School of Geography, Earth and Atmospheric Sciences - Research Publications
Now showing items 1-12 of 239
Influence of the 2015-2016 El Niño on the record-breaking mangrove dieback along northern Australia coast.
(Springer Science and Business Media LLC, 2021-10-14)
This study investigates the underlying climate processes behind the largest recorded mangrove dieback event along the Gulf of Carpentaria coast in northern Australia in late 2015. Using satellite-derived fractional canopy cover (FCC), variation of the mangrove canopies during recent decades are studied, including a severe dieback during 2015-2016. The relationship between mangrove FCC and climate conditions is examined with a focus on the possible role of the 2015-2016 El Niño in altering favorable conditions sustaining the mangroves. The mangrove FCC is shown to be coherent with the low-frequency component of sea level height (SLH) variation related to the El Niño Southern Oscillation (ENSO) cycle in the equatorial Pacific. The SLH drop associated with the 2015-2016 El Niño is identified to be the crucial factor leading to the dieback event. A stronger SLH drop occurred during austral autumn and winter, when the SLH anomalies were about 12% stronger than the previous very strong El Niño events. The persistent SLH drop occurred in the dry season of the year when SLH was seasonally at its lowest, so potentially exposed the mangroves to unprecedented hostile conditions. The influence of other key climate factors is also discussed, and a multiple linear regression model is developed to understand the combined role of the important climate variables on the mangrove FCC variation.
Megaphages infect Prevotella and variants are widespread in gut microbiomes
(NATURE RESEARCH, 2019-04-01)
Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences
(AMER SOC MICROBIOLOGY, 2017-11-01)
We report the 4.55-Mbp genome of "Candidatus Fluviicola riflensis" (Bacteroidetes) that was manually curated to completion from Illumina data. "Ca Fluviicola riflensis" is a facultative anaerobe. Its ability to grow over a range of O2 levels may favor its proliferation in an aquifer adjacent to the Colorado River in the United States.
Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.
(Springer Science and Business Media LLC, 2019-03-26)
The original version of this Article contained errors in Fig. 4. In panel a, the labels 'F420-reducing NiFe hydrogenase (group 3a)' and 'Group 2 NiFe hydrogenase' were misplaced. These errors have been corrected in both the PDF and HTML versions of the Article.
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.
(Springer Science and Business Media LLC, 2019-01-28)
The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Similarly, Melainabacteria have diverse energy metabolisms and are capable of fermentation and aerobic or anaerobic respiration. The ancestor of all these groups may have been an anaerobe in which fermentation and H2 metabolism were central metabolic features. The ability to use O2 as a terminal electron acceptor must have been subsequently acquired by these lineages.
The distinction of CPR bacteria from other bacteria based on protein family content.
(Springer Science and Business Media LLC, 2019-09-13)
Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.
Three ways social identity shapes climate change adaptation
(IOP Publishing Ltd, 2021-12-01)
Adaptation to climate change is inescapably influenced by processes of social identity-how people perceive themselves, others, and their place in the world around them. Yet there is sparse evidence into the specific ways in which identity processes shape adaptation planning and responses. This paper proposes three key ways to understand the relationship between identity formation and adaptation processes: (a) how social identities change in response to perceived climate change risks and threats; (b) how identity change may be an objective of adaptation; and (c) how identity issues can constrain or enable adaptive action. It examines these three areas of focus through a synthesis of evidence on community responses to flooding and subsequent policy responses in Somerset county, UK and the Gippsland East region in Australia, based on indepth longitudinal data collected among those experiencing and enacting adaptation. The results show that adaptation policies are more likely to be effective when they give individuals confidence in the continuity of their in-groups, enhance the self-esteem of these groups, and develop their sense of self-efficacy. These processes of identity formation and evolution are therefore central to individual and collective responses to climate risks.
The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia
(NATURE PUBLISHING GROUP, 2019-08-13)
The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.
Core-Shell Processing of Natural Pigment: Upper Palaeolithic Red Ochre from Lovas, Hungary
(PUBLIC LIBRARY SCIENCE, 2015-07-06)
Ochre is the common archaeological term for prehistoric pigments. It is applied to a range of uses, from ritual burials to cave art to medications. While a substantial number of Palaeolithic paint mining pits have been identified across Europe, the link between ochre use and provenance, and their antiquity, has never yet been identified. Here we characterise the mineralogical signature of core-shell processed ochre from the Palaeolithic paint mining pits near Lovas in Hungary, using a novel integration of petrographic and mineralogical techniques. We present the first evidence for core-shell processed, natural pigment that was prepared by prehistoric people from hematitic red ochre. This involved combining the darker red outer shell with the less intensely coloured core to efficiently produce an economical, yet still strongly coloured, paint. We demonstrate the antiquity of the site as having operated between 14-13 kcal BP, during the Epigravettian period. This is based on new radiocarbon dating of bone artefacts associated with the quarry site. The dating results indicate the site to be the oldest known evidence for core-shell pigment processing. We show that the ochre mined at Lovas was exported from the site based on its characteristic signature at other archaeological sites in the region. Our discovery not only provides a methodological framework for future characterisation of ochre pigments, but also provides the earliest known evidence for "value-adding" of products for trade.
