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Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics 1 . However, there has been considerable debate surrounding the reliability of these inferences 2 – 5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions. An infinite number of alternative diversification scenarios—which may have markedly different, but equally plausible, dynamics—can underpin a given time-calibrated phylogeny of extant species, suggesting many previous studies have over-interpreted phylogenetic evidence.

Morphological analysis of teeth found at Lida Ajer shows that these belong to Homo sapiens , indicating that modern humans were in Sumatra between 73,000 and 63,000 years ago. Early modern human presence in Sumatra Genetic evidence points to the presence of modern humans in southeast Asia before 60,000 years ago, but actual fossil evidence is scant and circumstantial. Kira Westaway et al . present evidence for a modern human presence in the region between 73,000 and 63,000 years based on three dating methods applied to consolidated breccia rocks in a cave in Sumatra, Indonesia, which had previously yielded human teeth. The findings establish that modern humans were present in the region at around the time of the catastrophic eruption of Toba that took place in Sumatra around 73,000 years ago. Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka) 1 and in island southeast Asia (ISEA) before 60 ka (93–61 ka) 2 predates accepted archaeological records of occupation in the region 3 . Claims that AMH arrived in ISEA before 60 ka (ref. 4 ) have been supported only by equivocal 5 or non-skeletal evidence 6 . AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications 7 , poor preservation and/or excavation strategies 8 and questionable taxonomic identifications 9 . Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth 7 , 10 . The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations 7 , palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA 2 . Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa.

Analysis of 200-million-year-old digested foods reveals how the animals became dominant. Analysis of 200-million-year-old digested foods reveals how the animals became dominant. An artists impression of a late Triassic scene with Plateosaurus and Liliensternus dinosaurs. Credit: Arthur Dorety/Stocktrek Images via Alamy

Remarkably preserved footprints of Homo erectus and Paranthropus boisei offer direct evidence that extinct hominin species coexisted. Remarkably preserved footprints of Homo erectus and Paranthropus boisei offer direct evidence that extinct hominin species coexisted. A footprint hypothesized to have been created by a Paranthropus boisei individual. Credit: Kevin G. Hatala

A phylogeny of birds is presented from targeted genomic sequencing of 198 species of living birds representing all major avian lineages; the results find five major clades forming successive sister taxa to the rest of Neoaves and do not support the recently proposed Neoavian clades of Columbea and Passerea. A new look at the bird lineage The evolutionary relationships of bird species remain a contentious issue. Richard Prum et al . used targeted genomic sequencing to compare more than 259 nuclear loci from each of 198 living bird species, representing all major avian lineages and two crocodilian outgroups. The results favour a phylogeny consisting of five major clades forming successive sister taxa to the rest of Neoaves, and do not support two recently proposed Neoavian clades — Columbea and Passerea — as natural groups. Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10 7 bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin ( Opisthocomus hoazin ) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea 1 —were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.

Climate change is a critical factor affecting biodiversity. However, the quantitative relationship between temperature change and extinction is unclear. Here, we analyze magnitudes and rates of temperature change and extinction rates of marine fossils through the past 450 million years (Myr). The results show that both the rate and magnitude of temperature change are significantly positively correlated with the extinction rate of marine animals. Major mass extinctions in the Phanerozoic can be linked to thresholds in climate change (warming or cooling) that equate to magnitudes >5.2 °C and rates >10 °C/Myr. The significant relationship between temperature change and extinction still exists when we exclude the five largest mass extinctions of the Phanerozoic. Our findings predict that a temperature increase of 5.2 °C above the pre-industrial level at present rates of increase would likely result in mass extinction comparable to that of the major Phanerozoic events, even without other, non-climatic anthropogenic impacts. The linkage between temperature change and extinction rates in the fossil record is well-known qualitatively but little explored quantitatively. Here the authors investigate the relationship of marine animal extinctions with rate and magnitude of temperature change across the last 450 million years, and identify thresholds in climate change linked to mass extinctions.

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies 1 – 3 . However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes 4 . In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties 5 , 6 , and thus the timescale of placental mammal evolution remains contentious 7 – 10 . Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene 8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets. Bayesian analysis of datasets comprising genomes from multiple mammalian species can efficiently and precisely decipher their evolutionary timeline.

Present knowledge of Late Triassic tetrapod evolution, including the rise of dinosaurs, relies heavily on the fossil-rich continental deposits of South America, their precise depositional histories and correlations. We report on an extended succession of the Ischigualasto Formation exposed in the Hoyada del Cerro Las Lajas (La Rioja, Argentina), where more than 100 tetrapod fossils were newly collected, augmented by historical finds such as the ornithosuchid Venaticosuchus rusconii and the putative ornithischian Pisanosaurus mertii . Detailed lithostratigraphy combined with high-precision U–Pb geochronology from three intercalated tuffs are used to construct a robust Bayesian age model for the formation, constraining its deposition between 230.2 ± 1.9 Ma and 221.4 ± 1.2 Ma, and its fossil-bearing interval to 229.20 + 0.11/− 0.15–226.85 + 1.45/− 2.01 Ma. The latter is divided into a lower Hyperodapedon and an upper Teyumbaita biozones, based on the ranges of the eponymous rhynchosaurs, allowing biostratigraphic correlations to elsewhere in the Ischigualasto-Villa Unión Basin, as well as to the Paraná Basin in Brazil. The temporally calibrated Ischigualasto biostratigraphy suggests the persistence of rhynchosaur-dominated faunas into the earliest Norian. Our ca. 229 Ma age assignment to Pi. mertii partially fills the ghost lineage between younger ornithischian records and the oldest known saurischians at ca. 233 Ma.

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages. Upper Palaeolithic and Mesolithic genomes from western Europe and the Caucasus reveal a previously undescribed strand of Eurasian ancestry with a deep divergence from other hunter-gatherer genomes. This had a profound impact on ancient and modern populations from the Atlantic to Central Asia.

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago. Perhaps the earliest known signs of life have been found in Quebec, where features such as haematite tubes suggest that filamentous microbes lived around hydrothermal vents at least 3,770 million years ago. Early life in hydrothermal vents (Dodd 21377, Biology Article, Henry Gee) Hydrothermal vents on the sea floor have been thought to be some of the earliest habitable environments on the planet. Now Matthew Dodd et al . suggest that possible signatures of life in and around hydrothermal vents at least 3,770 million years ago could represent the earliest evidence for life on Earth. Jasper and carbonate rocks from northern Quebec, Canada preserve features thought to indicate the presence of filamentous microorganisms. These features include haematite tubes that preserve morphologies that are indicative of microbial activity in much younger rocks.