixed models to assess the fit of 12 dinosaur phylogenies to three speciation models (null, slowdown to asymptote, downturn). We do not find strong support for the downturn model in our analyses, which suggests that dinosaur speciation rates were not in terminal decline prior to the K-Pg boundary and that the clade was still capable of generating new taxa. Nevertheless, we advocate caution in interpreting the results of such models, as they may not accurately reflect the complexities of the underlying data. Indeed, current phylogenetic methods may not provide the best test for hypotheses of dinosaur extinction; the collection of more dinosaur occurrence data will be essential to test these ideas further.

Abstract Background Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera. Results Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa. Conclusions Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.

Background: Understanding drivers of animal biodiversity has been a longstanding aim in evolutionary biology. Insects and fishes represent the largest lineages of invertebrates and vertebrates respectively, and consequently many ideas have been proposed to explain this diversity. Natural enemy interactions are often important in diversification dynamics, and key traits that mediate such interactions may therefore have an important role in explaining organismal diversity. Venom is one such trait which is intricately bound in antagonistic coevolution and has recently been shown to be associated with increased diversification rates in tetrapods. Despite ~ 10% of fish families and ~ 16% of insect families containing venomous species, the role that venom may play in these two superradiations remains unknown. Results: In this paper we take a broad family-level phylogenetic perspective and show that variation in diversification rates are the main cause of variations in species richness in both insects and fishes, and that venomous families have diversification rates twice as high as non-venomous families. Furthermore, we estimate that venom was present in ~ 10% and ~ 14% of the evolutionary history of fishes and insects respectively. Conclusions: Consequently, we provide evidence that venom has played a role in generating the remarkable diversity in the largest vertebrate and invertebrate radiations. [ABSTRACT FROM AUTHOR]

Parasitism is often invoked as a factor explaining the variation in diversification rates across the tree of life, while also representing up to half of Earth's diversity. Yet, patterns and processes of parasite diversification remain mostly unknown. In this study, we assess the patterns of parasite diversification and specifically determine the role of life‐history traits (i.e. life cycle complexity and host range) and major coevolutionary events in driving diversification across eight phylogenetic datasets spanning taxonomically different parasite groups. Aware of the degree of incomplete sampling among all parasite phylogenies, we also tested the impact of sampling bias on estimates of diversification. We show that the patterns and rates of parasite diversification differ among taxa according to life cycle complexity and to some extent major host transitions. Only directly transmitted parasites were found to be influenced by an effect of major host transitions on diversification rates. Although parasitism may be a main factor responsible for heterogeneity in diversification among the tree of life, the high degree of incomplete parasite phylogenies remains an obstacle when modelling diversification dynamics. Nevertheless, we provide the first comparative test of parasite diversification, revealing some consistent patterns and insight into the processes that shape it. [ABSTRACT FROM AUTHOR]

Explosive radiations—substantial increases in net species diversification—have been considered one of the most intriguing diversification patterns across the Tree of Life, but the subsequent change, movement, and extinction of the constituent lineages make radiations hard to discern or understand as geological time passes. We used the megadiverse angiosperm genus Solanum L. (Solanaceae), with ca. 1200 currently accepted species distributed worldwide in a wide array of habitats, to explore these patterns on a global scale. We synthesized phylogenetic and distributional data for this ongoing radiation to show how dispersal events and past climatic changes have interacted to shape diversification. We find that, despite the vast diversity of Solanum lineages in the Neotropics, lineages in the Old World are diversifying more rapidly. This recent increase in diversification coincides with a long‐distance dispersal event from the Neotropics to regions where major climatic changes were taking place. Two separate groups of Solanum have migrated and established in Australia, but only the arid‐adapted lineages underwent significant increases in diversification rate, as they were able to adapt to the continent's long‐term climatic trend towards seasonally dry and arid biomes (a pattern observed in the diversification of other arid‐adapted groups). Our findings provide a clear example of how successful colonization of new areas and niches can—but does not always—drive explosive diversifications. [ABSTRACT FROM AUTHOR]

