Post-glacial vegetation in the South Patagonian territory of the giant ground sloth, Mylodon

By comparison with the major modern plant communities of southern Patagonia, the changing post-glacial vegetation of the region is reconstructed from macrofossils derived from deposits in the Cueva del Mylodon, Ultima Esperanza, S. Chile. The oldest deposits, carbon-dated as c. 12,400 B.P., comprise dung of the extinct ground sloth Mylodon darwinii and show the animal to have fed entirely on Cyperaceae, Gramineae and species associated with these in the modern cool, wet sedge-grasslands of western Patagonia, communities which would be expected after the retreat of the ice. Overlying deposits of well-preserved, wind-blown leaf-litter permitted some quantitative analyses which show a rise of evergreen forest dominated by Nothofagus betuloides that reached its maximum c. 7000 B.P. and then declined as it was replaced by deciduous N. pumilio forest. A break in the fossil plant record, covering the human occupation about 5643 B.P. and the subsequent final appearance of Mylodon remains, is followed by evidence of mixed evergreen/deciduous forest in which Nothofagus pumilio gradually increases in importance to give deciduous forest some 2500 years ago similar to that found in the environs of the cave in historical times. Comparison with pollen diagrams shows that the modern climatic and vegetation difference between E. Fudgia and Ultima Eeperanza has persisted throughout the post-glacial period.     

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13–158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.     

Seasonal and habitat variation in the diet of the tawny owl ( Strix aluco ) in central Poland during unusually warm years

In the temperate climate zone in Europe the composition of the diet of predatory vertebrates shows evident variability between the warm and cold season. However, the recently observed climate warming can mitigate the effect of snow cover and low temperatures on the winter foraging ecology of raptors, thus affecting trophic webs in ecosystems. We analysed diet variability in the tawny owl Strix aluco, between the warm and cold seasons of four unusually warm years (as compared to reference years of 1950–2000) in two habitats (forest vs. farmland) in Central Poland. The most important prey group in the tawny owl’s diet were mammals, constituting over 80% of prey items. There were distinct diet differences between the two seasons: insectivorous mammals, birds and amphibians were caught more often during the warm season, and Muridae and Arvicolidae during the cold season. The proportion of insectivorous mammals, voles and amphibians was significantly higher in forest than in farmland. Diet diversity, analysed with rarefaction methods and expressed as the expected cumulative mammal species number for a given number of randomly sampled preyed mammals, was independent of season and higher in forest than in the agricultural habitat. We conclude that even during unusually warm years tawny owls change significantly their feeding habits between the warm and cold season. The effect of season, habitat and weather factors on diet variability in raptors are discussed.     

贵州白鹇湖沉积物中孢粉记录的5.5kaB.P.以来的气候变化

通过对白鹇湖沉积物柱芯孢粉组合的剖面变化分析,在有机质14C定年基础上,探讨了白鹇湖地区过去5.5 ka calB.P.以来的植被演替和气候变化过程.研究结果表明,5500-4500 aB.P.期间,各类植被比较丰富,气候温暖湿润;4500-2750 aB.P.期间,干旱草本和蕨类植物开始出现,是气候转变过渡期;2750-1500 aB.P.期间,木本植物组合类型发生明显变化,喜湿草本减少,耐旱草本增加,气候向温凉干旱化发展;1500 aB.P.至今,木本植被和喜湿草本继续减少,中生耐旱草本和蕨类植物数量继续大幅增加,干旱化趋势明显,植被组合向典型石漠化植被组合类型发展.白鹇湖沉积物剖面孢粉组合变化表明,该地区近5000a来气候变化以温度下降、降水减少为主要趋势,并存在明显的陆地植被退化现象.研究还揭示了自然气候变化事件(如气候持续干旱)可导致喀斯特地区发生石漠化,证实了喀斯特地区生态环境具先天脆弱性.科学评估白鹇湖地区气候干旱化趋势及其生态环境影响对指导该地区科学应对气候变化具重要意义,亟待加强.     

Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile

DNA was extracted from an 11,700-year-old rodent midden from the Atacama Desert, Chile and the chloroplast and animal mitochondrial DNA (mtDNA) gene sequences were analysed to investigate the floral environment surrounding the midden, and the identity of the midden agent. The plant sequences, together with the macroscopic identifications, suggest the presence of 13 plant families and three orders that no longer exist today at the midden locality, and thus point to a much more diverse and humid climate 11,700 years ago. The mtDNA sequences suggest the presence of at least four different vertebrates, which have been putatively identified as a camelid (vicuna), two rodents (Phyllotis and Abrocoma), and a cardinal bird (Passeriformes). To identify the midden agent, DNA was extracted from pooled faecal pellets, three small overlapping fragments of the mitochondrial cytochrome b gene were amplified and multiple clones were sequenced. These results were analysed along with complete cytochrome b sequences for several modern Phyllotis species to place the midden sequence phylogenetically. The results identified the midden agent as belonging to an ancestral P. limatus. Today, P. limatus is not found at the midden locality but it can be found 100 km to the north, indicating at least a small range shift. The more extensive sampling of modern Phyllotis reinforces the suggestion that P. limatus is recently derived from a peripheral isolate.     

