Nature Ecology & Evolution

A clever experimental design in bacteria with engineered obligate mutualisms shows that interdependency can allow pairs of bacteria to survive in environments that are uninhabitable by the individual strains.

Paranthropus robustus is a small-brained extinct hominin from South Africa characterized by derived, robust craniodental morphology. The most complete known skull of this species is DNH 7 from Drimolen Main Quarry, which differs from P. robustus specimens recovered elsewhere in ways attributed to sexual dimorphism. Here, we describe a new fossil specimen from Drimolen Main Quarry, dated from approximately 2.04–1.95 million years ago, that challenges this view. DNH 155 is a well-preserved adult male cranium that shares with DNH 7 a suite of primitive and derived features unlike those seen in adult P. robustus specimens from other chronologically younger deposits. This refutes existing hypotheses linking sexual dimorphism, ontogeny and social behaviour within this taxon, and clarifies hypotheses concerning hominin phylogeny. We document small-scale morphological changes in P. robustus associated with ecological change within a short time frame and restricted geography. This represents the most highly resolved evidence yet of microevolutionary change within an early hominin species.

Species distribution models are a powerful tool for ecological inference, but not every use is biologically justified. Applying these tools to the COVID-19 pandemic is unlikely to yield new insights, and could mislead policymakers at a critical moment.

The pandemic will allow us to fundamentally remodel the way field-based sciences are taught, conducted and funded — but only if we stop waiting for a ‘return to normal’.

Reduced human mobility during the pandemic will reveal critical aspects of our impact on animals, providing important guidance on how best to share space on this crowded planet.

Evolutionary biologist who proposed the handicap principle.

Naturalist, synthesizer and conservation champion.

Conservationist who changed how we think about threats to biodiversity.

The founder of plant functional ecology.

Founder of conservation biology, expansive thinker and inspiring mentor.

Bat biologist and inspirational mentor who developed the concept of aeroecology.

Archaeologist who emphasized the importance of chronology in understanding Palaeolithic Europe, and laid the framework for the archaeology of modern human origins.

Quantitative geneticist who made fundamental contributions to understanding the nature of genetic variation.

Biodiversity advocate and Amazon expert

Evolutionary biologist who brought taxonomy to life.

Primatologist who gave voice to animal communication and cognition.

Archaeologist who transformed our understanding of Neanderthals.

Ecologist who co-founded the discipline of macroecology.

Pioneer of molecular evolution.

Primate palaeontologist and passionate advocate for diversity in human origins research.

Coral biologist and tireless reef advocate.

Researcher who studied fundamental questions about sexual selection, and an inspiring and kind colleague and friend.

Inspirational conservation scientist.

Humid montane forests are challenging environments for human habitation. We used high-resolution fossil pollen, charcoal, diatom and sediment chemistry data from the iconic archaeological setting of Laguna de los Condores, Peru to reconstruct changing land uses and climates in a forested Andean valley. Forest clearance and maize cultivation were initiated during periods of drought, with periods of forest recovery occurring during wetter conditions. Between ad 800 and 1000 forest regrowth was evident, but this trend was reversed between ad 1000 and 1200 as drier conditions coincided with renewed land clearance, the establishment of a permanent village and the use of cliffs overlooking the lake as a burial site. By ad 1230 forests had regrown in the valley and maize cultivation was greatly reduced. An elevational transect investigating regional patterns showed a parallel, but earlier, history of reduced maize cultivation and forest regeneration at mid-elevation. However, a lowland site showed continuous maize agriculture until European conquest but very little subsequent change in forest cover. Divergent, climate-sensitive landscape histories do not support categorical assessments that forest regrowth and peak carbon sequestration coincided with European arrival. Multi-proxy palaeoecological methods reconstruct phases of land clearance, maize cultivation and forest regrowth in the High Andes centuries before European incursion, and do not support the idea that forest regrowth and peak carbon sequestration were coincident with European arrival.

Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces. Filaments branch and anastomose, touch and entangle each other. They are indistinguishable from mycelial fossils found in similar deep-biosphere habitats in the Phanerozoic, where they are attributed to fungi on the basis of chemical and morphological similarities to living fungi. The Ongeluk fossils, however, are two to three times older than current age estimates of the fungal clade. Unless they represent an unknown branch of fungus-like organisms, the fossils imply that the fungal clade is considerably older than previously thought, and that fungal origin and early evolution may lie in the oceanic deep biosphere rather than on land. The Ongeluk discovery suggests that life has inhabited submarine volcanics for more than 2.4 billion years.

Despite substantial conservation efforts, the loss of ecosystems continues globally, along with related declines in species and nature’s contributions to people. An effective ecosystem goal, supported by clear milestones, targets and indicators, is urgently needed for the post-2020 global biodiversity framework and beyond to support biodiversity conservation, the UN Sustainable Development Goals and efforts to abate climate change. Here, we describe the scientific foundations for an ecosystem goal and milestones, founded on a theory of change, and review available indicators to measure progress. An ecosystem goal should include three core components: area, integrity and risk of collapse. Targets—the actions that are necessary for the goals to be met—should address the pathways to ecosystem loss and recovery, including safeguarding remnants of threatened ecosystems, restoring their area and integrity to reduce risk of collapse and retaining intact areas. Multiple indicators are needed to capture the different dimensions of ecosystem area, integrity and risk of collapse across all ecosystem types, and should be selected for their fitness for purpose and relevance to goal components. Science-based goals, supported by well-formulated action targets and fit-for-purpose indicators, will provide the best foundation for reversing biodiversity loss and sustaining human well-being.

Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic–Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C30 sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic–Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.

Recent advances in AI-based 3D protein structure prediction could help address health-related questions, but may also have far-reaching implications for evolution. Here we discuss the advantages and limitations of high-quality 3D structural predictions by AlphaFold2 in unravelling the relationship between protein properties and their impact on fitness, and emphasize the need to integrate in silico structural predictions with functional genomic studies.

Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2–3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000–5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa. The authors present the genome sequence of a >45,000-year-old female Homo sapiens individual from the site of Zlatý kůň, Czechia. Although radiometric dating of the human remains was inconclusive, the authors were able to use molecular methods to demonstrate that she was probably among the earliest Eurasian inhabitants following expansion out of Africa.

Dairy pastoralism is integral to contemporary and past lifeways on the eastern Eurasian steppe, facilitating survival in agriculturally challenging environments. While previous research has indicated that ruminant dairy pastoralism was practiced in the region by circa 1300 bc, the origin, extent and diversity of this custom remain poorly understood. Here, we analyse ancient proteins from human dental calculus recovered from geographically diverse locations across Mongolia and spanning 5,000 years. We present the earliest evidence for dairy consumption on the eastern Eurasian steppe by circa 3000 bc and the later emergence of horse milking at circa 1200 bc, concurrent with the first evidence for horse riding. We argue that ruminant dairying contributed to the demographic success of Bronze Age Mongolian populations and that the origins of traditional horse dairy products in eastern Eurasia are closely tied to the regional emergence of mounted herding societies during the late second millennium bc.

Yuzhniy Oleniy Ostrov in Karelia, northwest Russia, is one of the largest Early Holocene cemeteries in northern Eurasia, with 177 burials recovered in excavations in the 1930s; originally, more than 400 graves may have been present. A new radiocarbon dating programme, taking into account a correction for freshwater reservoir effects, suggests that the main use of the cemetery spanned only some 100–300 years, centring on ca. 8250 to 8000 cal bp. This coincides remarkably closely with the 8.2 ka cooling event, the most dramatic climatic downturn in the Holocene in the northern hemisphere, inviting an interpretation in terms of human response to a climate-driven environmental change. Rather than suggesting a simple deterministic relationship, we draw on a body of anthropological and archaeological theory to argue that the burial of the dead at this location served to demarcate and negotiate rights of access to a favoured locality with particularly rich and resilient fish and game stocks during a period of regional resource depression. This resulted in increased social stress in human communities that exceeded and subverted the ‘normal’ commitment of many hunter-gatherers to egalitarianism and widespread resource sharing, and gave rise to greater mortuary complexity. However, this seems to have lasted only for the duration of the climate downturn. Our results have implications for understanding the context of the emergence—and dissolution—of socio-economic inequality and territoriality under conditions of socio-ecological stress.

