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Abstract In species distribution modelling (SDM), it is common practice to explore multiple machine learning (ML) algorithms and combine their results into ensembles. In R, many implementations of different ML algorithms are available but, as they were mostly developed independently, they often use inconsistent syntax and data structures. For this reason, repeating an analysis with multiple algorithms and combining their results can be challenging. Specialised SDM packages solve this problem by providing a simpler, unified interface by wrapping the original functions to tackle each specific requirement. However, creating and maintaining such interfaces is time‐consuming, and with this approach, the user cannot easily integrate other methods that may become available. Here, we present tidysdm, an R package that solves this problem by taking advantage of the tidymodels universe. tidymodels provide standardised grammar, data structures and modelling interfaces, and a well‐documented infrastructure to integrate new algorithms and metrics. The wide adoption of tidymodels means that most ML algorithms and metrics are already integrated, and the user can add additional ones. Moreover, because of the broad adoption of tidymodels, new statistical approaches tend to be implemented quickly, making them easily integrated into existing pipelines and analyses. tidysdm takes advantage of the tidymodels universe to provide a flexible and fully customisable pipeline to fit SDM. It includes SDM‐specific algorithms and metrics, and methods to facilitate the use of spatial data within tidymodels. Additionally, tidysdm is the first software that natively allows SDM to be performed using data from different periods, expanding the availability of SDM for scholars working in palaeontology, archaeology, palaeobiology, palaeoecology and other disciplines focussing on the past.

Predator-prey interactions in marine ecosystems control population sizes, maintain species richness, and provide intermediate disturbance. Such ecosystem structuring interactions may be rare in Antarctic epibenthic communities, which are unique among marine ecosystems worldwide for their dominance of soft bodied fauna (sponges, soft and hard corals, and echinoderms) and a simultaneous paucity of shell crushing predators (sharks, rays and durophagous decapods). In the shallow benthos, instead of durophagy, important Antarctic predators such as starfish, pycnogonids (sea spiders), nemertean worms, and nudibranchs employ grazing, scavenging, or sucking strategies. Far less is known about deep sea (>1000 m) Antarctic benthic communities due to the challenging nature of polar data collection, so that photographic surveys provide one of the only means of making in situ observations of these deep sea communities. We used seabed photographs of the deep (~2000m) slope of the Powell Basin, northwest Weddell Sea, taken by the Ocean Floor Observation and Bathymetry System on board the RV Polarstern (PS118, April 2019) to investigate the epibenthic community composition, and Bayesian Network Inference (BNI) to determine the ecological network, namely the ecological associations, including potential invertebrate predator-prey relationships between taxa. Photographs show that the rocky substrates of the basin slope support between 10-22 morphotaxa per photo, and highly abundant communities (density between 106 to 553 individuals/m2). BNI results reveal a network of associations between the sessile and mobile suspension and filter feeding organisms and their physical environment. However, associations between invertebrate predators like starfish, and other organisms, were not detected in the network. This lack of inclusion within the network suggests that, despite the presence of these normally important mobile predators, invertebrate predator-prey interactions on the rocky Powell Basin slope do not have the same ecosystem-regulating impact that they do on shallow Antarctic epibenthic communities.

Abstract Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.

European megafaunal ungulates living in open habitats over the last 50,000 years showed evidence for niche change, possibly driven by climatic change and extinction of competitors and predators

Summary: The Ihò Eléérú (or Iho Eleru) rock shelter, located in Southwest Nigeria, is the only site from which Pleistocene-age hominin fossils have been recovered in western Africa. Excavations at Iho Eleru revealed regular human occupations ranging from the Later Stone Age (LSA) to the present day. Here, we present chronometric, archaeobotanical, and paleoenvironmental findings, which include the taxonomic, taphonomic, and isotopic analyses of what is the only Pleistocene faunal assemblage documented in western Africa. Our results indicate that the local landscape surrounding Iho Eleru, although situated within a regional open-canopy biome, was forested throughout the past human occupation of the site. At a regional scale, a shift from forest- to savanna-dominated ecotonal environment occurred during a mid-Holocene warm event 6,000 years ago, with a subsequent modern reforestation of the landscape. Locally, no environmental shift was observable, placing Iho Eleru in a persistent forested “island” during the period of occupation.

