Large phylogenetic trees are often unbalanced near the root, with a species-depauperate lineage sister to a far more species-rich clade. The species-poor branches, sometimes referred to as "early diverging," are often viewed as key sources of information about deep evolutionary history. As a result, these lineages occupy a central role in debates about ancestral states. Using simulations and likelihood-based models of trait evolution, we show that the information contributed by species-depauperate lineages to ancestral state reconstructions is surprisingly limited. Instead, in unbalanced phylogenetic trees, the accuracy of ancestral state reconstructions at the root node is determined primarily by the species-rich clade and, more specifically, the evolutionary distance separating that clade from the root, rather than by the character state or evolutionary rate of the "early-diverging" sister lineage. This pattern reflects a general property of how phylogenetic inference aggregates information across descendant lineages: ancestral state reconstructions combine evidence from both descendant lineages rather than applying disproportionate weight to one of the descendants simply because fewer branching events separate it from the ancestral node. Our results highlight the limits of using extant, species-depauperate lineages to infer deep ancestors and the importance of fossils and other evidence that more directly sample early evolutionary history.

Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate[1]. However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth-death and dispersal-extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil †Vielasia in the oldest 'Eochiroptera' clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.

Paleoclimatic changes during the late Cenozoic led to substantial losses of tree diversity in Western and Central Europe. A modern synthesis linking which taxa were lost, the timing of these losses, and their implications for the adaptation of the region's forest ecosystems to ongoing climate change is needed. Here, we compile a dataset of fossil occurrences of tree genera from Western and Central Europe to analyze tree diversity changes during the Cenozoic (66 Ma - present). We find that tree genus richness declined 75% after its peak in the Miocene (23 - 5.3 Ma), with most losses already occurring during the Plio-Pleistocene transition (ca. 2 - 3 Ma). We then use genus-level niche models to explore how these changes unfolded within climate space. Our results show how the current regional tree flora was progressively filtered towards the colder and drier margins of climate space. This coincided with the losses of most heat-tolerant lineages, including many temperate genera that could have profited under modern climate warming (e.g., Castanea, Juglans, Aesculus). We foresee several ways in which our analyses of paleoecological data can inform forest management to increase regional tree diversity and enhance forest resilience under climate change.

Cellulose nanocrystals (CNCs), a bio-based nanoscale material derived from lignocellulosic biomass, have recently attracted significant attention as an additive to fabricate multifunctional nanocomposites owing to their physicochemical, thermomechanical, microstructural, and morphological properties and eco-friendly nature. Unlike fossil-based synthetic additives/materials (e.g., plastics), CNCs are derived from natural sources and exhibit superior mechanical strength, high crystallinity, and environmental compatibility, making them ideal green alternatives for sustainable applications. This study focuses on producing structurally pure CNCs from palm fruit waste shells (PFWSs), an agricultural residue (derived from secondary plant biomass, namely, palm trees), often discarded after collecting the edible parts. This residual mass has generally been considered organic solid waste and low-value biomass that is not suitable for use as cattle feed; rather, it is disposed of by conventional burning, leading to air, water, and soil pollution. Instead of extracting cellulose from primary plant sources (e.g., cotton and jute), which have vital industrial and agricultural roles, the target of this study is the utilization of secondary plant biomass to reduce the pressure on primary plant-derived lignocellulosic fibers. The current research addresses the gap by utilizing underexploited PFWSs as a sustainable feedstock for the extraction of high-quality CNCs. A stepwise chemical treatment was employed, including scouring (1% soap solution), alkali treatment (10% NaOH solution), bleaching (2% NaClO2 and 2% Na2S2O5 solution at pH 4.0), and acid hydrolysis with 40% H2SO4 to remove non-cellulosic components and isolate nanoscale crystalline cellulose. The extracted CNCs were characterized using FTIR-ATR spectroscopy, FE-SEM, OM, XRD, TGA, DSC, UV-vis spectroscopy, DLS, and zeta potential analysis. The results revealed high crystallinity (about 89.24%), thermal stability up to 600 °C and nanoscale morphology of the extracted CNCs. The zeta potential distribution ranged from -110 mV to +55 mV. The PFWS-derived CNCs demonstrate significant promise as a reinforcing agent in eco-friendly bionanocomposites for biomedical, packaging, and engineering applications.

