Fossil Sequences Research Articles

What does the occurrence of Sporormiella (Preussia) spores mean in Australian fossil sequences?

ABSTRACTUnderstanding the loss of the final few species of Australian megafauna is beset by a paucity of data on human arrival, well‐provenanced megafauna, human/megafauna population range and distribution (coexistence and interaction), and the range, scale and impact of environmental changes spanning the human–megafauna period. To overcome these shortcomings, the occurrence and decline of coprophilous fungal spores of Sporormiella in sediments have been used as a proxy for extinct megaherbivores. The Sporormiella evidence is presented as the key indicator of extinction timing and these reports are often from locations where there is no known archaeological record or megafauna remains. However, interpreting fungal spore occurrence is not straightforward, as demonstrated by studies investigating taphonomy, taxonomy and the types of animal dung where Sporormiella occurs. No detailed studies on these problems exist for Australia and no evidence supporting the use of Sporormiella as a valid proxy has been reported. Here we examine the occurrence of Sporormiella spores from Cuddie Springs in south‐eastern Australia. Despite a well‐preserved suite of megafauna fossils, Sporormiella occurrence is sporadic and frequencies are low. We conclude that using Sporormiella alone as an indicator for the presence of megafauna is premature for the Australian context.

Trajectories of change in Mediterranean Holocene vegetation through classification of pollen data

Quantification of vegetation cover from pollen analysis has been a goal of palynologists since the advent of the method in 1916 by the great Lennart von Post. Pollen-based research projects are becoming increasingly ambitious in scale, and the emergence of spatially extensive open-access datasets, advanced methods and computer power has facilitated sub-continental analysis of Holocene pollen data. This paper presents results of one such study, focussing on the Mediterranean basin. Pollen data from 105 fossil sequences have been extracted from the European Pollen database, harmonised by both taxonomy and chronologies, and subjected to a hierarchical agglomerative clustering method to synthesise the dataset into 16 main groupings. A particular focus of analysis was to describe the common transitions from one group to another to understand pathways of Holocene vegetation change in the Mediterranean. Two pollen-based indices of human impact (OJC: Oleaceae, Juglans, Castanea; API: anthropogenic pollen indicators) have been used to infer the degree of human modification of vegetation within each pollen grouping. Pollen-inferred cluster groups that are interpreted as representing more natural vegetation states show a restricted number of pathways of change. A set of cluster groups were identified that closely resemble anthropogenically-disturbed vegetation, and might be considered anthromes (anthopogenic biomes). These clusters show a very wide set of potential pathways, implying that all potential vegetation communities identified through this analysis have been altered in response to land exploitation and transformation by human societies in combination with other factors, such as climatic change. Future work to explain these ecosystem pathways will require developing complementary datasets from the social sciences and humanities (archaeology and historical sources), along with synthesis of the climatic records from the region.

Biostratigraphy and Depositional Environment of the Miocene Limestone Bed of Baripada, Mayurbhanj District, Odisha: Foraminiferal, Sedimentological and Bulk Organic Geochemical Evidences

ABSTRACT Baripada Marine Beds (BMB) have been studied extensively in terms of its mega fossil content. However, not much has been discussed about the foraminiferal content and the organic matter assemblage in these beds. The fossiliferous sequence of BMB consists of sandstone, shale and limestone units. The present study is persued on the limestone unit of BMB. Foraminiferal, thin section and rock-eval pyrolysis studies were performed on the 33 surface samples collected from five sections of Jamdapal and Mukurmatia region along the Budhabalang river bank. Foraminifera are less abundant in the samples of Jamdapal, whereas Mukurmatia is comparatively rich. First appearance datum of Globorotalia menardii[ranges since middle Miocene (12.6 Ma); FAD at planktic foraminiferal zone N12] and last appearance datum of Neogloboquadrina continuosa [ranges between early Miocene (23.2 Ma) to late Miocene (8.3 Ma); FAD at planktic foraminiferal zone N4B and LAD at N16] together suggest that the limestone unit was deposited in between 12.6 to 8.3 Ma within the upper Miocene. Also, the association of shallow water benthic foraminifera (Species of Ammonia, Asterorotalia, Bolivina, Buliminella, Cibicides, Challengerella, Criboelphidium, Cribononion, Elphidium, Hanzawaia, Nonionella) and planktic foraminifera (Globigerina falcoensis, Globigerina woodi, Globorotalia menardii, Neogloboquadrina continuosa) together with oyster bank and shark teeth suggest deposition of limestone within well oxygenated, tropical, shallow water, open marine condition (within 40m water depth). Lithological and thin section studies together with global sea level fluctuation history advocate that upper Miocene marine transgression promoted the formation of this unit. Bulk organic geochemical data obtained by the rock-eval pyrolysis studies on selected samples indicate a low total organic carbon (TOC), with low hydrogen index (HI), high oxygen index (OI). The organic facies is characterised by type-IV kerogen with major contribution from near shore terrestrial plants. This also suggests deposition in shallow, oxygenated environments that did not promote significant accumulation and preservation of organic content in sediments.