African paleoanthropological studies typically focus on regions of the continent such as Eastern, Southern and Northern Africa, which hold the highest density of Pleistocene archaeological sites. Nevertheless, lesser known areas such as West Africa also feature a high number of sites. Here, we present a high-resolution map synthesising all well contextualised Pleistocene archaeological sites present in Sub-Saharan West Africa. A detailed elevation and ecoregional map was developed and correlated with palaeoanthropological sites. This map is supplemented with 1,000- and 2000-year interval climate reconstructions over the last 120,000 years for three subregions of high archaeological interest. The presented archaeological sites were compiled by reviewing published literature, and selected based on: (1) documented archaeological stratification or >10 characteristic artefacts, (2) published coordinates, and (3) published chronometric ages or relative dating. The data presented here elucidates the current state of knowledge of Pleistocene West Africa, highlighting the regional potential for human evolutionary studies.

Optimising the spatial distribution of global croplands could substantially reduce carbon emissions and biodiversity loss associated with rain-fed crop production, according to a mathematical framework applied to environmental impact and crop yield data

Abstract Eastern Africa has played a prominent role in debates about human evolution and dispersal due to the presence of rich archaeological, palaeoanthropological and palaeoenvironmental records. However, substantial disconnects occur between the spatial and temporal resolutions of these data that complicate their integration. Here, we apply high-resolution climatic simulations of two key parameters, mean annual temperature and precipitation, and a biome model, to produce a highly refined characterisation of the environments inhabited during the eastern African Middle Stone Age. Occupations are typically found in sub-humid climates and landscapes dominated by or including tropical xerophytic shrubland. Marked expansions from these core landscapes include movement into hotter, low-altitude landscapes in Marine Isotope Stage 5 and cooler, high-altitude landscapes in Marine Isotope Stage 3, with the recurrent inhabitation of ecotones between open and forested habitats. Through our use of high-resolution climate models, we demonstrate a significant independent relationship between past precipitation and patterns of Middle Stone Age stone tool production modes overlooked by previous studies. Engagement with these models not only enables spatiotemporally explicit examination of climatic variability across Middle Stone Age occupations in eastern Africa but enables clearer characterisation of the habitats early human populations were adapted to, and how they changed through time.

It is still unclear when and by which route modern humans expanded out of Africa. Here, Beyer et al. use paleoclimate reconstructions and estimates of human precipitation requirements to evaluate the survivability of spatial and temporal migration corridors to Eurasia over the last 300,000 years.

Measurement(s) genome Technology Type(s) DNA sequencing Factor Type(s) modern/ancient human Sample Characteristic - Organism Homo sapiens Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14839329

Measurement(s) temperature • precipitation • cloud cover • net primary productivity Technology Type(s) computational modeling technique Factor Type(s) atmospheric carbon dioxide • orbital parameters • land surface type (ocean, land, land ice) Sample Characteristic - Environment climate system Sample Characteristic - Location Earth (planet) Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.15073479

Increasing body and brain size constitutes a key pattern in human evolution, but the mechanisms driving these changes remain debated. Using a large fossil dataset combined with global paleoclimatic reconstructions, the authors show that different environmental variables influenced the evolution of brain and body size in Homo.

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

It has been hypothesized that domestication can occur through the ‘commensal pathway’ in which the domesticate takes advantage of a niche created as a byproduct by the domesticator. Here, Brooker et al. provide evidence for a commensal domestication process between longfin damselfish and mysid shrimps.

The first animals appear during the late Ediacaran (572 to 541 Ma); an initial diversity increase was followed reduction in diversity, often interpreted as catastrophic mass extinction. We investigate Ediacaran ecosystem structure changes over this time period using the "Elements of Metacommunity Structure" framework to assess whether this diversity reduction in the Nama was likely caused by an external mass extinction, or internal metacommunity restructuring. The oldest metacommunity was characterised by taxa with wide environmental tolerances, and limited specialisation or intertaxa associations. Structuring increased in the second oldest metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting in competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran. These results reveal that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.

