Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions 1-3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Paleogene (K-Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Threats to reptiles at global and regional scales.

Reptiles are an important, yet often understudied, taxon in nature conservation. They play a significant role in ecosystems1 and can serve as indicators of environmental health, often responding more rapidly to human pressures than other vertebrate groups.2 At least 21% of reptiles are currently assessed as threatened with extinction by the IUCN.3 However, due to the lack of comprehensive global assessments until recently, they have been omitted from spatial studies addressing conservation or spatial prioritization (e.g., Rosauer et al.,4,5,6,7,8 Fritz and Rahbek,4,5,6,7,8 Farooq et al.,4,5,6,7,8 Meyer et al., 4,5,6,7,8 and Farooq et al.4,5,6,7,8). One important knowledge gap in conservation is the lack of spatially explicit information on the main threats to biodiversity,9 which significantly hampers our ability to respond effectively to the current biodiversity crisis.10,11 In this study, we calculate the probability of a reptile species in a specific location being affected by one of seven biodiversity threats-agriculture, climate change, hunting, invasive species, logging, pollution, and urbanization. We conducted the analysis at a global scale, using a 50 km × 50 km grid, and evaluated the impact of these threats by studying their relationship with the risk of extinction. We find that climate change, logging, pollution, and invasive species are most linked to extinction risk. However, we also show that there is considerable geographical variation in these results. Our study highlights the importance of going beyond measuring the intensity of threats to measuring the impact of these separately for various biogeographical regions of the world, with different historical contingencies, as opposed to a single global analysis treating all regions the same.

Idiosyncratic patterns of local species richness and turnover define global biodiversity hotspots.

Tropical mountains are global biodiversity hotspots, owing to a combination of high local species richness and turnover in species composition. Typically, the highest local richness and turnover levels are implicitly assumed to converge in the same mountain regions, resulting in extraordinary species richness at regional to global scales. We investigated this untested assumption using high-resolution distribution data for all 9,788 bird species found in 134 mountain regions worldwide. Contrary to expectations, the mountain regions with the highest local richness differed from those with the highest species turnover. This finding reflects dissimilarities in the regions' climates and habitat compositions. Forest habitats and humid tropical climates characterize the mountain regions with the highest local richness. In contrast, mountain regions with the highest turnover are generally colder with drier climates and have mostly open habitat types. The highest local species richness and turnover levels globally converge in only a few mountain regions with the greatest climate volumes and topographic heterogeneity, resulting in the most prominent global hotspots for avian biodiversity. These results underline that species-richness hotspots in tropical mountains arise from idiosyncratic levels of local species richness and turnover, a pattern that traditional analyses of overall regional species richness do not detect.

Millennial processes of population decline, range contraction and near extinction of the European bison.

European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.

Temperate species underfill their tropical thermal potentials on land.

Understanding how temperature determines the distribution of life is necessary to assess species' sensitivities to contemporary climate change. Here, we test the importance of temperature in limiting the geographic ranges of ectotherms by comparing the temperatures and areas that species occupy to the temperatures and areas species could potentially occupy on the basis of their physiological thermal tolerances. We find that marine species across all latitudes and terrestrial species from the tropics occupy temperatures that closely match their thermal tolerances. However, terrestrial species from temperate and polar latitudes are absent from warm, thermally tolerable areas that they could potentially occupy beyond their equatorward range limits, indicating that extreme temperature is often not the factor limiting their distributions at lower latitudes. This matches predictions from the hypothesis that adaptation to cold environments that facilitates survival in temperate and polar regions is associated with a performance trade-off that reduces species' abilities to contend in the tropics, possibly due to biotic exclusion. Our findings predict more direct responses to climate warming of marine ranges and cool range edges of terrestrial species.

Diversification of flowering plants in space and time.

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

Vegetation structure from LiDAR explains the local richness of birds across Denmark.