A peculiar climbing Megalonychidae from the Pleistocene of Peru and its implication for sloth history

The Xenarthra, particularly the Tardigrada, are with the Notoungulata and Marsupialia among the most diversified South American mammals. Lujanian South American Land Mammal Age localities from the coastal Piedra Escrita site and Andean Casa del Diablo Cave, Peru, have yielded three specimens of the Megalonychidae Diabolotherium nordenskioldi gen. nov. This singular fossil sloth exhibits a peculiar mosaic of cranial and postcranial characters. Some are considered convergent with those of other sloths (e.g. 5/4 quadrangular teeth, characteristic of Megatheriidae), whereas others clearly indicate climbing capabilities distinct from the suspensory mode of extant sloths. The arboreal mode of life of D. nordenskioldi is suggested by considerable mobility of the elbow, hip, and ankle joints, a posteriorly convex ulna with an olecranon shorter than in fossorial taxa, a radial notch that faces more anteriorly than in other fossil sloths and forms an obtuse angle with the coronoid process (which increases the range of pronation–supination), a proximodistally compressed scaphoid, and a wide range of digital flexion. D. nordenskioldi underscores the great adaptability of Tardigrada: an arboreally adapted form is now added to the already known terrestrial, subarboreal, and aquatic (marine and freshwater) fossil sloths. A preliminary phylogenetic analysis of the Tardigrada confirmed the monophyly of Megatherioidea, Nothrotheriidae, Megatheriidae, and Megalonychidae, in which Diabolotherium is strongly nested.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 179–235.     

How to survive a glaciation: the challenge of estimating biologically realistic potential distributions under freezing conditions

Correlative ecological niche models are increasingly used to estimate potential distributions during the Last Glacial Maximum (LGM) for biogeographical research. In the case of presence‐background/pseudoabsences techniques, cold environments that are poorly represented in existing geography can complicate the process of model calibration and transfer into more extreme cold environments that were very common during the LGM (non‐analog conditions). This may lead to biologically unrealistic estimations. Using one cold‐adapted North American mammal, we explore a real scenario to better understand the effect of restricting the range of environmental conditions over which niche models are calibrated and then transferred to LGM conditions. We performed two sets of experiments in Maxent: 1) we calibrated models in the context of only present‐day climate conditions, which is the most common practice, and compared predictions under LGM conditions based on two extrapolation methods (clamping versus unconstrained); 2) we calibrated single models using both present‐day and LGM conditions as part of the same background in order to include more extreme environments in the model calibration. Our experiments led to dramatically different estimates of species’ potential distributions, showing notable differences with respect to latitudinal and elevational shifts during the LGM. Models calibrated using present‐day climates yielded biologically unrealistic estimations, suggesting that species survived in the glaciers during the LGM. Even more unrealistic estimations were achieved when clamping was enforced as the method to extrapolate. Models calibrated in the context of both modern and past climates reduced the required degree of extrapolation and allowed more realistic potential distributions, suggesting that the species avoided extremely cold conditions during the LGM. This study alerts to the possibility of obtaining implausible potential distributions during the LGM due to restricted background datasets and offers recommendations that should promote better strategies to estimate distributional changes during glaciations.     

Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100

Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.     

A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change

Plant–herbivore interactions provide critical insights into the mechanisms that govern the spatiotemporal distributions of organisms. These interactions are crucial to understanding the impacts of climate change, which are likely to have an effect on the population dynamics of alpine herbivores. The Royle's pika (Ochotona roylei, hereafter pika) is a lagomorph found in the western Himalaya and is dependent on alpine plants that are at risk from climate change. As the main prey of many carnivores in the region, the pika plays a crucial role in trophic interactions. We examined topographical features, plant genera presence and seasonal dynamics as drivers of the plant richness in the pika's diet across an elevational gradient (2,600–4,450 m). We identified 79 plant genera in the faecal pellets of pikas, of which 89% were forbs, >60% were endemic to the Himalaya, and 97.5% of the diet plant genera identified followed the C₃ photosynthetic pathway. We found that, during the premonsoon season, the number of genera in the pika's diet decreased with increasing elevation. We demonstrate that a large area of talus supports greater plant diversity and, not surprisingly, results in higher species richness in the pika's diet. However, in talus habitat with deep crevices, pikas consumed fewer plant genera suggesting they may be foraging suboptimally due to predation risk. The continued increase in global temperature is expected to have an effect on the distribution dynamics of C₃ plants and consequently influence pika diet and distribution, resulting in a significant negative cascading effect on the Himalayan ecosystem.     