Long-term dynamics of species’ range sizes play a crucial role in determining extinction risks. Here the authors simulate global vegetation cover and scenarios of anthropogenic land cover change to estimate habitat range sizes of thousands of mammal, bird, and amphibian species since 1700, and project trajectories up to 2100 under four emission scenarios and five socio-economic pathways.

Abstract Background During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods. Results We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels. Conclusions Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

Abstract Background Foraging performance is widely hypothesized to play a key role in shaping age-specific demographic rates in wild populations, yet the underlying behavioral changes are poorly understood. Seabirds are among the longest-lived vertebrates, and demonstrate extensive age-related variation in survival, breeding frequency and success. The breeding season is a particularly critical phase during the annual cycle, but it remains unclear whether differences in experience or physiological condition related to age interact with the changing degree of the central-place constraint in shaping foraging patterns in time and space. Methods Here we analyze tracking data collected over two decades from congeneric black-browed (BBA) and grey-headed (GHA) albatrosses, Thalassarche melanophris and T. chrysostoma, breeding at South Georgia. We compare the foraging trip parameters, at-sea activity (flights and landings) and habitat preferences of individuals aged 10–45 years and contrast these patterns between the incubation and early chick-rearing stages. Results Young breeders of both species showed improvements in foraging competency with age, reducing foraging trip duration until age 26. Thereafter, there were signs of foraging senescence; older adults took gradually longer trips, narrowed their habitat preference (foraging within a smaller range of sea surface temperatures) (GHA), made fewer landings and rested on the water for longer (BBA). Some age-specific effects were apparent for each species only in certain breeding stages, highlighting the complex interaction between intrinsic drivers in determining individual foraging strategies. Conclusions Using cross-sectional data, this study highlighted clear age-related patterns in foraging behavior at the population-level for two species of albatrosses. These trends are likely to have important consequences for the population dynamics of these threatened seabirds, as young or old individuals may be more vulnerable to worsening environmental conditions.

It is unclear whether bird migration patterns are restricted to interglacial periods or are maintained during glacial maxima. Somveille et al. apply a global migration simulation model to climate reconstruction to show that the prevalence of this phenomenon has likely been largely maintained up to 50,000 years ago.

Knowledge of the 3-dimensional space use of large marine predators is central to our understanding of ecosystem dynamics and for the development of management recommendations. Horizontal movements of white sharks, Carcharodon carcharias, in eastern Australian and New Zealand waters have been relatively well studied, yet vertical habitat use is less well understood. We dual-tagged 27 immature white sharks with Pop-Up Satellite Archival Transmitting (PSAT) and acoustic tags in New South Wales coastal shelf waters. In addition, 19 of these individuals were also fitted with Smart Position or Temperature Transmitting (SPOT) tags. PSATs of 12 sharks provided useable data; four tags were recovered, providing highly detailed archival data recorded at 3-s intervals. Horizontal movements ranged from southern Queensland to southern Tasmania and New Zealand. Sharks made extensive use of the water column (0–632 m) and experienced a broad range of temperatures (7.8–28.9 °C). Archival records revealed pronounced diel-patterns in distinct fine-scale oscillatory behaviour, with sharks occupying relatively constant depths during the day and exhibiting pronounced yo-yo diving behaviour (vertical zig-zag swimming through the water column) during the night. Our findings provide valuable new insights into the 3-dimensional space use of Eastern Australasian (EA) white sharks and contribute to the growing body on the general ecology of immature white sharks.

The destruction of natural habitat for cropland and pasture represents a major threat to global biodiversity. Despite widespread societal concern about biodiversity loss associated with food production, consumer access to quantitative estimates of the impact of crop production on the world's species has been very limited compared to assessments of other environmental variables such as greenhouse gas emissions or water use. Here, we present a consistent dataset of the biodiversity footprints of pasture and 175 crops at the global and national level. The data were generated by combining maps of the global distribution of agricultural areas in the year 2000 with spatially explicit estimates of the biodiversity loss associated with the conversion of natural habitat to farmland. Estimates were derived for three common alternative measures of biodiversity – species richness, threatened species richness, and range rarity – of the world's mammals, birds, and amphibians. Our dataset provides important quantitative information for food consumers and policy makers, allowing them to take evidence-based decisions to reduce the biodiversity footprint of global food production.

