Reconstructing the geomorphic history of Liang Bua, Flores, Indonesia: a stratigraphic interpretation of the occupational environment

Liang Bua, in Flores, Indonesia, was formed as a subterranean chamber over 600 ka. From this time to the present, a series of geomorphic events influenced the structure of the cave and cave deposits, creating a complex stratigraphy. Within these deposits, nine main sedimentary units have been identified. The stratigraphic relationships between these units provide the evidence needed to reconstruct the geomorphic history of the cave. This history was dominated by water action, including slope wash processes, channel formation, pooling of water, and flowstone precipitation, which created waterfalls, cut-and-fill stratigraphy, large pools of water, and extensive flowstone cappings. The reconstructed sequence of events over the last 190 k.yr. has been summarized by a series of time slices that demonstrate the nature of the occupational environment in Liang Bua. The earliest artifacts at the site, dated to ∼190 ka, testify to hominin presence in the area, but the reconstructions suggest that occupation of the cave itself may not have been possible until after ∼100 ka. At ∼95 ka, channel erosion of a basal unit, which displays evidence of deposition in a pond environment, created a greater relief on the cave floor, and formed remanent areas of higher ground that later became a focus for hominin occupation from 74-61 ka by the west wall and in the center of the cave, and from ∼18-17 ka by the east wall. These zones have been identified according to the sloping nature of the stratigraphy and the distribution of artifacts, and their locations have implications for the archaeological interpretation of the site.     

Conclusions: implications of the Liang Bua excavations for hominin evolution and biogeography

Excavations at Liang Bua, on the Indonesian island of Flores, have yielded a stratified sequence of stone artifacts and faunal remains spanning the last 95 k.yr., which includes the skeletal remains of two human species, Homo sapiens in the Holocene and Homo floresiensis in the Pleistocene. This paper summarizes and focuses on some of the evidence for Homo floresiensis in context, as presented in this Special Issue edition of the Journal of Human Evolution and elsewhere. Attempts to dismiss the Pleistocene hominins (and the type specimen LB1 in particular) as pathological pygmy humans are not compatible with detailed analyses of the skull, teeth, brain endocast, and postcranium. We initially concluded that H. floresiensis may have evolved by insular dwarfing of a larger-bodied hominin species over 880 k.yr. or more. However, recovery of additional specimens and the numerous primitive morphological traits seen throughout the skeleton suggest instead that it is more likely to be a late representative of a small-bodied lineage that exited Africa before the emergence of Homo erectus sensu lato. Homo floresiensis is clearly not an australopithecine, but does retain many aspects of anatomy (and perhaps behavior) that are probably plesiomorphic for the genus Homo. We also discuss some of the other implications of this tiny, endemic species for early hominin dispersal and evolution (e.g., for the “Out of Africa 1” paradigm and more specifically for colonizing Southeast Asia), and we present options for future research in the region.     

Geochronology of cave deposits at Liang Bua and of adjacent river terraces in the Wae Racang valley, western Flores, Indonesia: a synthesis of age estimates for the type locality of Homo floresiensis

A robust timeframe for the extant cave deposits at Liang Bua, and for the river terraces in the adjoining Wae Racang valley, is essential to constrain the period of existence and time of extinction of Homo floresiensis and other biota that have been excavated at this hominin type locality. Reliable age control is also required for the variety of artifacts excavated from these deposits, and to assist in environmental reconstructions for this river valley and for the region more broadly. In this paper, we summarize the available geochronological information for Liang Bua and its immediate environs, obtained using seven numerical-age methods: radiocarbon, thermoluminescence, optically- and infrared-stimulated luminescence (collectively known as optical dating), uranium-series, electron spin resonance, and coupled electron spin resonance/uranium-series. We synthesize the large number of numerical age determinations reported previously and present additional age estimates germane to questions of hominin evolution and extinction.     

