The Natural History Museum repository: Recent submissions
Now showing items 41-60 of 1374
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Late Quaternary horses in Eurasia in the face of climate and vegetation changeWild horses thrived across Eurasia until the Last Glacial Maximum to collapse after the beginning of the Holocene. The interplay of climate change, species adaptability to different environments, and human domestication in horse history is still lacking coherent continental-scale analysis integrating different lines of evidence. We assembled temporal and geographical information on 3070 horse occurrences across Eurasia, frequency data for 1120 archeological layers in Europe, and matched them to paleoclimatic and paleoenvironmental simulations for the Late Quaternary. Climate controlled the distribution of horses, and they inhabited regions in Europe and Asia with different climates and ecosystem productivity, suggesting plasticity to populate different environments. Their decline in Europe during the Holocene appears associated with an increasing loss and fragmentation of open habitats. Europe was the most likely source for the spread of horses toward more temperate regions, and we propose both Iberia and central Asia as potential centers of domestication.
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An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to NeolithizationAbstract: 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 (<jats:italic>N</jats:italic><jats:sub>e</jats:sub>) 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 <jats:italic>N</jats:italic><jats:sub>e</jats:sub> 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.
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Quantitative decoding of Ediacaran locomotory trace fossil morphologies: Evidence for the emergence of slender anterior-posterior body profilesTrace fossils are vital for studying early animals and their co-evolution with paleoenvironments during the terminal Ediacaran, a period with sparse body fossil records. Thus, patterns of morphologic evolution are difficult to untangle for Ediacaran trace-makers and quantitatively unexplored. In this study, we use the integral scale, which reflects the distance within which a trajectory (i.e., force and displacement) is self-correlated, as a potential indicator for the characteristic length of trace-maker’s locomotion. By analyzing modern and fossilized animal-trace-correlated trajectories, a proportionality between the characteristic locomotory length and the trajectory integral scale is found. Since the length of the structure producing locomotion is no larger than that of the body, the characteristic locomotory length also reflects the minimal body length. Applying this scaling law to Ediacaran−Cambrian locomotory trace fossils (e.g., Archaeonassa, Gordia, Helminthopsis, Parapsammichnites), we identify clear evidence of slender anterior-posterior body axes after around 545 Ma, with gradually increasing minimal body length-to-width ratios to up to 4−12. The trace-makers probably had relatively rigid bodies with robust hydrostatic nerve-muscle systems enhancing directional sensation and movement, enabling them to thrive in dynamically complex, heterogeneous, and shifting habitats. These adaptations likely drove niche partitioning and cascading diversification, underpinning the evolutionary roots of the Cambrian Explosion and more familiar animals of the Phanerozoic. Our findings establish a novel quantitative approach to studying deep-time locomotory trace fossils, offering robust insights into early animal anatomy and paleoecological dynamics.
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Major expansion in the human niche preceded out of Africa dispersalAll contemporary Eurasians trace most of their ancestry to a small population that dispersed out of Africa about 50,000 years ago (ka)<jats:sup>1–9</jats:sup>. By contrast, fossil evidence attests to earlier migrations out of Africa<jats:sup>10–15</jats:sup>. These lines of evidence can only be reconciled if early dispersals made little to no genetic contribution to the later, major wave. A key question therefore concerns what factors facilitated the successful later dispersal that led to long-term settlement beyond Africa. Here we show that a notable expansion in human niche breadth within Africa precedes this later dispersal. We assembled a pan-African database of chronometrically dated archaeological sites and used species distribution models (SDMs) to quantify changes in the bioclimatic niche over the past 120,000 years. We found that the human niche began to expand substantially from 70 ka and that this expansion was driven by humans increasing their use of diverse habitat types, from forests to arid deserts. Thus, humans dispersing out of Africa after 50 ka were equipped with a distinctive ecological flexibility among hominins as they encountered climatically challenging habitats, providing a key mechanism for their adaptive success.