Ancient Lake Ohrid is the oldest and biologically most diverse freshwater lake in Europe. The recent deep-drilling campaign SCOPSCO provided detailed insights into the lake's limnological history over the past 1.36 my. However, it remains unclear what factors triggered the onset of radiations and whether diversification rates remained constant throughout their evolution. We therefore inferred time-calibrated molecular phylogenies for eight invertebrate groups endemic to Lake Ohrid and performed diversification-rate analyses for the four most species-rich groups. The molecular-clock analyses indicate that few groups possibly originated in springs or rivers in the 'proto-Balkans' during the pre-lake phase. The onset of all other radiations, however, can be correlated to one of the three limnological phases in the Ohrid Graben and in Lake Ohrid since 1.9 mya. We therefore assume that the onset of radiations was triggered by an increased ecological opportunity arising from massive environmental changes in the course of the lake deepening. The diversification-rate analyses further indicate that the groups examined diversified with a constant rate. Although the reconstruction of the early evolutionary history of these groups remains challenging, our data suggest that the relatively stable conditions in Lake Ohrid together with its high buffer capacity likely prevented significant changes in diversification rates over time. [ABSTRACT FROM AUTHOR]

Premise of research. Analyses of the evolution of floral morphology and symmetry broaden our understanding of the drivers of angiosperm diversification. Integrated within a flower, labile floral characters produce different phenotypes that promote variable interactions with pollinators. Thus, investigation of floral evolution may help with inferring potential historic transitions in pollinator modes and ecological pressures that generated present diversity. This study aims to explore the morphological evolution of flowers in Miconieae, a species-rich Neotropical tribe within the Melastomataceae. Despite a constrained floral plan, Melastomataceae manage to achieve a variety of floral phenotypes appealing to diverse pollinator types, with a majority of the species requiring specialized "buzz pollination" by bees. However, previous research of Miconieae documented several instances of convergent evolution of phenotypes associated with generalized pollination strategies. We explore the floral morphological evolution of Miconieae in a phylogenetic context to understand how diversification relates to different phenotypes and how common evolution of generalized pollination systems is within this tribe. Methodology. We constructed the largest species-level phylogeny of the Miconieae and combined it with morphological data on a variety of floral characteristics for more than 350 species scored from field photographs. Trait evolution was then analyzed using ancestral state reconstruction with stochastic character mapping. Trait correlation was estimated with Pagel's statistical method for discrete characters and with regression analysis of phylogenetically independent contrasts of continuous characters. We analyzed diversification in the tribe with Bayesian analysis of macroevolutionary mixtures and explored the effect of character state evolution on diversification with the binary state speciation and extinction approach. Pivotal results. Our analyses reveal rampant convergent and correlated evolution of multiple characters indicative of pollinator-mediated selective pressures. Conclusions. We confirm several parallel trends in the evolution of generalized floral phenotypes and find an association between generalization trends and increased diversification rates that may be related to colonization of highland environments. [ABSTRACT FROM AUTHOR]

Summary: The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction‐site associated DNA sequencing (RAD‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000 RAD‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome. See also the Editorial on this article by Plomion & Martin, 226: 943–946. [ABSTRACT FROM AUTHOR]

The Ronnbergia alliance is a lineage of two genera, Ronnbergia and Wittmackia , which diversified in three centres of distribution; the Pacific Forest, the Atlantic Forest and the Caribbean. In this study, we reconstructed the most plausible biogeographic scenario that explain the disjunct evolution of the Ronnbergia alliance in these centres of diversity. We also compared the evolutionary rate dynamics of lineage diversification and floral evolution in each of these areas. Our results suggested that the Ronnbergia alliance originated in the Atlantic Forest c. 5.2 Mya. Ronnbergia originated c. 3.5 Mya after a long-distance dispersal event to the Pacific Forest. The diversification of Wittmackia started in the Atlantic Forest, c. 3.2 Mya, and experienced more heterogeneous evolutionary rate dynamics than Ronnbergia during its radiation. In Wittmackia a long-distance dispersal from the Atlantic Forest to Jamaica gave rise to the Caribbean clade, which diversified rapidly and experienced significantly higher rates of floral evolution. This study helped in understanding how bromeliad diversification occurs differently among major centres of biodiversity. In our case, we found how the Caribbean is a much more dynamic area of diversification than the Atlantic Forest or the Pacific Forest. [ABSTRACT FROM AUTHOR]

