哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

RESEARCH ON THE VALIDITY OF EOSPALAX SMITHI INFERRED FROM MOLECULAR AND MORPHOLOGICAL EVIDENCES

为了探讨斯氏鼢鼠的物种地位,分别测得了4个斯氏鼢鼠、3个高原鼢鼠、2个秦岭鼢鼠个体的线粒体细胞色素b基因和12S rRNA基因的全序列,结合下载自GenBank中的鼢鼠序列,利用MEGA4.0,PHYLIP 3.57c软件包和Mrbayes 3.1.2软件以中华竹鼠做外群分别重建鼢鼠亚科的系统发育关系,并比较了采自3个地区的斯氏鼢鼠、高原鼢鼠和秦岭鼢鼠的头骨形态学特征.分子生物学研究结果支持斯氏鼢鼠的物种地位,且与秦岭鼢鼠和高原鼢鼠的亲缘关系较近.     

林跳鼠亚科的系统学研究述评

林跳鼠亚科分布在亚洲和北美洲,虽然种类及数量都不多,但对该亚科的分类和系统发育关系一直存在争议,近几年对林跳鼠哑科分子系统学的研究,产生了一些与形态学、生物地理学等研究不同的结果.本文对林跳鼠亚科系统学研究的一些工作加以述评,归纳出林跳鼠亚科在系统学方面还存在的问题,并对林跳鼠亚科系统学的进一步研究提出了一些建议.     

斯氏鼢鼠物种地位有效性的探讨

为了探讨斯氏鼢鼠的物种地位,分别测得了4个斯氏鼢鼠、3个高原鼢鼠、2个秦岭鼢鼠个体的线粒体细胞色素b基因和12SrRNA基因的全序列,结合下载自Gen Bank中的鼢鼠序列,利用MEG A4.0,PH YLIP 3.57c软件包和Mrbayes 3.1.2软件以中华竹鼠做外群分别重建鼢鼠亚科的系统发育关系,并比较了采自3个地区的斯氏鼢鼠、高原鼢鼠和秦岭鼢鼠的头骨形态学特征。分子生物学研究结果支持斯氏鼢鼠的物种地位,且与秦岭鼢鼠和高原鼢鼠的亲缘关系较近。     

须脚目动物系统学研究进展

须脚目是一类体型微小、形态特殊、生活于土壤或洞穴中的蛛形动物,目前全世界仅记录109种,隶属于2科8属,包括2个化石记录种。由于对该类群系统学研究比较欠缺,其系统发育地位仍不明确。基于形态学的支序系统学分析大部分支持须脚目与四肺类(蜘蛛目+无鞭目+鞭蝎目+裂盾目)聚为一支,但也有研究支持须脚目与真螨类关系较近;分子系统学方面的研究较少,其分析结果也存在分歧。目前中国须脚目动物仅有零星的报道,研究匮乏。现简要报道最近在广西发现的1种类须脚蝎属动物,分析须脚目已知科、属及其分布,比较世界各地区已知须脚目的物种数,列举须脚目研究学者及其研究区域,从经典分类学和系统发育两个方面对须脚目系统学研究的最新进展进行综述,同时给出了须脚目各科、属的中文学名翻译,以期推动中国须脚目动物系统学的开展。     

基于支序系统学的中国蓟马科系统发育研究

蓟马科Thripidae昆虫是重要的经济害虫之一,到目前为止,我国蓟马科的分类还比较混乱,亟需对其系统分类进行深入研究。本文基于西北农林科技大学昆虫博物馆(NWAFU)、中国科学院动物研究所(IZCAS)和华南农业大学资源与环境学院(SCAU)检视的实证标本,运用支序系统学的方法对中国蓟马科59属的系统发育进行了初步研究,并探讨了科内的系统发育关系。结果显示:蓟马科是一个单系群,但蓟马亚科Thripinae不是一个单系群;棍蓟马亚科Dendrothripinae和针蓟马亚科Panchaetothripinae亲缘关系较近,且互为姐妹群;绢蓟马亚科Sericothripinae的分类地位应降一级,作为蓟马亚科内的一个族或一个属团;针蓟马族Panchaetothripini的分类地位还有待进一步研究。     

角蟾科Megophryidae系统研究进展

角蟾科Megophryidae是原始无尾两栖类中分化最多的科,分布于亚洲东部、南部及东南部.但角蟾科各类群的分类地位长期以来存在较大争议.本文从形态、染色体、DNA水平方面详细介绍了角蟾科系统学研究的进展;从科的建立、亚科的分类、属的争议、种的争议等各级分类阶元讨论了其研究历史,包括不同阶元的订正、类群的系统发育关系、起源与分化等不同学者的见解;展望了将来的一些研究方向.     