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Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time SeriesHorse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.
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Phylogenetically informative proteins from an Early Miocene rhinocerotidIn the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference<sup>1-4</sup>. Still, even though ancient proteins have been reported from the Middle-Late Miocene<sup>5,6</sup>, the recovery of protein sequences providing subordinal-level phylogenetic insights does not exceed 3.7 million years ago (Pliocene)<sup>1</sup>. Here, we push this boundary back to 21-24 million years ago (Early Miocene) by retrieving enamel protein sequences of a rhinocerotid (Epiaceratherium sp.; CMNFV59632) from Canada's High Arctic. We recover partial sequences of seven enamel proteins and more than 1,000 peptide-spectrum matches, spanning at least 251 amino acids. Endogeneity is in line with thermal age estimates and is supported by indicators of protein damage, including several spontaneous and irreversible chemical modifications accumulated during prolonged diagenesis. Bayesian tip-dating places the divergence time of CMNFV59632 in the Middle Eocene-Oligocene, coinciding with a phase of high rhinocerotid diversification<sup>7</sup>. This analysis identifies a later Oligocene divergence for Elasmotheriinae, weakening alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae<sup>8,9</sup>. The findings are consistent with hypotheses on the origin of the enigmatic fauna of the Haughton Crater, which, in spite of considerable endemism, has similarity to distant Eurasian faunas<sup>10,11</sup>. Our findings demonstrate the potential of palaeoproteomics in obtaining phylogenetic information from a specimen that is approximately ten times older than any sample from which endogenous DNA has been obtained so far.
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Fauna Europaea: Helminths (Animal Parasitic)Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea), Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.
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Decapodiform cephalopods in focus: A case study on natural history illustration book creationDecapodiform cephalopods are ecologically significant marine animals known for their vivid coloration, complex behaviors, and key roles in trophic webs. Despite their importance, public recognition of these species in Japan remains limited. This study aims to enhance public awareness of decapodiform cephalopods by developing a science picture book that integrates narrative storytelling and natural history illustration as an educational tool. We conducted a case study in Japan involving the creation of a picture book based on a multidisciplinary approach, including scientific literature review, morphological and behavioral observations of live specimens in aquariums, diving-based fieldwork in Okinawa, and detailed examination of preserved museum specimens. Additionally, we designed a supplementary poster illustrating 17 decapodiform species to visually communicate their morphological diversity. Feedback from readers, including educators and museum visitors, indicated that the book was effective in increasing engagement and improving understanding of cephalopod ecology. The poster further supported species recognition and interest in marine biodiversity. Our findings underscore the potential of interdisciplinary collaboration among researchers, illustrators, museums, and aquariums in developing educational materials, and demonstrate the effectiveness of illustrated science communication in promoting marine ecological literacy.
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Towards sustainable treatments to preserve fossils from weathering, as part of the garden redevelopment project at the Natural History MuseumThe redevelopment of the gardens at the Natural History Museum (London, UK) required the preparation and stabilisation of several large fossil specimens to enable them to withstand exposure to typical weathering in an urban setting within the UK. Several specimens were considered to be at risk from damage: limestone dinosaur trackways, limestone invertebrate fossil blocks and some silicified sections of fossil tree. This project explores several options using literature searches, scanning electron microscopy and tape tests to identify sustainable but effective methods of preservation. The most appropriate treatment chosen for the limestones is CaLoSiL® E25 with TiO2 and for the silicious fossils SILRES® BS OH 100.