Rate of succession in restored wetlands and the role of site context

Question: Are changes in plant species composition, functional group composition and rates of species turnover consistent among early successional wetlands, and what is the role of landscape context in determining the rate of succession? Location: Twenty‐four restored wetlands in Illinois, USA. Methods: We use 4 years of vegetation sampling data from each site to describe successional trends and rates of species turnover in wetlands. We quantify: (1) the rate at which composition changes from early‐successional to late‐successional species and functional groups, as indicated by site movement in ordination space over time, and (2) the rate of change in the colonization and local extinction of individual species. We correlate the pace of succession to site area, isolation and surrounding land cover. Results: Some commonalities in successional trends were evident among sites. Annual species were replaced by clonal perennials, and colonization rates declined over time. However, differences among sites outweighed site age in determining species composition, and the pace of succession was influenced by a site's landscape setting. Rates of species turnover were higher in smaller wetlands. In addition, wetlands in agricultural landscapes underwent succession more rapidly, as indicated by a rapid increase in dominance by late‐successional plants. Conclusions: Although the outcome of plant community succession in restored wetlands was somewhat predictable, species composition and the pace of succession varied among sites. The ability of restoration practitioners to accelerate succession through active manipulation may be contingent upon landscape context.     

Assessing the impact of local habitat variables and landscape context on riparian birds in agricultural,urbanized, and native landscapes

Large tracts of natural habitat are being replaced by agriculture and urban sprawl in Mediterranean regions worldwide. We have limited knowledge about the effects of human activities on native species in these landscapes and which, if any, management practices might enhance the conservation of native biodiversity within them. Through a citizen volunteer bird-monitoring project, we compared bird abundance and species richness in northern Californian riparian zones surrounded by vineyards, urban areas, and natural areas. We assessed both local and landscape-level variables that may enhance native bird diversity in each land use type. We also demonstrate a new statistical approach, generalized estimating equations, to analyze highly variable data, such as that collected by volunteers. Avian abundance was highly correlated with both landscape context and local habitat variables, while avian richness was correlated with local habitat variables, specifically shrub richness, and percent of tree cover. In particular, shrub species richness has a strong positive correlation with riparian-preferring bird species. This suggests that active local management of riparian zones in human-dominated landscapes can increase our ability to retain native bird species in these areas.     

Development of tree-ring maximum latewood density chronologies for the western Tien Shan Mountains,China: Influence of detrending method and climate response

Three tree-ring maximum latewood density chronologies were developed from high elevation Picea schrenkiana sites in the western Tien Shan Mountains using different detrending methods. The new chronologies extend back to the early 16th and late 17th centuries, and contain significant late spring and summer temperature signals, respectively. An assessment of varying detrending methods and band-pass filtering the chronologies revealed only slightly differing low frequency trends retained in the maximum latewood densities. The distance between sampling sites and the varying seasonality of limiting climatic factors are identified as key drivers affecting the correlation among the maximum latewood density records in the study region. The new chronologies represent reliable proxies of high elevation late spring and summer temperature variability in an area underrepresented by such data, and are ready-to-use for network analyses addressing longer-term climate variations in eastern central Asia.     

Selecting agri-environmental indicators for monitoring and assessment of environmental management in the example of landscape parks in Poland

The objective of this article is to assess the condition of and hazards to the natural environment in selected landscape parks in Poland with respect to the impact of agricultural management using the DPSIR method. Our proposed set of indicators, based on generally available and applicable data, shows at the local scale, in a simple way, the condition of functioning of the balance between the natural environment and agricultural management and it assesses the level of repair works in the context of the records of the environmental protection program. The highest negative impact of agricultural management in the areas studied is noticed in the soil environment as well as the contexts of biodiversity and landscape. On the other hand, the lowest influence of agricultural economy was noted in the cases of the atmosphere and hydrosphere. The results of the aggregated indicators also showed lower or higher dependencies between the coverage and the use of the area in landscape parks and the condition of particular elements of the environment and the landscape.     

Effects of within-lake gradients on the distribution of fossil chironomids from maar lakes in western Alaska: implications for environmental reconstructions

