The evolving landscape and climate of western Flores: an environmental context for the archaeological site of Liang Bua

The rapidly changing landscape of the eastern Indonesian archipelago has evolved at a pace dictated by its tropical climate and its geological and tectonic history. This has produced accelerated karstification, flights of alluvial terraces, and complex, multi-level cave systems. These cave systems sometimes contain a wealth of archaeological evidence, such as the almost complete skeleton of Homo floresiensis found at the site of Liang Bua in western Flores, but this information can only be understood in the context of the geomorphic history of the cave, and the more general geological, tectonic, and environmental histories of the river valley and region. Thus, a reconstruction of the landscape history of the Wae Racang valley using speleothems, geological structure, tectonic uplift, karst, cave, and terrace development, provides the necessary evidence to determine the formation, age, evolution, and influences on the site. This evidence suggests that Liang Bua was formed as two subterranean chambers ∼600 ka, but could not be occupied until ∼190 ka when the Wae Racang wandered to the southern side of the valley, exposing the chamber and depositing alluvial deposits containing artifacts. During the next ∼190 k.yr., the chambers coalesced and evolved into a multi-level and interconnected cave that was subjected to channel erosion and pooling events by the development of sinkholes. The domed morphology of the front chamber accumulated deep sediments containing well stratified archaeological and faunal remains, but ponded water in the chamber further prevented hominin use of the cave until ∼100 ka. These chambers were periodically influenced by river inundation and volcanic activity, whereas the area outside the cave was greatly influenced by glacial phases, which changed humid forest environments into grassland environments. This combined evidence has important implications for the archaeological interpretation of the site.     

Preface: research at Liang Bua, Flores, Indonesia

Excavations at Liang Bua, Flores, Indonesia, have yielded evidence for an endemic human species, Homo floresiensis, a population that occupied the cave between ∼95-17 ka. This discovery has major implications for early hominin evolution and dispersal in Africa and Asia, attracting worldwide interest. This preface describes the rationale for the excavations in historical, geographical, and wider research contexts, as well as the methods used. It also introduces the other papers on aspects of Liang Bua research that feature in this edition of the Journal of Human Evolution.     

The Liang Bua faunal remains: a 95 k.yr. sequence from Flores, East Indonesia

Excavations at Liang Bua, a limestone cave on the island of Flores, East Indonesia, have yielded a well-dated archaeological and faunal sequence spanning the last 95 k.yr., major climatic fluctuations, and two human species - H. floresiensis from 95 to 17 k.yr.¹, and modern humans from 11 k.yr. to the present. The faunal assemblage comprises well-preserved mammal, bird, reptile and mollusc remains, including examples of island gigantism in small mammals and the dwarfing of large taxa. Together with evidence from Early-Middle Pleistocene sites in the Soa Basin, it confirms the long-term isolation, impoverishment, and phylogenetic continuity of the Flores faunal community. The accumulation of Stegodon and Komodo dragon remains at the site in the Pleistocene is attributed to Homo floresiensis, while predatory birds, including an extinct species of owl, were largely responsible for the accumulation of the small vertebrates. The disappearance from the sequence of the two large-bodied, endemic mammals, Stegodon florensis insularis and Homo floresiensis, was associated with a volcanic eruption at 17 ka and precedes the earliest evidence for modern humans, who initiated use of mollusc and shell working, and began to introduce a range of exotic animals to the island. Faunal introductions during the Holocene included the Sulawesi warty pig (Sus celebensis) at about 7 ka, followed by the Eurasian pig (Sus scrofa), Long-tailed macaque, Javanese porcupine, and Masked palm civet at about 4 ka, and cattle, deer, and horse - possibly by the Portuguese within historic times. The Holocene sequence at the site also documents local faunal extinctions - a result of accelerating human population growth, habitat loss, and over-exploitation.     

A new species of giant marabou stork (Aves: Ciconiiformes) from the Pleistocene of Liang Bua,Flores (Indonesia)

Fossils of the genus Leptoptilos from the Pleistocene of Liang Bua, Flores, Indonesia, belong to a new species of giant marabou stork, Leptoptilos robustus sp. nov. This giant bird, estimated at 1.80 m in length, was similar in dimensions to extant Leptoptilos dubius, except for the tibiotarsus. The thick cortical bone wall of the tibiotarsus and the estimated weight of 16 kg imply a reduced flight capability. Osteological and biometric characters suggest that L. robustus is most closely related to L. dubius. An evolutionary lineage is proposed in which a volant L. dubius‐like ancestor in the Middle Pleistocene evolved into the Late Pleistocene L. robustus on Flores, with a concomitant reduction of the ability to fly and an increase in body size. The large body size and terrestrial lifestyle of L. robustus are responses to an unbalanced, insular environment with abundant prey items and a lack of mammalian carnivores, and emphasize the extraordinary nature of the Homo floresiensis fauna. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 707–724.     