Examining bias in pollen-based quantitative climate reconstructions induced by human impact on vegetation in China

Abstract. Human impact is a well-known confounder in pollen-based quantitative climate reconstructions as most terrestrial ecosystems have been artificially affected to varying degrees. In this paper, we use a human-induced pollen dataset (H-set) and a corresponding natural pollen dataset (N-set) to establish pollen–climate calibration sets for temperate eastern China (TEC). The two calibration sets, taking a weighted averaging partial least squares (WA-PLS) approach, are used to reconstruct past climate variables from a fossil record, which is located at the margin of the East Asian summer monsoon in north-central China and covers the late glacial Holocene from 14.7 ka BP (thousands of years before AD 1950). Ordination results suggest that mean annual precipitation (Pann) is the main explanatory variable of both pollen composition and percentage distributions in both datasets. The Pann reconstructions, based on the two calibration sets, demonstrate consistently similar patterns and general trends, suggesting a relatively strong climate impact on the regional vegetation and pollen spectra. However, our results also indicate that the human impact may obscure climate signals derived from fossil pollen assemblages. In a test with modern climate and pollen data, the Pann influence on pollen distribution decreases in the H-set, while the human influence index (HII) rises. Moreover, the relatively strong human impact reduces woody pollen taxa abundances, particularly in the subhumid forested areas. Consequently, this shifts their model-inferred Pann optima to the arid end of the gradient compared to Pann tolerances in the natural dataset and further produces distinct deviations when the total tree pollen percentages are high (i.e. about 40 % for the Gonghai area) in the fossil sequence. In summary, the calibration set with human impact used in our experiment can produce a reliable general pattern of past climate, but the human impact on vegetation affects the pollen–climate relationship and biases the pollen-based climate reconstruction. The extent of human-induced bias may be rather small for the entire late glacial and early Holocene interval when we use a reference set called natural. Nevertheless, this potential bias should be kept in mind when conducting quantitative reconstructions, especially for the recent 2 or 3 millennia.

Xenarthra (Mammalia) from a new late Neogene fossiliferous locality in Northwestern Argentina

Northwestern Argentina contains one of the most complete continental late Neogene (ca. 9–2.58 Ma) fossiliferous sequences in South America, especially in the current territories of the Catamarca, Tucumán and Jujuy provinces. More precisely in Jujuy Province several localities bearing mainly fossil mammals have been reported at the Quebrada de Humahuaca in the Uquía, Maimará and Tilcara formations, in which the clade Xenarthra (Mammalia) is well-represented. In this scenario, the fossiliferous potential of other localities of Jujuy Province are less known, especially in those areas located at the northwest end of Argentina, bordering Bolivia in the Northern Puna. A new late Neogene fossiliferous locality near Calahoyo (3639 m.a.s.l), Jujuy Province, is here reported. The materials, belonging to Xenarthra, were exhumed from the base of the Tafna Formation which was deposited in a sedimentary basin by alluvial and/or fluvial currents, undergoing transitions of various lacustrine episodes. The taxa include the Tardigrada Pyramiodontherium bergi (Megatheriidae) and the Cingulata Eosclerocalyptus sp. (Glyptodontidae) and Macrochorobates chapalmalensis (Dasypodidae). From a biostratigraphic viewpoint, this assemblage suggests a Late Miocene-Pliocene age for the base of the Tafna Formation, and partially contradicts the supposed Plio-Pleistocene age of this unit. Finally, the new specimens here described indicate that Xenarthra were taxonomically and ecologically diverse during the late Neogene in the northwest end of Argentina, since they are represented by at least three main lineages (sloths, glyptodontids and armadillos).

