Over the past ~20 years, several forces have converged to potentially create a seismic shift in how new species are described. These forces include: (1) pleas for DNA-based taxonomy, (2) large-scale genomic datasets for species delimitation, (3) new statistical methods for molecular species delimitation, (4) the discovery of hundreds of cryptic species hiding within morphology-based species, (5) the possibility that most morphologically distinct species are already described, and (6) the putative decline of morphology-based taxonomy. But has a major shift towards molecular-based taxonomy actually happened? Here, we examined newly described species from 9 major groups across the Tree of Life and the evidence used to delimit them. We found five major results. First, in the largest groups, most new species were still described based on morphological data alone, including arthropods, mollusks, and plants (groups collectively including ~90% of all known species). Second, in other groups, most new species were described based on both molecular and morphological evidence, including chordates, fungi, bacteria, and archaeans. Third, species described based only on molecular data remain rare. Fourth, within animals, the majority of species descriptions that incorporated molecular data included only mitochondrial sequences. Fifth, molecular data were typically used to build a tree and generate genetic distances, rather than being used for statistical delimitation methods. Our results suggest that many new developments in species delimitation are underutilized by taxonomists (e.g. genomics), likely because these developments do not offer the fastest way to describe new species before they become extinct. Our results also suggest that many morphologically distinct species (and cryptic species) remain to be described.

AimA species' rate of climatic niche evolution may reflect its ability to survive changing climates. Yet large-scale studies of these rates remain limited. Here, we assessed global patterns in climatic niche rates among angiosperms and explored the potential drivers shaping these patterns.LocationGlobal.Time PeriodCurrent.Major Taxa StudiedAngiosperms.MethodsWe estimated broad-scale climatic niches for 231,567 angiosperm species based on distributional data from over 1100 sources. By integrating a published phylogeny of angiosperms, we estimated rates of climatic niche change for each extant species as the difference between its current and ancestral niche divided by the species' age. Global patterns were analysed by averaging rates for all the species found in each geographic unit. We used multiple statistical models to explore the relative contributions of niche width and climatic seasonality to shaping these geographic patterns of niche evolution. We analysed patterns of niche evolution and their underlying drivers separately for temperature-related and precipitation-related niches and for different directions of niche evolution (i.e., increases and decreases in species' temperature and precipitation niche values when compared to their most recent ancestors).ResultsRates for temperature variables increased with latitude, whereas rates for precipitation variables decreased with latitude. These opposing patterns in temperature and precipitation rates were related to opposing latitudinal patterns in climatic seasonality and species' niche widths for temperature and precipitation. Rates also differed for different directions of niche evolution, with different patterns associated with changes to warmer vs. cooler climates and wetter vs. drier climates.Main ConclusionsOur results revealed large-scale geographic patterns in rates of climatic niche change for temperature and precipitation for the largest clade of angiosperms and their underlying drivers. These findings may have important implications for species' abilities to respond to recent climate change.

The idea that Earth is currently experiencing a sixth mass extinction is widespread. We critically evaluate this claim. Very few studies have tested this idea. Some studies showed that recent extinction rates are faster than fossil background rates, but extinction rates can exceed background rates outside mass extinctions. Other studies extrapolated from recent extinctions to project 75% global species loss. But these recent extinctions were mostly of island species. No cause was specified for these future extinctions, and >50% of assessed species are considered non-threatened. We find numerous other issues. Proponents of the sixth mass extinction have made invaluable contributions by highlighting recent extinctions, but these extinctions may not be equivalent to past mass extinctions or relevant to current threats.

Biodiversity loss is one of the greatest challenges facing Earth today. The most direct information on species losses comes from recent extinctions. However, our understanding of these recent, human-related extinctions is incomplete across life, especially their causes and their rates and patterns among clades, across habitats and over time. Furthermore, prominent studies have extrapolated from these extinctions to suggest a current mass extinction event. Such extrapolations assume that recent extinctions predict current extinction risk and are homogeneous among groups, over time and among environments. Here, we analyse rates and patterns of recent extinctions (last 500 years). Surprisingly, past extinctions did not strongly predict current risk among groups. Extinctions varied strongly among groups, and were most frequent among molluscs and some tetrapods, and relatively rare in plants and arthropods. Extinction rates have increased over the last five centuries, but generally declined in the last 100 years. Recent extinctions were predominantly on islands, whereas the majority of non-island extinctions were in freshwater. Island extinctions were most frequently related to invasive species, but habitat loss was the most important cause (and current threat) in continental regions. Overall, we identify the major patterns in recent extinctions but caution against extrapolating them into the future.