We examined fossil chironomids (Diptera: Chironomidae) in the surface sediments of four maar lakes in western Alaska to determine chironomid distribution patterns with respect to within-lake gradients of water depth, LOI (loss-on-ignition), and bottom-water temperature. Linear and non-linear regressions were undertaken to test whether the within-lake distributions of fossil chironomids were uniform. Additionally, water depths where abrupt changes or breakpoints in the assemblages occur were identified using piecewise regression. Direct gradient analysis was then used to examine variation in the assemblages explained by the environmental data. For the shallowest lake, chironomid abundances of individual taxa and inferred temperatures varied little within the lake. For the three deep lakes, seven of the sixteen commonest fossil taxa varied significantly with water depth, although some lake-specific patterns were evident. Water depth was generally identified as the principal environmental variable in explaining variation in the assemblages, although sediment organic matter content and bottom-water temperature were also important. Abrupt changes in assemblages occurred at different water depths in each lake, and at only one lake did the breakpoint occur within the range of water depths defining the thermocline. Chironomid-inferred temperature trends from the lakes also showed depth-related patterns: the warmest inferred temperatures were generally from both the shallowest and deepest water depths, whereas intermediate depths yielded temperature inferences about 0.5 to 1.0°C cooler than the average within-lake value. Nevertheless, we conclude that these patterns had only a slight impact on temperature reconstructions relative to the prediction error of the model. A greater understanding of taphonomic processes is needed to determine their influence on environmental reconstructions based on chironomids. Handling editor: J. Saros     

The folding landscape of Streptomyces griseus protease B reveals the energetic costs and benefits associated with evolving kinetic stability

Like most extracellular bacterial proteases, Streptomyces griseus protease B (SGPB) and alpha-lytic protease (alphaLP) are synthesized with covalently attached pro regions necessary for their folding. In this article, we characterize the folding free energy landscape of SGPB and compare it to the folding landscapes of alphaLP and trypsin, a mammalian homolog that folds independently of its zymogen peptide. In contrast to the thermodynamically stable native state of trypsin, SGPB and alphaLP fold to native states that are thermodynamically marginally stable or unstable, respectively. Instead, their apparent stability arises kinetically, from unfolding free energy barriers that are both large and highly cooperative. The unique unfolding transitions of SGPB and alphaLP extend their functional lifetimes under highly degradatory conditions beyond that seen for trypsin; however, the penalty for evolving kinetic stability is remarkably large in that each factor of 2.4-8 in protease resistance is accompanied by a cost of ~10(5) in the spontaneous folding rate and ~5-9 kcal/mole in thermodynamic stability. These penalties have been overcome by the coevolution of increasingly effective pro regions to facilitate folding. Despite these costs, kinetic stability appears to be a potent mechanism for developing native-state properties that maximize protease longevity.     

Lessons learned and challenges for environmental management in Colombia: The role of communication,education and participation strategies

Environmental management has increasingly focused on promoting social engagement in biodiversity and ecosystem services conservation as a way to foster sustainability. However, a critical challenge that still remains is the adequate implementation of strategies of communication, education, and participation (CEPA) oriented to reconnect the social and ecological dimensions in the systems. This study analyzed the main features and types of CEPA implemented by the Colombian Regional Autonomous Corporations in environmental management projects that consider ecosystem services. We found a variety of CEPA focused on a wide range of stakeholders. Communication and education were the most frequently implemented in the projects. Within communication, spreading information about the projects was the most common, while education focused on instrumental training of local communities. Participation, the less frequently implemented, mainly aimed to ensure government and decision-makers involved in the initial phases of the projects. We conclude that there is a need to increase and improve education strategies in conservation projects to make decisions based on critical and reflective thinking, and foster the engagement of a broader set of stakeholders in the processes.     

The environmental context for the origins of modern human diversity: a synthesis of regional variability in African climate 150,000-30,000 years ago

We synthesize African paleoclimate from 150 to 30 ka (thousand years ago) using 85 diverse datasets at a regional scale, testing for coherence with North Atlantic glacial/interglacial phases and northern and southern hemisphere insolation cycles. Two major determinants of circum-African climate variability over this time period are supported by principal components analysis: North Atlantic sea surface temperature (SST) variations and local insolation maxima. North Atlantic SSTs correlated with the variability found in most circum-African SST records, whereas the variability of the majority of terrestrial temperature and precipitation records is explained by local insolation maxima, particularly at times when solar radiation was intense and highly variable (e.g., 150-75 ka). We demonstrate that climates varied with latitude, such that periods of relatively increased aridity or humidity were asynchronous across the northern, eastern, tropical and southern portions of Africa. Comparisons of the archaeological, fossil, or genetic records with generalized patterns of environmental change based solely on northern hemisphere glacial/interglacial cycles are therefore imprecise.We compare our refined climatic framework to a database of 64 radiometrically-dated paleoanthropological sites to test hypotheses of demographic response to climatic change among African hominin populations during the 150-30 ka interval. We argue that at a continental scale, population and climate changes were asynchronous and likely occurred under different regimes of climate forcing, creating alternating opportunities for migration into adjacent regions. Our results suggest little relation between large scale demographic and climate change in southern Africa during this time span, but strongly support the hypothesis of hominin occupation of the Sahara during discrete humid intervals ∼135-115 ka and 105-75 ka. Hominin populations in equatorial and eastern Africa may have been buffered from the extremes of climate change by locally steep altitudinal and rainfall gradients and the complex and variable effects of increased aridity on human habitat suitability in the tropics. Our data are consistent with hominin migrations out of Africa through varying exit points from ∼140-80 ka.     