The Late-Glacial and Holocene Marboré Lake sequence (2612 m a.s.l., Central Pyrenees, Spain): Testing high altitude sites sensitivity to millennial scale vegetation and climate variability

This paper presents the environmental, climate and vegetation changes reconstructed for the last 14.6kyrcal BP from the Marboré Lake sedimentary sequence, the highest altitude record (2612m a.s.l.) in the Pyrenees studied up to date. We investigate the sensitivity of this high altitude site to vegetational and climate dynamics and altitudinal shifts during the Holocene by comparing palynological spectra of the fossil sequence and pollen rain content from current moss pollsters. We hypothesize that the input of sediments in lakes at such altitude is strongly controlled by ice phenology (ice-free summer months) and that during cold periods Pollen Accumulation Rate (PAR) and Pollen Concentration (PC) reflect changes in ice-cover and thus is linked to temperature changes. Low sedimentation rates and low PC and PAR occurred during colder periods as the Younger Dryas (GS-1) and the Holocene onset (12.6–10.2kyrcal BP), suggesting that the lake-surface remained ice-covered for most of the year during these periods. Warmer conditions are not evident until 10.2kyrcal BP, when an abrupt increase in sedimentation rate, PC and PAR occur, pointing to a delayed onset of the Holocene temperature increase at high altitude. Well-developed pinewoods and deciduous forest dominated the mid montane belt since 9.3kyrcal BP until mid-Holocene (5.2kyrcal BP). A downwards shift in the deciduous forest occurred after 5.2kyrcal BP, in agreement with the aridity trend observed at a regional and Mediterranean context. The increase of herbaceous taxa during the late-Holocene (3.5kyrcal BP-present) reflects a general trend to reduced montane forest, as anthropogenic disturbances were not evident until 1.3kyrcal BP when Olea proportions from lowland areas and other anthropogenic indicators clearly expand. Our study demonstrates the need to perform local experimental approaches to check the effect of ice phenology on high altitude lakes sensitivity to vegetation changes to obtain more realistic reconstructions of mountain vegetation belts dynamics.

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

Abstract DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.

Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis

ABSTRACTGeometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.

Self-regulation of trilobite diversity in Murero (middle Cambrian, Spain) due to compensatory extinction

As species accumulate in a community, competition for available ecospace is expected to prevent the addition of new species and to facilitate species extinction, thus producing a dynamic equilibrium of diversity. This mechanism remains under debate since its empirical support comes mainly from indirect or partial evidence, with very few direct tests at the species level. Here a new method is described to detect the presence of selfregulation feedbacks between species richness and turnover rates. It consists of Monte Carlo simulations which randomize the distribution of species ranges among stratigraphic intervals, providing predictions which allow the detection of genuine self-regulation feedbacks in the real data. Since the simulations include any potential bias due to preservation, sampling, or change in depositional environment, and these biases would also affect the real dataset, they are thus ruled out as explanations for any difference found. This method is applied to one of the best known fossiliferous sequences worldwide, the Rambla de Valdemiedes in Murero (RV1 section, middle Cambrian, Spain), a classic locality that has been studied for more than 150 years and which stands out due to its excellent sampling density, continuous deposition, and homogeneous fossil preservation. The results show that trilobite species richness was self-regulated due to positive feedback with extinction rate, which implies that compensatory extinction regulated this fauna in spite of the on-going Cambrian radiation. The lack of evidence of any origination feedback suggests ecological opportunities were not limiting for new species to colonize this Cambrian community

The Sri Lankan ‘Microlithic’ Tradition c. 38,000 to 3,000 Years Ago: Tropical Technologies and Adaptations of Homo sapiens at the Southern Edge of Asia