• Low-altitudinal soil had a wider niche for specialists and generalists. • pH had the greatest impact on soil bacterial community in the three altitudinal soils. • The species turnover rate was ranked as low->middle->high-altitudinal soils. • Low-altitudinal soil was more suitable for the growth of soil bacterias on Fanjing Mountain. Recent evidence suggests that Abies fanjingshanensis , endemic to China's Fanjing Mountain—a UNESCO World Heritage site—is facing a worrying decline. It is postulated that this decline is intricately linked to soil conditions. In response, this study has categorized microbial communities as generalists or specialists within soils from varying altitudes and has examined their relationship with soil nutrient status, as well as their implications for species extinction and diversification rates. Our findings indicate that low-altitude soils provide a more expansive and significant ecological niche for both specialist and generalist species compared to those from mid- and high-altitudes. Moreover, microbial diversity was markedly higher in the low-altitude soils. Soil pH emerged as the predominant factor influencing microbial communities across all elevations. In accordance with pH variations, species turnover rates followed an ascending order from low to high altitudes, corroborated by the specialization rates of generalists, which were 16.83, 1.50, and 3.06 times higher in low-, mid-, and high-altitude soils, respectively. Network stability analysis revealed that low-altitude soils exhibited greater robustness compared to their higher altitude counterparts. These results suggest that low-altitude soils on Fanjing Mountain present a more favorable environment for soil bacterial growth, potentially elucidating the marked decline of rare plant species in the mid- and high-altitude regions. This research contributes to a more nuanced understanding of the interplay between microbial communities and soil nutrition on Fanjing Mountain, with broader implications for the conservation of rare montane flora. [ABSTRACT FROM AUTHOR]

Mesophotic Coral Ecosystems (MCEs) develop on a unique environment, where abrupt environmental changes take place. Using a time-calibrated molecular phylogeny (mtDNA: mtMutS), we examined the lineage membership of mesophotic gorgonian corals (Octocorallia: Cnidaria) in comparison to shallow and deep-sea lineages of the wider Caribbean-Gulf of Mexico and the Tropical Eastern Pacific. Our results show mesophotic gorgonians originating multiple times from old deep-sea octocoral lineages, whereas shallow-water species comprise younger lineages. The mesophotic gorgonian fauna in the studied areas is related to their zooxanthellate shallow-water counterparts in only two clades (Gorgoniidae and Plexauridae), where the bathymetrical gradient could serve as a driver of diversification. Interestingly, mesophotic clades have diversified faster than either shallow or deep clades. One of this groups with fast diversification is the family Ellisellidae, a major component of the mesophotic gorgonian coral assemblage worldwide.

Aim To document the geographical structure of the historical signal in the continental species richness gradient of birds and evaluate the influences of contemporary and historical climatic conditions on the generation and maintenance of the richness pattern. Location Australia. Methods We used range maps of breeding birds to generate the spatial pattern of species richness at four grain sizes, and two molecular phylogenies to measure the level of evolutionary development of avifaunas at each grain size. We then used simple correlation and path analysis to generate a statistical model of species richness using environmental predictor variables and compared the spatial patterns of richness and mean evolutionary development to identify possible environmental links between richness and net diversification rates across the continent. Results The contemporary richness pattern is well explained statistically by actual evapotranspiration (a measure of water-energy balance), operating both directly and indirectly through plant production, and this is robust to the spatial resolution of the analysis. Further, species richness and the mean level of evolutionary development of faunas show a strong spatial correspondence, such that dry areas support both fewer species and species from more highly derived families, whereas wet areas support more species of both basal and derived families. The evolutionary pattern conforms to a similar pattern known for plants and is probably explained by the increase in aridity in western and central Australia arising in the Miocene. Main conclusions The contemporary bird richness gradient contains a historical signal and reflects the effects of both current levels of water availability as well as changes in rainfall patterns extending over evolutionary time. The historical signal persists even in the absence of obvious hard barriers to dispersal.

