Exposing hidden endemism in a Neotropical forest raptor using citizen science

Gaps in our knowledge of the geographical distribution of species represent a fundamental challenge to biogeographers and conservation biologists alike, and are particularly pervasive in the tropics. Here we highlight the case of the Rufous‐thighed Kite Harpagus diodon, a South American raptor commonly mapped as resident across half the continent. Recent observations at migration watch points have indicated it may be partially migratory in the southernmost parts of its range. To investigate this possibility, we collated contemporary and historical specimen records, published sight records and ‘digital vouchers’ – photographs and sound‐recordings archived online (from citizen science initiatives) – and explored the spatiotemporal distribution of records. We were unable to trace any documented records of this species from Amazonia during the austral summer (October–March), or records from the Atlantic Forest biome during the peak of the Austral winter (June–August), and all proven breeding records stem from the Atlantic Forest region. We compared this pattern with that of a ‘control’ species, the congeneric Double‐toothed Kite H. bidentatus, again using specimens and digital vouchers. For this species we found no evidence of seasonality between biomes and can disregard spatiotemporal variation in observer effort as a cause of seasonal biases. We consider that all populations of Rufous‐thighed Kites are fully migratory, wintering in Equatorial forests in the Amazonian basin. We provide evidence that this pattern was previously obscured by erroneous undocumented records and poor or erroneous specimen metadata, and its discovery was primarily facilitated by digital vouchers. This discovery requires a reassessment of the species’ global conservation status as an Atlantic Forest breeding endemic, threatened by habitat loss and degradation, as it was previously considered to be resident across large swathes of undisturbed Amazonian Forest on the Guiana Shield. The bulk of the digital voucher data used to elucidate this pattern were extracted from a Brazilian citizen science initiative WikiAves, which may serve as a model for collating biodiversity data in megadiverse countries and help catalyse environmental awareness.     

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

山地景观遗传学研究文献综述

山地生态系统是生物多样性分布与保护的热点。山地景观遗传学（Mountain Landscape Genetics）研究在山地景观尺度上野生生物的种群遗传格局及其驱动机制和影响因素,是景观遗传学（Landscape Genetics）的重要分支。山地景观遗传学研究对于深入理解物种的空间遗传结构、形成过程、物种形成与分化机制具有重要意义与价值,同时可以为珍稀濒危物种和山地生物多样性的有效保护与管理提供科学指导。为了更好地掌握目前山地景观遗传学的发展趋势与重点研究问题,为未来生物多样性与山地生态系统的保护管理提供科学参考,基于对Web of Science核心数据库和中国知网数据库的系统检索,全面汇总分析了1999-2020年山地景观遗传学领域发表的192篇英文文献与31篇中文文献。结果显示,该领域自2008年起迅速发展,截至2020年共有46个国家的研究机构发表了山地景观遗传相关研究,研究热点地区包括北美洲的落基山脉、内华达山脉、阿巴拉契亚山脉,欧洲的阿尔卑斯山脉、比利牛斯山脉,以及亚洲的喜马拉雅-横断山脉。研究对象类群涵盖真菌、植物、节肢动物、脊椎动物,其中脊椎动物是研究发表最多的类群,占发表文献总数的62.0%;脊椎动物中,又以对哺乳类（占脊椎动物发表文献总数的52.9%）与两栖类（23.5%）的研究最多。目前主要的研究方向包括：（1）识别山地景观中的基因流路径或阻碍;（2）量化山地景观特征对种群遗传结构时空变化的影响。中国是发表山地景观遗传学文章数量最多的亚洲国家,近十年来相关研究发展迅速,研究类群以植物（占在中国发表文献总数的62.3%）与脊椎动物（35.8%）为主,对脊椎动物的研究中以两栖动物为最多（占所有脊椎动物发文数量的52.6%）,研究区域主要集中在喜马拉雅-横断山脉与秦岭。本文进一步对目前山地景观遗传学研究中存在的空缺及未来重点关注问题提出建议。     

佛山市禅城区小型兽类组成及多样性的时空变化

城市化导致的野生动物生境破碎化,会使野栖小型兽类更多聚集分布于城区斑块化的农区和公园生境中,因而其多样性组成及时空变化模式可能会与其他区域不同,了解这些模式对防控城区野栖小型兽类的危害具有重要支撑作用。本研究于2020年12月至2021年10月,分4个季节在佛山市禅城区3个公园和7处农区生境中以夹捕法调查小型兽类,比较了小型兽类的种类、密度和生态学指标的时空差异。共有效置夹1843夹次,捕获小型兽类2目2科4属7种共244只。其中劳亚食虫目（Eulipotyphla）的臭鼩（Suncus murinus）占总捕获动物的48.77%;啮齿目中黑缘齿鼠（Rattus andamanensis,20.90%）和卡氏小鼠（Mus caroli,18.03%）为优势鼠种,黑缘齿鼠为佛山市新增记录,卡氏小鼠为禅城区新增记录。4次调查总捕获率达13.28%±0.93%,12月的啮齿类捕获率显著低于4月;公园的总捕获率和啮齿类捕获率都比农区略高,而臭鼩捕获率比农区略低,但差异不显著。12月的物种丰富度和优势度指数最高,均匀度指数最低;4月的多样性指数最高,优势度指数最低;而10月的均匀度指数最高,物种...     