The prehistoric archaeology of Sri Lanka is of considerable significance for investigations of the evolution, dispersal and adaptation of our species within a variety of environments beyond Africa during the Late Pleistocene. In particular, the archaeological and fossil sequences of Sri Lanka’s ‘Microlithic tradition’, c. 38,000–3,000 cal. years BP, have yielded some of the earliest Homo sapiens fossils, microlithic technologies, osseous toolkits, and evidence for symbolic ornamentation and long-distance contacts anywhere in South Asia. The further association of the Late Pleistocene portion of these records with the tropical rainforest of Sri Lanka’s Wet Zone also makes Sri Lanka of particular interest for debates regarding the viability of tropical rainforest for early human foraging and specialization. Yet beyond mentions of its fossil evidence, the archaeology and palaeoenvironmental contexts of the ‘Microlithic tradition’ have remained little-explored in the international literature. Here we present the first critical review of this period of Sri Lankan prehistory, examining its local chronologies, the spatial and diachronic patterns of its material cultural sequence, and relating its technological and fossil record to broader international archaeological, anthropological and genetic debates.

Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.

No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.

A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution

Although some creationist objections to evolutionary biology are simplistic and thus are easily refuted, when more technical arguments become widespread it is important for science educators to explain the relevant science in a straightforward manner. An interesting case study is provided by misguided allegations about how cytochrome c data pertain to molecular evolution. The most common of these misrepresentations bears a striking similarity to a particularly glaring misunderstanding of what should be expected of a transitional form in a fossil sequence. Although evangelist Kirk Cameron's ridiculous injunction of a hypothetical 'crocoduck' as an example of a potential transitional form is frequently invoked to illustrate the ignorance of many critics of evolutionary science, a strikingly analogous argument was applied to cytochrome c data by biochemist Michael Denton in 1985. The details of this analogy are worth exploring to clarify the fallacy of the widely circulated molecular argument.

Dinosaurs and Indians: Fossil Resource Dispossession of Sioux Lands, 1846-1875

The emergence of vertebrate paleontology as an established, scientific discipline can in part be attributed to large vertebrate fossils found on land dispossessed from indigenous populations from around the world. Specifically, geographic locations of the North American continental interior are known to yield fossiliferous stratagraphic sequences. I argue that vertebrate fossils are another natural resource dispossessed from Native peoples within the historical boundaries of Sioux lands. This body of research discusses the physical and geographical evidence of the first quarter-century of fossil dispossession in Indian country between the years 1846 and 1875.

The early Rhuddanian survival interval in the Lower Silurian of the Oslo Region: A third pulse of the end-Ordovician extinction

Ordovician/Silurian boundary layers with Rhuddanian strata are exposed as a long, continuously fossiliferous sequence in the Solvik Formation in the Asker area, central Oslo Region, Norway. Brachiopods belonging to Benthic Assemblage 5 are preserved in the lower parts of the formation. This level is investigated for the presence of a survival interval after the last end-Ordovician extinction event. The criteria for a survival interval include taxa that are dwarfed, long ranging, eurytopic, often opportunistic, as well as assemblages that show low density and diversity.Four species, Isorthis prima, Leangella scissa, Dicoelosia osloensis and Eoplectodonta duplicata, were collected and measured. The three former were dwarfed compared to a younger Aeronian fauna belonging to the same Benthic Assemblage. Detailed investigations showed a statistically significant two-step reduction in size for all but D. osloensis. The first interval, immediately above the last end-Ordovician extinction event, displays dwarfed brachiopods, but diversity is high and the number of long-ranging and eurytopic species is low due to the presence of globally and locally “relict” Ordovician species. The second interval, the upper parts of lower Rhuddanian, shows all the characteristics of a survival interval in which the sizes are statistically significantly smaller than both those in the interval below and those in the Aeronian interval above. No lithological change within lower Rhuddanian strata could be linked to the pronounced reduction in size. The second step in size reduction may be related to global occurrence of anoxia in the deep oceans with a pulse of anoxic water pushed onto the shelf at that time. It is coeval with a short negative ∂13C excursion found in some locales, signifying a brief period of global warming. The results suggest a protracted extinction event through parts of the early Rhuddanian and a third and final extinction event followed by a clear survival interval.