The legacy of past climate and landscape change on species' current experienced climate and elevation ranges across latitude: a multispecies study utilizing mammals in western North America

Aim Elevation and climate ranges across latitude experienced by 21 wide‐ranging mammal species in western North America were summarized to examine two questions: (1) do populations in the northern and southern portions of a species’ range experience different climates or are environments selected to remain similar to climates at the core of ranges; and (2) how do species’ elevational ranges, experienced temperature seasonality and temperature ranges change across latitude? Given the larger effects of climate oscillations in the north vs. the south, a predicted outcome is for species to conserve climate niches across latitude and to show reduced climate and elevation ranges in the north. An alternative outcome is latitudinal niche diversification and increased climate variation in the north. Location Western North America. Methods The questions above were examined using a combination of species occurrence data bases, climate data bases, simple summaries of means and standard deviations and by testing summaries against random distributions across latitude for 21 mammal species from a variety of orders. Results The results showed that: (i) most species conserve their niche strongly or weakly given overall temperature gradients from north to south; (ii) seasonality experienced by species is relatively static until the highest latitudes despite directional trends across the region; and (iii) the elevation range and temperature variation that species experience decreases from south to north. Main conclusions Populations at range edges appear to partition environments to remain closer to temperature values similar to those at the core of the range. In addition, seasonality is not a likely explanatory factor of genetic diversity in latitudinal gradients. The data are instead more consistent with predictions that a combination of higher gene‐flow, increasing environmental instability and decreasing elevation gradients in the north compared to the south may lead to negative correlations between latitude and species’ climate variation. The results corroborate risks faced by northern mammal populations to global climate changes.     

A review on the potential effects of environmental and economic factors on sheep genetic diversity: Consequences of climate change

Climate change has a significant effect on the productivity of livestock including milk, meat, and reproduction. This could be attributed to the internal diversion of energy resources towards adaptive mechanisms. Among the climate change variables, thermal stress seems to be the major limiting factor in animal agriculture. A better understanding of the effects of climate change-influenced ecological factors on the genetic diversity of livestock species is warranted. Sheep is an ideal livestock species to be used in investigating environmental adaptation due to its wide range of agroecological habitats, genetic and phenotypic variability. There is a heavy reliance on sheep genetic diversity for future animal protein security, but the implications of climate change on their genetic diversity receive less attention.Here, the potential environmental factors influencing natural selection in sheep populations are presented. We argue that prolonged exposure to these factors plays a major role in influencing the development of adaptation traits in indigenous sheep breeds, consequently leading to the alteration of genetic diversity at specific loci. The factors discussed include hot temperatures (heat stress), insufficient water, low quantity and quality of forage, and prevalence of parasites, pests, and diseases. In addition, genetic diversity, some signatures of selection for adaptation and economic angles of selection are also briefly discussed.A better understanding of environmental factors influencing the genetic diversity of sheep populations will inform breeding and management programs and may offer an opportunity for greater production efficiency with low input costs.     

The value of scattered trees for wildlife: Contrasting effects of landscape context and tree size

Aim

The biodiversity value of scattered trees in modified landscapes is often overlooked in planning and conservation decisions. We conducted a multitaxa study to determine how wildlife abundance, species richness and community composition at individual trees are affected by (1) the landscape context in which trees are located; and (2) the size of trees.

Location

Canberra, south‐eastern Australia.