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Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation CaptureABSTRACT: New approaches are urgently needed to enrich rare or low‐abundant DNA in complex samples. Soil‐transmitted helminths (STHs) inhabit heterogeneous environments, including the gastrointestinal tract of their host as adults and are excreted as eggs and larvae in faeces, complicating our understanding of their biology and the use of genetic tools for species monitoring and population tracking. We have developed a hybridisation capture approach to enrich mitochondrial genome sequences of two STH species, the roundworm <jats:italic>Ascaris lumbricoides</jats:italic> and whipworm <jats:italic>Trichuris trichiura,</jats:italic> from extracted DNA from faecal material and worm specimens. Employing ~1000 targeted probes, we achieved > 6000 and > 12,000 fold enrichment for <jats:italic>A. lumbricoides</jats:italic> and <jats:italic>T. trichiura,</jats:italic> respectively, relative to direct whole genome shotgun (WGS) sequencing. Sequencing coverage was highly concordant with probe targets and correlated with the number of eggs per gram (EPG) of parasites present, from which DNA from as few as 336 EPG for <jats:italic>Ascaris</jats:italic> and 48 EPG for <jats:italic>Trichuris</jats:italic> were efficiently captured and sufficient to provide effective mitochondrial genome data. Finally, allele frequencies were highly concordant between WGS and hybridisation capture, suggesting little genetic information is lost with additional sample processing required for enrichment. Our hybridisation capture design and approach enable sensitive and flexible STH mitochondrial genome sampling from faecal DNA extracts and pave the way for broader hybridisation capture‐based genome‐wide applications and molecular epidemiology studies of STHs.
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Fenestella and other bryozoans in the Carboniferous rocks of the British IslesAsk a geologist to name a fossil bryozoan found in the rocks of the British Isles and the most likely answer will be Fenestella. The net-like fossils of Fenestella are especially abundant in the Carboniferous Limestone (Figs 1 and 2), although the genus, as used in its broadest sense, is also present in the Silurian, Devonian and Permian deposits of Britain.
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New species and a key to members of the Geminata clade (Solanum L.; Solanaceae) in ColombiaAs part of ongoing studies of Solanum in South America, three new species of the Geminata clade are described for Colombia. Solanum caquetense J.D.Tovar sp. nov., from the Department of Caquetá, is a riverside shrub found in lowland rainforests, with willow-like leaves characteristic of rheophyte plants. Solanum pinguiculum J.D. Tovar sp. nov. is confined to the understory of cloud forests on the eastern Andean slopes in the Departments of Cauca, Huila, and Putumayo, and is a tiny subshrub with somewhat watery stems and minute flowers. Solanum sabu J.D. Tovar sp. nov. is a rare plant, represented by a single collection from the eastern Andean slopes of the Cordillera Central in the Department of Tolima; it is a shrub with loose dendritic trichomes on abaxial leaf surface, and is described here to encourage further investigation in the field and herbaria. Differences between these new taxa and morphologically similar species are discussed, and photos, preliminary conservation status, and distribution maps are provided for all newly described species. To facilitate the identification of these morphologically very similar plants, a dichotomous key for all members of the Geminata clade occurring in Colombia is provided together with a synopsis of their distribution by Department.
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Phylogeny and Evolutionary History of Respiratory Complex I Proteins in MelainabacteriaThe evolution of oxygenic photosynthesis was one of the most transformative evolutionary events in Earth’s history, leading eventually to the oxygenation of Earth’s atmosphere and, consequently, the evolution of aerobic respiration. Previous work has shown that the terminal electron acceptors (complex IV) of aerobic respiration likely evolved after the evolution of oxygenic photosynthesis. However, complex I of the respiratory complex chain can be involved in anaerobic processes and, therefore, may have pre-dated the evolution of oxygenic photosynthesis. If so, aerobic respiration may have built upon respiratory chains that pre-date the rise of oxygen in Earth’s atmosphere. The Melainabacteria provide a unique opportunity to examine this hypothesis because they contain genes for aerobic respiration but likely diverged from the Cyanobacteria before the evolution of oxygenic photosynthesis. Here, we examine the phylogenies of translated complex I sequences from 44 recently published Melainabacteria metagenome assembled genomes and genomes from other Melainabacteria, Cyanobacteria, and other bacterial groups to examine the evolutionary history of complex I. We find that complex I appears to have been present in the common ancestor of Melainabacteria and Cyanobacteria, supporting the idea that aerobic respiration built upon respiratory chains that pre-date the evolution of oxygenic photosynthesis and the rise of oxygen.