Explaining global species richness patterns is a major goal of evolution, ecology, and biogeography. These richness patterns are often attributed to spatial variation in diversification rates (speciation minus extinction). Surprisingly, prominent studies of birds, fish, and plants have reported higher speciation and/or diversification rates at higher latitudes, where species richness is lower. We hypothesize that these surprising findings are explained by the focus of those studies on relatively recent macroevolutionary rates, within the last ~20 million years. Here, we analyze global richness patterns among 10,213 squamates (lizards and snakes) and explore their underlying causes. We find that when diversification rates were quantified at more recent timescales, we observed mismatched patterns of rates and richness, similar to previous studies in other taxa. Importantly, diversification rates estimated over longer timescales were instead positively related to geographic richness patterns. These observations may help resolve the paradoxical results of previous studies in other taxa. We found that diversification rates were largely unrelated to climate, even though climate and richness were related. Instead, higher tropical richness was related to the ancient occupation of tropical regions, with colonization time the variable that explained the most variation in richness overall. We suggest that large-scale diversity patterns might be best understood by considering climate, deep-time diversification rates, and the time spent in different regions, rather than recent diversification rates alone.

An important aspect of the current extinction crisis is the loss of distinct clades (e.g., genera). A recent study suggested that there is rapidly accelerating extinction of genera (and other higher taxa), indicating a current mass extinction event that endangers human survival. However, that study was based only on land vertebrates, which include only about half of vertebrates and <2% of living species. Here, we examine the recent extinction (last 500 years) of higher taxa across living organisms. We find that 102 genera have gone extinct (90 animals, 12 plants), along with 10 families and two orders. Yet, the majority of these genus-level extinctions were among mammals and birds, as were all extinctions of families and orders. There were very few extinctions among the thousands of genera of ray-finned fishes (n = 4; 0.08%), squamate reptiles (n = 2; 0.17%), and amphibians (n = 1; 0.18%). Documented extinctions were also rare among the thousands of assessed genera of arthropods (n = 11; 0.32%) and plants (n = 12; 0.17%), which together encompass most known species. Most extinct genera were monotypic (~80%), and most were island endemics (76%). Moreover, despite the claim that extinctions of higher taxa are rapidly accelerating, the highest rates of genus-level extinctions occurred more than 100 years ago, and have declined subsequently. Overall, the recent extinctions of higher taxa are not as dire as previously suggested.

Rapid radiations, including adaptive radiations, are of considerable interest to evolutionary biologists, in large part because they are thought to underlie much of the species diversity of life. Yet, this fundamental idea has only been tested at a limited scale, within frogs. Here, we test this idea across living organisms and within many of the largest clades (e.g. animals, plants). Specifically, we quantify how much of Earth’s species richness is contained within rapid radiations (clades with high net diversification rates). We find that among the major clades of living organisms and among land plant phyla and animal phyla, >80% of known species richness is contained within the few clades in the upper 90th percentile for diversification rates in each group. Thus, these exceptionally rapid radiations contain most of Earth’s extant species diversity. Patterns were broadly similar using smaller clades (orders, families) and in insects and vertebrates, with the majority of species generally contained within clades in the upper 75th percentile. Results were also similar using large-scale clades defined by their ages instead of taxonomic ranks. Overall, these results show for the first time that most of the known species richness of life is explained by rapid radiations. Moreover, phenotypic evidence from previous studies suggests that some of the most species-rich rapid radiations across life, animals, and plants may also qualify as adaptive radiations.

Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22-45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.

Understanding the origins of species richness patterns (especially high tropical richness) is a long-standing challenge at the intersection of biogeography, ecology, and evolutionary biology. One hypothesis that can potentially explain the latitudinal richness gradient is the tropical conservatism hypothesis (TCH). The TCH proposes that there are presently more species in tropical regions because many clades originated in the tropics and have only colonised the temperate zones more recently, leaving less time for speciation to build up temperate richness, and with niche conservatism limiting temperate colonisation by tropical clades. Here, we review the empirical evidence for the TCH. We first define this hypothesis, outline its major predictions, and describe its relationship to similar hypotheses. We then perform a systematic review to quantitatively evaluate the support for (and against) its major predictions. Finally, we describe several areas for future research. Global. Present to ~750 million years ago. All (especially plants and animals). We perform a systematic review of the evidence for the TCH over the last ~20 years. Most predictions of the TCH were supported in a significant majority of the studies that examined them. Further, a significant majority of relevant studies rejected the role of higher tropical diversification rates in driving the latitudinal diversity gradient (contrary to the diversification-rate and out-of-the-tropics hypotheses). Surprisingly, the importance of diversification rates did not depend on the ages of the clades studied. Our results generally support the TCH, but also highlight several important issues moving forward. Most studies tested very few predictions of the TCH, and the pivotal role of colonisation time was often untested. Many studies analysed phylogenetic diversity measures, but their relevance for explaining richness patterns remains disturbingly unclear. Finally, we discuss several unresolved questions about the TCH and the origins of richness patterns.