鲤科鲌亚科鱼类的系统发育及动物地理学

以雅罗鱼亚科为外群,采用分支系统学的原理和方法对鲌亚科17个属(须鳊属除外)进行了系统发育和动物地理学的分析.结果表明,(1)鲌亚科这17个属为一个单系群,并由4个较小的单系群组成;(2)鲌亚科现在的地理分布格局除源自离散事件外,主要源于扩散事件.鲌亚科的特征演化还表明,东亚地区地质历史的反转演化和平行演化可能在鲌亚科系统发育过程中起了重要的作用.     

鲤科鲴亚科鱼类的系统发育及动物地理学

以雅罗鱼亚科为外群,采用分支系统学的原理和方法对鲐亚科17个属(须鳊属除外)进行了系统发育和动物地理学的分析。结果表明,(1)鲴亚科这17个属为一个单系群,并由4个较小的单系群组成;(2)鲴亚科现在的地理分布格局除源自离散事件外,主要源于扩散事件。鲐亚科的特征演化还表明,东亚地区地质历史的反转演化和平行演化可能在鲴亚科系统发育过程中起了重要的作用。     

中英科研机构五年宏观动物学研究进展比较分析——以中国科学院动物进化与系统学重点实验室和英国自然历史博物馆为例

在全球资源和环境危机下,物种和生态层面的宏观动物学研究已成为可持续发展的重要课题。本文基于英国自然历史博物馆和中国科学院动物进化与系统学重点实验室2009~2013年动物学领域研究进展的可视化对比分析,以揭示两机构近5年宏观动物学研究的现状、热点、差异以及未来发展趋势。分析发现,两机构在动物分类、系统进化与生物多样性等宏观动物学研究方向十分类似;作者聚类方面中国科学院动物进化与系统学重点实验室多侧重于中国昆虫纲研究,而英国自然历史博物馆研究的动物类群更具多样性且地区跨度更广;中国科学院动物进化与系统学重点实验室目前最主要的研究热点乃至未来相当一段时间的研究前沿仍为中国新物种的经典分类学研究;英国自然历史博物馆的研究热点则已转向中国和印度等发展中国家的新物种发现与描记,在经典分类学基础上的物种多样性和系统发育学研究则是英国自然历史博物馆宏观动物学的研究前沿。     

Soil pH determines fungal diversity along an elevation gradient in Southwestern China

Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units(OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis(DistLM) identified that soil pH dominated the explanatory power of the species richness(23.72%),phylogenetic diversity(24.25%) and beta diversity(28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH(P0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China.     

Hybrid ecosystems can contribute to local biodiversity conservation

Calcareous grasslands have become severely threatened habitats in Europe. The aim of this study was to investigate the changes in plant species richness, and functional and phylogenetic diversity in northern Estonian calcareous (alvar) grasslands resampled after 90 years of land-use change. Functional traits characterizing species that have benefited most from decreased habitat area and altered environmental conditions, and additional species that can potentially inhabit the remaining grassland patches were identified. Also changes in the relative amount of habitat-specific species were studied to detect a possible decrease in habitat integrity. Although grasslands in the studied region had lost most of their original area (~90 %), species richness had substantially increased due to invasion by more competitive, nutrient-demanding native species. Functional diversity generally increased, whereas phylogenetic diversity showed no response to altered conditions. Overall, these grasslands have lost their integrity as calcareous grassland habitat type in the region, because the relative amount of habitat-specific characteristic species has declined significantly. However, although the grasslands have transformed to a ‘hybrid’ habitat type and restoration to their previous state is likely not reasonable, such degraded species-rich grassland fragments can still be recognized as important habitats to preserve high local biodiversity and several characteristic species of calcareous grasslands. As current landscapes consist of an increasing number of hybrid and novel communities, new tools to supplement traditional conservation or restoration practices are necessary to recognize and maintain regions and habitats of high local biodiversity.     

Multiple facets of stream macroinvertebrate alpha diversity are driven by different ecological factors across an extensive altitudinal gradient