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Population genomics and morphological data bridge the centuries of cyanobacterial taxonomy along the continuum of Microcoleus speciesThe filamentous cyanobacterium <i>Microcoleus</i> is among the most important global primary producers, especially in hot and cold desert ecosystems. This taxon represents a continuum consisting of a minimum of 12 distinct species with varying levels of gene flow and divergence. The notion of a species continuum is poorly understood in most lineages but is especially challenging in cyanobacteria. Here we show that genomic diversification of the <i>Microcoleus</i> continuum is reflected by morphological adaptation. We compiled a dataset of morphological data from 180 cultured strains and 300 whole genome sequences, including eight herbarium specimens and the type specimen of <i>Microcoleus</i>. We employed a combination of phylogenomic, population genomic, and population-level morphological data analyses to delimit species boundaries. Finally, we suggest that the shape of the filament apices may have an adaptive function to environmental conditions in the soil.
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A new Cambrian stem-group echinoderm reveals the evolution of the anteroposterior axisEchinoderms are among the most morphologically distinctive animal phyla, encompassing familiar forms like starfish and sea urchins. Uncovering how their unique pentaradial body plan evolved from a bilaterally symmetrical ancestor has long proved challenging, as this involved fundamental changes to adult morphology and body plan development, associated with a complete reorganization of the anteroposterior (A-P) axis,1–3 obfuscating homologies between disparate groups.4,5 This has greatly limited our understanding of one of the most radical transformations in bilaterian evolutionary history.6–8 Here, we describe a new bilaterally symmetrical echinoderm, Atlascystis acantha, from the Cambrian of Morocco.9 This is the oldest bilaterally symmetrical echinoderm and the first with this body plan known from different ontogenetic stages, allowing us to elucidate mechanisms ofits growth. Thisdemonstrates thatAtlascystis possessed ambulacra—structures accommodating extensions of the characteristic echinoderm water vascular system—providing a clear point of homology betweenAtlascystis andradially symmetricalforms. By integrating the Cambrian fossilrecordandour newphylogeny with developmental biology,10 we uncover how changes to the ancestral bilaterian A-P patterning network alongside stepwise morphological transformations gave rise to the pentaradial structure of extant echinoderms, transforming our understanding of the origin and earliest evolution of this major animal phylum.
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Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, AntarcticaABSTRACT: Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.
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Using Captain Scott's Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years?Evidence of climate-driven environmental change is increasing in Antarctica, and with it comes concern that this will propagate to impacts on biological communities. Recognition and prediction of change needs to incorporate the extent and timescales over which communities vary under extant conditions. However, few observations of Antarctic microbial communities, which dominate inland habitats, allow this. We therefore carried out the first molecular comparison of Cyanobacteria in historic herbarium microbial mats from freshwater ecosystems on Ross Island and the McMurdo Ice Shelf, collected by Captain R.F. Scott's ‘Discovery’ Expedition (1902–1903), with modern samples from those areas. Using 16S rRNA gene surveys, we found that modern and historic cyanobacteria assemblages showed some variation in community structure but were dominated by the same genotypes. Modern communities had a higher richness, including genotypes not found in historic samples, but they had the highest similarity to other cyanobacteria sequences from Antarctica. The results imply slow cyanobacterial 16S rRNA gene genotype turnover and considerable community stability within Antarctic microbial mats. We suggest that this relates to Antarctic freshwater 'organisms requiring a capacity to withstand diverse stresses, and that this could also provide a degree of resistance and resilience to future climatic-driven environmental change in Antarctica.
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A phylogenetically novel cyanobacterium most closely related to GloeobacterAbstract: Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.