Climate change may be an important threat to global biodiversity, potentially leading to the extinction of numerous species. But how many? There have been various attempts to answer this question, sometimes yielding strikingly different estimates. Here, we review these estimates, assess their disagreements and methodology, and explore how we might reach better estimates. Large-scale studies have estimated the extinction of ~1% of sampled species up to ~70%, even when using the same approach (species distribution models; SDMs). Nevertheless, worst-case estimates often converge near 20%-30% species loss, and many differences shrink when using similar assumptions. We perform a new review of recent SDM studies, which show ~17% loss of species to climate change under worst-case scenarios. However, this review shows that many SDM studies are biased by excluding the most vulnerable species (those known from few localities), which may lead to underestimating global species loss. Conversely, our analyses of recent climate change responses show that a fundamental assumption of SDM studies, that species' climatic niches do not change over time, may be frequently violated. For example, we find mean rates of positive thermal niche change across species of ~0.02°C/year. Yet, these rates may still be slower than projected climate change by ~3-4 fold. Finally, we explore how global extinction levels can be estimated by combining group-specific estimates of species loss with recent group-specific projections of global species richness (including cryptic insect species). These preliminary estimates tentatively forecast climate-related extinction of 14%-32% of macroscopic species in the next ~50 years, potentially including 3-6 million (or more) animal and plant species, even under intermediate climate change scenarios.

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.

Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China’s described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.

Booth (2024) recently criticized our review on climate change and global species extinctions because we mentioned studies of introduced species but not forestry trials (deliberately introduced trees). However, as noted by Booth (2024), a relevant database is lacking for these trials, thus preventing their inclusion. More broadly, we suggest that researchers interested in extinction and other impacts of climate change should focus directly on studying the recent effects of climate change, rather than on introduced species, forestry trials, or other more indirect lines of evidence.

ABSTRACT Plants and animals are often adorned with potentially conspicuous colours (e.g. red, yellow, orange, blue, purple). These include the dazzling colours of fruits and flowers, the brilliant warning colours of frogs, snakes, and invertebrates, and the spectacular sexually selected colours of insects, fish, birds, and lizards. Such signals are often thought to utilize pre‐existing sensitivities in the receiver's visual systems. This raises the question: what was the initial function of conspicuous colouration and colour vision? Here, we review the origins of colour vision, fruit, flowers, and aposematic and sexually selected colouration. We find that aposematic colouration is widely distributed across animals but relatively young, evolving only in the last ~150 million years (Myr). Sexually selected colouration in animals appears confined to arthropods and chordates, and is also relatively young (generally <100 Myr). Colourful flowers likely evolved ~200 million years ago (Mya), whereas colourful fruits/seeds likely evolved ~300 Mya. Colour vision ( sensu lato ) appears to be substantially older, and likely originated ~400–500 Mya in both arthropods and chordates. Thus, colour vision may have evolved long before extant lineages with fruit, flowers, aposematism, and sexual colour signals. We also find that there appears to have been an explosion of colour within the last ~100 Myr, including >200 origins of aposematic colouration across nine animal phyla and >100 origins of sexually selected colouration among arthropods and chordates.