How global climatic changes are translated into ice-sheet fluctuations and sea-level change is not well understood. Here the authors present a compilation of empirical data and numerical modelling results of pre-LGM Northern Hemisphere ice sheet changes and show pronounced ice-sheet asymmetry within the last glacial cycle and significant variations in ice-marginal positions between older glacial cycles.

Abstract Background Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators.

Abstract Background Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura’s jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. Results We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura’s jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). Conclusions Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

Many organisms avoid habitats posing risks of parasitism. Parasites are not generally conspicuous, however, which raises the question of what cues individuals use to detect parasitism risk. Here, we provide evidence in alpine newts (Ichthyosaura alpestris) that non-visual cues from parasite-exposed conspecifics inform habitat avoidance. Alpine newts breed in aquatic habitats and occasionally move among adjacent terrestrial habitat during breeding seasons. We completed experiments with newts whereby individuals had access to both habitats, and the aquatic habitats varied in prior occupancy by conspecifics with different histories of exposure to the parasitic skin fungus, Batrachochytrium dendrobatidis (Bd). Continuous filming of newt activity for 2 days provided little evidence that prior use of aquatic habitats by conspecifics, regardless of their Bd exposure history, immediately influenced newt habitat use. However, newts that encountered aquatic habitats used specifically by Bd-exposed conspecifics on day 1 spent less time aquatic on day 2, whereas other newts did not alter habitat use. Responses could have been elicited by cues generated by Bd stages on the conspecifics or, perhaps more likely, cues emitted by the conspecifics themselves. In either case, these observations suggest that newts use non-visual cues sourced from exposed conspecifics to detect Bd risk and that those cues cause newts to avoid aquatic habitats. Bd may therefore influence host behavior in early phases of interactions, and possibly before any contact with infectious stages is made, creating potential for non-consumptive effects.

The Welfare Genome Project (WGP) provided 1,000 healthy Korean volunteers with detailed genetic and health reports to test the social perception of integrating personal genetic and healthcare data at a large-scale. WGP was launched in 2016 in the Ulsan Metropolitan City as the first large-scale genome project with public participation in Korea. The project produced a set of genetic materials, genotype information, clinical data, and lifestyle survey answers from participants aged 20–96. As compensation, the participants received a free general health check-up on 110 clinical traits, accompanied by a genetic report of their genotypes followed by genetic counseling. In a follow-up survey, 91.0% of the participants indicated that their genetic reports motivated them to improve their health. Overall, WGP expanded not only the general awareness of genomics, DNA sequencing technologies, bioinformatics, and bioethics regulations among all the parties involved, but also the general public’s understanding of how genome projects can indirectly benefit their health and lifestyle management. WGP established a data construction framework for not only scientific research but also the welfare of participants. In the future, the WGP framework can help lay the groundwork for a new personalized healthcare system that is seamlessly integrated with existing public medical infrastructure.

The contamination of natural systems with plastic debris has become one of the most pressing global environmental issues. Microplastics (MPs) are of particular concern because their ubiquity and small size make them available for ingestion by a range of aquatic biota. MP exposure studies are hence proliferating rapidly but are typically limited to the analyses of population-level responses in toxicity endpoints across treatments. Potential contaminant-induced alterations in behavioural patterns, however, could manifest on numerous levels of variation: at the population-level, between individuals and within individuals. Here, we used repeated measures on startle response durations – a risk-avoidance mechanism – in European hermit crabs, Pagurus bernhardus, to measure behavioural responses to MP exposure across multiple levels of variation. We found that MP exposure led to a significant decrease of startle duration at the population-level as well as a reduction of intra-individual variation. In other words, crabs became less risk averse on average and their behaviour became more predictable with increasing MP concentrations. Collectively, our findings indicate that MP pollution might increase susceptibility to predation in hermit crabs.

