Major Environmental Shifts Research Articles

Middle and Late Holocene paleolimnological changes in central Lake Tanganyika: Integrated evidence from the Kavala Island Ridge (Tanzania)

Middle and Late Holocene sediments have not been extensively sampled in Lake Tanganyika, and much remains unknown about the response of the Rift Valley’s largest lake to major environmental shifts during the Holocene, including the termination of the African Humid Period (AHP). Here, we present an integrated study (sedimentology, mineralogy, and geochemistry) of a radiocarbon-dated sediment core from the Kavala Island Ridge (KIR) that reveals paleoenvironmental variability in Lake Tanganyika since the Middle Holocene with decadal to centennial resolution. Massive blue-gray sandy silts represent sediments deposited during the terminal AHP (~5880–4640 cal yr BP), with detrital particle size, carbon concentrations, light stable isotopes, and mineralogy suggesting an influx of river-borne soil organic matter and weathered clay minerals to the lake at that time. Enhanced by the AHP’s warm and wet conditions, chemical weathering and erosion of Lake Tanganyika’s watershed appears to have promoted considerable nutrient recharge to the lake system. Following a relatively gradual termination of the AHP over the period from ~4640 cal yr BP to ~3680 cal yr BP, laminated and organic carbon-rich sediments began accumulating on the KIR. δ15Nbulk, C/N, and hydrogen index data suggest high relative primary production from a mix of algae and cyanobacteria, most likely in response to nutrient availability in the water column under a cooler and seasonally dry climate from ~3680 to 1100 cal yr BP. Sediments deposited during the Common Era show considerable variability in magnetic susceptibility, total organic carbon content, carbon isotopes, and C/N, consistent with dynamic hydroclimate conditions that affected the depositional patterns, including substantial changes around the Medieval Climate Anomaly and Little Ice Age. Data from this study highlight the importance of sedimentary records to constrain boundary conditions in hydroclimate and nutrient flux that can inform long-term ecosystem response in Lake Tanganyika.

Life cycle assessment of lithium-sulfur batteries with carbon nanotube hosts: Insights from lab experiments

Lithium‑sulfur (Li-S) batteries are candidates for next-generation batteries. It can be produced sustainably using sulfur instead of controversial cathode minerals like cobalt. However, Li-S batteries must improve their energy density and cycle life at their current state of development. Hosting the sulfur on carbon nanotubes (CNT) is a potential solution. This study investigated the environmental performance of a CNT-based Li-S battery based on original experiment data. The CNT in the batteries functioned as binders, conductive fillers, and current collectors, reducing auxiliary materials and simplifying manufacturing processes. We conducted a cradle-to-gate life cycle assessment (LCA) to clarify the environmental performance. We showed that the global warming potential (GWP) of the Li-S battery pack in a conventional battery structure was 105 kg CO2e/kWh. By partially substituting current collectors, increasing lithium anode efficiency, and reducing solvent usage, we could achieve 87, 82, and 78 kg CO2e, respectively. The lowest GWP of Li-S battery was 20 % lower when compared to a graphite‑nickel manganese cobalt oxides (NMC) battery. In addition, the other environmental indicators, including human toxicity, ecotoxicity, and acidification, were 26 % to 79 % lower, showing no major environmental burden shift. One exception was the mineral resource depletion, which was 2 % higher because lithium metal, instead of synthetic graphite, was used as a high-capacity anode pair. This study also found that modifying the cathode production process by using a less energy-intensive filtration before evaporating the remaining solvent could significantly reduce the energy required, thus mitigating the previously identified environmental hotspot. Our finding highlighted that a prospective LCA collaborating with battery experimentalists could lead to novel discoveries for environmentally sustainable battery production. Overall, we showed that Li-S batteries are environmentally preferred at the production stage, as supported by advanced experiments. Further research into improving the cycle life of Li-S batteries is crucial when considering the use stage to reduce the environmental impact per functional unit of energy delivered over the battery lifetime.