Abstract Background A large number of taxa have undergone evolutionary radiations in mountainous areas, rendering alpine systems particularly suitable to study the extrinsic and intrinsic factors that have shaped diversification patterns in plants. The species-rich genus Saxifraga L. is widely distributed throughout the Northern Hemisphere, with high species numbers in the regions adjacent to the Qinghai-Tibet Plateau (QTP) in particular the Hengduan Mountains and the Himalayas. Using a dataset of 297 taxa (representing at least 60% of extant Saxifraga species), we explored the variation of infrageneric diversification rates. In addition, we used state-dependent speciation and extinction models to test the effects of geographic distribution in the Hengduan Mountains and the entire QTP region as well as of two morphological traits (cushion habit and specialized lime-secreting glands, so-called hydathodes) on the diversification of this genus. Results We detected two to three rate shifts across the Saxifraga phylogeny and two of these shifts led to radiations within two large subclades of Saxifraga, sect. Ciliatae Haworth subsect. Hirculoideae Engl. & Irmsch. and sect. Porphyrion Tausch subsect. Kabschia Engl. GEOSSE analyses showed that presence in the Hengduan Mountains had a positive effect on diversification across Saxifraga. Influence of these mountains was strongest in Saxifraga sect. Ciliatae subsect. Hirculoideae given its pronounced distribution there, and thus the radiation in this group can be classified at least partially as geographic. In contrast, the evolution of the cushion life form and lime-secreting hydathodes had positive effects on diversification only in selected Saxifraga sections, including sect. Porphyrion subsect. Kabschia. We therefore argue that radiation in this group was likely adaptive. Conclusions Our study underlines the complexity of processes and factors underpinning plant radiations: Even in closely related lineages occupying the same life zone, shifts in diversification are not necessarily governed by similar factors. In conclusion, alpine plant radiations result from a complex interaction among geographical settings and/or climatic modifications providing key opportunities for diversification as well as the evolution of key innovations.

Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

The diversification dynamics of the Australian temperate flora remains poorly understood. Here, we investigate whether differences in plant richness in the southwest Australian (SWA) biodiversity hotspot and southeast Australian (SEA) regions of the Australian continent can be attributed to higher net diversification, more time for species accumulation, or both. We assembled dated molecular phylogenies for the 21 most species-rich flowering plant families found across mesic temperate Australia, encompassing both SWA and SEA regions, and applied a series of diversification models to investigate responses across different groups and timescales. We show that the high richness in SWA can be attributed to a higher net rate of lineage diversification and more time for species accumulation. Different pulses of diversification were retrieved in each region. A decrease in diversification rate across major flowering plant lineages at the Eocene–Oligocene boundary (ca 34 Ma) was witnessed in SEA but not in SWA. Our study demonstrates the importance of historical diversification pulses and differential responses to global events as drivers of present-day diversity. More broadly, we show that diversity within the SWA biodiversity hotspot is not only the result of recent radiations, but also reflects older events over the history of this planet. [ABSTRACT FROM AUTHOR]

The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a "museum" of extant species diversity. Subsequent "out‐of‐Asia" colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space. [ABSTRACT FROM AUTHOR]

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta', which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the 'Symphyta', with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms. [ABSTRACT FROM AUTHOR]