A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA

We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes, which fall within haplogroups X and C, consistent with Northeastern Native populations today. In addition we have sexed the male using a novel-sexing assay and confirmed the authenticity of his Y chromosome with the presence of the Native American specific Y-QM3 single nucleotide polymorphism (SNP). This is the first ancient nuclear SNP typed from a Native population in the Americas. In addition, using the same teeth we conducted a stable isotopes analysis of collagen and dentine to show that both individuals relied on marine sources (fresh and salt water fish, seals) with no hierarchy seen between them, and that their water sources were pooled or stored water. Both mtDNA sequence data and Y SNP data hint at possible gene flow or a common ancestral population for both the Beothuk and the current day Mikmaq, but more importantly the data do not lend credence to the proposed idea that the Beothuk (specifically, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots are not hypervariable because they are more prone to damage.     

Lutz's spontaneous sedimentation technique and the paleoparasitological analysis of sambaqui (shell mound) sediments

Parasite findings in sambaquis (shell mounds) are scarce. Although the 121 shell mound samples were previously analysed in our laboratory, we only recently obtained the first positive results. In the sambaqui of Guapi, Rio de Janeiro, Brazil, paleoparasitological analysis was performed on sediment samples collected from various archaeological layers, including the superficial layer as a control. Eggs of Acanthocephala, Ascaridoidea and Heterakoidea were found in the archaeological layers. We applied various techniques and concluded that Lutz''s spontaneous sedimentation technique is effective for concentrating parasite eggs in sambaqui soil for microscopic analysis.     

Promises and pitfalls of using high‐throughput sequencing for diet analysis

The application of high‐throughput sequencing‐based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic composition and diversity. Here, we review these studies in the light of high‐throughput sequencing‐based assessment of trophic interactions. We address how the study design can account for distortion factors, and how acknowledging limitations and biases inherent to sequencing‐based diet analyses are essential for obtaining reliable results, thus drawing appropriate conclusions. Furthermore, we suggest strategies to minimize the effect of distortion factors, measures to increase reproducibility, replicability and comparability of studies, and options to scale up DNA sequencing‐based diet analyses. In doing so, we aim to aid end‐users in designing reliable diet studies by informing them about the complexity and limitations of DNA sequencing‐based diet analyses, and encourage researchers to create and improve tools that will eventually drive this field to its maturity.     

气候变化背景下定量解析生态工程对植被动态的影响研究方法概述

植被动态变化受气候和人类活动双重作用力的驱动。在气候变化的背景下,如何定量剖析人类活动在植被动态变化中的作用力,对增加植被生态系统碳储量和缓解气候变化具有重要意义。随着生态文明建设和环境保护意识的加强,就植被生态系统而言,生态工程作为一项巨大的人类活动,对植被影响的广度和深度日益加强。系统分析气候变化背景下生态工程对植被的生态效应影响,对后期生态恢复措施的制定和实施具有十分重要的理论指导意义。虽已有一些生态工程对植被影响的定量化研究方法,但不同方法之间的结果难以进行比较研究。比较探讨各定量研究方法的优缺点有利于推动植被驱动机制的研究,有助于恢复生态学和人类生态学的应用和发展。系统梳理了定量研究生态工程对植被动态的影响主要研究方法:回归分析、残差趋势分析、基于生物物理过程模型方法和阈值分割方法。对比发现,基于生物物理过程模型方法具有较高的应用潜力,趋势分析方法和阈值分割方法仍需进一步完善。目前,定量剖析生态工程对植被变化的影响研究主要侧重于模型模拟,野外实证研究和模型验证较为缺乏,是恢复生态学未来研究的重点和难点之一。     

Application of a Gondwanan perspective to restore ecological integrity in the south‐western Australian global biodiversity hotspot

Bounded by ocean and desert, the isolated, predominately Mediterranean‐climate region of south‐western Australia (SWA) includes nine bioregions (circa 44 million hectares). The ecological integrity of the landscapes in this global biodiversity hotspot has been compromised by deforestation, fragmentation, exploitation, and introduced biota. Nature and degree of transformation varies between four interconnected landscapes (Swan Coastal Plain; South‐west Forests; Wandoo Woodlands; and Great Western Woodlands). A Gondwanan perspective emphasizes a venerable biota and a cultural component to deep time. The particular importance of remnants and protected areas is recognized in restoring ecological integrity to Gondwanan landscapes. The nature and magnitude of the restoration task in these ancient, and neighboring, landscapes require higher levels of investment and more time than do recent landscapes. The protection, conservation, restoration, and rehabilitation of ecological integrity require multiple approaches in each landscape as well as consideration of the whole. Active conservation of biota and minimizing the impact of industrial‐ and agricultural‐use are priorities. Integrating a climate focus and rethinking fire are critical restoration considerations to future trajectories under anthropogenic climate change. A legislative mandate to coordinate industrial‐scale restoration and active conservation to build from protected areas must become a societal priority to restore ecological integrity.     