The Mungo Mega-Lake Event, Semi-Arid Australia: Non-Linear Descent into the Last Ice Age, Implications for Human Behaviour
(PUBLIC LIBRARY SCIENCE, 2015-06-17)
The Willandra Lakes complex is one of the few locations in semi-arid Australia to preserve both paleoenvironmental and Paleolithic archeological archives at high resolution. The stratigraphy of transverse lunette dunes on the lakes' downwind margins record a late Quaternary sequence of wetting and drying. Within the Willandra system, the Lake Mungo lunette is best known for its preservation of the world's oldest known ritual burials, and high densities of archeological traces documenting human adaptation to changing environmental conditions over the last 45 ka. Here we identify evidence at Lake Mungo for a previously unrecognised short-lived, very high lake filling phase at 24 ka, just prior to the Last Glacial Maximum. Mega-lake Mungo was up to 5 m deeper than preceding or subsequent lake full events and represented a lake volume increase of almost 250%. Lake Mungo was linked with neighboring Lake Leaghur at two overflow points, creating an island from the northern part of the Mungo lunette. This event was most likely caused by a pulse of high catchment rainfall and runoff, combined with neotectonic activity which may have warped the lake basin. It indicates a non-linear transition to more arid ice age conditions. The mega-lake restricted mobility for people living in the area, yet archeological traces indicate that humans rapidly adapted to the new conditions. People repeatedly visited the island, transporting stone tools across water and exploiting food resources stranded there. They either swam or used watercraft to facilitate access to the island and across the lake. Since there is no evidence for watercraft use in Australia between initial colonization of the continent prior to 45 ka and the mid-Holocene, repeated visits to the island may represent a resurrection of waterfaring technologies following a hiatus of at least 20 ky.
The Campanian Ignimbrite Eruption: New Data on Volcanic Ash Dispersal and Its Potential Impact on Human Evolution
(PUBLIC LIBRARY SCIENCE, 2013-06-17)
The Campanian Ignimbrite (CI) volcanic eruption was the most explosive in Europe in the last 200,000 years. The event coincided with the onset of an extremely cold climatic phase known as Heinrich Event 4 (HE4) approximately 40,000 years ago. Their combined effect may have exacerbated the severity of the climate through positive feedbacks across Europe and possibly globally. The CI event is of particular interest not only to investigate the role of volcanism on climate forcing and palaeoenvironments, but also because its timing coincides with the arrival into Europe of anatomically modern humans, the demise of Neanderthals, and an associated major shift in lithic technology. At this stage, however, the degree of interaction between these factors is poorly known, based on fragmentary and widely dispersed data points. In this study we provide important new data from Eastern Europe which indicate that the magnitude of the CI eruption and impact of associated distal ash (tephra) deposits may have been substantially greater than existing models suggest. The scale of the eruption is modelled by tephra distribution and thickness, supported by local data points. CI ashfall extends as far as the Russian Plain, Eastern Mediterranean and northern Africa. However, modelling input is limited by very few data points in Eastern Europe. Here we investigate an unexpectedly thick CI tephra deposit in the southeast Romanian loess steppe, positively identified using geochemical and geochronological analyses. We establish the tephra as a widespread primary deposit, which blanketed the topography both thickly and rapidly, with potentially catastrophic impacts on local ecosystems. Our discovery not only highlights the need to reassess models for the magnitude of the eruption and its role in climatic transition, but also suggests that it may have substantially influenced hominin population and subsistence dynamics in a region strategic for human migration into Europe.
A New Chronology for Rhafas, Northeast Morocco, Spanning the North African Middle Stone Age through to the Neolithic
(PUBLIC LIBRARY SCIENCE, 2016-09-21)
Archaeological sites in northern Africa provide a rich record of increasing importance for the origins of modern human behaviour and for understanding human dispersal out of Africa. However, the timing and nature of Palaeolithic human behaviour and dispersal across north-western Africa (the Maghreb), and their relationship to local environmental conditions, remain poorly understood. The cave of Rhafas (northeast Morocco) provides valuable chronological information about cultural changes in the Maghreb during the Palaeolithic due to its long stratified archaeological sequence comprising Middle Stone Age (MSA), Later Stone Age (LSA) and Neolithic occupation layers. In this study, we apply optically stimulated luminescence (OSL) dating on sand-sized quartz grains to the cave deposits of Rhafas, as well as to a recently excavated section on the terrace in front of the cave entrance. We hereby provide a revised chronostratigraphy for the archaeological sequence at the site. We combine these results with geological and sedimentological multi-proxy investigations to gain insights into site formation processes and the palaeoenvironmental record of the region. The older sedimentological units at Rhafas were deposited between 135 ka and 57 ka (MIS 6 -MIS 3) and are associated with the MSA technocomplex. Tanged pieces start to occur in the archaeological layers around 109 ka, which is consistent with previously published chronological data from the Maghreb. A well indurated duricrust indicates favourable climatic conditions for the pedogenic cementation by carbonates of sediment layers at the site after 57 ka. Overlying deposits attributed to the LSA technocomplex yield ages of ~21 ka and ~15 ka, corresponding to the last glacial period, and fall well within the previously established occupation phase in the Maghreb. The last occupation phase at Rhafas took place during the Neolithic and is dated to ~7.8 ka.