Methods

Trunk arthropod, bat and bird surveys were undertaken over 3 years (2012–2014) at 72 trees of three sizes (small (20–50 cm DBH), medium (51–80 cm), large (≥80 cm)) located in four landscape contexts (reserves, pasture, urban parklands, urban built‐up areas).

Results

Landscape context affected all taxa surveyed. Trunk arthropod communities differed between trees in urban built‐up areas and reserves. Bat activity and richness were significantly reduced at trees in urban built‐up areas suggesting that echolocating bats may be disturbed by high levels of urbanization. Bird abundance and richness were highest at trees located in modified landscapes, highlighting the value of scattered trees for birds. Bird communities also differed between non‐urban and urban trees. Tree size had a significant effect on birds but did not affect trunk arthropods and bats. Large trees supported higher bird abundance, richness and more unique species compared to medium and small trees.

Main conclusions

Scattered trees support a diversity of wildlife. However, landscape context and tree size affected wildlife in contrasting ways. Land management strategies are needed to collectively account for responses exhibited by multiple taxa at varying spatial scales. We recommend that the retention and perpetuation of scattered trees in modified landscapes should be prioritized, hereby providing crucial habitat benefits to a multitude of taxa.     

The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa

In considering the best possible solutions for answering phylogenetic questions from genomic sequences, we have chosen a strategy that we suggest is superior to others that have gone previously. We have ignored multigene families and instead have used single-gene families. This minimizes the inadvertent analysis of paralogs. We have employed strict data controls and have reasoned that if a protein is not capable of recovering the uncontroversial parts of a phylogenetic tree, then why should we use it for the more controversial parts? We have sliced and diced the data in as many ways as possible in order to uncover the signals in that data. Using this strategy, we have tested two controversial hypotheses concerning eukaryotic phylogenetic relationships: the placement of arthropoda and nematodes and the relationships of animals, plants, and fungi. We have constructed phylogenetic trees from 780 single-gene families from 10 completed genomes and amalgamated these into a single supertree. We have also carried out a total evidence analysis on the only universally distributed protein families that can accurately reconstruct the uncontroversial parts of the phylogenetic tree: a total of five families. In doing so, we ignore the majority of single-gene families that are universally distributed as they do not have the appropriate signals to recover the uncontroversial parts of the tree. We have also ignored every protein that has ever been used previously to address this issue, simply because none of them meet our strict criteria. Using these data controls, site stripping, and multiple analyses, 24 out of 26 analyses strongly support the grouping of vertebrates with arthropods (Coelomata hypothesis) and plants with animals. In the other two analyses, the data were ambivalent. The latter finding overturns an 11-year theory of Eukaryotic evolution; the first confirms what has already been said by others. In the light of this new tree, we re-analyze the evolution of intron gain and loss in the rpL14 gene and find that it is much more compatible with the hypothesis presented here than with the Opisthokonta hypothesis.     

The importance of biotic interactions and local adaptation for plant response to environmental changes: field evidence along an elevational gradient

Predicting the response of species to environmental changes is a great and on‐going challenge for ecologists, and this requires a more in‐depth understanding of the importance of biotic interactions and the population structuration in the landscape. Using a reciprocal transplantation experiment, we tested the response of five species to an elevational gradient. This was combined to a neighbour removal treatment to test the importance of local adaptation and biotic interactions. The trait studied was performance measured as survival and biomass. Species response varied along the elevational gradient, but with no consistent pattern. Performance of species was influenced by environmental conditions occurring locally at each site, as well as by positive or negative effects of the surrounding vegetation. Indeed, we observed a shift from competition for biomass to facilitation for survival as a response to the increase in environmental stress occurring in the different sites. Unlike previous studies pointing out an increase of stress along the elevation gradient, our results supported a stress gradient related to water availability, which was not strictly parallel to the elevational gradient. For three of our species, we observed a greater biomass production for the population coming from the site where the species was dominant (central population) compared to population sampled at the limit of the distribution (marginal population). Nevertheless, we did not observe any pattern of local adaptation that could indicate adaptation of populations to a particular habitat. Altogether, our results highlighted the great ability of plant species to cope with environmental changes, with no local adaptation and great variability in response to local conditions. Our study confirms the importance of taking into account biotic interactions and population structure occurring at local scale in the prediction of communities’ responses to global environmental changes.     