Infectious diseases are considered major threats to biodiversity, however strategies to mitigate their impacts in the natural world are scarce and largely unsuccessful. Chytridiomycosis is responsible for the decline of hundreds of amphibian species worldwide, but an effective disease management strategy that could be applied across natural habitats is still lacking. In general amphibian larvae can be easily captured, offering opportunities to ascertain the impact of altering the abundance of hosts, considered to be a key parameter affecting the severity of the disease. Here, we report the results of two experiments to investigate how altering host abundance affects infection intensity in amphibian populations of a montane area of Central Spain suffering from lethal amphibian chytridiomycosis. Our laboratory-based experiment supported the conclusion that varying density had a significant effect on infection intensity when salamander larvae were housed at low densities. Our field experiment showed that reducing the abundance of salamander larvae in the field also had a significant, but weak, impact on infection the following year, but only when removals were extreme. While this suggests adjusting host abundance as a mitigation strategy to reduce infection intensity could be useful, our evidence suggests only heavy culling efforts will succeed, which may run contrary to objectives for conservation.

Recent decades have seen the rapid expansion of scholarship that identifies societal responses to past climatic fluctuations. This fast-changing scholarship, which was recently synthesized as the History of Climate and Society (HCS), is today undertaken primary by archaeologists, economists, geneticists, geographers, historians and paleoclimatologists. This review is the first to consider how scholars in all of these disciplines approach HCS studies. It begins by explaining how climatic changes and anomalies are reconstructed by paleoclimatologists and historical climatologists. It then provides a broad overview of major changes and anomalies over the 300,000-year history of Homo sapiens, explaining both the causes and environmental consequences of these fluctuations. Next, it introduces the sources, methods, and models employed by scholars in major HCS disciplines. It continues by describing the debates, themes, and findings of HCS scholarship in its major disciplines, and then outlines the potential of transdisciplinary, ‘consilient’ approaches to the field. It concludes by explaining how HCS studies can inform policy and activism that confronts anthropogenic global warming.

Anthropogenic land use and climate change in the Industrial age have had substantial impacts on the geographic ranges of the world’s terrestrial animal species. How do these impacts compare against those in the millennia preceding the Industrial era? Here, we combine reconstructions of global climate and land use from 6000 BCE to 1850 CE with empirical data on the spatial distributions and habitat requirements of 16,919 mammal, bird, and amphibian species to estimate changes in their range sizes through time. We find that land use had only a small, yet almost entirely negative impact during most of the study period, whilst natural climatic variability led to some range expansions and contractions; but, overall it had a small impact on the majority of species. Our results provide a baseline for comparison with studies of range changes during the Industrial period, demonstrating that contemporary rates of range loss exceed the magnitude of range changes seen over many thousands of years prior to the Industrial period by an alarming extent.

Abstract Archaeological evidence shows that, in the long run, Neolitization (the transition from foraging to food production) was associated with demographic growth. We used two methods (patterns of linkage disequilibrium from whole-genome SNPs and MSMC estimates on genomes) to reconstruct the demographic profiles for respectively 64 and 24 modern-day populations with contrasting lifestyles across the Old World (sub-Saharan Africa, south-eastern Asia, Siberia). Surprisingly, in all regions, food producers had larger effective population sizes (Ne) than foragers already 20 k years ago, well before the Neolithic revolution. As expected, this difference further increased ~12–10 k years ago, around or just before the onset of food production. Using paleoclimate reconstructions, we show that the early difference in Ne cannot be explained by food producers inhabiting more favorable regions. A number of mechanisms, including ancestral differences in census size, sedentism, exploitation of the natural resources, social stratification or connectivity between groups, might have led to the early differences in Ne detected in our analyses. Irrespective of the specific mechanisms involved, our results provide further evidence that long term cultural differences among populations of Palaeolithic hunter-gatherers are likely to have played an important role in the later Neolithization process.