Classic ecological research into the determinants of biodiversity patterns emphasised the important role of three-dimensional (3D) vegetation heterogeneity. Yet, measuring vegetation structure across large areas has historically been difficult. A growing focus on large-scale research questions has caused local vegetation heterogeneity to be overlooked compared with more readily accessible habitat metrics from, for example, land cover maps. Using newly available 3D vegetation data, we investigated the relative importance of habitat and vegetation heterogeneity for explaining patterns of bird species richness and composition across Denmark (42,394 km2 ). We used standardised, repeated point counts of birds conducted by volunteers across Denmark alongside metrics of habitat availability from land-cover maps and vegetation structure from rasterised LiDAR data (10 m resolution). We used random forest models to relate species richness to environmental features and considered trait-specific responses by grouping species by nesting behaviour, habitat preference and primary lifestyle. Finally, we evaluated the role of habitat and vegetation heterogeneity metrics in explaining local bird assemblage composition. Overall, vegetation structure was equally as important as habitat availability for explaining bird richness patterns. However, we did not find a consistent positive relationship between species richness and habitat or vegetation heterogeneity; instead, functional groups displayed individual responses to habitat features. Meanwhile, habitat availability had the strongest correlation with the patterns of bird assemblage composition. Our results show how LiDAR and land cover data complement one another to provide insights into different facets of biodiversity patterns and demonstrate the potential of combining remote sensing and structured citizen science programmes for biodiversity research. With the growing coverage of LiDAR surveys, we are witnessing a revolution of highly detailed 3D data that will allow us to integrate vegetation heterogeneity into studies at large spatial extents and advance our understanding of species' physical niches.

Mechanistic models project bird invasions with accuracy.

Invasive species pose a major threat to biodiversity and inflict massive economic costs. Effective management of bio-invasions depends on reliable predictions of areas at risk of invasion, as they allow early invader detection and rapid responses. Yet, considerable uncertainty remains as to how to predict best potential invasive distribution ranges. Using a set of mainly (sub)tropical birds introduced to Europe, we show that the true extent of the geographical area at risk of invasion can accurately be determined by using ecophysiological mechanistic models that quantify species' fundamental thermal niches. Potential invasive ranges are primarily constrained by functional traits related to body allometry and body temperature, metabolic rates, and feather insulation. Given their capacity to identify tolerable climates outside of contemporary realized species niches, mechanistic predictions are well suited for informing effective policy and management aimed at preventing the escalating impacts of invasive species.

An updated floristic map of the world.

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

Species-specific traits mediate avian demographic responses under past climate change.

Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.

Changes in the functional diversity of modern bird species over the last million years.

Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturbances. We combine morphological, ecological, and life-history trait data for >260 extant bird species with genomic-based estimates of changing effective population size (Ne) to quantify demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. We show that functional diversity was relatively stable over this period, but underwent significant changes in some key areas of trait space due to changing species abundances. Our results suggest that patterns of population decline over the Pleistocene have been concentrated in particular regions of trait space associated with extreme reproductive strategies and low dispersal ability, consistent with an overall erosion of functional diversity. Further, species most sensitive to climate warming occupied a relatively narrow region of functional space, indicating that the largest potential population increases and decreases under climate change will occur among species with relatively similar trait sets. Overall, our results identify fluctuations in functional space of extant species over evolutionary timescales and represent the demographic-based vulnerability of different regions of functional space among these taxa. The integration of paleodemographic dynamics with functional trait data enhances our ability to quantify losses of biosphere integrity before anthropogenic disturbances and attribute contemporary biodiversity loss to different drivers over time.

Novel plant-frugivore network on Mauritius is unlikely to compensate for the extinction of seed dispersers.

Insular communities are particularly vulnerable to anthropogenic extinctions and introductions. Changes in composition of island frugivore communities may affect seed dispersal within the native plant community, risking ecological shifts and ultimately co-extinction cascades. Introduced species could potentially mitigate these risks by replacing ecological functions of extinct species, but conclusive evidence is lacking. Here, we investigate changes in plant-frugivore interactions involving frugivorous birds, mammals and reptiles in Mauritius, an oceanic island with an exceptionally well-specified frugivore community and well-described species introduction history. We demonstrate substantial losses of binary interaction partnerships (at the species level) resulting from native species extinctions, but also gains of equal numbers of novel interactions with introduced species, potentially supporting the idea that non-native species might compensate for lost seed dispersal. However, closer investigation of animal seed handling behaviour reveals that most interactions with seed dispersers are replaced by ecologically different interactions with seed predators. Therefore, restoration of seed dispersal functionality in this novel plant-frugivore community is unlikely.

Biodiversity cradles and museums segregating within hotspots of endemism.