Modeling Land Use Transformations and Flood Hazard on Ibaraki’s Coastal in 2030: A Scenario-Based Approach Amid Population Fluctuations

Coastal areas, influenced by human activity and natural factors, face major environmental shifts, including climate-induced flood risks. This highlights the importance of forecasting coastal land use for effective flood defense and ecological conservation. Japan’s distinct demographic path necessitates flexible strategies for managing its urban development. The study examines the Ibaraki Coastal region to analyze the impacts of land-use changes in 2030, predicting and evaluating future floods from intensified high tides and waves in scenario-based forecasts. The future roughness map is derived from projected land-use changes, and we utilize this information in DioVISTA 3.5.0 software to simulate flood scenarios. Finally, we analyzed the overlap between simulated floods and each land-use category. The results indicate since 2020, built-up areas have increased by 52.37 sq. km (39%). In scenarios of constant or shrinking urban areas, grassland increased by 28.54 sq. km (42%), and urban land cover decreased by 7.47 sq. km (5.6%) over ten years. Our research examines two separate peaks in water levels associated with urban flooding. Using 2030 land use maps and a peak height of 4 m, which is the lower limit of the maximum run-up height due to storm surge expected in the study area, 4.71 sq. km of residential areas flooded in the urban growth scenario, compared to 4.01 sq. km in the stagnant scenario and 3.96 sq. km in the shrinkage scenario. With the upper limit of 7.2 m, which is the extreme case in most of the study area, these areas increased to 49.91 sq. km, 42.52 sq. km, and 42.31 sq. km, respectively. The simulation highlights future flood-prone urban areas for each scenario, guiding targeted flood prevention efforts.

Divergent vertebral formulae shape the evolution of axial complexity in mammals

Complexity, defined as the number of parts and their degree of differentiation, is a poorly explored aspect of macroevolutionary dynamics. The maximum anatomical complexity of organisms has undoubtedly increased through evolutionary time. However, it is unclear whether this increase is a purely diffusive process or whether it is at least partly driven, occurring in parallel in most or many lineages and with increases in the minima as well as the means. Highly differentiated and serially repeated structures, such as vertebrae, are useful systems with which to investigate these patterns. We focus on the serial differentiation of the vertebral column in 1,136 extant mammal species, using two indices that quantify complexity as the numerical richness and proportional distribution of vertebrae across presacral regions and a third expressing the ratio between thoracic and lumbar vertebrae. We address three questions. First, we ask whether the distribution of complexity values in major mammal groups is similar or whether clades have specific signatures associated with their ecology. Second, we ask whether changes in complexity throughout the phylogeny are biased towards increases and whether there is evidence of driven trends. Third, we ask whether evolutionary shifts in complexity depart from a uniform Brownian motion model. Vertebral counts, but not complexity indices, differ significantly between major groups and exhibit greater within-group variation than recognized hitherto. We find strong evidence of a trend towards increasing complexity, where higher values propagate further increases in descendant lineages. Several increases are inferred to have coincided with major ecological or environmental shifts. We find support for multiple-rate models of evolution for all complexity metrics, suggesting that increases in complexity occurred in stepwise shifts, with evidence for widespread episodes of recent rapid divergence. Different subclades evolve more complex vertebral columns in different configurations and probably under different selective pressures and constraints, with widespread convergence on the same formulae. Further work should therefore focus on the ecological relevance of differences in complexity and a more detailed understanding of historical patterns.

Glacial Outburst Floods Responsible for Major Environmental Shift in Arctic Coastal Catchment, Rekvedbukta, Albert I Land, Svalbard

Small Arctic coastal catchments and coastal lagoon systems are some of the most vulnerable to climate change. Glacial retreat and the development of glacial lakes and drainage systems provide opportunities for hazardous events such as GLOFs. We observe that the stability of lagoons and their associated barriers are controlled by the frequency and magnitude of storms approaching the coasts, access to sediment supplies and resilience to sea-level rise. Based on multidecadal remote sensing data, we were able to identify the rate of glacial recession, the development of glacial lakes, vegetation response to climate change and a GLOF event, and shoreline and lagoon responses to the environmental shifts within the small catchment. Here we present an example of lagoon system evolution where a glacial outburst flood exerted significant control over lagoon drainage and coastal barrier stability.