The global distribution of language diversity mirrors that of several variables related to ecosystem productivity. It has been argued that this is driven by the size of social networks, which tend to be larger in harsher climates to ensure food security, leading to reduced language divergence. Is this pattern purely synchronic, or is there also a quantifiable relationship between environmental conditions and language diversification over time? We used a spatio-temporal phylogeny of the Bantu language family to estimate local diversification rates at the times and locations of language divergence. We compared these data against spatially-explicit reconstructions of several palaeoclimate and palaeovegetation variables (mean annual temperature and the temperature of the coldest and warmest quarter, annual precipitation and the precipitation of the wettest and driest quarter, growing degree days, the length of the growing season, and net primary production), to investigate a potential link between local environmental factors and diversification rates in the Bantu languages. A regression analysis does not suggest a statistically significant relationship between climatic or ecological variables and linguistic diversification over time. We find a strong positive correlation between pairwise linguistic and geographic distances in the Bantu languages, arguing for a dominant role of isolation as a result of the rapid Bantu expansion that might have overwhelmed any potential influence of local environmental factors.

Social groups composed of familiar individuals exhibit better coordination than unfamiliar groups; however, the ways familiarity contributes to coordination are poorly understood. Prior social experience probably allows individuals to learn the tendencies of familiar group-mates and respond accordingly. Without prior experience, individuals would benefit from strategies for enhancing coordination with unfamiliar others. We used a social catfish, Corydoras aeneus, that uses discrete, observable tactile interactions to assess whether active interactions could facilitate coordination, and how their role might be mediated by familiarity. We describe this previously understudied physical interaction, ‘nudges’, and show it to be associated with group coordination and cohesion. Furthermore, we investigated nudging and coordination in familiar/unfamiliar pairs. In all pairs, we found that nudging rates were higher during coordinated movements than when fish were together but not coordinating. We observed no familiarity-based difference in coordination or cohesion. Instead, unfamiliar pairs exhibited significantly higher nudging rates, suggesting that unfamiliar pairs may be able to compensate for unfamiliarity through increased nudging. By contrast, familiar individuals coordinated with comparatively little nudging. Second, we analysed nudging and cohesion within triplets of two familiar and one unfamiliar individual (where familiar individuals had a choice of partner). Although all individuals nudged at similar rates, the unfamiliar group-mate was less cohesive than its familiar group-mates and spent more time alone. Unfamiliar individuals that nudged their group-mates more frequently exhibited higher cohesion, indicating that nudging may facilitate cohesion for the unfamiliar group-mate. Overall, our results suggest that nudges can mitigate unfamiliarity, but that their usage is reduced in the case of familiar individuals, implying a cost is associated with the behaviour.

The utility of a universal reference sequence for human genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean reference genome and consensus variome, and show that an ethnically-relevant reference can improve variant detection.

An ongoing elephant poaching crisis is threatening not only elephant populations but also the local economies that rely on nature-based tourism. Here, Naidoo and colleagues use an economic model to estimate the financial contribution of elephants to tourism and the possible consequences of their loss.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by an RNA-associated molecular assembly built on Sm proteins. Despite the availability of several 3D-structures of Sm-like archaeal proteins (SmAPs), their function has remained elusive. The aim of this study was to shed light on the function of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso). Using co-purification followed by RNASeq different classes of non-coding RNAs and mRNAs were identified that co-purified either with both paralogues or solely with Sso-SmAP1 or Sso-SmAP2. The large number of associated intron-containing tRNAs and tRNA/rRNA modifying RNAs may suggest a role of the two Sso-SmAPs in tRNA/rRNA processing. Moreover, the 3D structure of Sso-SmAP2 was elucidated. Like Sso-SmAP1, Sso-SmAP2 forms homoheptamers. The binding of both proteins to distinct RNA substrates is discussed in terms of surface conservation, structural differences in the RNA binding sites and differences in the electrostatic surface potential of the two Sso-SmAP proteins. Taken together, this study may hint to common and different functions of both Sso-SmAPs in Sso RNA metabolism.

How often do people visit the world's protected areas (PAs)? Despite PAs covering one-eighth of the land and being a major focus of nature-based recreation and tourism, we don't know. To address this, we compiled a globally-representative database of visits to PAs and built region-specific models predicting visit rates from PA size, local population size, remoteness, natural attractiveness, and national income. Applying these models to all but the very smallest of the world's terrestrial PAs suggests that together they receive roughly 8 billion (8 x 109) visits/y-of which more than 80% are in Europe and North America. Linking our region-specific visit estimates to valuation studies indicates that these visits generate approximately US $600 billion/y in direct in-country expenditure and US $250 billion/y in consumer surplus. These figures dwarf current, typically inadequate spending on conserving PAs. Thus, even without considering the many other ecosystem services that PAs provide to people, our findings underscore calls for greatly increased investment in their conservation.

