A protocol for temporal calibration of general area cladograms

Aim To describe a protocol for incorporating a temporal dimension into historical biogeographical analysis, while maintaining the essential independence of all datasets, involving the generation of general area cladograms. Location Global. Methods General area cladograms (GACs) are a reconstruction of the evolutionary history of a set of areas and unrelated clades within those areas. Nodes on a GAC correspond to speciation events in a group of taxa; general nodes are those at which multiple unrelated clades speciate. We undertake temporal calibration of GACs using molecular clock estimates of splitting events between extant taxa as well as first appearance data from the fossil record. We present two examples based on re‐analysis of previously published data: first, a temporally calibrated GAC generated from secondary Brooks parsimony analysis (BPA) of six extant bird clades from the south‐west of North America using molecular clock estimates of divergence times; and second, an analysis of African Neogene mammals based on a phylogenetic analysis for comparing trees (PACT) analysis. Results A hypothetical example demonstrates how temporal calibration reveals potentially critical information about the timing of both unique and general events, while also illustrating instances of incongruence between dates generated from molecular clock estimates and fossils. For the African Neogene mammal dataset, our analysis reveals that most mammal clades underwent geodispersal associated with the Neogene climatic optimum (c. 16 Ma) and vicariant speciation in central Africa correlated with increased aridity and cooler temperatures around 2.5 Ma. Main conclusions Temporally calibrated GACs are valuable tools for assessing whether coordinated patterns of speciation are associated with large‐scale climatic or tectonic phenomena.     

Germination ecology of drupelets of the fig (Ficus carica L.)

Abiotic and biotic factors and their effects on germination of fig drupelets were studied. The drupelets germinated between 10^oC and 30^oC.Constant humidity was necessary for germination and frequent drying out of the substrate was unfavourable. Total darkness for the whole duration of the experiments had a slighly negative effect on germination. The fastest germination occurred at constant humidity and an alternating temperature of 20/30^oC with exposure to light for 8 hours (at the higher temperature) and to darkness for 16 hours (at the lower temperature).Natural or artificial removal of drupelets from the syconium guaranteed a high germination percentage, whereas no germination occurred in drupelets left inside the syconium. Hence birds and mammals act as dispersal agents and mediators of germination. As they eat pieces of fig syconium, they free the drupelets from the flesh, eliminating the effect of inhibitors and/or microenvironments with high osmotic pressure inside the syconium. These findings support the hypothesis that germination occurs in autumn or spring depending on the climatic zone in which the species grows.     

生物复苏——大绝灭后生物演化历史的第一幕

生命史是一部生物界短期,快速剧变与长期,慢速稳定相互交替的历史。大绝灭（即集群绝灭）事件反映了全球环境的大突变,点断了地质历史中的生命记录及其发展历程,预示着生物界的演化出现了最有意义的飞跃,近年来尝试研究大绝灭后全球生物界的残存－复苏及其基本型式,并探索复苏的控制因素,标志着地质科学中一个重心的转移（即从大绝灭转向其后的生物残存与复苏的研究）。生物复苏揭示了大绝灭后生物演化历史的第一幕,其研究的     

Disentangling the historical routes to community assembly in the global epicentre of biodiversity

Aim

The exceptional turnover in biota with elevation and number of species coexisting at any elevation makes tropical mountains hotspots of biodiversity. However, understanding the historical processes through which species arising in geographical isolation (i.e. allopatry) assemble along the same mountain slope (i.e. sympatry) remains a major challenge. Multiple models have been proposed including (1) the sorting of already elevationally divergent species, (2) the displacement of elevation upon secondary contact, potentially followed by convergence, or (3) elevational conservatism, in which ancestral elevational ranges are retained. However, the relative contribution of these processes to generating patterns of elevational overlap and turnover is unknown.

Location

Tropical mountains of Central- and South-America.

Time Period

The last 12 myr.

Major Taxa Studied

Birds.

Methods

We collate a dataset of 165 avian sister pairs containing estimates of phylogenetic age, geographical and regional elevational range overlap. We develop a framework based on continuous-time Markov models to infer the relative frequency of different historical pathways in explaining present-day overlap and turnover of sympatric species along elevational gradients.

Results

We show that turnover of closely related bird species across elevation can predominantly be explained by displacement of elevation ranges upon contact (81%) rather than elevational divergence in allopatry (19%). In contrast, overlap along elevation gradients is primarily (88%) explained by conservatism of elevational ranges rather than displacement followed by elevational expansion (12%).