Has Biomimicry in Architecture Arrived in France? Diversity of Challenges and Opportunities for a Paradigm Shift.

Biomimicry is a growing field of developing environmental innovations for materials, facade systems, buildings, and urban planning. In France, we observe an extensive diversity of initiatives in biomimicry for the development of regenerative cities. These initiatives blossom in a large range of areas, from education to urban policies, to achieve a major environmental, social and economic paradigm shift. To provide a comprehensive understanding of this development at the national scale, this paper presents and discusses the diversity of the developed initiatives over the last 10 years in six main fields-education, urban policies, fundamental and applied research, design demonstrators, arts, and communication. This research is an opportunistic study based on the analysis of these initiatives enriched by the feedback of the stakeholders collected by the authors working in the field of biomimicry over the last seven years. We identify that biomimicry in France has mainly extended through individual initiatives of teachers, territorial authorities, architectural studios, or researchers rather than through the support of public policies. Putting into perspective developments in biomimicry by other countries, this cross-discipline analysis provides recommendations for the extensive development of regenerative architecture and urbanism at the national scale.

Tracking habitat or testing its suitability? Similar distributional patterns can hide very different histories of persistence versus nonequilibrium dynamics.

The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.

Resilient biotic response to long-term climate change in the Adriatic Sea.

Preserving adaptive capacities of coastal ecosystems, which are currently facing the ongoing climate warming and a multitude of other anthropogenic impacts, requires an understanding of long‐term biotic dynamics in the context of major environmental shifts prior to human disturbances. We quantified responses of nearshore mollusk assemblages to long‐term climate and sea‐level changes using 223 samples (~71,300 specimens) retrieved from latest Quaternary sediment cores of the Adriatic coastal systems. These cores provide a rare chance to study coastal systems that existed during glacial lowstands. The fossil mollusk record indicates that nearshore assemblages of the penultimate interglacial (Late Pleistocene) shifted in their faunal composition during the subsequent ice age, and then reassembled again with the return of interglacial climate in the Holocene. These shifts point to a climate‐driven habitat filtering modulated by dispersal processes. The resilient, rather than persistent or stochastic, response of the mollusk assemblages to long‐term environmental changes over at least 125 thousand years highlights the historically unprecedented nature of the ongoing anthropogenic stressors (e.g., pollution, eutrophication, bottom trawling, and invasive species) that are currently shifting coastal regions into novel system states far outside the range of natural variability archived in the fossil record.

The Jurassic Laberge Group in the Whitehorse Trough of the Canadian Cordillera: Using Detrital Mineral Geochronology and Thermochronology to Investigate Tectonic Evolution