Females of the parasitoid wasp Dinocampus coccinellae are known to parasitise both male and female coccinellid hosts. It is suggested that female hosts provide more resources for developing wasp larvae because they tend to be larger than male hosts, and female coccinellids have a much greater food intake than males. Thus the wasp's lifetime reproductive success should be increased by ovipositing preferentially in female rather than male hosts when given a choice. Laboratory experiments, using Coccinella septempunctata as a host, show that such a preference does exist. Wasps preferentially oviposit in females, and this preference is not simply a result of the larger mean size of females compared to males. These results corroborate higher rates of prevalence in female compared to male hosts reported previously.

Nature Communications 7: Article number: 13637 (2016): Published 24 November 2016; Updated 9 October 2017. The original version of this Article contained an error in the email address of the corresponding author George Church. The correct email is gchurch@genetics.med.harvard.edu. The error has beencorrected in the HTML and PDF versions of the Article.

Nearly one in five bird species has separate breeding and overwintering distributions, and the regular migrations of these species cause a substantial seasonal redistribution of avian diversity across the world. However, despite its ecological importance, bird migration has been largely ignored in studies of global avian biodiversity, with few studies having addressed it from a macroecological perspective. Here, we analyse a dataset on the global distribution of the world's birds in order to examine global spatial patterns in the diversity of migratory species, including: the seasonal variation in overall species diversity due to migration; the contribution of migratory birds to local bird diversity; and the distribution of narrow-range and threatened migratory birds. Our analyses reveal a striking asymmetry between the Northern and Southern hemispheres, evident in all of the patterns investigated. The highest migratory bird diversity was found in the Northern Hemisphere, with high inter-continental turnover in species composition between breeding and non-breeding seasons, and extensive regions (at high latitudes) where migratory birds constitute the majority of the local avifauna. Threatened migratory birds are concentrated mainly in Central and Southern Asia, whereas narrow-range migratory species are mainly found in Central America, the Himalayas and Patagonia. Overall, global patterns in the diversity of migratory birds indicate that bird migration is mainly a Northern Hemisphere phenomenon. The asymmetry between the Northern and Southern hemispheres could not have easily been predicted from the combined results of regional scale studies, highlighting the importance of a global perspective.

Recent applications of population genetic models to human craniodental traits have revealed a strong neutral component to patterns of global variation. However, little work has been undertaken to determine whether neutral processes might also be influencing the postcranium, perhaps due to substantial evidence for selection and plastic environmental responses in these regions. Recent work has provided evidence for neutral effects in the pelvis, but has been limited in regard to shape data (small numbers of linear measurements) and restricted only to males. Here, we use geometric morphometric methods to examine population variation in the human os coxae (pelvic bone) in both males and females. Neutrality is examined via apportionment of variance patterns and fit to an Out-of-Africa serial founder effect model, which is known to structure neutral genetic patterns. Moreover, we compare males and females directly, and the true versus false pelvis, in order to examine potential obstetrical effects. Our results indicate evidence for substantial neutral population history effects on pelvic shape variation. They also reveal evidence for the effect of obstetrical constraints, but these affect males and females to equivalent extents. Our results do not deny an important role for selection in regard to specific aspects of human pelvic variation, especially in terms of features associated with body size and proportions. However, our analyses demonstrate that at a global level, the shape of the os coxae reveals substantial evidence for neutral variation. Our analyses thus indicate that population variation in the human pelvis might be used to address important questions concerning population history, just as the human cranium has done.