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.     

Correlation of (Ordovician, Mohawkian) K-bentonites in the upper Mississippi valley using apatite chemistry: implications for stratigraphic interpretation of the mixed carbonate-siliciclastic Decorah Formation

Four Ordovician K-bentonites have been chemically fingerprinted using trace element content of apatite phenocrysts contained within the altered ash layers. Trace element analysis was performed using electron microprobe on individual crystals. The bentonites include the Deicke, Millbrig, Elkport, and Dickeyville beds. These beds lie within the Decorah Formation of the northern Mississippi Valley outcrop area. All four K-bentonite beds are believed to have a Taconic source whereas volcanic ash was transported by wind and deposited in the Ordovician North America epeiric sea.

The Decorah is a marine unit, shaly to the north and west and carbonate-rich to the south and east. Thirteen K-bentonite samples were collected from six localities. Only one locality (Dickeyville, WI) contains all four beds in succession. One hundred seventy-one apatite crystals were handpicked and analyzed for major, minor and trace elements using an electron microprobe. Each crystal was analyzed at three to six separate spots to ascertain compositional variation. The most discriminating and diagnostic elements were Mg and Mn; plotting Mg vs. Mn content produces data clusters characteristic for each K-bentonite. Clusters show only minimal change between localities, allowing individual K-bentonites to be identified and used for stratigraphic correlation.

Time slices provided by the K-bentonite horizons show that the Decorah Formation is composed of reciprocal wedges (stratigraphic sequences) of shale and carbonate. Shale was deposited in deeper water within the Hollandale Embayment but pinched out southeastward onto the flank of the Wisconsin Dome. Carbonates were formed largely in shoal water on the arch, prograding northwestward and shaling out downramp into the embayment.     

Reconstructing the history of log-drifting in the Reichraminger Hintergebirge, Austria

The watersheds of the rivers Enns and Steyer border the Reichraminger Hintergebirge. This area has a long tradition in the iron processing industry. Because mineral coal was not available, charcoal has been produced for the iron industry for the past 500 years, leading to a heavy exploitation of the vast forests (180 km²).

From the logging sites in the mountains the timber had to be transported up to 12 km to the forges in the lowland. Most of the small rivers had insufficient water to drift logs efficiently. Therefore, at gorges or at places where there were narrow steep sided valleys wooden dams (klausen) were built to block the water, using the first cut trees of a newly targeted harvesting area. By abruptly opening the dams, the rapid flow of the raised water level carried the logs to the next klausen. Up to seven klausen were built in a valley before the rechen (rake-like grids within the river to collect the logs) of the Enns and Steyer were reached.

To reconstruct the history of log drifting in the Reichraminger Hintergebirge, 33 klausen and rechen were visited and dendrochronologically sampled. The remaining wood of the dam constructions showed progressive stages of degradation, and in some cases only a few logs remained preserved under the water. With cores from living trees added to the dataset, master chronologies were established for spruce (576 years), fir (569 years) and larch (342 years). The construction history of the klausen can be sequentially traced back to 1563 AD. The time spans of the individual chronologies varied between 40 and 392 years. All available conifer species were utilized to build the dams, except during the 19th century, when the most suitable species - larch - was used to a higher degree.     

How seals divide up the world: environment, life history, and conservation

Pinnipeds display a remarkable variation in life history adaptations while successfully inhabiting almost every marine environment. We explore how they have done this by grouping the world’s pinniped species according to their environmental conditions, mating systems, lactation strategies, and timing of life histories. Next, we tested whether any of these clusters provide information about risk of extinction (using the International Union for Nature and the Conservation of Natural Resources status ranks). Seals at risk were not characterized by differences in lactation pattern (22% short vs. 46% long), mating system (24% multi-male vs. 35% harems), or timing of life history events (23% fast vs. 42% slow) but did differ based on four environmental groupings. Grouping traits (rather than seals) described two clusters: one that included the environmental trait, primary productivity, and a second one that included all other environmental variables (seasonality, latitude, and temperature). Based on this result and theoretical considerations, we plotted seals according to energy (primary productivity) and variation (seasonality) and found a pattern analogous to that of the same four groups determined by cluster analysis of all environmental variables. Of the two pinniped groups representing low variation (equatorial and high productivity), ten of 21 seal species have been designated at risk, in contrast to none of the 13 seal species adapted to high variation. We conclude that seals appear to be best adapted to seasonal environments and thus, conservation efforts may benefit by concentrating on species inhabiting less variable environments.     

Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization

The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo‐, FeV‐, or FeFe‐cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active‐site sequence features can reliably distinguish extant Mo‐nitrogenases from V‐ and Fe‐nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo‐nitrogenases. Taxa representing early‐branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo‐cofactor in studied organisms, suggesting that early Mo‐nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein‐level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism‐level innovations that characterize the Phanerozoic Eon.     