Environmental filtering and spatial structuring are important ecological processes for the generation and maintenance of biodiversity. However, the relative importance of these ecological drivers for multiple facets of diversity is still poorly understood in highland streams. Here, we examined the responses of three facets of stream macroinvertebrate alpha diversity to local environmental, landscape‐climate and spatial factors in a near‐pristine highland riverine ecosystem. Taxonomic (species richness, Shannon diversity, and evenness), functional (functional richness, evenness, divergence, and Rao's Quadratic entropy), and a proxy of phylogenetic alpha diversity (taxonomic distinctness and variation in taxonomic distinctness) were calculated for macroinvertebrate assemblages in 55 stream sites. Then Pearson correlation coefficient was used to explore congruence of indices within and across the three diversity facets. Finally, multiple linear regression models and variation partitioning were employed to identify the relative importance of different ecological drivers of biodiversity. We found most correlations between the diversity indices within the same facet, and between functional richness and species richness were relatively strong. The two phylogenetic diversity indices were quite independent from taxonomic diversity but correlated with functional diversity indices to some extent. Taxonomic and functional diversity were more strongly determined by environmental variables, while phylogenetic diversity was better explained by spatial factors. In terms of environmental variables, habitat‐scale variables describing habitat complexity and water physical features played the primary role in determining the diversity patterns of all three facets, whereas landscape factors appeared less influential. Our findings indicated that both environmental and spatial factors are important ecological drivers for biodiversity patterns of macroinvertebrates in Tibetan streams, although their relative importance was contingent on different facets of diversity. Such findings verified the complementary roles of taxonomic, functional and phylogenetic diversity, and highlighted the importance of comprehensively considering multiple ecological drivers for different facets of diversity in biodiversity assessment.     

Dark diversity: shedding light on absent species

Ecological theory and nature conservation have traditionally relied solely on observed local diversity. In this review, we recommend including those species that are absent from an ecosystem but which belong to its species pool; that is, all species in the region that can potentially inhabit those particular ecological conditions. We call the set of absent species 'dark diversity'. Relating local and dark diversities enables biodiversity comparisons between regions, ecosystems and taxonomic groups, and the evaluation of the roles of local and regional processes in ecological communities. Dark diversity can also be used to counteract biodiversity loss and to estimate the restoration potential of ecosystems. We illustrate the dark diversity concept by globally mapping plant dark diversity and the local:dark diversity ratio.     

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

Studying patterns of species distributions along elevation gradients is frequently used to identify the primary factors that determine the distribution, diversity and assembly of species. However, despite their crucial role in ecosystem functioning, our understanding of the distribution of below‐ground fungi is still limited, calling for more comprehensive studies of fungal biogeography along environmental gradients at various scales (from regional to global). Here, we investigated the richness of taxa of soil fungi and their phylogenetic diversity across a wide range of grassland types along a 2800 m elevation gradient at a large number of sites (213), stratified across a region of the Western Swiss Alps (700 km²). We used 454 pyrosequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs). The OTU diversity–area relationship revealed uneven distribution of fungal taxa across the study area (i.e. not all taxa are everywhere) and fine‐scale spatial clustering. Fungal richness and phylogenetic diversity were found to be higher in lower temperatures and higher moisture conditions. Climatic and soil characteristics as well as plant community composition were related to OTU alpha, beta and phylogenetic diversity, with distinct fungal lineages suggesting distinct ecological tolerances. Soil fungi, thus, show lineage‐specific biogeographic patterns, even at a regional scale, and follow environmental determinism, mediated by interactions with plants.     

Interactive effects of keystone rodents on the structure of desert grassland arthropod communities

Certain species play particularly large roles in ecosystems, and are often referred to as keystones. However, little is known about the interactive effects of these species where they co-occur. Prairie dogs ( Cynomys spp.) and banner-tailed kangaroo rats Dipodomys spectabilis are commonly considered keystone species of grassland ecosystems, creating a mosaic of unique habitats on the landscape through ecosystem engineering and herbivory. We examined the separate and interactive effects of these species on the structure of grassland arthropod communities. We conducted a cross-site study at two locations in the northern Chihuahuan Desert, and evaluated the impacts of these rodents on ground-dwelling arthropod and grasshopper communities in areas where prairie dogs and kangaroo rats co-occurred compared to areas where each rodent species occurred alone. Our results demonstrate that prairie dogs ( C. gunnisoni and C. ludovicianus ) and banner-tailed kangaroo rats had keystone-level impacts on arthropod communities both separately and interactively. Their burrow systems provided important habitats for multiple trophic and taxonomic groups of arthropods, and increased overall arthropod abundance and species richness. Many arthropods also were attracted to the aboveground habitats around the mounds and across the landscapes where the rodents occurred. Detritivores, predators, ants, grasshoppers, and rare rodent burrow inhabitants were especially associated with prairie dog and kangaroo rat activity. The impacts of prairie dogs and kangaroo rats were unique, and the habitats they created supported different assemblages of arthropods. Where both rodent species co-occurred, there was greater heterogeneity and arthropod diversity on the landscape. Our results suggest that the interaction of multiple keystones, especially those with engineering roles, results in unique and more diverse communities in time and space.     