Behavioural leads in evolution: evidence from the fossil record

There has been much discussion of the role of behaviour in evolution, especially its potential to lead morphological evolution by placing the organism in a novel selective environment. Many adaptations of living species can be imagined to have originated in this way, although documented examples are relatively few. A fruitful arena for testing hypotheses about behavioural innovation is the fossil record. Traditionally, the behaviour of fossil species has been deduced from their morphology, precluding the observation of a behavioural lead preceding morphological evolution. This circularity can be broken by examining behavioural proxies independent of the adaptive morphology itself. Examples applicable to fossil remains include dietary information (e.g. wear traces on teeth, stable isotopes) and trace fossils indicating locomotor mode (footprints). The signature of a behavioural lead would be an observed shift in behaviour from one horizon (or taxon) to another, followed later by a functionally-related morphological change. This pattern can be sought either in finely-stratified anagenetic sequences of fossils (stratophenetic approach) or among fossils with well-resolved species-level phylogenies (cladistic approach). An array of case studies from the literature is presented. These include feeding shifts in finely-resolved sequences of vertebrates ranging from freshwater fish to terrestrial ungulates, as well as locomotor changes crucial to major evolutionary transitions in the origin of tetrapods, birds, and humans. The latter examples highlight the role of behaviour in initiating exaptation (the requisitioning of structure for a new function). The case studies also illustrate the challenges of using fossil sequences to elucidate behavioural roles, including insufficient stratigraphic resolution and uncertainty over the adaptive function of observed traits. By the same token, they suggest criteria for choosing promising cases for research, as well as for formulating testable hypotheses about evolutionary modes. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 315–331.

Strontium isotope dating of bivalve faunas from the Upper Miocene Cacela Formation, eastern Algarve, Portugal: Evidence from Messinian bivalve fauna

The study is focused on the determination of the geological age of bivalve fauna recovered from four fossiliferous sequences in the Cacela Formation of Algarve, southern Portugal, by means of the strontium isotope stratigraphy. Forty two analyses of bivalve samples from Barroquinha, Cabanas, the Cacela River and Lacem were performed. The estimated age based on the 87Sr/86Sr ratios in bivalve shell samples from the Cacela River (a reference section for the Cacela Formation) is 7.6 ± 0.4 Ma and is consistent with a late Tortonian age suggested by micropalaeontological data (calcareous nannofossils and planktonic foraminifers). Moreover, strontium isotopic data record that the oldest age of the bivalves of the Cacela Formation (Lacem site) is at least 8.9 ± 0.4 Ma whilst the age of about 7.0 ± 0.5 Ma can be inferred for bivalves from Barroquinha. An intriguing new datum comes, however, from the bivalve strontium isotopic data of the Cabanas section which records the estimated age of about 6.7 ± 0.4 Ma and, therefore, an early Messinian age. This is the first report of the early Messinian marine bivalve fauna in Portugal. Sixty one bivalve species have been recovered in the Messinian of Cabanas. Four of them: Pseudopythina macandrewi (P. Fischer), Coripia corbis (Philippi), Glossus (Glossus) humanus (Linnaeus) and Cyathodonta dollfusi (Cossmann et Peyrot) have previously not been reported from the Miocene of southern Portugal.

Functional Characterization of the Human Mariner Transposon Hsmar2

DNA transposons are mobile elements with the ability to mobilize and transport genetic information between different chromosomal loci. Unfortunately, most transposons copies are currently inactivated, little is known about mariner elements in humans despite their role in the evolution of the human genome, even though the Hsmar2 transposon is associated to hotspots for homologous recombination involved in human genetic disorders as Charcot–Marie–Tooth, Prader-Willi/Angelman, and Williams syndromes. This manuscript describes the functional characterization of the human HSMAR2 transposase generated from fossil sequences and shows that the native HSMAR2 is active in human cells, but also in bacteria, with an efficiency similar to other mariner elements. We observe that the sub-cellular localization of HSMAR2 is dependent on the host cell type, and is cytotoxic when overexpressed in HeLa cells. Finally, we also demonstrate that the binding of HSMAR2 to its own ITRs is specific, and that the excision reaction leaves non-canonical footprints both in bacteria and eukaryotic cells.

