Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2–3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3–4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.     

祁连山气候变化特征及其对水资源的影响

祁连山作为我国重要的生态功能区、西北地区重要的生态安全屏障和河流产流区,是气候变化敏感区和生态环境脆弱区,其生态环境对西北地区经济发展起着重要作用。本研究利用祁连山区气温和降水观测数据、MOD10A2积雪产品以及石羊河、黑河和疏勒河流量资料,系统分析了1961—2020年祁连山区的气候变化特征,以及在气候变暖背景下,气候变化对祁连山区水资源的影响。结果表明: 1961—2020年,祁连山区平均气温呈显著上升趋势,升温速率达0.39 ℃·(10 a)^-1,西段升温速率最大,中、东段次之,冬季升温趋势最显著,春季最小;祁连山区平均气温在1997年发生突变。祁连山区年降水量总体呈波动增加趋势[10 mm·(10 a)^-1],中段增加最明显,2004年以来祁连山区处于多雨时期,气候呈暖湿化趋势;四季降水量均呈增加趋势,夏季降水增加对年降水贡献最大;年降水以年际尺度变化为主,2.8年的年际尺度贡献率高达64.3%。祁连山积雪面积受气温和降雪影响明显,与夏季气温存在负相关,与降雪量存在正相关;2016—2020年,祁连山增温趋缓、降雪增多,积雪面积呈增加趋势。2000年以来,祁连山升温加剧,降水增多,冰雪融水增加,石羊河、黑河和疏勒河出山径流均呈增加趋势。研究结果对祁连山区生态文明建设和应对气候变化具有重要意义。     

天山一号冰川表面冰尘和底部沉积层中可培养酵母菌系统发育类群的分布及生态生理特征

【目的】揭示乌鲁木齐河源天山1号冰川表面冰尘(CS)和底部沉积层(DS)可培养酵母菌系统发育类群及其结构组成差异,分析低温酵母菌代表菌株之间的生态、生理生化特性。【方法】利用4种培养基分离天山1号冰川可培养酵母菌,采用ITS基因序列分析确定菌种的系统进化地位。对分离菌株的最适生长温度、耐盐性和产酶等生态、生理学特性进行分析。【结果】从冰尘和底部沉积层中共分离出152株酵母菌菌株,通过ITSrRNA基因序列的NCBI比对和Rep-PCR指纹分型,结果表明酵母菌类群包括担子菌门(Basidiomycota)和子囊菌(Ascomycota),分属于14个属26种,其中担子菌门柄锈菌亚门(Pucciniomycotina)88株、伞菌亚门(Agariomycotina)24株,子囊菌门40株,冰川广布酵母菌Vishniacozyma victoriae为优势菌株(占比21.84%)。17种酵母的最适生长温度为15°C、2种为10°C、6种为20°C。25株代表酵母菌株产酶分析显示,产脂肪酶、淀粉酶、蛋白酶菌株分别为11株、11株、5株,6株3种酶都不产。【结论】天山1号冰川冰尘及底部沉积层可培养低温酵母系统发育类群结构存在差异,产低温酶活性高、稳定性好,为今后冰川低温酵母菌的研究提供有价值的数据支持。     

长白山群落交错带长白松和鱼鳞云杉径向生长对气候变暖的响应

长白山是典型的温性针阔叶混交林分布区,也是受全球气候变化影响最为显著的地区之一.为了解该区森林生态系统对气候变化的响应,本研究选取该区阔叶红松林与云冷杉林(又称暗针叶林)群落交错带内优势乔木树种长白松和鱼鳞云杉作为对象,获取树木年轮宽度资料建立标准年表,明确限制2个树种径向生长的关键气候因子.结果表明:长白松和鱼鳞云杉...     

Current biogeographical roles of the Kunlun Mountains

Large‐scale patterns of biodiversity and formation have garnered increasing attention in biogeography and macroecology. The Qinghai‐Tibet Plateau (QTP) is an ideal area for exploring these issues. However, the QTP consists of multiple geographic subunits, which are understudied. The Kunlun Mountains is a geographical subunit situated in the northern edge of the QTP, in northwest China. The diversity pattern, community phylogenetic structures, and biogeographical roles of the current flora of the Kunlun Mountains were analyzed by collecting and integrating plant distribution, regional geological evolution, and phylogeography. A total of 1911 species, 397 genera, and 75 families present on the Kunlun Mountains, of which 29.8% of the seed plants were endemic to China. The mean divergence time (MDT) of the Kunlun Mountains flora was in the early Miocene (19.40 Ma). Analysis of plant diversity and MDT indicated that the eastern regions of the Kunlun Mountains were the center of species richness, endemic taxa, and ancient taxa. Geographical origins analysis showed that the Kunlun Mountains flora was diverse and that numerous clades were from East Asia and Tethyan. Analysis of geographical origins and geological history together highlighted that the extant biodiversity on the Kunlun Mountains appeared through species recolonization after climatic fluctuations and glaciations during the Quaternary. The nearest taxon index speculated that habitat filtering was the most important driving force for biodiversity patterns. These results suggest that the biogeographical roles of the Kunlun Mountains are corridor and sink, and the corresponding key processes are species extinction and immigration. The Kunlun Mountains also form a barrier, representing a boundary among multiple floras, and convert the Qinghai‐Tibet Plateau into a relatively closed geographical unit.     