The immense concentrations of vertebrate species in tropical mountains remain a prominent but unexplained pattern in biogeography. A long-standing hypothesis suggests that montane biodiversity hotspots result from endemic species aggregating within ecologically stable localities. Here, the persistence of ancient lineages coincides with frequent speciation events, making such areas both 'cradles' (where new species arise) and 'museums' (where old species survive). Although this hypothesis refers to processes operating at the scale of valleys, it remains supported primarily by patterns generated from coarse-scale distribution data. Using high-resolution occurrence and phylogenetic data on Andean hummingbirds, we find that old and young endemic species are not spatially aggregated. The young endemic species tend to have non-overlapping distributions scattered along the Andean treeline, a long and narrow habitat where populations easily become fragmented. By contrast, the old endemic species have more aggregated distributions, but mainly within pockets of cloud forests at lower elevations than the young endemic species. These findings contradict the premise that biogeographical cradles and museums should overlap in valley systems where pockets of stable climate persist through periods of climate change. Instead, Andean biodiversity hotspots may derive from large-scale fluctuating climate complexity in conjunction with local-scale variability in available area and habitat connectivity.

Process-explicit models reveal the structure and dynamics of biodiversity patterns.

With ever-growing data availability and computational power at our disposal, we now have the capacity to use process-explicit models more widely to reveal the ecological and evolutionary mechanisms responsible for spatiotemporal patterns of biodiversity. Most research questions focused on the distribution of diversity cannot be answered experimentally, because many important environmental drivers and biological constraints operate at large spatiotemporal scales. However, we can encode proposed mechanisms into models, observe the patterns they produce in virtual environments, and validate these patterns against real-world data or theoretical expectations. This approach can advance understanding of generalizable mechanisms responsible for the distributions of organisms, communities, and ecosystems in space and time, advancing basic and applied science. We review recent developments in process-explicit models and how they have improved knowledge of the distribution and dynamics of life on Earth, enabling biodiversity to be better understood and managed through a deeper recognition of the processes that shape genetic, species, and ecosystem diversity.

Potential for invasion of traded birds under climate and land-cover change.

Humans have moved species away from their native ranges since the Neolithic, but globalization accelerated the rate at which species are being moved. We fitted more than half million distribution models for 610 traded bird species on the CITES list to examine the separate and joint effects of global climate and land-cover change on their potential end-of-century distributions. We found that climate-induced suitability for modelled invasive species increases with latitude, because traded birds are mainly of tropical origin and much of the temperate region is 'tropicalizing.' Conversely, the tropics are becoming more arid, thus limiting the potential from cross-continental invasion by tropical species. This trend is compounded by forest loss around the tropics since most traded birds are forest dwellers. In contrast, net gains in forest area across the temperate region could compound climate change effects and increase the potential for colonization of low-latitude birds. Climate change has always led to regional redistributions of species, but the combination of human transportation, climate, and land-cover changes will likely accelerate the redistribution of species globally, increasing chances of alien species successfully invading non-native lands. Such process of biodiversity homogenization can lead to emergence of non-analogue communities with unknown environmental and socioeconomic consequences.

Behavioural and morphological traits influence sex-specific floral resource use by hummingbirds.

Research on resource partitioning in plant-pollinator mutualistic systems is mainly concentrated at the levels of species and communities, whereas differences between males and females are typically ignored. Nevertheless, pollinators often show large sexual differences in behaviour and morphology, which may lead to sex-specific patterns of resource use with the potential to differentially affect plant reproduction and diversification. We investigated variation in behavioural and morphological traits between sexes of hummingbird species as potential mechanisms underlying sex-specific flower resource use in ecological communities. To do so, we compiled a dataset of plant-hummingbird interactions based on pollen loads for 31 hummingbird species from 13 localities across the Americas, complemented by data on territorial behaviour (territorial or non-territorial) and morphological traits (bill length, bill curvature, wing length and body mass). We assessed the extent of intersexual differences in niche breadth and niche overlap in floral resource use across hummingbird species. Then, we tested whether floral niche breadth and overlap between sexes are associated with sexual dimorphism in behavioural or morphological traits of hummingbird species while accounting for evolutionary relatedness among the species. We found striking differences in patterns of floral resource use between sex. Females had a broader floral niche breadth and were more dissimilar in the plant species visited with respect to males of the same species, resulting in a high level of resource partitioning between sexes. We found that both territoriality and morphological traits were related to sex-specific resource use by hummingbird species. Notably, niche overlap between sexes was greater for territorial than non-territorial species, and moreover, niche overlap was negatively associated with sexual dimorphism in bill curvature across hummingbird species. These results reveal the importance of behavioural and morphological traits of hummingbird species in sex-specific resource use and that resource partitioning by sex is likely to be an important mechanism to reduce intersexual competition in hummingbirds. These findings highlight the need for better understanding the putative role of intersexual variation in shaping patterns of interactions and plant reproduction in ecological communities.