The Laberge Group is an Early to Middle Jurassic sequence of mostly siliciclastic sedimentary rocks that were deposited in a marginal marine environment in the northern Canadian Cordillera. It forms a long narrow belt with a total thickness of 3–4 km extending for more than 600 km across southern Yukon and northwestern British Columbia. These sedimentary rocks overlap the Yukon-Tanana, Stikinia and Cache Creek terranes that form the main components of the Intermontane superterrane. The Laberge Group contains a record of the erosion of some of these terranes, and also offers some constraints on the timing of their amalgamation and accretion to the Laurentian margin. The Laberge Group was deposited with local unconformity on the Late Triassic Stuhini Group (in British Columbia) and correlative Lewes River Group (in Yukon), both of which are volcanic-rich, and assigned to the Stikinia terrane. The Laberge Group is in turn overlain by Middle Jurassic to Cretaceous clastic rocks, including the Bowser Lake Group in BC and the Tantalus Formation in Yukon. Clast compositions and detrital zircon populations within the Laberge Group and between it and these bounding units indicate major shifts in depositional environment, basin extent and detrital sources from Late Triassic to Late Jurassic. During the Early Jurassic clast compositions in the Laberge Group shifted from sediment- and volcanic-dominated to plutonic-dominated, and detrital zircon populations are dominated by grains that yield ages that approach or overlap their inferred depositional ages. This pattern is consistent with progressive dissection and unroofing of (an) active arc(s) to eventually expose Triassic to Jurassic plutonic suites. Detrital rutile and muscovite data from the Laberge Group indicate rapid cooling and then exhumation of adjoining metamorphic rocks during the Early Jurassic, allowing these to contribute detritus on a more local scale. The most likely source for such metamorphic detritus is within the Yukon-Tanana terrane, and its presence in the Laberge Group may constrain the timing of amalgamation and accretion of the Yukon-Tanana and Stikinia terranes. Thermochronological data also provide new insights into the evolution of the Laberge Group basin. Results from the U–Th/(He) method on detrital apatite suggest that most areas experienced post-depositional heating to 60°C or more, whereas U–Th/(He) results from detrital zircon show that heating to more than 200°C occurred on a more local scale. In detail, Laberge Group cooling and exhumation was at least in part structurally controlled, with more strongly heated areas situated in the footwall of an important regional fault system. The thermochronological data are preliminary, but they suggest potential to eventually constrain the kinematics and timing of inversion across the Laberge Group basin and may also have implications for its energy prospectivity. In summary, the Laberge Group is a complex package of sedimentary rocks developed in an active, evolving tectonic realm, and many questions remain about the details of its sources and evolution. Nevertheless, the available information demonstrates the potential of combined geochronological and thermochronological methods applied to detrital minerals to unravel links between regional tectonics, basin development and clastic sedimentation.

Editorial 2022

Editorial 2022

A 350-year multiproxy record of climate-driven environmental shifts in the Amundsen Sea Polynya, Antarctica

With a growing concern over rapid Antarctic ice loss in recent years, the Amundsen Sea, one of the fastest-melting areas in Antarctica, currently becomes a hotspot for the Earth sciences in the context of its linkage to global climate. As a center of strong physical and biological coupling processes, polynyas of the Amundsen Sea could act as sentinels of changes in atmosphere–ice–ocean interactions, offering a unique perspective into its sensitivity to climate variability. Here, we present a new, multiproxy-based high-resolution sedimentary record from the Amundsen Sea polynya, which provides new insights into environmental conditions of the region over the last 350 years and their linkages to climatic factors. Our results show that the polynya witnessed step-wise environmental shifts in parallel with the phases and strength of large-scale climate patterns, i.e., the Southern Annular Mode (SAM) and El Niño–Southern Oscillation (ENSO). Notably, intersite correlation of on-shelf Circumpolar Deep Water (CDW) intrusion signals at different locals suggests that the CDW may have gained increased access to the shelves at the time of a strong coupling of positive SAM and El Niño states. We tentatively speculate that anomalous large-scale atmospheric and oceanic circulation patterns over the Southern Hemisphere, forced by increasing greenhouse gas levels, were strongly involved in the mid-20 th century CDW invigoration, which may be greater in scale that goes well beyond the Amundsen Sea region. This result is relevant to the current debate on spatial heterogeneity in the timing and phasing of major climatic events in Antarctica, underscoring an unambiguous connection of the Antarctic climate state to the large-scale ocean–atmosphere reorganizations. Our study also extends a growing evidence that today's global warming trend is expected to have a severe effect on future configuration of Antarctic continental ice-shelf environment. • Sedimentary data capture major shifts in the Amundsen Sea polynya environment. • Stepwise environmental shifts are linked to large-scale climate variabilities. • The mid-20th century's continental-scale CDW increase under anthropogenic forcings. • Today's global warming trend may severely affect future configuration of Antarctica.