大兴安岭原麝冬季的生境选择

2005年3～4月和2006年3月,在黑龙江省大兴安岭呼中自然保护区,采用机械布点法随机设置样线,对原麝(Moschus moschiferus)冬季生境选择进行了研究。对海拔、乔木密度、雪深、隐蔽度、食物丰富度、坡度和倒木数量进行2个独立样本的Mann-Whitey U检验,找出生境利用样方与任意样方的生态因子的差异。U检验的结果表明,原麝冬季喜欢活动在相对海拔高、乔木密度小、雪层浅、隐蔽度高、坡度陡且喜食食物丰富的区域;对植被类型、坡位、坡向、距水源距离、距人为干扰距离、动物干扰和碎石坡7个名词性变量采用卡方(Chi-square)统计进行显著性检验,卡方检验的结果表明:原麝冬季偏好远离人为干扰、接近碎石坡、阳坡和其他动物干扰较少的针阔混交林中;对以上14个生态因子进行主成分分析,结果表明,前6个特征值的累计贡献率达到72·318%,可以较好地反映原麝生境特征,根据主成分分析结果,将原麝冬季生境选择影响因子分别命名为空间因子(海拔、坡度、距碎石坡距离)、干扰因子(距人为干扰距离、距水源距离)、坡向因子(坡向、乔木密度)、坡位因子(坡位、动物干扰)、食物因子(食物丰富度、隐蔽度)和倒木因子(倒木数量)。     

Effects of a hydropower plant on Coleopteran diversity and abundance in the Udzungwa Mountains, Tanzania

The effects of river flow diversion on biodiversity were assessed using Coleoptera as an indicator group in three habitats of the Kihansi Gorge (Udzungwa Mountains, Tanzania), before and after commissioning of a hydropower plant. Data collected using sweep netting and pitfall traps showed that the effect of diversion of the river flow was site-specific, affecting particularly the spray habitat. Rarefaction analysis of both sweep netting and pitfall samples indicated that the expected richness of Coleoptera declined significantly in all habitats after commissioning of the power plant. Sweep netting and pitfall samples showed that the highest Shannon–Wiener diversity index value before the diversion of the river flow was in the spray zone, but the index value decreased after diversion. Changes in the other two habitats were less prominent. Analysis of variance using diversity index values from five pitfall samples in each habitat type before and after commissioning indicated that there were no statistically significant differences in the diversity index between the two sampling periods or among the three habitat types. Renkonen's similarity index between habitats showed that pitfall samples had higher similarity (87%) than did samples from sweep netting (69%). It is suggested that for mitigation purposes, artificial spray systems, which have been installed in other wetlands of the Kihansi Gorge, also be installed to cover the whole Lower Wetland in which this study was undertaken. In order to maintain overall biodiversity in the Kihansi Gorge, it is suggested that the ecosystem conservation approach be prioritised.     

Sampling adequacy in an extreme environment: species richness patterns in Slovenian caves

Caves harbor a rich fauna unique to subterranean environments. Although extensive records of cave animals are available, only a small fraction of known caves in any region have been biologically assessed. We investigated the impact of incomplete sampling using one of the richest, best documented cave faunas in the world – that of the Dinaric karst of Slovenia. We utilized time snapshots (1940, 1970, and 2000) of the caves and cave fauna to analyze stability of hotspots, spatial pattern, and relationship between number of species and number of caves. Using data aggregated into 100km² hexagons, the location of hotspots, black–white joins, Moran's I, and spatial autocorrelation all remained constant, at least from 1970 on. The linear regression coefficient of the relationship between number of caves and number of species declined with time. Most hexagons had been sampled, but there was no indication that any hexagon had been sampled intensively enough for the accumulation curve of number of caves versus number of species within a hexagon to reach an asymptote. This appeared to be the result of a highly skewed distribution of species richness among caves. Number and position of hotspots can be predicted from information on these few high diversity caves.     

北极-第三纪成分在喜马拉雅-横断山的发展及演化

通过古植物学及古地史资料,论述了北极地区在第三纪早期气候变迁对喜马拉雅-横断山地区植物区系形成的影响,并通过一些喜马拉雅-横断山地区的特征类群;杜鹃属,槭树属,柳属,桦木属和桤木属以及一些草本类群虎耳草科的落新妇族,金腰属和虎耳草属,忍冬科的莛子镳属的分布式样和起源分化的分析,说明了喜马拉雅-横断山区系中有相当一部分是这些北方起源的,北极-第三纪成分迁移是现代喜马拉雅-横断山植物区系成分的一个重要来源,并且讨论了喜马拉雅-横断山植物区系同北方植物区系可能的迁移路线,指出西南-秦岭-东北通道即西南沿四川盆地经秦岭和黄河至东北和西伯利亚和“中亚高地通道”即向西经帕米尔高原同北方交流,向东经西南-秦岭-东北通道迁移交流是喜马拉雅-横断山植物区系成分同北方交流的主要路线,由于第四纪冰期间冰期反复作用,各类成分在该地区保存,汇集,分化发展,使得该喜马拉雅-横断山地区成了北极-第三纪中心消失以后,在近代形成的温带和高山植物区系新的发展和分化中心。     

Extraordinarily low bone mineral density in an old female chimpanzee (<Emphasis Type="Italic">Pan troglodytes schweinfurthii</Emphasis>) from the Mahale Mountains National Park

We examined bone mineral density (BMD) of the femoral neck and lumbar vertebrae of four chimpanzee skeletons from Mahale Mountains National Park, Tanzania, and four captive ones, with a dual energy X-ray absorptiometer. The BMD of Wansombo, an old female chimpanzee from Mahale , was remarkably lower than the mean of the other six younger adult female chimpanzees and categorized as osteoporosis. Posture, locomotion, and trunk-sacral anatomy of chimpanzees may have prevented fractures in Wansombo, whose BMD was below human osteoporosis criteria. Electronic Publication