Africa’s Middle Stone Age preserves sporadic evidence for novel behaviours among early modern humans, prompting a range of questions about the influence of social and environmental factors on patterns of human behavioural evolution. Here we document a suite of novel adaptations dating approximately 92–80 thousand years before the present at the archaeological site Varsche Rivier 003 (VR003), located in southern Africa’s arid Succulent Karoo biome. Distinctive innovations include the production of ostrich eggshell artefacts, long-distance transportation of marine molluscs and systematic use of heat shatter in stone tool production, none of which occur in coeval assemblages at sites in more humid, well-studied regions immediately to the south. The appearance of these novelties at VR003 corresponds with a period of reduced regional wind strength and enhanced summer rainfall, and all of them disappear with increasing winter rainfall dominance after 80 thousand years before the present, following which a pattern of technological similarity emerges at sites throughout the broader region. The results indicate complex and environmentally contingent processes of innovation and cultural transmission in southern Africa during the Middle Stone Age.

To the Editor — In 1879 in a private letter to Joseph Hooker, Charles Darwin grumbled 1 : “The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.”Although this abominable mystery is often cited today, and sometimes declared solved, few realize that the mystery is deeper today than it was for Darwin.

Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. Theoretical analyses and computer simulations of proteins under purifying selection for thermodynamic stability show that substitution rates and the stabilization of resident amino acids (the 'evolutionary Stokes shift') can be predicted from biophysics and the effect of sequence entropy alone. Furthermore, we demonstrate that substitutions predominantly occur when epistatic interactions result in near neutrality; substitution rates are determined by how often epistasis results in such nearly neutral conditions. This theory provides a general framework for modelling protein sequence change under purifying selection, potentially explains patterns of convergence and mutation rates in real proteins that are incompatible with previous models, and provides a better null model for the detection of adaptive changes.

Climate change, land-use change, pollution and exploitation are among the main drivers of species’ population trends; however, their relative importance is much debated. We used a unique collection of over 1,000 local population time series in 22 communities across terrestrial, freshwater and marine realms within central Europe to compare the impacts of long-term temperature change and other environmental drivers from 1980 onwards. To disentangle different drivers, we related species’ population trends to species- and driver-specific attributes, such as temperature and habitat preference or pollution tolerance. We found a consistent impact of temperature change on the local abundances of terrestrial species. Populations of warm-dwelling species increased more than those of cold-dwelling species. In contrast, impacts of temperature change on aquatic species’ abundances were variable. Effects of temperature preference were more consistent in terrestrial communities than effects of habitat preference, suggesting that the impacts of temperature change have become widespread for recent changes in abundance within many terrestrial communities of central Europe.

We talk to Dr Swanne Gordon, a Jamaican-Canadian Assistant Professor of Biology at Washington University in St. Louis, United States, about her research on natural diversity and experience as a Black person in academia.

The postdoctoral workforce comprises a growing proportion of the science, technology, engineering and mathematics (STEM) community, and plays a vital role in advancing science. Postdoc professional development, however, remains rooted in outdated realities. We propose enhancements to postdoc-centred policies and practices to better align this career stage with contemporary job markets and work life. By facilitating productivity, wellness and career advancement, the proposed changes will benefit all stakeholders in postdoc success—including research teams, institutions, professional societies and the scientific community as a whole. To catalyse reform, we outline recommendations for (1) skills-based training tailored to the current career landscape, and (2) supportive policies and tools outlined in postdoc handbooks. We also invite the ecology and evolution community to lead further progressive reform. The postdoctoral experience is in need of reform. Here the authors outline concrete steps that institutions, postdocs and mentors can take to improve the landscape.

Many academics move countries in pursuit of career opportunities. With every move, personal identities are renegotiated as people shift between belonging to majority and minority groups in different contexts. Institutes should consider people’s dynamic and intersectional identities in their diversity, equity and inclusion practices.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges. A decentralized community is introduced that aims to standardize and integrate species trait data across organismal groups, based on principles of Open Science.