Fecal stanol ratios indicate shifts in camelid pastoralism in the highlands of Peru across a 4,000-year lacustrine sequence

Subsistence adaptations respond to environmental instability as well as sociopolitical demands. On the Andean altiplano, camelid husbandry is a key adaptation utilized for thousands of years to mitigate environmental risks to agricultural productivity, to facilitate transport and to generate wealth for political purposes. Here, we reconstruct the history of camelid utilization on the altiplano with fecal stanol biomarkers from Lake Orurillo in southern Peru. Biomarker samples span a 4000-year interval and document changes at centennial timescales. The abundances of individual fecal stanols appear to be less diagnostic of changes in human occupation in the Orurillo region where human population levels apparently remained far lower than those of domesticated camelids. However, ratios of human (coprostanol) to ruminant (24-ethylcoprosanol) fecal stanol concentrations demonstrate that these proxies are reliable indicators of variations in camelid herd sizes. Our data show that camelid utilization intensified after ca. 1050 CE during a severe and protracted drought that was coincident with widespread population movement away from fertile farmlands to higher elevations favorable for grazing. Camelid herds remained in high abundance around Orurillo during improved climate conditions and through the Inca era until after ca. 1500 CE when our data point to a significant disruption after European conquest. The intensification of camelid husbandry among Andean cultures is therefore linked to major environmental and sociopolitical shifts.

Frequency of exceptional Nile flood events as an indicator of Holocene hydro-climatic changes in the Ethiopian Highlands

Climate conditions in Africa have varied substantially during the Late Quaternary with alternating humid and arid periods controlled mainly by the African monsoonal regime. However, the duration and termination of the last African Humid Period (14–6 ka BP) and its internal climatic variability are still debated. Using a laminated sequence from the Nile Deep-Sea Fan, we reconstruct for the first time the monsoon-induced frequency of exceptional Nile floods at centennial resolution during the African Humid Period. By combining sedimentological, geochemical and microscopic tools and comparing our record with two proximal piston cores and with regional paleoclimatic records, we show: a) the occurrence of recurrent high-energy floods between 10.1 and 9 ka BP, during the height of the African Humid Period; b) a shift in the hydro-climatic regime as early as 9 ka BP, with a progressive reduction in flood frequency and magnitude until 8.2 ka BP, likely related to a southward migration of the monsoon rainfall belt; c) a drastic reduction of flood activity between 8.2 and 7.8 ka BP; d) an unstable Ethiopian-Nile hydrological system from 7.8 ka BP, followed by a further decrease in river runoff until ∼4 ka BP. The occurrence of a stepwise hydro-climatic deterioration over the Ethiopian Highlands from ∼9 ka BP brings into question the climatic linkages and feedbacks between low and high latitudes during the Early to Mid-Holocene and in particular around the 8.2 ka BP North Atlantic cooling event. Our unique record of flood frequency at centennial-resolution therefore allows us to draw new insights on fluvial and geomorphic feedbacks of the Nile hydrologic system to monsoonal regimes during a period of major environmental shifts.

A major environmental shift by the middle Eocene in southern China: Evidence from palynological records

The modern environment of southern China is dominated by a humid monsoon climate, and presents a striking contrast to the widespread deserts found at similar latitudes elsewhere. The formation of a monsoon climate marks a major environmental shift in southern China during the Cenozoic; however, the origin and possible driving mechanism of the climate transition remain unclear. Paleogene palynological records from seven basins across southern China offer an exceptional opportunity to address this knowledge gap. The Paleogene palynoflora reveals two completely different vegetation and climate patterns: the Paleocene to early Eocene was characterized by a relatively high abundance of xerophilous taxa, suggesting an arid/semi-arid climate; while the middle Eocene to Oligocene supported subtropical wet evergreen and deciduous broad-leaved mixed forest, characterized by a significant increase in broad-leaved, coniferous taxa and the almost complete disappearance of xerophilous taxa, together indicating the emergence of a warm–humid climate at this time. Combined palynological, sedimentological, paleozoological, and paleobotanical proxy evidence reveal that the major environmental transition occurred roughly around the middle Eocene; this transition may mark the establishment of the monsoon climate. Furthermore, middle Eocene climatic parameters obtained through the Coexistence Approach (CA) were compared with those of modern sites with known climate regimes. The middle Eocene parameters were most similar to those exposed to the modern East Asian Monsoon (EAM), further indicating that the middle Eocene climate of southern China was predominantly influenced by the EAM. The evolution of the Paleogene palynoflora in southern China is largely consistent with global climate change. We infer that the enhancement of the East Asian winter monsoon (EAWM) during the middle Eocene was closely related to long-term global cooling, while the intensified East Asian summer monsoon (EASM) was primarily caused by the northward drift of the Indian Subcontinent and the uplift of the Tibetan Plateau.