Background The genus Podosphaeraster comprises seven species, characterised by a distinctive spherical body, all currently known from the seabed at depths below approximately 70 m. Its peculiar morphology has made its phylogenetic placement a subject of ongoing debate. It was initially suggested to be placed in Sphaerasteridae, the same family as fossil species. However, subsequent detailed skeletal analyses of the fossil forms suggested that this similarity was likely due to convergent evolution. Recent molecular analyses have revealed that Valvatida, in which the genus is currently placed, is likely a large polyphyletic group, leaving its taxonomic position still unresolved. New information A detailed examination of the internal skeletal structure of Podosphaeraster toyoshiomaruae, collected from the seas around Japan, was conducted using micro-focus X-ray computed tomography. Concurrently, shotgun sequencing was performed to identify key molecular markers for recent asteroid phylogeny. Additionally, shotgun sequencing determined the complete mitochondrial genome. Despite conservative evolution amongst asteroidean mitochondrial genomes, a translocation of the COX2 gene was revealed, representing the first discovery of a major protein-coding gene translocation within Asteroidea. In the phylogenetic tree, P. toyoshiomaruae was positioned as the most basal lineage within Valvatida. However, the statistical support for this placement was low, potentially due to the long-branch attraction caused by the excessively rapid evolutionary rate. Images reconstructed by micro-CT confirmed the presence of calcified reinforcement in the mesentery and showed its detailed structure for the first time. The mesentery skeleton was found to connect to the V-plate and five pairs of plates, including three kinds of marginal plates. This suggests that the marginal plates of this species may not be homologous with those of other asteroids. Although varying degrees of marginal plate reduction are shared with the order Velatida, we consider this to be a case of convergent evolution. Our phylogenetic analysis indicates a close relationship between P. toyoshiomaruae and Poraniidae (and other Valvatida), all of which possess marginal plates differentiated to varying extents, the homology of which remains uncertain.

The extinct "American cheetah" (Miracinonyx trumani) has long been considered a North American ecological analog of the African cheetah[1][,][2] (Acinonyx jubatus) based on convergent cursorial morphology, yet this paradigm rests on limited data[3] and untested assumptions about its evolutionary relationships and ecology.[2][,][4] Here, we generate nuclear paleogenomes from M. trumani specimens from Wyoming (∼23 kya; thousand years ago) and Yukon (∼31 kya), definitively placing this enigmatic felid within the evolutionary tree of cats. Phylogenomic analyses confirm M. trumani as sister to pumas (Puma concolor), not cheetahs, with a divergence of ∼2.6 million years ago (mya) during rapid Pliocene-Pleistocene climate oscillations. The Yukon specimens extend the species' known range[2] by over 20° latitude into the Arctic, and stable isotope analyses reveal striking ecological differentiation, with the Yukon population occupying an elevated trophic position consistent with exploitation of anadromous fish, while the Wyoming population functioned as a generalist terrestrial predator. This evidence suggests that M. trumani exhibited remarkable ecological versatility, while loss-of-function mutations in circadian genes may reflect relaxed constraints on circadian regulation. Together, these findings underscore how morphological convergence can obscure the true diversity and complexity of extinct megafaunal ecosystems.

Giant viruses of the phylum Nucleocytoviricota have emerged as particularly notable due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes, and they have been detected in hosts that span the eukaryotic tree of life. But surprisingly, such viruses have not been definitively found in Kingdom Fungi, though earlier genomic and metagenomic work suggests putative associations. Here we report both "viral fossils" and active infection by giant viruses in fungi, particularly in the zoosporic phyla Blastocladiomycota and Chytridiomycota. The recovered viral assemblies span up to 350 kb, encode over 300 genes, and form a monophyletic family-level clade within the Nucleocytoviricota related to orders Imitervirales and Algavirales, which we name Mycodnaviridae. We observed variation in infection status among the isolates including apparent active infection and transcriptionally suppressed states, suggesting that viral activation may be constrained to certain life stages of the host. Our experimental findings add to the limited natural virus-host systems available in culture for the study of giant viruses and expand the known host range of Nucleocytoviricota into a new kingdom that contains many model species. Mycodnaviridae have a global distribution, which invites inquiry into the implications of these infections for host traits, host genome evolution, and the metabolic impacts on ecosystems.

The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placental mammals, at least 720 Myr of basal lineages are ghost lineages, that is, lineages that have left no fossil evidence of their past history. In contrast, some studies have suggested that the fossil record is a faithful temporal archive of evolutionary history and thus the times of diversification of clades must be close to the ages of their oldest fossils. Such literalist interpretations have been contradicted by analysis of molecular datasets which, in many cases, indicate that groups including placental mammals and animals may have originated at times substantially older than their fossil records. Some of those studies have further argued that, in the case of animals and placental mammals, molecular clocks are uninformative, suffer from characteristic pathologies, and thus cannot distinguish between recent and ancient hypotheses of diversification. Here, we reexamine these two cases and show, using Bayesian model selection theory, that the explosive diversification models previously proposed for animals and placental mammals have a posterior probability of ∼0. We show the characteristic pathologies purportedly discovered do not exist, highlight errors in previous analyses, and provide advice on best practice for molecular-clock dating analysis.