Thermal sensitivity of escape response performance by the scallop Placopecten magellanicus: Impact of environmental history

To examine the impact of environmental history on the thermal sensitivity of escape response performance in juvenile giant scallops, Placopecten magellanicus, we compared animals sampled in late May, when water temperatures and day length were increasing, to animals sampled in late September, when water temperature and day length were decreasing. Habitat temperature was approximately 12 °C at both sampling times. For May scallops, performance was better at 6 than at 12 or 18 °C whereas September scallops performed better at 6 and 12 °C than at 19 °C. Regardless of environmental history, the rate of phasic contractions consistently declined at 18–19 °C, due to a decrease in the number of phasic contractions. Force measurements during escape responses of May scallops showed that phasic force production and the minimal interval between contractions changed little with temperature, whereas the minimum and mean durations of phasic contractions decreased as temperature rose. Phasic contraction rate in the first series increased with temperature. Reliance upon tonic contractions was higher in scallops tested at 18 °C than in those tested at 6 °C. Environmental history, more than habitat temperature at the time of sampling, seems to set the thermal sensitivity of phasic contraction rate in P. magellanicus. Phasic force production did not change within the thermal range tested.     

Liang Bua Homo floresiensis mandibles and mandibular teeth: a contribution to the comparative morphology of a new hominin species

In 2004, a new hominin species, Homo floresiensis, was described from Late Pleistocene cave deposits at Liang Bua, Flores. H. floresiensis was remarkable for its small body-size, endocranial volume in the chimpanzee range, limb proportions and skeletal robusticity similar to Pliocene Australopithecus, and a skeletal morphology with a distinctive combination of symplesiomorphic, derived, and unique traits. Critics of H. floresiensis as a novel species have argued that the Pleistocene skeletons from Liang Bua either fall within the range of living Australomelanesians, exhibit the attributes of growth disorders found in modern humans, or a combination of both. Here we describe the morphology of the LB1, LB2, and LB6 mandibles and mandibular teeth from Liang Bua. Morphological and metrical comparisons of the mandibles demonstrate that they share a distinctive suite of traits that place them outside both the H. sapiens and H. erectus ranges of variation. While having the derived molar size of later Homo, the symphyseal, corpus, ramus, and premolar morphologies share similarities with both Australopithecus and early Homo. When the mandibles are considered with the existing evidence for cranial and postcranial anatomy, limb proportions, and the functional anatomy of the wrist and shoulder, they are in many respects closer to African early Homo or Australopithecus than to later Homo. Taken together, this evidence suggests that the ancestors of H. floresiensis left Africa before the evolution of H. erectus, as defined by the Dmanisi and East African evidence.     

Late Holocene stratigraphic evolution of a back-barrier tidal basin in the East Frisian Wadden Sea, southern North Sea: transgressive deposition and its preservation potential

The late Holocene stratigraphic evolution of a back-barrier tidal basin in the East Frisian Wadden Sea, southern North Sea, was investigated on the basis of a conceptual model relating the rate of sea-level rise to the rate of sediment supply. For this purpose, more than 20 vibra-cores and box-cores were evaluated, complemented by ¹⁴C ages of in situ peats and historical charts. In spite of interspersed short regressive events, the late Holocene stratigraphy generally reveals upward-coarsening grain-size trends indicative of transgressive deposition in the course of sea-level rise rather than erosion and redeposition by migrating channels. A particular feature is the general absence of down-core bioturbation traces, which stands out in sharp contrast to the intensely burrowed modern surface layer. Thus, in the Wadden Sea, high sediment turnover in the course of rapid transgression evidently obliterates most bioturbation traces and other tidal signals such as minor regressive deposits, thereby emphasising the importance of preservation potential.     

The Messinian reef complex of the Salento Peninsula (southern Italy): Stratigraphy, facies and paleoenvironmental interpretation

Summary An integrated study of the early Messinian reef complex cropping out along the eastern coast of the Salento Peninsula (southern Italy), including stratigraphy, facies analysis and paleoecological aspects, is here presented. Fourteen facies types belonging to three main facies associations (back reef and shelf, shelf-edge, slope) have been recognized. They document a wide spectrum of depositional environments, reef building organisms and growth fabrics, in response to depth and other environmental factors in different parts of the reef complex. The biotic structure of the reef is also described and discussed in detail. It consists of different types of reef building organisms and of their bioconstructions (mainlyPorites coral reefs,Halimeda bioherms and vermetidmicrobial “trottoirs”), that differ in composition and structure according to their position on the shelf edge-toslope profile. Results indicate that the reef complex of the Salento Peninsula has strong similarities with the typical early Messinian reefs of the Mediterranean region. However, the recognition of some peculiar features, i.e. the remarkable occurrence ofHalimeda bioherms and of vermetid-microbial “trottoirs”, gives new insights for better understanding reef patterns and development of the reef belt during the Late Miocene in the Mediterranean.     