我国三北地区植被变化的动因分析

地表植被变化是气候变化、人类活动等多种因素共同作的结果。然而,以往的研究要么集中在与气候变化有关的气象因素,要么集中在与人类活动有关的人为因素,鲜有基于长期数据监测下对自然与社会因素之间相互作用的定量评估。因此,气候变化和人为因素对地表植被变化的相互作用并不明确,各个因素对植被变化影响的量化贡献仍然不确定。为了评价生态修复项目对荒漠化防治的效果、以及在土地荒漠化防治中自然与社会因素对我国植被变化的影响、及其复杂的相互作用机理,该研究应用卫星遥感影像资料,通过面板数据混合回归模型大数据分析方法,计算了1983年至2012年气候变化和人类活动对我国北方地区植被变化的贡献率。结果表明,气候变化和人类活动对NDVI变化均有重要作用,其中人类活动对植被覆盖度变化的影响占58.2%—90.4%、气候变化占9.6%—41.8%;不同地区表现出不同的地理分异特征,并存在时滞效应。由此可见,荒漠化防治必须充分考虑不同因素的综合作用和地域特征,才能取得事半功倍的效果。研究结果较好地体现了卫星遥感影像资料在大尺度(省域尺度)下与社会经济统计指标的融合,为进一步中尺度(县域尺度)研究提供了方法借鉴。     

Molecular diet analysis of neotropical bats based on fecal DNA metabarcoding

Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defined dietary guilds (e.g., insectivores, carnivores, and frugivores). Apart from these broad guilds, we lack detailed dietary information for many species and therefore have only a limited understanding of interaction networks linking bats and their diet items. In this study, we used DNA metabarcoding of plants, arthropods, and vertebrates to investigate the diets of 25 bat species from the tropical dry forests of Lamanai, Belize. Our results report some of the first detection of diet items for the focal bat taxa, adding rich and novel natural history information to the field of bat ecology. This study represents a comprehensive first effort to apply DNA metabarcoding to bat diets at Lamanai and provides a useful methodological framework for future studies testing hypotheses about coexistence and niche differentiation in the context of modern high‐throughput molecular data.     

青藏高原地区气候图解数据集

气候图解可以直观反映气象台站基本信息和气温、降水等气象数据,是研究植被与气候关系的有效方式。为便于了解青藏高原不同植被区域气候特征,进一步认识青藏高原植被与气候关系,该文基于1951–1980年与1981–2010年青藏高原地区国家地面气象台站基本信息和各30年平均观测数据,依据《中国植被》所述标准制作每个气象台站的气候图解。论文提供了青藏高原地区主要台站气候图解集,包括两个30年时间段共计205幅图解。研究表明:(1)青藏高原地区气温和降水总体水平偏低,前后30年年平均气温和年降水量整体呈上升趋势;(2)青藏高原地区各气象台站记录值随植被区域不同表现出较大差异。虽然青藏高原西部地区的气象台站数量很少,但该数据集仍涵盖了高原面上的不同植被地带,可有效运用于高原植被与气候关系研究,为展示高原气候环境等提供便利。     

Size increase in high elevation ground squirrels over the last century

There is increasing evidence for morphological change in response to recent environmental change, but how this relates to fluctuations in geographic range remains unclear. We measured museum specimens from two time periods (1902–1950 and 2000–2008) that vary significantly in climate to assess if and how two high elevation contracting species of ground squirrels in the Sierra Nevada of California, Belding's ground squirrel (Urocitellus beldingi) and the golden‐mantled ground squirrel (Callospermophilus lateralis), and one lower elevation, stable species, the California ground squirrel (Otospermophilus beecheyi), have responded morphologically to changes over the last century. We measured skull length (condylobasal length), an ontogenetically more labile trait highly correlated with body size, and maxillary toothrow length, a more developmentally constrained trait predictive of skull shape. C. lateralis and U. beldingi, both obligate hibernators, have increased in body size, but have not changed in shape. In contrast, O. beecheyi, which only hibernates in parts of its range, has shown no significant change in either morphometric trait. The increase in body size in the higher elevation species, hypothesized to be a plastic effect due to a longer growing season and thus prolonged food availability, opposes the expected direction of selection for decreased body size under chronic warming. Our study supports that population contraction is related to physiological rather than nutritional constraints.     

A consensus view of the proteome of the last universal common ancestor

The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide‐derived organic cofactors.