Major radiations have given rise to huge swathes of life on Earth, and understanding their dynamics reveals the process of biodiversity generation itself. The rise of dinosaurs and other archosaurs during the Triassic was a spectacular example of such a radiation; it set the stage for Mesozoic faunas and gave rise to the largest land animals on Earth. Previous attempts to understand its dynamics have relied on phylogeny, necessitating the exclusion of much data. We use the Bayesian occurrence-based approach PyRate, allowing speciation and extinction dynamics to be estimated without recourse to phylogeny. We analyse stratigraphic range-based data for all archosauromorphs from the late Permian to the Early Jurassic, and test for association of body size with diversification using a body size proxy. We find an 'early burst' pattern of diversification, with initial high speciation giving way to increased extinction. Falling speciation is consistent with niche-filling following extinction, but increasing extinction may indicate a role for neutral dynamics during radiation. Cryptic diversification may be evidenced by a peak earlier than inferred using phylogenetic estimates. Body size is not statistically associated with diversification, but the positive direction of association potentially reflects the concurrent passive 'trend' of increasing size.

Why do tree species' distributions occasionally collapse? Paleoecologists have puzzled over the problem since recognizing that eastern hemlock (Tsuga canadensis (L.) Carr.), a North American conifer tree, declined abruptly range-wide amid the ostensibly stable climates of the Holocene. The decline c. 5000 yr before 1950 CE (YBP) highlights risks that either ecological tipping points or unknown modes of climate variation could amplify biotic changes today. Synchrony tests, regression, and gradient analyses applied to fossil pollen and paleoclimatic records from across hemlock's range were used to test hypotheses about the decline. The analyses reveal a time-transgressive decline directly linked to climatic shifts associated with Atlantic Meridional Overturning Circulation. The surprising extent of decline arose from complex regional patterns of climate change that compressed the geographic realization of hemlock's climate niche. Eastern droughts triggered an initial phase of decline after 5800 YBP even as hemlock increased in snowbelts near the Great Lakes and upslope in Appalachian highlands. Added climatic stress then eliminated these refuges during a second phase of declines c. 4900 YBP. Overall, the regionally patterned collapses of hemlock populations point to a strong sensitivity to interacting temperature and precipitation changes, but not a precedent for exotic insect and pathogen infestations today.

Like many of Earth's subtropical open ecosystems, the African savanna originated in the Miocene Epoch (23.0 to 5.3 Ma), one of the best historical analogs for future climate states. The first C4 grass, C3 tree, and shrub savanna developed in the subtropics after ~10 Ma in northwest Africa, but the terrestrial sedimentary record of the region is not well preserved, making it difficult to determine when, how, and why the African landscape opened. Here, we leverage plant-wax biomarkers extracted from the marine sedimentary archive to document the origination and history of open ecosystems through Miocene northwest Africa. We show that a C3 grass-rich savanna with no modern analog replaced closed woodlands and forests during the middle Miocene (~15 to 14 Ma), a period of global cooling and aridification. This nonanalog ecosystem transitioned into the C4 savanna in stages in the late Miocene (most rapidly between 7.4 to 6.4 Ma) as global temperatures cooled and aridity increased, roughly coincident with several C4 expansions in other subtropical regions. Our new vegetation history, put in the context of other records, links initial ecosystem opening and C4 expansion to periods of global cooling and drying. It is consistent with a nonlinear system of feedbacks between climate, consumers (herbivory and fire), and plant-trait interactions that allows small changes in one parameter to have dramatic effects on regional vegetation structure and composition. The geologic record indicates that the response of subtropical open ecosystems to future climate perturbations will depend on the nature and strength of these feedbacks.

Coprolites-fossil material extruded from an animal's digestive system-represent a rare insight into trophic interactions in deep time. However, while the first animals appeared about 600 million years ago, the first coprolites are only observed in the earliest Cambrian. Conversely, in modern oceans, fecal pellets are an important part of the particulate organic carbon in the water column and the global flux of organic carbon to deep water. In this review, we analyze the impact of the advent of fecal matter on the Cambrian Radiation by examining coprolites, analyzing animal biology, and contextualizing this through the role of fecal pellets in the oceanic nutrient cycle. We illustrate the central position of coprolites in driving the Cambrian Radiation.

Forests constitute the dominant terrestrial ecosystems and play a critical role in global carbon cycling. However, the changing structure and function of forests through geological time remain poorly understood due to the scarcity of in situ fossil forests preserving detailed and physiologically important anatomical characters. On the basis of 78 in situ permineralized conifer stumps in the Yiwu Jurassic Forest of Xinjiang, China, we quantitatively reconstruct the forest using paleobotanical observations and ecological analyses. We found that this fossil forest has a random tree distribution with an average density of 126 trees per hectare, showing limited postestablishment competitive thinning; its estimated canopy height ranged from 10.47 to 43.95 meters, stand-level biomass was 276,192 to 386,946 kilograms per hectare, and a notable net primary productivity of 21.11 to 31.9 t/hm[2]·a, which is three times higher than that of modern temperate conifer forests. Elevated temperature and atmospheric pCO2 in the Middle Jurassic probably contributed to this high productivity. Our study indicates that tree density, canopy height, and biomass equivalent to modern forests had already emerged by the Middle Jurassic and that forests were functioning as major terrestrial carbon sinks.