• Complex models of chromosome evolution fit better in Cyperaceae megaphylogeny. • Three transitions in the model of chromosome number evolution in sedges. • Chromosome number evolution may explain shifts in diversification rates in sedges. Large-scale changes in chromosome number have been associated with diversification rate shifts in many lineages of plants. For instance, several ancient rounds of polyploidization events have been inferred to promote genomic differentiation and/or isolation and, consequently, angiosperm diversification. Dysploidy, although less studied, has been suggested to also play an important role in angiosperm diversification. In this article, we aim to elucidate the role of chromosomal rearrangements on lineage diversification by analyzing a new comprehensive sedge (Cyperaceae) phylogenetic tree. Our null hypothesis is that the mode and tempo of chromosome evolution are to be homogeneous across the complete phylogeny. In order to discern patterns of diversification shifts and chromosome number changes within the family tree, we tested clade-specific chromosome evolution models for several subtrees according to previously reported increments of diversification rates. Results show that a complex, heterogeneous model composed of different clade-specific chromosome evolution transitions are significantly supported against the null hypothesis of a model with no chromosome number model transition events along the phylogeny. This could suggest a link between diversification and changes in chromosome number evolution although other possibilities are not discarded. Our methodological approach may allow identifying different patterns of chromosome evolution, as found for Cyperaceae, for other lineages at different evolutionary levels. [ABSTRACT FROM AUTHOR]

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth‐death models has made it possible to detect their signature based on extant‐taxa phylogenies. Most birth‐death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree ("single pulse" approach), in contrast to the paleontological record, where MEEs have a time duration. Here, we explore the power of a Bayesian Birth‐Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a "time‐slice" approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on the phylogeny's size and MEE intensity. Comparisons of BDSKY with the single‐pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Agave sensu lato appeared around 8 Mya. • The best supported diversification model for Agavoidae shows two shifts around 8 Mya. • Agave sensu lato speciation rate has been increasing towards the present. • Nectarivorous bats from the Glossophaginae subfamily originated around 7 Mya. • Agave and their pollinating bats share a diffuse coevolutionary history. Abstract The genus Agave sensu lato contains ca. 211 described species, many of which are considered keystone species because of their ecological dominance and the quantity of resources they provide with their massive, nectar-rich inflorescences. The large diversity of Agave species has been hypothesized as being related to their reproductive strategy (predominantly monocarpic) and diverse pollinators (e.g., bats, hummingbirds, hawkmoths). In particular, Agave species provide resources that a few genera of nectar feeding bats from the subfamily Glosophaginae are dependent upon. To explore a possible coevolutionary relationship between Agave and the bat species that pollinate them, we calibrated molecular phylogenies of both groups and looked for a correlation in their dates of divergence. One coding and two non-coding regions of the chloroplast genome were sequenced from 49 species of the Agavoideae (Asparagaceae), and the mitochondrial gene Cyt-b and nuclear coding gene RAG2 were either sequenced or obtained from gene bank for 120 Phyllostomid bats. Results from the analyses indicate that Agave sensu lato is a young genus (estimated crown age 2.7–8.5/stem age 4.6–12.3 Ma), with an increasing diversification rate, and the highest speciation rate among Agavoideae's clades. The origin of the Glossophaginae bats (stem age 20.3–23.5 Ma) occurred prior to the stem age of Agave sensu lato , while the origin of the current pollinators of Agave species, members of the genera Glossophaga , Leptonycteris, Anoura, Choeronyscus, Musonycteris and Choeronycteris , was estimated to be around 6.3–16.2 Ma, overlapping with the stem age of Agave sensu lato , supporting the hypothesis of diffuse coevolution. [ABSTRACT FROM AUTHOR]

The importance of ecologically mediated divergent selection in accelerating trait evolution has been poorly studied in the most species‐rich biome of the planet, the continental Neotropics. We performed macroevolutionary analyses of trait divergence and diversification rates across closely related pairs of Andean and Amazonian passerine birds, to assess whether the difference in elevational range separating species pairs – a proxy for the degree of ecological divergence – influences the speed of trait evolution and diversification rates. We found that elevational differentiation is associated with faster divergence of song frequency, a trait important for pre‐mating isolation, and several morphological traits, which may contribute to extrinsic post‐mating isolation. However, elevational differentiation did not increase recent speciation rates, possibly due to early bursts of diversification during the uplift of the eastern Andes followed by a slow‐down in speciation rate. Our results suggest that ecological differentiation may speed up trait evolution, but not diversification of Neotropical birds. [ABSTRACT FROM AUTHOR]