Ungulate diversity and precipitation history since the Last Glacial Maximum in the Western Cape, South Africa

This study reviews the precipitation history of the winter and year-round rainfall zones in the Western Cape (South Africa) in light of its fossil ungulate communities. Fossil sequences spanning the Last Glacial Maximum (LGM) and Lateglacial through the Holocene document a decline in ungulate richness through time. Based on the observed relationship between ungulate community richness and annual precipitation in Southern and East Africa, this implies increased effective precipitation during the LGM-Lateglacial at sites located in both the winter and year-round rainfall zones. These results are consistent with other lines of paleoenvironmental evidence from the winter rainfall zone, although they contradict records from the year-round rainfall zone that have been interpreted as reflecting aridity. A critical review of these records suggests that the patterns interpreted in terms of aridity can be explained by other mechanisms, including vegetation change. Current evidence is consistent with paleoclimatic models indicating that altered rainfall patterns during the LGM-Lateglacial were primarily related to the position of westerly frontal systems, which were displaced northward due to the expansion of Antarctic sea ice. Seasonal migration of these systems resulted in an expanded winter rainfall zone across much of southwestern Africa, but perhaps with some summer rains reaching the southern coast.

Bayesian age-depth modelling of Late Quaternary deposits from Wet and Blanche Caves, Naracoorte, South Australia: A framework for comparative faunal analyses

Bayesian age-depth models were constructed for two Late Quaternary aged fossil-bearing sedimentary sequences from caves in south eastern South Australia. The deposits in Wet and Blanche Caves contain dense assemblages of vertebrate fossils, largely the result of owl pellet accumulation. While individually calibrated radiocarbon determinations from the fossil sequences have provided a chronology for their accumulation, there was limited capacity available with such data to (a) temporally constrain assemblages associated with different depositional units and layers within the two sites, (b) interpret the chronological relationships among successive units and layers and (c) correlate sedimentary units and layers of similar age between the two deposits. Here, Bayesian age-depth models were constructed in OxCal for the Wet and Blanche Cave sequences, incorporating the available radiocarbon data and stratigraphic information collected during their excavation. Despite the low precision of the age-depth models for Wet and Blanche Caves which results in part from there being only single radiocarbon determinations available for a number of units and layers, the models enabled the relationships within and between the two sites to be established. Of particular utility for future faunal analyses is quantification of the temporal relationship between strata from the two sites, where groups of individual layers from Blanche Cave were found to be temporally equivalent with the longer-duration units in Wet Cave. We suggest that the use of Phase modelling, as performed here, is useful for cave deposits that have complex depositional histories and even in such instances where, as is common for palaeontological sites, few radiocarbon data are collected relative to the time-spans of tens of millennia that are often represented by them.

Chronology and stratigraphy of the Wet Cave vertebrate fossil deposit, Naracoorte, and relationship to paleoclimatic conditions of the Last Glacial Cycle in south-eastern Australia

The Wet Cave vertebrate fossil deposit of the Naracoorte Caves in south-eastern South Australia contains a rich and diverse assemblage of small mammal fauna known to span the Upper Pleistocene–Holocene. Here, we describe five previously unidentified in situ units (A, B, C, E and F) and one likely reworked unit (D) in the Wet Cave sedimentary profile, which are correlated with paleoclimatic conditions associated with the Last Glacial Cycle. Additional radiocarbon dates presented here provide a finer temporal resolution for the upper sections of the sequence than previously available and reveal rapid deposition of polished quartz sands laminated with brown silts during the last glacial maximum (LGM). Change in sediment type and depositional processes are dated from 16.8 to 16.4 k cal y BP and are associated with the onset of deglaciation. The characteristics of the five in situ depositional units are similar to those identified from the contemporaneous fossil and sedimentary sequence of Blanche Cave 3rd Chamber, located approximately 400 m away, reflecting interactions between paleoclimate, sediment mobility and deposition at this locality. Greater variation is evident between the Wet Cave sedimentary profile and the inner chamber of Robertson Cave, located approximately 6 km away and shows that local processes and cave structure exerted some control on sediment accumulation. Paleoclimatic inferences from the depositional sequence of Wet Cave are broadly consistent with those inferred from regional landforms for south-eastern Australia but provide a local signal more suitable for cross-correlation of the fossil faunas. In particular, the Wet Cave sequence suggests that local conditions were relatively stable in the lead up to the LGM despite fluctuation in both local and regional effective precipitation. Sedimentary units associated with the post-LGM deglaciation are characterised by alternating sand and sandy-silt layers, assumed to reflect the impact of enhanced seasonality and/or climatic fluctuation leading towards the Holocene.