Twenty years of understorey bird extinctions from Amazonian rain forest fragments: consistent trends and landscape-mediated dynamics

Aim We analysed presence/absence data for understorey bird species in rain forest fragments sampled from 1979 through 2001. Here we consider extinctions between 1992, when most fragments had been isolated for at least 8 years, and 2001. Our objectives were to determine whether high extinction rates documented soon after isolation continued through up to 20 years after isolation, and to examine fragment size and landscape effects on extinction. Location Biological Dynamics of Forest Fragments Project, near Manaus, Brazil. Methods Through 1992, birds were surveyed with standardized mist net sampling in ten 1‐ to 100‐ha fragments. We repeated the mist net protocol in 2000–01. We also added remote taping of the dawn chorus and tape playback surveys for species captured in 1991–92 but not in 2000–01. Results Between 1992 and 2001, 37 species went extinct in at least one fragment. As expected, extinction rate decreased with increasing fragment size. Over 30% of species went extinct in 1‐ha fragments, compared to about 5% in 100‐ha fragments. Extinction followed a predictable pattern: most species lost from 100‐ha fragments between 1992 and 2001 had already gone extinct in smaller fragments before 1992. Despite extinctions, fragments gained species between 1992 and 2001, apparently due to species moving through the developing second growth matrix. Fragments surrounded by old second growth had lower extinction rates than predicted based on fragment size alone. Main conclusions Sequential extinctions occurred for at least 20 years. Some additional species previously lost from smaller fragments may continue to go extinct in 100‐ha fragments. At the same time, species assemblages in 1‐ and 10‐ha fragments mostly reflect second‐growth dynamics by 20 years after isolation. High species loss predicted from the first few years after isolation has not occurred, almost certainly because of recolonization.     

Population genetic structure of rock ptarmigan in the 'sky islands' of French Pyrenees: implications for conservation

Expected consequences of global warming include habitat reduction in many cool climate species. Rock ptarmigan is a Holarctic grouse that inhabits arctic and alpine tundra. In Europe, the Pyrenean ptarmigan inhabits the southern edge of the species' range and since the last glacial maximum its habitat has been severely fragmented and is restricted to high-alpine zones or 'sky islands'. A recent study of rock ptarmigan population genetic in Europe found that the Pyrenean ptarmigan had very low genetic diversity compared with that found in the Alps and Scandinavia. Habitat fragmentation and reduced genetic diversity raises concerns about the viability of ptarmigan populations in the Pyrenees. However, information on population structuring and gene flow across the Pyrenees, which is essential for designing a sound management plan, is absent. In this study, we use seven microsatellites and mitochondrial control region sequences to investigate genetic variation and differentiation among five localities across the Pyrenees. Our analyses reveal the presence of genetic differentiation among all five localities and a significant isolation-by-distance effect that is likely the result of short dispersal distances and high natal and breeding philopatry of Pyrenean ptarmigan coupled with severe habitat fragmentation. Furthermore, analysis of molecular variance, principal component analysis and Bayesian analysis of genetic structuring identified the greatest amount of differentiation between the eastern and main parts of the Pyrenean chain separated by the Sègre Valley. Our data also show that the Canigou massif may host an isolated population and requires special conservation attention. We propose a management plan which includes the translocation of birds. If a sky island structure affects genetic divergence in rock ptarmigan, it may also affect the genetic structure of other sky island species having low dispersal abilities.     

Use of cultivated foods and matrix habitat by Bale monkeys in forest fragments: Assessing local human attitudes and perceptions

Primates inhabiting human-modified landscapes often exploit matrix habitat to supplement their diet with cultivated foods, at times resulting in economic losses and conflict with local people. Understanding human-nonhuman primate interactions and the attitudes and perceptions of local people towards crop feeding species are crucial to designing effective species-based management plans. Over a 12-month period, we used scan sampling to study the consumption of cultivated foods and matrix use patterns by two habituated groups of Bale monkeys (Chlorocebus djamdjamensis), Ethiopian-endemic bamboo specialists, in two forest fragments (Kokosa and Afursa) set amidst human settlements and farmland in the southern Ethiopian Highlands. Further, we conducted interviews with local people to document their attitudes and perceptions towards Bale monkeys at the two sites. We found that Bale monkeys at Kokosa, a more degraded habitat by most measures, consumed significantly more cultivated foods than their counterparts at Afursa. Moreover, Bale monkeys at Kokosa spent significantly more time in the matrix than in the forest habitat, while monkeys at Afursa spent significantly less time in the matrix than in the forest habitat. Not surprisingly, local people displayed a more negative attitude towards monkeys inhabiting Kokosa than those inhabiting Afursa. The differences in Bale monkey cultivated food consumption and matrix use patterns—as well as in local people's attitudes and perceptions towards Bale monkeys—between Kokosa and Afursa are probably associated with differences in habitat structure, degree of habitat alteration, and land-use practices between the sites. We conclude that to ensure long-term coexistence between Bale monkeys and local people in human-modified landscapes, it is vital to incorporate nearby matrix habitats into management plans and to work closely with local communities to develop effective nonlethal crop protection strategies, thereby reducing the likelihood of negative interactions between Bale monkeys and humans.     

DNA fragmentation and morphological changes in apoptotic human lymphocytes

Cell suspensions enriched in cells at various stages of apoptosis were obtained by separation of irradiated human peripheral blood lymphocytes on density gradients at different post-irradiation times. The state of DNA fragmentation in the cells was determined by comet assay and pulsed field gel electrophoresis. The morphologically distinguishable features of apoptosis such as chromatin condensation and cell shrinkage correlated with discrete stages of DNA fragmentation. It was found that >/=50 kbp fragmentation of DNA occurs already in cells of normal density whereas the subsequent DNA fragmentation onto fragments <50 kbp occurs in parallel with cell shrinkage and simultaneous increase in cell density.The observed stages of DNA fragmentation seem to be separated in time that could allow in case of abortive apoptosis formation of chromosomal aberrations.