Algal lipids reveal unprecedented warming rates in alpine areas of SW Europe during the industrial period

Abstract. Alpine ecosystems of the southern Iberian Peninsula are among the most vulnerable and the first to respond to modern climate change in southwestern Europe. While major environmental shifts have occurred over the last ∼1500 years in these alpine ecosystems, only changes in the recent centuries have led to abrupt environmental responses, but factors imposing the strongest stress have been unclear until now. To understand these environmental responses, this study, for the first time, has calibrated an algal lipid-derived temperature proxy (based on long-chain alkyl diols) to instrumental historical data extending alpine temperature reconstructions to 1500 years before present. These novel results highlight the enhanced effect of greenhouse gases on alpine temperatures during the last ∼200 years and the long-term modulating role of solar forcing. This study also shows that the warming rate during the 20th century (∼0.18 ∘C per decade) was double that of the last stages of the Little Ice Age (∼0.09 ∘C per decade), even exceeding temperature trends of the high-altitude Alps during the 20th century. As a consequence, temperature exceeded the preindustrial record in the 1950s, and it has been one of the major forcing processes of the recent enhanced change in these alpine ecosystems from southern Iberia since then. Nevertheless, other factors reducing the snow and ice albedo (e.g., atmospheric deposition) may have influenced local glacier loss, since almost steady climate conditions predominated from the middle 19th century to the first decades of the 20th century.

Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer.

Knowledge of the molecular basis of phenotypic responses to environmental cues is key to understanding the process of adaptation. Insights to adaptation at an evolutionary time scale can be gained by observing organismal responses before and after a shift in environmental conditions, but such observations can rarely be made. Using the ecological and genomic model Daphnia, we linked transcriptomic responses and phosphorus (P)-related phenotypic traits under high and low P availability. We mapped weighted gene coexpression networks to traits previously assessed in resurrected ancient (600 years old) and modern Daphnia pulicaria from a lake with a historic shift in P-enrichment. Subsequently, we assessed evolutionary conservation or divergence in transcriptional networks of the same isolates. We discovered highly preserved gene networks shared between ancient genotypes and their modern descendants, but also detected clear evidence of transcriptional divergence between these evolutionarily separated genotypes. Our study highlights that phenotypic evolution is a result of molecular fine-tuning on different layers ranging from basic cellular responses to higher order phenotypes. In a broader context, these findings advance our understanding how populations are able to persist throughout major environmental shifts.

Attributing drivers to spatio-temporal changes in tree density across a suburbanizing landscape since 1944

Urban expansion, especially suburbanization, represents a major social, economic and environmental shift that has escalated since the mid-1900s in North America. Suburban development leads to corresponding changes in the treed environment of urban-rural fringes. It is important to understand where, when and why trees change in response to development over many decades, but this is difficult since long-term data are scarce. We used 70+ years (1944–2017) of leaf-off aerial photographs, often representing the only long-term landscape record, to quantify and map spatio-temporal changes in tree density through the entirety of the agricultural-suburban transitional period. Photo-interpretation of individual tree locations, along with recording observable drivers of change, was completed across six different modern landscapes in Mississauga, Ontario, Canada. Results indicate that tree density often recovers, or even increases, post-development. There are differences between landscapes, but most tree density gains are associated with forest expansion and tree planting, while most losses are associated with building and road construction. The influence of these drivers, along with the temporal trajectory of tree density changes, are shaped by a landscape’s socioecological legacy and the length, scope and intensity of development (as decided by decision makers). Processes include initial tree losses followed by recovery from tree planting, and forest succession in abandoned fields after land purchase and nearby development. We assert that the spatio-temporal changes in tree density and related drivers quantified here can be generalized to gain knowledge on how tree density and distribution across agricultural landscapes will change under different development scenarios.

Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

Abstract The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

Early cave art and ancient DNA record the origin of European bison.

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.