Behavioural traits that co-vary across contexts or situations often reflect fundamental trade-offs which individuals experience in different contexts (e.g. fitness trade-offs between exploration and predation risk). Since males tend to experience greater variance in reproductive success than females, there may be considerable fitness benefits associated with "bolder" behavioural types, but only recently have researchers begun to consider sex-specific and life-history strategies associated with these. Here we test the hypothesis that male three-spined sticklebacks (Gasterosteus aculeatus) show high risk but potentially high return behaviours compared to females. According to this hypothesis we predicted that male fish would show greater exploration of their environment in a foraging context, and be caught sooner by an experimenter than females. We found that the time fish spent out of cover exploring their environment was correlated over two days, and males spent significantly more time out of cover than females. Also, the order in which fish were net-caught from their holding aquarium by an experimenter prior to experiments was negatively correlated with the time spent out of cover during tests, and males tended to be caught sooner than females. Moreover, we found a positive correlation between the catch number prior to our experiments and nine months after, pointing towards consistent, long-term individual differences in behaviour.

Studies on leadership have focused either on physiological state as the key predictor (i.e. "leading according to need"), or else on temperamental asymmetries among group members (i.e. intrinsic leadership). In this paper, we explore how both factors interact in determining the emergence of leaders. We observed pairs of sticklebacks with varying degrees of temperamental difference, and recorded their movements back and forth between a safe covered area and a risky foraging area, both before and after satiating one of the two pair members (but not the other). Before satiation, when the fish had similar hunger levels, temperament was a good predictor of social roles, with the bolder member of a pair leading and the shyer member following. The effect of satiation depended on which fish received the additional food. When the shyer member of a pair was fed, and consequently became less active, the bolder fish did not change its behaviour but continued to lead. By contrast, when the bolder member of a pair was fed, and consequently initiated fewer trips out of cover, the shyer partner compensated by initiating trips more frequently itself. In pairs that differed only a little in temperament, feeding the bolder fish actually led to a role reversal, with the shyer fish emerging as a leader in the majority of joint trips out of cover. Our results show that leadership emerges as the consequence of multiple factors, and that their interaction can be complex.

Studies of coordinated movement have found that, in many animal species, bolder individuals are more likely to initiate movement and shyer individuals to follow. Here, we show that in pairs of foraging stickleback fish, leadership is not merely a passive consequence of temperamental differences. Instead, the act of initiating a joint foraging trip out of cover itself brings about a change in the role that an individual plays throughout the subsequent trip, and success in recruiting a partner affects an individual's tendency to initiate the next trip. On each joint trip, whichever fish took the initiative in leading out of cover gains greater influence over its partner's behaviour, which persists even after several changes in position (i.e. termination attempts and re-joining). During any given trip, the initiator is less responsive to its partner's movements than during trips initiated by the partner. An individual's personality had an important effect on its response to failure to recruit a partner: while bold fish were unaffected by failures to initiate a joint trip, shy individuals were less likely to attempt another initiation after a failure. This difference provides a positive feedback mechanism that can partially stabilise social roles within the pair, but it is not strong enough to prevent occasional swaps, with individuals dynamically adjusting their responses to one another as they exchange roles.

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.

Reports of rapid growth in nature-based tourism and recreation add significant weight to the economic case for biodiversity conservation but seem to contradict widely voiced concerns that people are becoming increasingly isolated from nature. This apparent paradox has been highlighted by a recent study showing that on a per capita basis, visits to natural areas in the United States and Japan have declined over the last two decades. These results have been cited as evidence of "a fundamental and pervasive shift away from nature-based recreation"-but how widespread is this phenomenon? We address this question by looking at temporal trends in visitor numbers at 280 protected areas (PAs) from 20 countries. This more geographically representative dataset shows that while PA visitation (whether measured as total or per capita visit numbers) is indeed declining in the United States and Japan, it is generally increasing elsewhere. Total visit numbers are growing in 15 of the 20 countries for which we could get data, with the median national rate of change unrelated to the national rate of population growth but negatively associated with wealth. Reasons for this reversal of growth in the richest countries are difficult to pin down with existing data, but the pattern is mirrored by trends in international tourist arrivals as a whole and so may not necessarily be caused by disaffection with nature. Irrespective of the explanation, it is clear that despite important downturns in some countries, nature-related tourism is far from declining everywhere, and may still have considerable potential both to generate funds for conservation and to shape people's attitudes to the environment.