河西走廊土地利用/覆盖变化的景观生态效应——以肃州绿洲为例

近来,在土地利用／覆被变化研究中,都纷纷结合景观格局变化分析模型来研究其空间结构变化趋势及其生态效应,以期为土地持续利用规划设计提供依据。景观格局及其变化既是各种干扰因素相互作用的结果,又影响着区域的生态过程。运用景观生态学原理,借助GIS技术(Arc GIS8．1)和Fragstas 3．3软件,基于1988、2000年Landsat5的4、3、2(RGB)波段合成影像解译结果,对河西走廊中西段肃州绿洲LUCC及其景观生态效应进行了研究。结果表明：(1)受自然地理要素的影响,景观类型空间分布表现出明显的区域差异。耕地主要分布于水系两岸和河流冲积扇;草地主要分布于祁连山地及绿洲边缘;林地主要分布于河流两岸、祁连山北坡一带;戈壁、沙漠广泛分布于绿洲之间,景观格局呈现出以戈壁为基质的戈壁、绿洲、沙漠相间分布的态势;(2)各土地利用类型及景观格局指数均发生了重要变化,耕地、水域明显增加,城镇用地和农村居民点也逐步增加,草地、林地和未利用地呈减少趋势,尤其是高覆盖度草地全部消失;(3)斑块破碎化程度在减小,异质性也在减小,但生态环境质量仍在下降,表现为大部分草地、林地被开垦为耕地,降低了绿洲维护生态平衡的能力,加大了干旱绿洲业已超负的水资源载荷;(4)景观中斑块优势度在减小,斑块类型在景观中趋于均匀分布,异质性的减小和均质化发展必然导致景观稳定性的降低;(5)林地和草地边缘效应降低,使其对周围斑块类型的影响相应减小,原有的景观生态功能减弱;相反,水体、盐碱地和裸地边缘效应有所增强,盐碱地和裸地等对景观发展影响的增强则是景观退化的表现。     

Being a burden to others and wishes to die: The importance of the sociopolitical context

All articles in May 2019’s special issue of Bioethics offer profound insights into the issue of “being a burden to others” in relation to wishes to die, which are highly relevant for ethical debates about end-of-life care and physician-assisted dying. In this reply, we wish to stress the importance of acknowledging and analyzing the sociopolitical context of the phenomenon “being a burden” in relation to wishes to die and we will show how this analysis could benefit from a care ethical approach. As discussions in care ethics have made clear, caring practices are both social and political practices. An empirical and ethical analysis of “being a burden” therefore needs to take institutional and societal norms and structures into account, in addition to first-person experiences and concepts such as caring needs, relational autonomy, and interdependency. Besides the relevance of the sociopolitical context for the phenomenon “being a burden” as such, the sociopolitical context also seems relevant for the investigation of the phenomenon, which we will illustrate by reflecting on “being a burden” in relation to the practice of physician-assisted dying in the Netherlands.     

The Middle Stone Age of the northern Kenyan Rift: age and context of new archaeological sites from the Kapedo Tuffs

Rift Valley sites in southern Ethiopia and northern Kenya preserve the oldest fossil remains attributed to Homo sapiens and the earliest archaeological sites attributed to the Middle Stone Age (MSA). New localities from the Kapedo Tuffs augment the sparse sample of MSA sites from the northern Kenya Rift. Tephrostratigraphic correlation with dated pyroclastic deposits from the adjacent volcano Silali suggests an age range of 135-123 ka for archaeological sites of the Kapedo Tuffs. Comparisons of the Kapedo Tuffs archaeological assemblages with those from the adjacent Turkana and Baringo basins show broad lithic technological similarity but reveal that stone raw material availability is a key factor in explaining typologically defined archaeological variability within this region. Spatially and temporally resolved comparisons such as this provide the best means to link the biological and behavioral variation manifest in the record of early Homo sapiens.     

Comparative cradle to grave environmental life cycle assessment of traditional and extensive vegetative roofs: an application for the Lebanese context

The International Journal of Life Cycle Assessment - Vegetative roofs (VRs) are fully planted roof spaces that offer aesthetic view, storm water management, sound insulation, energy savings, and...