La investigación sobre la partición de recursos en los sistemas mutualistas planta-polinizador se concentra principalmente en los niveles de especies y comunidades, mientras que las diferencias entre machos y hembras suelen ser ignoradas. Sin embargo, los polinizadores suelen mostrar grandes diferencias sexuales en su comportamiento y morfología, lo que puede dar lugar a patrones específicos de uso de recursos para cada sexo con el potencial de afectar de forma diferencial la reproducción y la diversificación de las plantas. Se estudió la variación en los rasgos de comportamiento y morfológicos entre sexos de las especies de colibríes como posibles mecanismos que explican el uso de recursos florales específicos para cada sexo en las comunidades ecológicas. Para ello, se recopiló un conjunto de datos de interacciones planta-colibrí con base en las cargas de polen de 31 especies de colibríes de 13 localidades en las Américas, además de datos sobre su comportamiento territorial (territorial o no territorial) y rasgos morfológicos (longitud y curvatura del pico, longitud del ala y masa corporal). Se evaluaron las diferencias intersexuales en la amplitud y el solapamiento del nicho en el uso de los recursos florales para las distintas especies de colibríes. Posteriormente, se comprobó si la amplitud del nicho floral y el solapamiento entre sexos están asociados con el dimorfismo sexual en los rasgos de comportamiento o morfológicos de las especies de colibríes, teniendo en cuenta el parentesco evolutivo entre las especies. Se encontraron diferencias notables en los patrones de uso de los recursos florales entre sexos. Las hembras presentaron una mayor amplitud de nicho floral y fueron más disímiles en las especies de plantas visitadas con respecto a los machos de la misma especie, lo que resultó en un alto nivel de partición de recursos entre los sexos. Se encontró que tanto la territorialidad como los rasgos morfológicos están relacionados con el uso de recursos específicos por sexo en las especies de colibríes. En particular, el solapamiento de nicho entre sexos fue mayor para las especies territoriales que para las no territoriales y, además, el solapamiento de nicho se asoció negativamente con el dimorfismo sexual en la curvatura del pico en las especies de colibríes. Estos resultados revelan la importancia de los rasgos conductuales y morfológicos de las especies de colibríes en el uso de recursos según el sexo y que la partición de recursos entre sexos es probablemente un mecanismo importante para reducir la competencia intersexual en los colibríes. Estos resultados ponen de manifiesto la necesidad de comprender mejor el rol que tiene la variación intersexual en los patrones de interacción y en la reproducción de las plantas en las comunidades ecológicas.

Extinction, coextinction and colonization dynamics in plant-hummingbird networks under climate change.

Climate-driven range shifts may cause local extinctions, while the accompanying loss of biotic interactions may trigger secondary coextinctions. At the same time, climate change may facilitate colonizations from regional source pools, balancing out local species loss. At present, how these extinction-coextinction-colonization dynamics affect biological communities under climate change is poorly understood. Using 84 communities of interacting plants and hummingbirds, we simulated patterns in climate-driven extinctions, coextinctions and colonizations under future climate change scenarios. Our simulations showed clear geographic discrepancies in the communities' vulnerability to climate change. Andean communities were the least affected by future climate change, as they experienced few climate-driven extinctions and coextinctions while having the highest colonization potential. In North America and lowland South America, communities had many climate-driven extinctions and few colonization events. Meanwhile, the pattern of coextinction was highly dependent on the configuration of networks formed by interacting hummingbirds and plants. Notably, North American communities experienced proportionally fewer coextinctions than other regions because climate-driven extinctions here primarily affected species with peripheral network roles. Moreover, coextinctions generally decreased in communities where species have few overlapping interactions, that is, communities with more complementary specialized and modular networks. Together, these results highlight that we should not expect colonizations to adequately balance out local extinctions in the most vulnerable ecoregions.