Main Conclusions

Bird communities across elevation gradients are assembled through a mix of processes, including the sorting, displacement and conservatism of species elevation ranges. The dominant role of conservatism in explaining co-occurrence of species on mountain slopes rejects more complex scenarios requiring displacement followed by expansion. The ability of closely related species to coexist without elevational divergence provides a direct and faster pathway to sympatry and helps explain the exceptional species richness of tropical mountains.     

关帝山云杉次生林树木径向生长的空间关联及其影响因子

以关帝山4 hm²云杉次生林样地为研究对象,按照CTFS(Center for Tropical Forest Science)技术规范对样地树木进行连续定位监测。利用2010至2015年间样地主要树种生长量观测数据,结合地形、土壤等环境因子调查及采样测定数据,分析了树木种群径向生长的空间关联性及其随生境的变化,并探讨了树木种群径向生长的影响因素。结果表明,青杄、华北落叶松、红桦、白桦和辽东栎为云杉次生林主要树种,在样地4个生境型(山脊生境、低海拔缓坡生境、高海拔缓坡生境、低洼地陡坡生境)中均有分布且呈现不同的径级结构。标记相关函数分析显示,同一生境型中,5树种径向生长的空间关联性各异;对于同一树种,径向生长的空间自相关性不仅具有尺度依赖性,同时生境型的不同导致树木径向生长的空间关联性发生变化。线性混合效应模型分析显示,初始胸径对树木径向生长的显著正效应在样地各类生境型的所有种群中普遍存在;生物因子对树木径向生长的显著影响只在特定生境型的青杄种群中被检测到,表明树木径向生长受同种邻体影响,但其影响显著性因树种而异;环境因子中,海拔和凹凸度对树木径向生长呈显著负效应...     

桑树磷脂酶MaPLA1-2D亚型4个基因的克隆与胁迫应答分析

磷脂酶(phospholipase)是一类在植物生长发育和胁迫应答中起重要调控作用的磷脂水解酶,也是一类重要的信号转导酶。而磷脂酶A1(PLA1)在植物应答生物胁迫和非生物胁迫中的功能研究鲜见报道。研究从桑树(Morus alba L.)中克隆了磷脂酶PLA1的1个亚型MaPLA1-2D基因,对其进行了序列分析、组织表达、胁迫诱导表达和蛋白亚细胞定位分析。结果表明,桑树PLA1-2D亚型基因包括4个成员,命名为MaPLA1-2D.1~MaPLA1-2D.4。4个基因在桑树根和叶中高水平表达,蛋白亚细胞定位在叶绿体。序列和进化分析表明MaPLA1-2D基因4个成员与拟南芥AtDAD1基因的保守结构域序列具有较高相似度且进化关系紧密。MaPLA1-2D基因4个成员的启动子含有多种胁迫应答顺式元件和激素响应元件;胁迫诱导表达模式分析表明MaPLA1-2D基因表达受干旱和脱落酸处理显著诱导。以上结果说明,MaPLA1-2D基因与拟南芥DAD同源,可能在桑树非生物胁迫应答中发挥重要功能。     

A qualitative procedure for the assessment of the habitat integrity status of the Luvuvhu River (Limpopo system,South Africa)

The riparian zone and instream habitat integrity of the Luvuvhu River were assessed based on a qualitative rating of the impacts of major disturbance factors such as water abstraction, flow regulation, bed and channel modification, etc. A system was devised to assess the impact of these factors on the relative frequency and variability of habitats on a spatial and temporal scale gauged against habitat characteristics that could have been expected to occur under conditions not anthropogenically influenced. It was found that deterioration of habitat integrity can be ascribed primarily to water abstraction. This has resulted in the cessation of surface flow in a naturally perennial river during the dry season and during droughts with consequent tree deaths and a loss of fast flowing instream habitat types in the main stem of the river. The relatively small high rainfall area in the catchment, the highly variable rainfall pattern and the occurrence of sporadic severe droughts exacerbate the impact of water abstraction on the instream and riparian habitats with expected detrimental consequences for the associated biota. The effect of water abstraction is particularly severe in the lower part of the river which flows through the Kruger National Park as no perennial tributaries join the Luvuvhu River in this section. Other factors which affect the habitat integrity of the river are the removal of indigenous riparian vegetation in some river sections, encroachment by exotic vegetation, bank erosion and stream bed modification.