ABSTRACTAimDiet is a key aspect of life in animals. There have been numerous independent origins of herbivorous diet across animals, but the factors that explain these origins remain poorly understood. One potentially crucial factor is body temperature (Tb), as the gut‐dwelling bacteria that help digest cellulose in many herbivores are thought to require high temperatures. However, analyses in birds, lizards and mammals found only limited evidence for higher Tb in herbivores than in carnivores. These analyses tested whether diet explains Tb evolution. Here, we focus instead on testing whether Tb helps explain the evolution of diet across tetrapods.LocationGlobal.Time PeriodPast 350 million years.Major Taxa StudiedTetrapods.MethodsWe analysed 1712 species with matched data on diet and Tb using diverse phylogenetic methods.ResultsAncestral reconstructions indicated that tetrapods likely had a carnivorous ancestor, followed by repeated transitions to omnivory and herbivory, especially in the last 110 million years. Thus, extant herbivorous lineages in tetrapods are relatively young, in contrast to many older carnivorous lineages. They are also relatively unstable in that reversals from herbivory back to omnivory and from omnivory back to carnivory were as frequent as the origins of herbivory and omnivory. Using phylogenetic logistic regression, we support the hypothesis that higher Tb helps explain the evolution of herbivory across tetrapods and within birds, mammals, lepidosaurs and turtles. Phylogenetic path analyses suggest that Tb generally drives the evolution of herbivory, and not vice versa. Our analyses also suggest that Tb is more important for the evolution of herbivory than large body size or diurnal diel activity, which are both significant predictors of herbivory in some cases.Main ConclusionsOur results show for the first time that Tb is a significant predictor of diet evolution among and within many major animal clades.

Abstract Speciation is the original source of all species richness. Here, I address two questions: (i) what might typical speciation look like across life? and (ii) how has speciation led to the diversity of life we see today? What is ‘typical’ depends on the richness of different groups. In groups associated with host organisms (which may dominate numerically), the processes of co-speciation and host switching are crucial. Among free-living organisms, allopatric speciation, ecological divergence, and prezygotic isolation appear widely important. Yet, the processes by which species become allopatric (and initially split) remain highly unclear. Among macroscopic organisms, the processes underlying the speciation of cryptic insect lineages may predominate, and are briefly reviewed here. Analyses of diversification rates among clades can illuminate the factors that drive speciation and species richness, and I review the advantages and disadvantages of different methods for estimating diversification rates. Patterns of species richness among named clades are generally related to variation in diversification rates, and specific types of ecological variables seem to underlie variation in diversification rates at different scales. Nevertheless, many richness patterns are unrelated to diversification rates and may be related to the time available for speciation instead, including richness among regions, clades, and traits.

AimThe climatic niche is associated with diversification in many groups of animals and plants. However, the relationships between climatic-niche breadth evolution, climatic-niche position evolution, and speciation remain underexplored. It is particularly unclear whether changes in climatic-niche breadth are related to diversification. We tested two hypotheses relating niche breadth, niche position, and speciation using climatic data in Squamata (lizards and snakes), one of the largest radiations of tetrapods. These hypotheses were: (1) the oscillation hypothesis (niche breadth changes along with niche position and speciation) and (2) the musical-chairs hypothesis (niche breadth remains relatively constant when niche position changes during speciation).LocationGlobal.TaxonSquamata (lizards and snakes).MethodsWe estimated rates of speciation and evolutionary rates for both climatic-niche position and climatic-niche breadth for 5320 squamate species. We tested relationships among these rates using Bayesian phylogenetic generalised linear-mixed models.ResultsHigher speciation rates were associated with higher rates of evolution in niche position and in niche breadth. Faster rates of change in niche breadth were related to narrower niches and faster rates of change in niche position.Main ConclusionsOur results support the oscillation hypothesis to explain the relationships between speciation and changes in climatic-niche position and climatic-niche breadth. We found that species that changed climatic-niche breadths more rapidly: (1) speciated faster; (2) evolved towards narrower niche breadths; and (3) changed climatic-niche positions more rapidly. These results suggest that oscillation between wider and narrower niches is coupled with climatic-niche divergence and speciation. These conclusions may apply to many other groups of plants and animals in which speciation is often related to climatic-niche divergence.

Two major types of species richness patterns are spatial (e.g. the latitudinal diversity gradient) and clade-based (e.g. the dominance of angiosperms among plants). Studies have debated whether clade-based richness patterns are explained primarily by larger clades having faster rates of species accumulation (speciation minus extinction over time; diversification-rate hypothesis) or by simply being older (clade-age hypothesis). However, these studies typically compared named clades of the same taxonomic rank, such as phyla and families. This study design is potentially biased against the clade-age hypothesis, since clades of the same rank may be more similar in age than randomly selected clades. Here, we analyse the causes of clade-based richness patterns across the tree of life using a large-scale, time-calibrated, species-level phylogeny and random sampling of clades. We find that within major groups of organisms (animals, plants, fungi, bacteria, archaeans), richness patterns are most strongly related to clade age. Nevertheless, weaker relationships with diversification rates are present in animals and plants. These overall results contrast with similar large-scale analyses across life based on named clades, which showed little effect of clade age on richness. More broadly, these results help support the overall importance of time for explaining diverse types of species richness patterns.