A new and highly divergent mitochondrial lineage in the Small Five-toed Jerboa,Allactaga elater,from Iran (Mammalia: Rodentia)

The Small Five-toed Jerboa, Allactaga elater, is a small rodent adapted to desert and semi-arid habitats with a widespread distribution around the Caucasus. Previous studies have suggested the occurrence of subspecific variation within the species but, except for a recent phylogeny of the genus Allactaga, most of the work done on the taxonomy of the group relies on morphological data only. To contribute to the current understanding of patterns of genetic diversity of A. elater we analysed one mitochondrial locus, cytochrome b, from 13 Iranian specimens. Comparing to a recent phylogeny, our results suggest the existence of two additional mitochondrial lineages, one that clusters within previously described lineages and a new and highly divergent one. The two novel mitochondrial lineages occur in the north and form two highly divergent monophyletic groups (Dxy = 14%), which likely separated during the Pleistocene.     

Reappraisal of Schaubcylindrichnus: A probable dwelling/feeding structure of a solitary funnel feeder

The ichnogenus Schaubcylindrichnus has been considered as a cluster of multiple J-shaped tubes, all of which show congruency. Based on such a reconstruction, the trace fossil has commonly been regarded as dwelling tubes of gregarious, head-down deposit-feeding animals.

Well-preserved specimens of Schaubcylindrichnus are found in Miocene and Pleistocene strata of Japan. The trace fossil consists of a bundle of closely spaced, thickly lined tubes, each of which shows a gentle bow-like bend curving downward in a vertical to oblique plane. As individual tubes in a single bundle frequently show size-gradation of diameter, branching and/or cross-cutting, it is probable that the bundle was formed through successive burrowing by a solitary producer. In a longitudinal section of well-preserved specimens, a funnel-like, sediment-filled structure, which is attached to an upper end of a limb of the bow-shaped bundle, is observed. At the other end of the limb, there is a mound-like structure of sediment that is piled up from the bedding surface. The trace fossil was probably a burrow system of a solitary funnel-feeding animal, like an enteropneust.

According to comparisons with type specimens of the ichnospecies of Schaubcylindrichnus, namely, topotypes of Schaubcylindrichnus coronus and holotype and paratypes of S. freyi, S. freyi can be regarded as a junior synonym of S. coronus. As the topotype specimens of S. coronus have many common features with the traces in Japan, the latter should be included in the former. S. coronus therefore is concluded as the burrow system of a solitary funnel feeder.     

Recent vicariance and the origin of the rare, edaphically specialized Sandhills lily, Lilium pyrophilum (Liliaceae): evidence from phylogenetic and coalescent analyses

Establishing the phylogenetic and demographic history of rare plants improves our understanding of mechanisms that have led to their origin and can lead to valuable insights that inform conservation decisions. The Atlantic coastal plain of eastern North America harbours many rare and endemic species, yet their evolution is poorly understood. We investigate the rare Sandhills lily (Lilium pyrophilum), which is endemic to seepage slopes in a restricted area of the Atlantic coastal plain of eastern North America. Using phylogenetic evidence from chloroplast, nuclear internal transcribed spacer and two low-copy nuclear genes, we establish a close relationship between L. pyrophilum and the widespread Turk's cap lily, L. superbum. Isolation-with-migration and coalescent simulation analyses suggest that (i) the divergence between these two species falls in the late Pleistocene or Holocene and almost certainly post-dates the establishment of the edaphic conditions to which L. pyrophilum is presently restricted, (ii) vicariance is responsible for the present range disjunction between the two species, and that subsequent gene flow has been asymmetrical and (iii) L. pyrophilum harbours substantial genetic diversity in spite of its present rarity. This system provides an example of the role of edaphic specialization and climate change in promoting diversification in the Atlantic coastal plain.     

Historical connectivity,contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan,Rhododendron oldhamii (Ericaceae)

Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168–13,092 years ago and ending 1584–3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale.     

西沙群岛琛科二井中新世和更新世的一些珊瑚

提要西沙群岛琛航岛琛科二井(CK-2)有878.3 m厚的新生代珊瑚礁灰岩(Cenozoic reef limestone)。新生代珊瑚礁灰岩自上而下包括了第四系的全新统和更新统以及新近系的上新统和中新统。其中,中新统厚514.3 m,产19属石珊瑚(Scleractinia corals)。更新统厚215.6 m,产21属石珊瑚(Scleractinia)和1属八射珊瑚(Octocorallia)。珊瑚是营底栖固着生活的动物,在地层断代方面它没有能像一些浮游动物(例如浮游有孔虫等)那么“精准”。但也有一些珊瑚的地质历程相对比较短暂的,它们在地层划分和对比方面还是能起到重要作用。本研究在琛科二井井深364–878.3 m的中新世地层中鉴定出有若干只见于中新世或者常见于中新世的珊瑚,如:星日珊瑚(Astrhelia)、安的列斯珊瑚(Antillophyllia)和大安的列斯珊瑚(Antillia)等。另外在井深21.4–237 m的更新世地层中也发现了数只限于第四纪的珊瑚,如:叶状珊瑚(Lobophyllia)、合叶珊瑚(Symphyllia)、轮沙珊瑚(Trochopsammia)和苍...     

中国亚热带地区阔叶林植物的谱系地理历史

中国亚热带地区因丰富的植物物种多样性备受生物地理学研究关注,丰富的多样性与中新世以来的地质气候变化密切相关。谱系地理学已成为探讨植物分布模式和遗传格局受地质气候变化影响的主要手段。总结了该地区阔叶林植物对中新世以来地质气候变化的响应模式和种群分化的历史成因。在中新世和上新世时,由于全球变冷、青藏高原抬升和亚洲内陆干旱,阔叶林植物被迫向南退缩,形成不同的谱系。同时,亚洲季风的增强为遗传多样性的增加提供了良好的环境。在更新世冰期和间冰期时,大部分落叶阔叶林和常绿阔叶林植物在多个避难所间存在长期隔离,不同的避难所种群各自经历局部地区的收缩和扩张。长期的隔离使不同谱系间进一步分化,形成高水平的遗传多样性和遗传分化。少部分植物在冰期时向南退缩,并在间冰期时明显向北扩张。最后,就分化时间的准确估计和探究遗传格局背后的机制两方面展望了未来的研究趋势。     

Shifting distributions and speciation: species divergence during rapid climate change

Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species distributions.     

Microbial origin of travertine fabrics—two examples from Southern Germany (Pleistocene stuttgart travertines and miocene riedöschingen Travertine)

Summary In Southern Germany, two examples of travertines of different age and depositional morphology were examined in detail. Travertines are laminated carbonate rocks formed by precipitation from mineral and/or thermal waters. They include characteristic facies types, such as bushy layers (‘shrubs’) referred to calcification of branching microbes (‘Dichothrix’-morphotype), laminar microbial mats, peloidal layers, and gas bubble layers formed within the sediment. In travertines, microbial activity is the most important factor for carbonate precipitation. Tufas differ from travertines by their abundance of molds of higher plants (leaves, reed, moss, green algae). They may be associated with travertines, but do not exhibit strict travertine facies types. Tufas are common in normal fresh water environments. Contrary to travertines and tufas, calcareous sinters usually occur in restricted areas like spring fissures, caves, or in pores, where microbial activity is not totally absent, but not of paramount importance for precipitation. Pedogenetic processes, which can alter travertine deposits, are responsible for large-scale features such as tepee-structures, and some intraclastic layers, and microscopic structures like endolithic borings andMicrocodium. Travertines may also grade into lacustrine limestones with Characeae, ostracods, and aquatic gastropods.