A fitness function for optimal life history in relation to density effects,competition, predation and stability of the environment

A fitness function (function maximized under natural selection) is studied in a population model in which the growth of a population is suppressed by crowding, density-independent continuous mortality (by euryphagous predators) and periodic disturbances. The dynamics of the population density between occurrence of disturbance can be expressed as,dN/dt=(F(N/K)−D)N, whereN is the population density,K is the carrying capacity,D is the density-independent continuous mortality, andF is the growth regulation factor described as a function of crowding (N/K). The period of disturbance isS. The survival rate under disturbance isu. It is concluded that the fitness function is (approximately) a product of competitive ability (C), carrying capacity, and degree of saturation, and is given byCKF ⁻¹(D−(lnu)/S). The degree of saturation is the inverse function of regulation factor (F) at the death rate due to predators and disturbance. I assume a population in which density is regulated only through survival. In this case, a low survival rate at the critical age-group means a high value ofCKF ⁻¹(D−(lnu)/S). Therefore, the reciprocal of the density-dependent survival rate at critical age-group is a measure of the fitness function. Using this measure, I predict the optimal age (body size) at first reproduction of a species of salamander. I also found that fitness calculated from observed values ofl(x) andm(x) includes a tautology. When the concept of fitness function is compared with the ESS method, the latter is more flexible. However, there is a possibility that an ESS is at the minimum of fitness function.     

Life history traits variation in heterogeneous environment: The case of a freshwater snail resistance to pond drying

Ecologists and population geneticists have long suspected that the diversity of living organisms was connected to the structure of their environment. In heterogeneous environments, diversifying selection combined to restricted gene flow may indeed lead to locally adapted populations. The freshwater snail, Galba truncatula, is a good model to address this question because it is present in a heterogeneous environment composed of temporary and permanent waters. In order to test the selective importance of those environments, we proposed here to measure survival of lineages from both habitats during drought episodes. To this purpose, we experimentally submitted adults and juveniles individuals from both habitats to drought. We found a difference in desiccation resistance between temporary and permanents waters only for adults. Adults from temporary habitats were found more resistant to drought. This divergence in desiccation resistance seems to explain the unexpected life history traits differences between habitats observed.     

Reconstructing the genetic admixture history of Tai-Kadai and Sinitic people: Insights from genome-wide SNP data from South China

South China (SC) was a region with mixed rice–millet farming during the Middle Neolithic period and was also suggested to be the homeland of Tai-Kadai (TK)-speaking people. However, the formations of inland TK-speaking people and southwestern Hans are far from clear due to very few studies on this subject. Here, we reveal the spatiotemporally demographic history of SC by analyzing newly-generated genome-wide SNP data of 115 modern southwestern individuals and find that inland TK-speaking Dongs and Bouyeis have a close genomic affinity to coastal TK/Austronesian (AN)-speaking people and Neolithic Yangtze River basin (YZRB) farmers, while southwestern Hans and TK-speaking Gelaos possess a close genomic affinity to Neolithic Yellow River basin (YRB) farmers. Genetic differentiations are identified among TK people from SC and Southeast Asia, and between northern and southern inland Chinese TK people, in which the identified shared genetic ancestry between TK and AN people highlights a common origin of AN/TK groups. Conclusively, our findings indicate that millet farmers deriving from the YRB and rice farmers deriving from the YZRB substantially contribute to the present-day inland TK speakers and southwestern Hans via a two-way admixture scenario of bi-directional gene-flow events, which facilitates the formation of a modern two-way genetic admixture profile.     

羊肚菌的多样性、演化历史及栽培研究进展

羊肚菌属Morchella真菌是一类珍稀食用和药用真菌,具有重要的经济和科研价值。从羊肚菌属的分类研究、物种多样性、物种分布与生态多样性、演化历史、人工栽培等方面,对新近的研究成果进行了综述,总结了世界羊肚菌研究中取得的主要成绩,指出了仍然存在的主要问题及解决这些问题的相应思路和对策。     

Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.     

Life history strategies and psychopathology: the faster the life strategies,the more symptoms of psychopathology

There is little extant empirical literature examining the associations between life history strategies and symptoms of psychopathology. The current study (N = 138) investigated the associations between life history strategies, symptoms of psychopathology, aggression, incidence of self-harm behaviour, and attachment (perceived parental support) in sample drawn from the general population and community mental health service providers. The results from the study indicate those with a faster life strategy report greater levels of aggression and symptoms of psychopathology. Further, perceptions of poorer parental support were associated with a faster life history strategy. Implications for life history theory, conceptualising psychopathology, and future research directions are discussed.