Comparative thermal adaptation in cicadas (Hemiptera: Cicadidae) inhabiting Mediterranean ecosystems

The thermal responses of cicadas inhabiting the Mediterranean ecosystems in Europe, North America, South Africa, and Australia are investigated. A total of 37 species and two subspecies from 17 genera representing eight tribes and three subfamilies of cicadas are investigated. The analysis includes species that are restricted to the Mediterranean ecosystem as well as those which also inhabit additional environments. The data suggest that cicadas adapt to the climate type regardless of particular types of plants within the various Mediterranean communities. Similarly, cicada thermal responses are independent of body size or taxonomic affinities. There is a wider range of body temperatures for the maximum voluntary tolerance temperature than for heat torpor or minimum flight temperatures. This diversity seems to be determined by the subdivision of the habitat used and the behavior of the species. All species possess relatively elevated heat torpor temperatures adapting to the general thermal characteristics of the Mediterranean ecosystem. The data suggest that cicadas adapt to the Mediterranean climate type regardless of the diversity of particular types of plants within the various communities, of body size or of taxonomic position.     

Phylogeny and temporal diversification of Calomys (Rodentia, Sigmodontinae): implications for the biogeography of an endemic genus of the open/dry biomes of South America

A thorough analysis of character evolution and biogeography of a group is only possible with a comprehensive sampling of its diversity. The sigmodontine genus Calomys is particularly interesting for the study of neotropical biogeography as it occurs exclusively in the dry and grassland biomes: Cerrado, Caatinga, Chaco, Pampas, Venezuelan Llanos, Puna, and a diversity of dry forests biomes. Although Brazil encompasses a large part of the geographic distribution of the genus and at least three endemic species, the last published phylogeny of Calomys included only two specimens (both representing the same species) from a single locality in this country. In the present paper we add complete cytochrome b sequences of Brazilian karyomorphs to previously published sequences in order to provide a phylogenetic hypothesis including most of the genus diversity. The main objectives of this study were to clarify taxonomic issues related to Brazilian karyomorphs and to study the diversification processes of the genus by analyzing its biogeography in combination with cladogenesis dates estimated with a molecular clock. The phylogeny indicates that at least six different species inhabit the Brazilian territory, one of them still undescribed. Date estimates indicate that two sequential basal splits, the first separating Andean from lowland species and the second isolating species north and south of the Amazonia, took place in the Pliocene between 3 and 4 Ma. A large-bodied and speciose clade of lowland species associated with dry forests and ecotones of the core Cerrado and Chaco areas with adjacent biomes diversified in the Pleistocene. This indicates the importance of safeguarding ecotones and the Cerrado at a time where this biome is being rapidly destroyed.     

Parasitic plants—impacts on nutrient cycling

Whilst it is widely accepted that different plant species influence ecosystem processes such as nutrient cycling, we are still far from understanding and predicting the effects of changes in vegetation composition on biogeochemical cycles. Ameloot E, Verlinden G, Boeckx P, Verheyen K, Hermy M. Impact of hemiparasitic Rhinanthus angustifolius and Rhinanthus minor on nitrogen availability in grassland (this issue) examine, for the first time, the impact of root hemiparasitic plants on in-situ nitrogen dynamics in intact field vegetation, using ¹⁵N techniques. This represents an important step forward in elucidating the unusual roles of parasitic plants in ecosystem function, and builds on a small set of recent studies indicating that parasitic plants have the potential to substantially alter the quantity and quality of resources returned to the soil by the plant community. These results reinforce the need to include parasitic plants in community and ecosystem theory, and emphasise that understanding the roles of parasitic plants in ecosystems is relevant for understanding ecosystem dynamics in a changing world.     

Environmental filtering is the main assembly rule of ground beetles in the forest and its edge but not in the adjacent grassland

In a fragmented landscape,transitional zones between neighboring habitats are common,and our understanding of community organizational forces across such habitats is important.Edge studies are numerous,but the majority of them utilize information on species richness and abundance.Abundance and taxonomic diversity,however,provide little information on the functioning and phylogeny of the co-existing species.Combining the evaluation of their functional and phylogenetic relationships,we aimed to assess whether ground beetle assemblages are deterministically or stochastically structured along grassland-forest gradients.Our results showed different community assembly rules on opposite sides of the forest edge.In the grassland,co-occurring species were functionally and phylogenetically not different from the random null model,indicating a random assembly process.Contrary to this,at the forest edge and the interior,co-occurring species showed functional and phylogenetic clustering,thus environmental filtering was the likely process structuring carabid assemblages.Community assembly in the grassland was considerably affected by asymmetrical species flows (spillover)across the forest edge:more forest species penetrated into the grassland than open-habitat and generalist species entered into the forest.This asymmetrical species flow underlines the importance of the filter function of forest edges.As unfavorable,human-induced changes to the structure,composition and characteristics of forest edges may alter their filter function,edges have to be specifically considered during conservation management.